--- _id: '411' abstract: - lang: eng text: Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins. alternative_title: - Methods in Molecular Biology author: - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: 'Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10' apa: Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10 chicago: Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10. ieee: M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143. ista: 'Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.' mla: Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10. short: M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143. date_created: 2018-12-11T11:46:20Z date_published: 2018-03-11T00:00:00Z date_updated: 2021-01-12T07:54:34Z day: '11' department: - _id: JiFr doi: 10.1007/978-1-4939-7747-5_10 editor: - first_name: Daniela full_name: Ristova, Daniela last_name: Ristova - first_name: Elke full_name: Barbez, Elke last_name: Barbez intvolume: ' 1761' language: - iso: eng month: '03' oa_version: None page: 131 - 143 publication: Root Development. Methods and Protocols publication_status: published publisher: Springer publist_id: '7418' quality_controlled: '1' scopus_import: 1 series_title: MIMB status: public title: Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1761 year: '2018' ... --- _id: '456' abstract: - lang: eng text: 'Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. ' article_number: eaar7514 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514' apa: 'Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514' chicago: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.' ieee: 'G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.' ista: 'Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.' mla: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.' short: G. Novarino, Science Translational Medicine 10 (2018). date_created: 2018-12-11T11:46:34Z date_published: 2018-01-10T00:00:00Z date_updated: 2021-01-12T07:59:42Z day: '10' department: - _id: GaNo doi: 10.1126/scitranslmed.aar7514 intvolume: ' 10' issue: '423' language: - iso: eng month: '01' oa_version: None publication: Science Translational Medicine publication_status: published publisher: American Association for the Advancement of Science publist_id: '7365' quality_controlled: '1' scopus_import: 1 status: public title: 'Zika-associated microcephaly: Reduce the stress and race for the treatment' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '53' abstract: - lang: eng text: In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation. author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: 'Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993' apa: 'Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993' chicago: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.' ieee: 'B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.' ista: 'Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.' mla: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.' short: B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206. date_created: 2018-12-11T11:44:22Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:01:26Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v71i1.1993 file: - access_level: open_access checksum: 7ac61bade5f37db011ca435ebcf86797 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:40:27Z date_updated: 2020-07-14T12:46:38Z file_id: '5702' file_name: 2018_VOEB_Petritsch.pdf file_size: 509434 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 71' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version page: 199 - 206 publication: VÖB Mitteilungen publication_status: published publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publist_id: '8001' scopus_import: 1 status: public title: 'IST PubRep and IST DataRep: the institutional repositories at IST Austria' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 71 year: '2018' ... --- _id: '536' abstract: - lang: eng text: 'We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.' article_processing_charge: Yes (via OA deal) author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Valerie full_name: King, Valerie last_name: King - first_name: Jared full_name: Saia, Jared last_name: Saia citation: ama: Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1 apa: Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1 chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1. ieee: D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018. ista: Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501. mla: Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1. short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501. date_created: 2018-12-11T11:47:01Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-02-23T12:23:25Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00446-017-0315-1 file: - access_level: open_access checksum: 69b46e537acdcac745237ddb853fcbb5 content_type: application/pdf creator: dernst date_created: 2019-01-22T07:25:51Z date_updated: 2020-07-14T12:46:38Z file_id: '5867' file_name: 2017_DistribComp_Alistarh.pdf file_size: 595707 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 31' issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 489-501 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_identifier: issn: - '01782770' publication_status: published publisher: Springer publist_id: '7281' quality_controlled: '1' scopus_import: 1 status: public title: Communication-efficient randomized consensus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '554' abstract: - lang: eng text: We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.). author: - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski - first_name: Robin full_name: Reuvers, Robin last_name: Reuvers - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: ama: 'Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x' apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x' chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.' ieee: 'M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.' ista: 'Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.' mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.' short: M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403. date_created: 2018-12-11T11:47:09Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:02:35Z day: '01' department: - _id: RoSe doi: 10.1007/s00220-017-3064-x external_id: arxiv: - '1511.05953' intvolume: ' 360' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.05953 month: '05' oa: 1 oa_version: Submitted Version page: 347-403 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_identifier: issn: - '00103616' publication_status: published publisher: Springer publist_id: '7260' quality_controlled: '1' scopus_import: 1 status: public title: 'The Bogoliubov free energy functional II: The dilute Limit' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 360 year: '2018' ... --- _id: '562' abstract: - lang: eng text: Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Dimitar full_name: Dimitrov, Dimitar last_name: Dimitrov - first_name: Laurent full_name: Guillaud, Laurent last_name: Guillaud - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15' apa: Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15 chicago: Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15. ieee: D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215. ista: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.' mla: Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15. short: D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215. date_created: 2018-12-11T11:47:11Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:03:05Z day: '01' ddc: - '570' department: - _id: RySh doi: 10.1007/978-1-4939-7571-6_15 editor: - first_name: Stephen D. full_name: Skaper, Stephen D. last_name: Skaper external_id: pmid: - '29222783' file: - access_level: open_access checksum: 8aa174ca65a56fbb19e9f88cff3ac3fd content_type: application/pdf creator: dernst date_created: 2019-11-19T07:47:43Z date_updated: 2020-07-14T12:47:09Z file_id: '7046' file_name: 2018_NeurotrophicFactors_Dimitrov.pdf file_size: 787407 relation: main_file file_date_updated: 2020-07-14T12:47:09Z has_accepted_license: '1' intvolume: ' 1727' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 201 - 215 pmid: 1 publication: Neurotrophic Factors publication_status: published publisher: Springer publist_id: '7252' quality_controlled: '1' scopus_import: 1 status: public title: Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1727 year: '2018' ... --- _id: '59' abstract: - lang: eng text: Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches. author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann citation: ama: 'Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27' apa: Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27 chicago: Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27. ieee: R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962. ista: 'Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.' mla: Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27. short: R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962. date_created: 2018-12-11T11:44:24Z date_published: 2018-05-19T00:00:00Z date_updated: 2021-01-12T08:05:10Z day: '19' department: - _id: KrCh doi: 10.1007/978-3-319-10575-8_27 edition: '1' editor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Edmund M. full_name: Clarke, Edmund M. last_name: Clarke - first_name: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem language: - iso: eng month: '05' oa_version: None page: 921 - 962 publication: Handbook of Model Checking publication_identifier: isbn: - 978-3-319-10574-1 publication_status: published publisher: Springer publist_id: '7995' quality_controlled: '1' scopus_import: 1 status: public title: Graph games and reactive synthesis type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '60' abstract: - lang: eng text: Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking. author: - first_name: Edmund full_name: Clarke, Edmund last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Helmut full_name: Veith, Helmut last_name: Veith citation: ama: 'Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1' apa: Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1 chicago: Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1. ieee: E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26. ista: 'Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.' mla: Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1. short: E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26. date_created: 2018-12-11T11:44:25Z date_published: 2018-05-19T00:00:00Z date_updated: 2021-01-12T08:05:35Z day: '19' department: - _id: ToHe doi: 10.1007/978-3-319-10575-8_1 editor: - first_name: Thomas A full_name: Henzinger, Thomas A last_name: Henzinger language: - iso: eng month: '05' oa_version: None page: 1 - 26 publication: Handbook of Model Checking publication_status: published publisher: Springer publist_id: '7994' quality_controlled: '1' scopus_import: 1 series_title: Handbook of Model Checking status: public title: Introduction to model checking type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '61' abstract: - lang: eng text: 'We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ' article_processing_charge: No author: - first_name: Andriy full_name: Bondarenko, Andriy last_name: Bondarenko - first_name: Anton full_name: Mellit, Anton id: 388D3134-F248-11E8-B48F-1D18A9856A87 last_name: Mellit - first_name: Andriy full_name: Prymak, Andriy last_name: Prymak - first_name: Danylo full_name: Radchenko, Danylo last_name: Radchenko - first_name: Maryna full_name: Viazovska, Maryna last_name: Viazovska citation: ama: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7' apa: Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7 chicago: Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7. ieee: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134. ista: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.' mla: Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7. short: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134. date_created: 2018-12-11T11:44:25Z date_published: 2018-05-23T00:00:00Z date_updated: 2021-01-12T08:06:06Z day: '23' department: - _id: TaHa doi: 10.1007/978-3-319-72456-0_7 extern: '1' external_id: arxiv: - '1509.06286' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.06286 month: '05' oa: 1 oa_version: Preprint page: 131 - 134 publication: Contemporary Computational Mathematics publication_status: published publisher: Springer publist_id: '7993' quality_controlled: '1' status: public title: There is no strongly regular graph with parameters (460; 153; 32; 60) type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6111' abstract: - lang: eng text: 'Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending.' article_number: e1007435 author: - first_name: Ian G. full_name: McLachlan, Ian G. last_name: McLachlan - first_name: Isabel full_name: Beets, Isabel last_name: Beets - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Maxwell G. full_name: Heiman, Maxwell G. last_name: Heiman citation: ama: McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435 apa: McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435 chicago: McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007435. ieee: I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of Science, 2018. ista: McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435. mla: McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435. short: I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018). date_created: 2019-03-19T13:09:28Z date_published: 2018-06-07T00:00:00Z date_updated: 2021-01-12T08:06:11Z day: '07' ddc: - '570' doi: 10.1371/journal.pgen.1007435 extern: '1' external_id: pmid: - '29879119' file: - access_level: open_access checksum: 622036b945365dbc575bea2768aa9bc8 content_type: application/pdf creator: kschuh date_created: 2019-03-19T13:18:01Z date_updated: 2020-07-14T12:47:19Z file_id: '6112' file_name: 2018_PLOS_McLachlan.pdf file_size: 13011506 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 14' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '6109' abstract: - lang: eng text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels. author: - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: QueeLim full_name: Ch’ng, QueeLim last_name: Ch’ng - first_name: Maëlle full_name: Jospin, Maëlle last_name: Jospin - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Ramiro full_name: Lorenzo, Ramiro last_name: Lorenzo - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115 apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115 chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115. ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018. ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899. mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115. short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899. date_created: 2019-03-19T12:41:33Z date_published: 2018-07-17T00:00:00Z date_updated: 2021-01-12T08:06:09Z day: '17' ddc: - '570' doi: 10.1073/pnas.1714610115 extern: '1' external_id: pmid: - '29959203' file: - access_level: open_access checksum: 5e81665377441cdd8d99ab952c534319 content_type: application/pdf creator: kschuh date_created: 2019-03-19T13:01:58Z date_updated: 2020-07-14T12:47:19Z file_id: '6110' file_name: 2018_PNAS_Laurent.pdf file_size: 1567765 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 115' issue: '29' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: E6890-E6899 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '6164' abstract: - lang: eng text: In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity. alternative_title: - LNCS article_processing_charge: No author: - first_name: Girish full_name: Koshti, Girish last_name: Koshti - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Gaëlle full_name: Largeteau-Skapin, Gaëlle last_name: Largeteau-Skapin - first_name: Rita full_name: Zrour, Rita last_name: Zrour - first_name: Eric full_name: Andres, Eric last_name: Andres - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7' apa: 'Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7' chicago: 'Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.' ieee: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96. ista: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.' mla: Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7. short: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96. conference: end_date: 2018-11-24 location: Porto, Portugal name: 'IWCIA: International Workshop on Combinatorial Image Analysis' start_date: 2018-11-22 date_created: 2019-03-21T12:16:58Z date_published: 2018-11-22T00:00:00Z date_updated: 2022-01-27T15:26:39Z day: '22' doi: 10.1007/978-3-030-05288-1_7 extern: '1' intvolume: ' 11255' language: - iso: eng month: '11' oa_version: None page: 82-96 place: Cham publication: 19th International Workshop publication_identifier: eisbn: - 978-3-030-05288-1 eissn: - 1611-3349 isbn: - 978-3-030-05287-4 issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11255 year: '2018' ... --- _id: '6354' abstract: - lang: eng text: Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow. acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)' article_number: e3018 author: - first_name: Shuxia full_name: Fan, Shuxia last_name: Fan - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 citation: ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018 apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018 chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018. ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018. ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018. mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018. short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018). date_created: 2019-04-29T09:40:33Z date_published: 2018-09-20T00:00:00Z date_updated: 2021-01-12T08:07:12Z day: '20' ddc: - '570' department: - _id: MiSi doi: 10.21769/bioprotoc.3018 ec_funded: 1 file: - access_level: open_access checksum: d4588377e789da7f360b553ae02c5119 content_type: application/pdf creator: dernst date_created: 2019-04-30T08:04:33Z date_updated: 2020-07-14T12:47:28Z file_id: '6360' file_name: 2018_BioProtocol_Fan.pdf file_size: 2928337 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' intvolume: ' 8' issue: '18' keyword: - Platelets - Cell migration - Bacteria - Shear flow - Fibrinogen - E. coli language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Bio-Protocol publication_identifier: issn: - 2331-8325 publication_status: published publisher: Bio-Protocol quality_controlled: '1' status: public title: Platelet migration and bacterial trapping assay under flow tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2018' ... --- _id: '6368' abstract: - lang: eng text: An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate. author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: P. S. full_name: Burns, P. S. last_name: Burns - first_name: M. D. full_name: Urmey, M. D. last_name: Urmey - first_name: R. W. full_name: Peterson, R. W. last_name: Peterson - first_name: N. S. full_name: Kampel, N. S. last_name: Kampel - first_name: B. M. full_name: Brubaker, B. M. last_name: Brubaker - first_name: G. full_name: Smith, G. last_name: Smith - first_name: K. W. full_name: Lehnert, K. W. last_name: Lehnert - first_name: C. A. full_name: Regal, C. A. last_name: Regal citation: ama: Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042. doi:10.1038/s41567-018-0210-0 apa: Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0210-0 chicago: Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0. ieee: A. P. Higginbotham et al., “Harnessing electro-optic correlations in an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018. ista: Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042. mla: Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0. short: A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042. date_created: 2019-05-03T09:17:20Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:07:15Z day: '01' doi: 10.1038/s41567-018-0210-0 extern: '1' external_id: arxiv: - '1712.06535' intvolume: ' 14' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.06535 month: '10' oa: 1 oa_version: Preprint page: 1038-1042 publication: Nature Physics publication_identifier: issn: - 1745-2473 - 1745-2481 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Harnessing electro-optic correlations in an efficient mechanical converter type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '6369' abstract: - lang: eng text: We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before. article_number: '220301' author: - first_name: Eric I. full_name: Rosenthal, Eric I. last_name: Rosenthal - first_name: Nicole K. full_name: Ehrlich, Nicole K. last_name: Ehrlich - first_name: Mark S. full_name: Rudner, Mark S. last_name: Rudner - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: K. W. full_name: Lehnert, K. W. last_name: Lehnert citation: ama: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 2018;97(22). doi:10.1103/physrevb.97.220301 apa: Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., & Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301 chicago: Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301. ieee: E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018. ista: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301. mla: Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:10.1103/physrevb.97.220301. short: E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018). date_created: 2019-05-03T09:29:49Z date_published: 2018-06-04T00:00:00Z date_updated: 2021-01-12T08:07:16Z day: '04' doi: 10.1103/physrevb.97.220301 extern: '1' external_id: arxiv: - '1802.02243' intvolume: ' 97' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.02243 month: '06' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: issn: - 2469-9950 - 2469-9969 publication_status: published publisher: American Physical Society (APS) quality_controlled: '1' status: public title: Topological phase transition measured in a dissipative metamaterial type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2018' ... --- _id: '6459' author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279 apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279' chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279. ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018. ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p. mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279. short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018. conference: end_date: 2018-09-26 location: Graz, Austria name: Open-Access-Tage start_date: 2018-09-24 date_created: 2019-05-16T07:27:14Z date_published: 2018-09-24T00:00:00Z date_updated: 2020-07-14T23:06:21Z day: '24' ddc: - '020' department: - _id: E-Lib doi: 10.5281/zenodo.1410279 file: - access_level: open_access checksum: 9063ab4d10ea93353c3a03bbf53fbcf1 content_type: application/pdf creator: dernst date_created: 2019-05-16T07:26:25Z date_updated: 2020-07-14T12:47:30Z file_id: '6460' file_name: Poster_Beitrag_125_Petritsch.pdf file_size: 1967778 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' keyword: - Open Access - Publication Analysis language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria status: public title: Open Access at IST Austria 2009-2017 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6525' abstract: - lang: eng text: This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal. author: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Anton full_name: Mellit, Anton id: 388D3134-F248-11E8-B48F-1D18A9856A87 last_name: Mellit - first_name: Du full_name: Pei, Du last_name: Pei citation: ama: 'Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009' apa: 'Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009' chicago: 'Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.' ieee: 'T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' ista: 'Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.' mla: 'Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.' short: 'T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' date_created: 2019-06-06T12:42:01Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:07:52Z day: '01' department: - _id: TaHa doi: 10.1093/oso/9780198802013.003.0009 language: - iso: eng month: '01' oa_version: None page: 189-218 publication: 'Geometry and Physics: Volume I' publication_identifier: isbn: - '9780198802013' - '9780191840500' publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: 1 status: public title: Mirror symmetry with branes by equivariant verlinde formulas type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6664' abstract: - lang: eng text: Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: 'Warren ' full_name: 'Gross, Warren ' last_name: Gross citation: ama: 'Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes by successive factor graph permutations. In: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281' apa: 'Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller and polar codes by successive factor graph permutations. In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing (pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281' chicago: Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, 1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281. ieee: S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and polar codes by successive factor graph permutations,” in 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, Hong Kong, China, 2018, pp. 1–5. ista: 'Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar codes by successive factor graph permutations. 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo Codes & Iterative Information Processing, 1–5.' mla: Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281. short: S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5. conference: end_date: 2018-12-07 location: Hong Kong, China name: 'ISTC: Symposium on Turbo Codes & Iterative Information Processing' start_date: 2018-12-03 date_created: 2019-07-23T09:12:43Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:29Z day: '01' doi: 10.1109/istc.2018.8625281 extern: '1' external_id: arxiv: - '1807.03912' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.03912 month: '12' oa: 1 oa_version: Preprint page: 1-5 publication: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Decoding Reed-Muller and polar codes by successive factor graph permutations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6674' abstract: - lang: eng text: Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Carlo full_name: Condo, Carlo last_name: Condo - first_name: Rudiger L. full_name: Urbanke, Rudiger L. last_name: Urbanke - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207' apa: 'Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., & Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207' chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018. https://doi.org/10.1109/tcomm.2018.2832207.' ieee: 'S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W. J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,” IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759, 2018.' ista: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 66(9), 3749–3759.' mla: 'Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66, no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207.' short: S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross, IEEE Transactions on Communications 66 (2018) 3749–3759. date_created: 2019-07-24T08:59:41Z date_published: 2018-09-01T00:00:00Z date_updated: 2021-01-12T08:08:31Z day: '01' doi: 10.1109/tcomm.2018.2832207 extern: '1' intvolume: ' 66' issue: '9' language: - iso: eng month: '09' oa_version: None page: 3749-3759 publication: IEEE Transactions on Communications publication_identifier: eissn: - 1558-0857 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'Decoder partitioning: Towards practical list decoding of polar codes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2018' ... --- _id: '6728' abstract: - lang: eng text: Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 . author: - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on permuted factor graphs. In: 2018 IEEE Global Communications Conference . IEEE; 2018. doi:10.1109/glocom.2018.8647308' apa: 'Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308' chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308. ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of polar codes on permuted factor graphs,” in 2018 IEEE Global Communications Conference , Abu Dhabi, United Arab Emirates, 2018. ista: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar codes on permuted factor graphs. 2018 IEEE Global Communications Conference . GLOBECOM: Global Communications Conference.' mla: Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.” 2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308. short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications Conference , IEEE, 2018. conference: end_date: 2018-12-13 location: Abu Dhabi, United Arab Emirates name: 'GLOBECOM: Global Communications Conference' start_date: 2018-12-09 date_created: 2019-07-30T06:43:15Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:42Z day: '01' doi: 10.1109/glocom.2018.8647308 extern: '1' external_id: arxiv: - '1806.11195' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.11195 month: '12' oa: 1 oa_version: Preprint publication: '2018 IEEE Global Communications Conference ' publication_identifier: isbn: - '9781538647271' publication_status: published publisher: IEEE quality_controlled: '1' status: public title: On the decoding of polar codes on permuted factor graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6678' abstract: - lang: eng text: We survey coding techniques that enable reliable transmission at rates that approach the capacity of an arbitrary discrete memoryless channel. In particular, we take the point of view of modern coding theory and discuss how recent advances in coding for symmetric channels help provide more efficient solutions for the asymmetric case. We consider, in more detail, three basic coding paradigms. The first one is Gallager's scheme that consists of concatenating a linear code with a non-linear mapping so that the input distribution can be appropriately shaped. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Furthermore, we derive a scaling law between the gap to capacity, the cardinality of the input and output alphabets, and the required size of the mapper. The second one is an integrated scheme in which the code is used both for source coding, in order to create codewords distributed according to the capacity-achieving input distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates the two tasks of source coding and channel coding by a chaining construction that binds together several codewords. We present conditions for the source code and the channel code, and we describe how to combine any source code with any channel code that fulfill those conditions, in order to provide capacity-achieving schemes for asymmetric channels. In particular, we show that polar codes, spatially coupled codes, and homophonic codes are suitable as basic building blocks of the proposed coding strategy. Rather than focusing on the exact details of the schemes, the purpose of this tutorial is to present different coding techniques that can then be implemented with many variants. There is no absolute winner and, in order to understand the most suitable technique for a specific application scenario, we provide a detailed comparison that takes into account several performance metrics. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: 'Rudiger ' full_name: 'Urbanke, Rudiger ' last_name: Urbanke citation: ama: Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393. doi:10.1109/tit.2018.2789885 apa: Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2018.2789885 chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory. IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE, pp. 3371–3393, 2018. ista: Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 64(5), 3371–3393. mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp. 3371–93, doi:10.1109/tit.2018.2789885. short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 64 (2018) 3371–3393. date_created: 2019-07-24T12:38:49Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T12:50:46Z day: '01' doi: 10.1109/tit.2018.2789885 extern: '1' external_id: arxiv: - '1406.7373' intvolume: ' 64' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1406.7373 month: '05' oa: 1 oa_version: Preprint page: 3371-3393 publication: IEEE Transactions on Information Theory publication_identifier: issn: - 0018-9448 - 1557-9654 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '6740' relation: earlier_version status: public status: public title: How to achieve the capacity of asymmetric channels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2018' ... --- _id: '690' abstract: - lang: eng text: We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1. article_number: 543-616 author: - first_name: Jii full_name: Lee, Jii last_name: Lee - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8 apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8 chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8. ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018. ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616. mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8. short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018). date_created: 2018-12-11T11:47:56Z date_published: 2018-06-14T00:00:00Z date_updated: 2021-01-12T08:09:33Z day: '14' department: - _id: LaEr doi: 10.1007/s00440-017-0787-8 ec_funded: 1 external_id: arxiv: - '1605.08767' intvolume: ' 171' issue: 1-2 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.08767 month: '06' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability Theory and Related Fields publication_status: published publisher: Springer publist_id: '7017' quality_controlled: '1' scopus_import: 1 status: public title: Local law and Tracy–Widom limit for sparse random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2018' ... --- _id: '6675' abstract: - lang: eng text: 'We present a coding paradigm that provides a new achievable rate for the primitive relay channel by combining compress-and-forward and decode-and-forward with a chaining construction. In the primitive relay channel model, the source broadcasts a message to the relay and to the destination; and the relay facilitates this communication by sending an additional message to the destination through a separate channel. Two well-known coding approaches for this setting are decode-and-forward and compress-and-forward: in the former, the relay decodes the message and sends some of the information to the destination; in the latter, the relay does not attempt to decode, but it sends a compressed description of the received sequence to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs of blocks and we use compress-and-forward for the first block and decode-and-forward for the second. In particular, in the first block, the relay does not attempt to decode and it sends only a part of the compressed description of the received sequence; in the second block, the relay decodes the message and sends this information plus the remaining part of the compressed sequence relative to the first block. As a result, we strictly outperform both compress-and- forward and decode-and-forward. Furthermore, this paradigm can be implemented with a low-complexity polar coding scheme that has the typical attractive features of polar codes, i.e., quasi-linear encoding/decoding complexity and super-polynomial decay of the error probability. Throughout the paper we consider as a running example the special case of the erasure relay channel and we compare the rates achievable by our proposed scheme with the existing upper and lower bounds.' author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: ama: 'Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive relay channel. In: 2018 IEEE International Symposium on Information Theory. IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479' apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm for the primitive relay channel. In 2018 IEEE International Symposium on Information Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479' chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” in 2018 IEEE International Symposium on Information Theory, Vail, CO, United States, 2018, pp. 351–355. ista: 'Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive relay channel. 2018 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory , 351–355.' mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–55, doi:10.1109/isit.2018.8437479. short: M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–355. conference: end_date: 2018-06-22 location: Vail, CO, United States name: 'ISIT: International Symposium on Information Theory ' start_date: 2018-06-17 date_created: 2019-07-24T09:10:38Z date_published: 2018-06-16T00:00:00Z date_updated: 2023-02-23T12:56:49Z day: '16' doi: 10.1109/isit.2018.8437479 extern: '1' external_id: arxiv: - '1801.03153' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.03153 month: '06' oa: 1 oa_version: Preprint page: 351-355 publication: 2018 IEEE International Symposium on Information Theory publication_identifier: eissn: - 2157-8117 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '7007' relation: later_version status: public status: public title: A new coding paradigm for the primitive relay channel type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '703' abstract: - lang: eng text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision. author: - first_name: Alexander full_name: Shekhovtsov, Alexander last_name: Shekhovtsov - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Bogdan full_name: Savchynskyy, Bogdan last_name: Savchynskyy citation: ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884 apa: Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884 chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884. ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018. ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682. mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884. short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682. date_created: 2018-12-11T11:48:01Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:32Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2017.2730884 external_id: arxiv: - '1508.07902' intvolume: ' 40' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.07902 month: '07' oa: 1 oa_version: Preprint page: 1668-1682 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: issn: - '01628828' publication_status: published publisher: IEEE publist_id: '6992' quality_controlled: '1' scopus_import: 1 status: public title: Maximum persistency via iterative relaxed inference with graphical models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2018' ... --- _id: '7063' abstract: - lang: eng text: The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed. article_processing_charge: No article_type: original author: - first_name: Edoardo full_name: Martino, Edoardo last_name: Martino - first_name: Alla full_name: Arakcheeva, Alla last_name: Arakcheeva - first_name: Gabriel full_name: Autès, Gabriel last_name: Autès - first_name: Andrea full_name: Pisoni, Andrea last_name: Pisoni - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Toni full_name: Helm, Toni last_name: Helm - first_name: Oleg V. full_name: Yazyev, Oleg V. last_name: Yazyev - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: László full_name: Forró, László last_name: Forró - first_name: Sergiy full_name: Katrych, Sergiy last_name: Katrych citation: ama: 'Martino E, Arakcheeva A, Autès G, et al. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 2018;5(4):470-477. doi:10.1107/s2052252518007303' apa: 'Martino, E., Arakcheeva, A., Autès, G., Pisoni, A., Bachmann, M. D., Modic, K. A., … Katrych, S. (2018). Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. International Union of Crystallography (IUCr). https://doi.org/10.1107/s2052252518007303' chicago: 'Martino, Edoardo, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja D. Bachmann, Kimberly A Modic, Toni Helm, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ. International Union of Crystallography (IUCr), 2018. https://doi.org/10.1107/s2052252518007303.' ieee: 'E. Martino et al., “Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity,” IUCrJ, vol. 5, no. 4. International Union of Crystallography (IUCr), pp. 470–477, 2018.' ista: 'Martino E, Arakcheeva A, Autès G, Pisoni A, Bachmann MD, Modic KA, Helm T, Yazyev OV, Moll PJW, Forró L, Katrych S. 2018. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 5(4), 470–477.' mla: 'Martino, Edoardo, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ, vol. 5, no. 4, International Union of Crystallography (IUCr), 2018, pp. 470–77, doi:10.1107/s2052252518007303.' short: E. Martino, A. Arakcheeva, G. Autès, A. Pisoni, M.D. Bachmann, K.A. Modic, T. Helm, O.V. Yazyev, P.J.W. Moll, L. Forró, S. Katrych, IUCrJ 5 (2018) 470–477. date_created: 2019-11-19T13:11:15Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '01' ddc: - '530' doi: 10.1107/s2052252518007303 extern: '1' file: - access_level: open_access checksum: 5c6180c7d19da599dd50a067eb2efd50 content_type: application/pdf creator: dernst date_created: 2019-11-20T14:00:27Z date_updated: 2020-07-14T12:47:48Z file_id: '7090' file_name: 2018_IUCrJ_Martino.pdf file_size: 1563353 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 470-477 publication: IUCrJ publication_identifier: eissn: - 2052-2525 publication_status: published publisher: International Union of Crystallography (IUCr) quality_controlled: '1' status: public title: 'Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2018' ... --- _id: '7062' abstract: - lang: eng text: 'Weyl fermions are a recently discovered ingredient for correlated states of electronic matter. A key difficulty has been that real materials also contain non-Weyl quasiparticles, and disentangling the experimental signatures has proven challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal TaAs far into its quantum limit, where only the purely chiral 0th Landau levels of the Weyl fermions are occupied. We find the electrical resistivity to be nearly independent of magnetic field up to 50 T: unusual for conventional metals but consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a two-order-of-magnitude increase in resistivity, indicating that a gap opens in the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation below 2 K, suggesting a mesoscopically textured state of matter. These results point the way to inducing new correlated states of matter in the quantum limit of Weyl semimetals.' article_number: '2217' article_processing_charge: No article_type: original author: - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Yi full_name: Zhang, Yi last_name: Zhang - first_name: Eun-Ah full_name: Kim, Eun-Ah last_name: Kim - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: M. K. full_name: Chan, M. K. last_name: Chan - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: F. full_name: Balakirev, F. last_name: Balakirev - first_name: A. full_name: Migliori, A. last_name: Migliori - first_name: N. J. full_name: Ghimire, N. J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: F. full_name: Ronning, F. last_name: Ronning - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald citation: ama: Ramshaw BJ, Modic KA, Shekhter A, et al. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04542-9 apa: Ramshaw, B. J., Modic, K. A., Shekhter, A., Zhang, Y., Kim, E.-A., Moll, P. J. W., … McDonald, R. D. (2018). Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04542-9 chicago: Ramshaw, B. J., Kimberly A Modic, Arkady Shekhter, Yi Zhang, Eun-Ah Kim, Philip J. W. Moll, Maja D. Bachmann, et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04542-9. ieee: B. J. Ramshaw et al., “Quantum limit transport and destruction of the Weyl nodes in TaAs,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: Ramshaw BJ, Modic KA, Shekhter A, Zhang Y, Kim E-A, Moll PJW, Bachmann MD, Chan MK, Betts JB, Balakirev F, Migliori A, Ghimire NJ, Bauer ED, Ronning F, McDonald RD. 2018. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 9(1), 2217. mla: Ramshaw, B. J., et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications, vol. 9, no. 1, 2217, Springer Nature, 2018, doi:10.1038/s41467-018-04542-9. short: B.J. Ramshaw, K.A. Modic, A. Shekhter, Y. Zhang, E.-A. Kim, P.J.W. Moll, M.D. Bachmann, M.K. Chan, J.B. Betts, F. Balakirev, A. Migliori, N.J. Ghimire, E.D. Bauer, F. Ronning, R.D. McDonald, Nature Communications 9 (2018). date_created: 2019-11-19T13:10:33Z date_published: 2018-06-07T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '07' ddc: - '530' doi: 10.1038/s41467-018-04542-9 extern: '1' file: - access_level: open_access checksum: 9c53f9a1f06a4d83d5fe879d2478b7d7 content_type: application/pdf creator: dernst date_created: 2019-11-20T13:55:44Z date_updated: 2020-07-14T12:47:48Z file_id: '7089' file_name: 2018_NatureComm_Ramshaw.pdf file_size: 1794797 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Quantum limit transport and destruction of the Weyl nodes in TaAs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7059' abstract: - lang: eng text: Unusual behavior in quantum materials commonly arises from their effective low-dimensional physics, reflecting the underlying anisotropy in the spin and charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2, the second derivative of the free energy F with respect to the magnetic field orientation θ in the crystal. We show that the magnetotropic coefficient can be quantitatively determined from a shift in the resonant frequency of a commercially available atomic force microscopy cantilever under magnetic field. This detection method enables part per 100 million sensitivity and the ability to measure magnetic anisotropy in nanogram-scale samples, as demonstrated on the Weyl semimetal NbP. Measurement of the magnetotropic coefficient in the spin-liquid candidate RuCl3 highlights its sensitivity to anisotropic phase transitions and allows a quantitative comparison to other thermodynamic coefficients via the Ehrenfest relations. article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: F. full_name: Arnold, F. last_name: Arnold - first_name: K. R. full_name: Shirer, K. R. last_name: Shirer - first_name: Amelia full_name: Estry, Amelia last_name: Estry - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: Nirmal J. full_name: Ghimire, Nirmal J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: Marcus full_name: Schmidt, Marcus last_name: Schmidt - first_name: Michael full_name: Baenitz, Michael last_name: Baenitz - first_name: E. full_name: Svanidze, E. last_name: Svanidze - first_name: Ross D. full_name: McDonald, Ross D. last_name: McDonald - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll citation: ama: Modic KA, Bachmann MD, Ramshaw BJ, et al. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 2018;9(1):3975. doi:10.1038/s41467-018-06412-w apa: Modic, K. A., Bachmann, M. D., Ramshaw, B. J., Arnold, F., Shirer, K. R., Estry, A., … Moll, P. J. W. (2018). Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06412-w chicago: Modic, Kimberly A, Maja D. Bachmann, B. J. Ramshaw, F. Arnold, K. R. Shirer, Amelia Estry, J. B. Betts, et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06412-w. ieee: K. A. Modic et al., “Resonant torsion magnetometry in anisotropic quantum materials,” Nature Communications, vol. 9, no. 1. Springer Nature, p. 3975, 2018. ista: Modic KA, Bachmann MD, Ramshaw BJ, Arnold F, Shirer KR, Estry A, Betts JB, Ghimire NJ, Bauer ED, Schmidt M, Baenitz M, Svanidze E, McDonald RD, Shekhter A, Moll PJW. 2018. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 9(1), 3975. mla: Modic, Kimberly A., et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications, vol. 9, no. 1, Springer Nature, 2018, p. 3975, doi:10.1038/s41467-018-06412-w. short: K.A. Modic, M.D. Bachmann, B.J. Ramshaw, F. Arnold, K.R. Shirer, A. Estry, J.B. Betts, N.J. Ghimire, E.D. Bauer, M. Schmidt, M. Baenitz, E. Svanidze, R.D. McDonald, A. Shekhter, P.J.W. Moll, Nature Communications 9 (2018) 3975. date_created: 2019-11-19T13:02:20Z date_published: 2018-09-28T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '28' ddc: - '530' doi: 10.1038/s41467-018-06412-w extern: '1' file: - access_level: open_access checksum: 46a313c816e66899d4dad2cf3583e5b0 content_type: application/pdf creator: dernst date_created: 2019-11-20T12:48:58Z date_updated: 2020-07-14T12:47:48Z file_id: '7088' file_name: 2018_NatureComm_Modic.pdf file_size: 1257681 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '3975' publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Resonant torsion magnetometry in anisotropic quantum materials tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7058' abstract: - lang: eng text: We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3 and RuCl3, which have been discussed as possible realizations of the Kitaev model. The analysis of the reported discontinuity in torque, as an external magnetic field is rotated across the c axis in both crystals, suggests that they have a translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the ground state and persisting over a very wide range of magnetic field and temperature. An extraordinary |B|B2 dependence of the torque for small fields, beside the usual B2 part, is predicted by the chiral spin order. Data for small fields are available for γ−Li2IrO3 and are found to be consistent with the prediction upon further analysis. Other experiments such as inelastic scattering and thermal Hall effect and several questions raised by the discovery of chiral spin order, including its topological consequences, are discussed. article_number: '205110 ' article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: A. full_name: Shekhter, A. last_name: Shekhter - first_name: C. M. full_name: Varma, C. M. last_name: Varma citation: ama: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 2018;98(20). doi:10.1103/physrevb.98.205110 apa: Modic, K. A., Ramshaw, B. J., Shekhter, A., & Varma, C. M. (2018). Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. APS. https://doi.org/10.1103/physrevb.98.205110 chicago: Modic, Kimberly A, B. J. Ramshaw, A. Shekhter, and C. M. Varma. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B. APS, 2018. https://doi.org/10.1103/physrevb.98.205110. ieee: K. A. Modic, B. J. Ramshaw, A. Shekhter, and C. M. Varma, “Chiral spin order in some purported Kitaev spin-liquid compounds,” Physical Review B, vol. 98, no. 20. APS, 2018. ista: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. 2018. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 98(20), 205110. mla: Modic, Kimberly A., et al. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B, vol. 98, no. 20, 205110, APS, 2018, doi:10.1103/physrevb.98.205110. short: K.A. Modic, B.J. Ramshaw, A. Shekhter, C.M. Varma, Physical Review B 98 (2018). date_created: 2019-11-19T13:01:31Z date_published: 2018-11-05T00:00:00Z date_updated: 2021-01-12T08:11:36Z day: '05' doi: 10.1103/physrevb.98.205110 extern: '1' external_id: arxiv: - '1807.06637' intvolume: ' 98' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.06637 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: APS quality_controlled: '1' status: public title: Chiral spin order in some purported Kitaev spin-liquid compounds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '7060' abstract: - lang: eng text: The anomalous metallic state in the high-temperature superconducting cuprates is masked by superconductivity near a quantum critical point. Applying high magnetic fields to suppress superconductivity has enabled detailed studies of the normal state, yet the direct effect of strong magnetic fields on the metallic state is poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4 cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that the metallic state exposed by suppressing superconductivity is characterized by magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude of the linear-in-field resistivity mirrors the magnitude and doping evolution of the well-known linear-in-temperature resistivity that has been associated with quantum criticality in high-temperature superconductors. article_processing_charge: No article_type: original author: - first_name: P. full_name: Giraldo-Gallo, P. last_name: Giraldo-Gallo - first_name: J. A. full_name: Galvis, J. A. last_name: Galvis - first_name: Z. full_name: Stegen, Z. last_name: Stegen - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: F. F. full_name: Balakirev, F. F. last_name: Balakirev - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: X. full_name: Lian, X. last_name: Lian - first_name: C. full_name: Moir, C. last_name: Moir - first_name: S. C. full_name: Riggs, S. C. last_name: Riggs - first_name: J. full_name: Wu, J. last_name: Wu - first_name: A. T. full_name: Bollinger, A. T. last_name: Bollinger - first_name: X. full_name: He, X. last_name: He - first_name: I. full_name: Božović, I. last_name: Božović - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald - first_name: G. S. full_name: Boebinger, G. S. last_name: Boebinger - first_name: A. full_name: Shekhter, A. last_name: Shekhter citation: ama: Giraldo-Gallo P, Galvis JA, Stegen Z, et al. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 2018;361(6401):479-481. doi:10.1126/science.aan3178 apa: Giraldo-Gallo, P., Galvis, J. A., Stegen, Z., Modic, K. A., Balakirev, F. F., Betts, J. B., … Shekhter, A. (2018). Scale-invariant magnetoresistance in a cuprate superconductor. Science. AAAS. https://doi.org/10.1126/science.aan3178 chicago: Giraldo-Gallo, P., J. A. Galvis, Z. Stegen, Kimberly A Modic, F. F. Balakirev, J. B. Betts, X. Lian, et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science. AAAS, 2018. https://doi.org/10.1126/science.aan3178. ieee: P. Giraldo-Gallo et al., “Scale-invariant magnetoresistance in a cuprate superconductor,” Science, vol. 361, no. 6401. AAAS, pp. 479–481, 2018. ista: Giraldo-Gallo P, Galvis JA, Stegen Z, Modic KA, Balakirev FF, Betts JB, Lian X, Moir C, Riggs SC, Wu J, Bollinger AT, He X, Božović I, Ramshaw BJ, McDonald RD, Boebinger GS, Shekhter A. 2018. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 361(6401), 479–481. mla: Giraldo-Gallo, P., et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science, vol. 361, no. 6401, AAAS, 2018, pp. 479–81, doi:10.1126/science.aan3178. short: P. Giraldo-Gallo, J.A. Galvis, Z. Stegen, K.A. Modic, F.F. Balakirev, J.B. Betts, X. Lian, C. Moir, S.C. Riggs, J. Wu, A.T. Bollinger, X. He, I. Božović, B.J. Ramshaw, R.D. McDonald, G.S. Boebinger, A. Shekhter, Science 361 (2018) 479–481. date_created: 2019-11-19T13:03:16Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '03' doi: 10.1126/science.aan3178 extern: '1' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 479-481 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: Scale-invariant magnetoresistance in a cuprate superconductor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7116' abstract: - lang: eng text: 'Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.' article_processing_charge: No author: - first_name: Demjan full_name: Grubic, Demjan last_name: Grubic - first_name: Leo full_name: Tam, Leo last_name: Tam - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14' apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14' chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.' ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.' ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.' mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.' short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156. conference: end_date: 2018-03-29 location: Vienna, Austria name: 'EDBT: Conference on Extending Database Technology' start_date: 2018-03-26 date_created: 2019-11-26T14:19:11Z date_published: 2018-03-26T00:00:00Z date_updated: 2023-02-23T12:59:17Z day: '26' ddc: - '000' department: - _id: DaAl doi: 10.5441/002/EDBT.2018.14 file: - access_level: open_access checksum: ec979b56abc71016d6e6adfdadbb4afe content_type: application/pdf creator: dernst date_created: 2019-11-26T14:23:04Z date_updated: 2020-07-14T12:47:49Z file_id: '7118' file_name: 2018_OpenProceedings_Grubic.pdf file_size: 1603204 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 145-156 publication: Proceedings of the 21st International Conference on Extending Database Technology publication_identifier: isbn: - '9783893180783' issn: - 2367-2005 publication_status: published publisher: OpenProceedings quality_controlled: '1' scopus_import: 1 status: public title: 'Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '7126' abstract: - lang: eng text: In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are taken as generative models of samples, they generate samples with broad empirical distributions and with a high value of the relevance, defined as the entropy of the empirical frequencies. These results are derived for different statistical models (Dirichlet model, independent and pairwise dependent spin models, and restricted Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition point where the symmetry between the sampled outcomes is spontaneously broken. The order parameter controlling the phase transition is the coding cost of the samples. The phase transition is a manifestation of the optimality of MDL codes, and it arises because codes that achieve a higher compression do not exist. These results suggest a clear interpretation of the widespread occurrence of statistical criticality as a characterization of samples which are maximally informative on the underlying generative process. article_number: '755' article_processing_charge: No article_type: original author: - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi citation: ama: Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical. Entropy. 2018;20(10). doi:10.3390/e20100755 apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2018). Minimum description length codes are critical. Entropy. MDPI. https://doi.org/10.3390/e20100755 chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description Length Codes Are Critical.” Entropy. MDPI, 2018. https://doi.org/10.3390/e20100755. ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes are critical,” Entropy, vol. 20, no. 10. MDPI, 2018. ista: Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are critical. Entropy. 20(10), 755. mla: Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” Entropy, vol. 20, no. 10, 755, MDPI, 2018, doi:10.3390/e20100755. short: R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018). date_created: 2019-11-26T22:18:05Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:11:56Z day: '01' ddc: - '519' doi: 10.3390/e20100755 extern: '1' file: - access_level: open_access checksum: d642b7b661e1d5066b62e6ea9986b917 content_type: application/pdf creator: rcubero date_created: 2019-11-26T22:23:08Z date_updated: 2020-07-14T12:47:50Z file_id: '7127' file_name: entropy-20-00755-v2.pdf file_size: 1366813 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 20' issue: '10' keyword: - Minimum Description Length - normalized maximum likelihood - statistical criticality - phase transitions - large deviations language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Entropy publication_identifier: issn: - 1099-4300 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Minimum description length codes are critical tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2018' ... --- _id: '7277' abstract: - lang: eng text: 'Solid alkali metal carbonates are universal passivation layer components of intercalation battery materials and common side products in metal‐O2 batteries, and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs. Li/Li+. However, O2 evolution, as would be expected according to the decomposition reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted for, which was previously ascribed to unidentified parasitic reactions. Here, we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3 in an aprotic electrolyte and therefore does not evolve as O2. These results have substantial implications for the long‐term cyclability of batteries: they underpin the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and help explain the interfacial reactivity of transition‐metal cathodes with residual Li2CO3.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Sara E. full_name: Renfrew, Sara E. last_name: Renfrew - first_name: Bryan D. full_name: McCloskey, Bryan D. last_name: McCloskey - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 2018;57(19):5529-5533. doi:10.1002/anie.201802277 apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201802277 chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201802277. ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Electrochemical oxidation of Lithium Carbonate generates singlet oxygen,” Angewandte Chemie International Edition, vol. 57, no. 19. Wiley, pp. 5529–5533, 2018. ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 57(19), 5529–5533. mla: Mahne, Nika, et al. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition, vol. 57, no. 19, Wiley, 2018, pp. 5529–33, doi:10.1002/anie.201802277. short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie International Edition 57 (2018) 5529–5533. date_created: 2020-01-15T07:20:09Z date_published: 2018-03-15T00:00:00Z date_updated: 2021-01-12T08:12:42Z day: '15' ddc: - '540' doi: 10.1002/anie.201802277 extern: '1' file: - access_level: open_access checksum: 45868d0adc2d13a506bb9a59eb4f409c content_type: application/pdf creator: dernst date_created: 2020-01-22T16:28:31Z date_updated: 2020-07-14T12:47:55Z file_id: '7357' file_name: 2018_AngewChemie_Mahne.pdf file_size: 657963 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 57' issue: '19' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 5529-5533 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Electrochemical oxidation of Lithium Carbonate generates singlet oxygen tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '7271' abstract: - lang: eng text: The recent demand of multifunctional materials and devices for advanced applications in energy conversion and data storage resulted into a revival of multiferroics, that is, materials characterized by the coexistence of ferromagnetism and ferroelectricity. Despite intense efforts made in the past decade, single-phase room temperature multiferroics are yet to be discovered/fabricated. Nanostructured ferroic materials could potentially exhibit multiferroism since a high fraction of their atoms/ions are superficial, thereby altering significantly the properties of the bulk phase. Alternately, a magnetic order can be induced into ferroelectric materials upon aliovalent doping with magnetic ions. Here, we report on the synthesis of aggregate-free single-phase transition-metal-doped BaTiO3 quasi-monodisperse cuboidal nanocrystals (NC) which exhibit multiferroic properties at room temperature and can be suitable for applications in data storage. The proposed synthetic route allows the inclusion of a high concentration of magnetic ions such as Mn+ (M = Cr, Mn, Fe, Co) up to a nominal concentration of 4% without the formation of any secondary phase. The size of the nanocrystals was controlled in a wide range from ∼15 up to ∼70 nm by varying the reaction time from 48 to 144 h. The presence of unpaired electrons and their magnetic ordering have been probed by electron paramagnetic resonance spectroscopy (EPR), and a vibrating sample magnetometer (VSM). Likewise, an acentric structure, associated with the existence of a dielectric polarization, was observed by lattice dynamics analysis and piezoresponse force microscopy (PFM). These results show that high-quality titanium-containing perovskite nanocrystals which display multiferroic properties at room temperature can be fabricated via soft solution-based synthetic routes, and the properties of these materials can be modulated by changing the size of the nanocrystals and the concentration of the dopant thereby opening the door to the design and study of single-phase multiferroic materials. article_processing_charge: No article_type: original author: - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: John full_name: McCracken, John last_name: McCracken - first_name: Aurelian full_name: Rotaru, Aurelian last_name: Rotaru - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: ama: Costanzo T, McCracken J, Rotaru A, Caruntu G. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 2018;1(9):4863-4874. doi:10.1021/acsanm.8b01036 apa: Costanzo, T., McCracken, J., Rotaru, A., & Caruntu, G. (2018). Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. ACS. https://doi.org/10.1021/acsanm.8b01036 chicago: Costanzo, Tommaso, John McCracken, Aurelian Rotaru, and Gabriel Caruntu. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials. ACS, 2018. https://doi.org/10.1021/acsanm.8b01036. ieee: T. Costanzo, J. McCracken, A. Rotaru, and G. Caruntu, “Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties,” ACS Applied Nano Materials, vol. 1, no. 9. ACS, pp. 4863–4874, 2018. ista: Costanzo T, McCracken J, Rotaru A, Caruntu G. 2018. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 1(9), 4863–4874. mla: Costanzo, Tommaso, et al. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials, vol. 1, no. 9, ACS, 2018, pp. 4863–74, doi:10.1021/acsanm.8b01036. short: T. Costanzo, J. McCracken, A. Rotaru, G. Caruntu, ACS Applied Nano Materials 1 (2018) 4863–4874. date_created: 2020-01-13T21:58:27Z date_published: 2018-09-28T00:00:00Z date_updated: 2023-02-23T13:02:57Z day: '28' doi: 10.1021/acsanm.8b01036 extern: '1' intvolume: ' 1' issue: '9' language: - iso: eng month: '09' oa_version: None page: 4863-4874 publication: ACS Applied Nano Materials publication_identifier: issn: - 2574-0970 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2018' ... --- _id: '7287' abstract: - lang: eng text: Passivation layers on electrode materials are ubiquitous in nonaqueous battery chemistries and strongly govern performance and lifetime. They comprise breakdown products of the electrolyte including carbonate, alkyl carbonates, alkoxides, carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar products and is tied to the deviation of the O2 balance from the ideal stoichiometry during formation/decomposition of alkaline peroxides or superoxides. Accurate and integral quantification of carbonaceous species and peroxides or superoxides in battery electrodes remains, however, elusive. We present a refined procedure to quantify them accurately and sensitively by pointing out and rectifying pitfalls of previous procedures. Carbonaceous compounds are differentiated into inorganic and organic ones. We combine mass and UV–vis spectrometry to quantify evolved O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid treatment and Fenton’s reaction. The capabilities of the method are exemplified by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2 cathodes. article_processing_charge: No article_type: letter_note author: - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Anjana R. full_name: Raju, Anjana R. last_name: Raju - first_name: Musthafa Ottakam full_name: Thotiyl, Musthafa Ottakam last_name: Thotiyl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl B, Mourad E, Schafzahl L, et al. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 2018;3(1):170-176. doi:10.1021/acsenergylett.7b01111 apa: Schafzahl, B., Mourad, E., Schafzahl, L., Petit, Y. K., Raju, A. R., Thotiyl, M. O., … Freunberger, S. A. (2018). Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. ACS. https://doi.org/10.1021/acsenergylett.7b01111 chicago: Schafzahl, Bettina, Eléonore Mourad, Lukas Schafzahl, Yann K. Petit, Anjana R. Raju, Musthafa Ottakam Thotiyl, Martin Wilkening, Christian Slugovc, and Stefan Alexander Freunberger. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters. ACS, 2018. https://doi.org/10.1021/acsenergylett.7b01111. ieee: B. Schafzahl et al., “Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase,” ACS Energy Letters, vol. 3, no. 1. ACS, pp. 170–176, 2018. ista: Schafzahl B, Mourad E, Schafzahl L, Petit YK, Raju AR, Thotiyl MO, Wilkening M, Slugovc C, Freunberger SA. 2018. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 3(1), 170–176. mla: Schafzahl, Bettina, et al. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters, vol. 3, no. 1, ACS, 2018, pp. 170–76, doi:10.1021/acsenergylett.7b01111. short: B. Schafzahl, E. Mourad, L. Schafzahl, Y.K. Petit, A.R. Raju, M.O. Thotiyl, M. Wilkening, C. Slugovc, S.A. Freunberger, ACS Energy Letters 3 (2018) 170–176. date_created: 2020-01-15T12:13:52Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '01' ddc: - '540' - '543' - '546' - '547' doi: 10.1021/acsenergylett.7b01111 extern: '1' file: - access_level: open_access checksum: 461ccf575ba077af90314fe72d20521e content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:19:36Z date_updated: 2020-07-14T12:47:55Z file_id: '8049' file_name: O2 TIOC_fin_incl_SI.pdf file_size: 1892355 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 170-176 publication: ACS Energy Letters publication_identifier: issn: - 2380-8195 - 2380-8195 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2018' ... --- _id: '7285' abstract: - lang: eng text: Hydrogelation, the self-assembly of molecules into soft, water-loaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for long-range conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its long-range conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbon-like structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels. article_processing_charge: No article_type: original author: - first_name: Max full_name: Burian, Max last_name: Burian - first_name: Francesco full_name: Rigodanza, Francesco last_name: Rigodanza - first_name: Nicola full_name: Demitri, Nicola last_name: Demitri - first_name: Luka full_name: D̵ord̵ević, Luka last_name: D̵ord̵ević - first_name: Silvia full_name: Marchesan, Silvia last_name: Marchesan - first_name: Tereza full_name: Steinhartova, Tereza last_name: Steinhartova - first_name: Ilse full_name: Letofsky-Papst, Ilse last_name: Letofsky-Papst - first_name: Ivan full_name: Khalakhan, Ivan last_name: Khalakhan - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Maurizio full_name: Prato, Maurizio last_name: Prato - first_name: Zois full_name: Syrgiannis, Zois last_name: Syrgiannis citation: ama: Burian M, Rigodanza F, Demitri N, et al. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 2018;12(6):5800-5806. doi:10.1021/acsnano.8b01689 apa: Burian, M., Rigodanza, F., Demitri, N., D̵ord̵ević, L., Marchesan, S., Steinhartova, T., … Syrgiannis, Z. (2018). Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. ACS. https://doi.org/10.1021/acsnano.8b01689 chicago: Burian, Max, Francesco Rigodanza, Nicola Demitri, Luka D̵ord̵ević, Silvia Marchesan, Tereza Steinhartova, Ilse Letofsky-Papst, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano. ACS, 2018. https://doi.org/10.1021/acsnano.8b01689. ieee: M. Burian et al., “Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels,” ACS Nano, vol. 12, no. 6. ACS, pp. 5800–5806, 2018. ista: Burian M, Rigodanza F, Demitri N, D̵ord̵ević L, Marchesan S, Steinhartova T, Letofsky-Papst I, Khalakhan I, Mourad E, Freunberger SA, Amenitsch H, Prato M, Syrgiannis Z. 2018. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 12(6), 5800–5806. mla: Burian, Max, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano, vol. 12, no. 6, ACS, 2018, pp. 5800–06, doi:10.1021/acsnano.8b01689. short: M. Burian, F. Rigodanza, N. Demitri, L. D̵ord̵ević, S. Marchesan, T. Steinhartova, I. Letofsky-Papst, I. Khalakhan, E. Mourad, S.A. Freunberger, H. Amenitsch, M. Prato, Z. Syrgiannis, ACS Nano 12 (2018) 5800–5806. date_created: 2020-01-15T12:13:25Z date_published: 2018-06-05T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '05' ddc: - '540' - '541' doi: 10.1021/acsnano.8b01689 extern: '1' file: - access_level: open_access checksum: 050f7f0ba5d845c5c71779ef14ad5ef3 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:56:40Z date_updated: 2020-07-14T12:47:55Z file_id: '8052' file_name: Manuscript 20092017_subm.pdf file_size: 1333353 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 12' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 5800-5806 publication: ACS Nano publication_identifier: issn: - 1936-0851 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2018' ... --- _id: '7286' abstract: - lang: eng text: The solid electrolyte interphase (SEI) in Li and Na ion batteries forms when highly reducing or oxidizing electrode materials come into contact with a liquid organic electrolyte. Its ability to form a mechanically robust, ion-conducting, and electron-insulating layer critically determines performance, cycle life, and safety. Li or Na alkyl carbonates (LiAC and NaAC, respectively) are lead SEI components in state-of-the-art carbonate based electrolytes, and our fundamental understanding of their charge transport and mechanical properties may hold the key to designing electrolytes forming an improved SEI. We synthesized a homologous series of LiACs and NaACs from methyl to octyl analogues and characterized them with respect to structure, ionic conductivity, and stiffness. The compounds assume layered structures except for the lithium methyl carbonate. Room-temperature conductivities were found to be ∼10–9 S cm–1 for lithium methyl carbonate, <10–12 S cm–1 for the other LiACs, and <10–12 S cm–1 for the NaACs with ion transport mostly attributed to grain boundaries. While LiACs show stiffnesses of ∼1 GPa, NaACs become significantly softer with increasing chain lengths. These findings will help to more precisely interpret the complex results from charge transport and mechanical characterization of real SEIs and can give a rationale for influencing the SEI’s mechanical properties via the electrolyte. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Heike full_name: Ehmann, Heike last_name: Ehmann - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Jürgen full_name: Sattelkow, Jürgen last_name: Sattelkow - first_name: Thomas full_name: Ganner, Thomas last_name: Ganner - first_name: Harald full_name: Plank, Harald last_name: Plank - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: 'Schafzahl L, Ehmann H, Kriechbaum M, et al. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 2018;30(10):3338-3345. doi:10.1021/acs.chemmater.8b00750' apa: 'Schafzahl, L., Ehmann, H., Kriechbaum, M., Sattelkow, J., Ganner, T., Plank, H., … Freunberger, S. A. (2018). Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.8b00750' chicago: 'Schafzahl, Lukas, Heike Ehmann, Manfred Kriechbaum, Jürgen Sattelkow, Thomas Ganner, Harald Plank, Martin Wilkening, and Stefan Alexander Freunberger. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials. ACS, 2018. https://doi.org/10.1021/acs.chemmater.8b00750.' ieee: 'L. Schafzahl et al., “Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties,” Chemistry of Materials, vol. 30, no. 10. ACS, pp. 3338–3345, 2018.' ista: 'Schafzahl L, Ehmann H, Kriechbaum M, Sattelkow J, Ganner T, Plank H, Wilkening M, Freunberger SA. 2018. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 30(10), 3338–3345.' mla: 'Schafzahl, Lukas, et al. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials, vol. 30, no. 10, ACS, 2018, pp. 3338–45, doi:10.1021/acs.chemmater.8b00750.' short: L. Schafzahl, H. Ehmann, M. Kriechbaum, J. Sattelkow, T. Ganner, H. Plank, M. Wilkening, S.A. Freunberger, Chemistry of Materials 30 (2018) 3338–3345. date_created: 2020-01-15T12:13:37Z date_published: 2018-05-03T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '03' doi: 10.1021/acs.chemmater.8b00750 extern: '1' intvolume: ' 30' issue: '10' language: - iso: eng month: '05' oa_version: None page: 3338-3345 publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: ACS quality_controlled: '1' status: public title: 'Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2018' ... --- _id: '7407' abstract: - lang: eng text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems where a prover can convince a verifier that he "wastes" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO''15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ' alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59' apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59' chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59. ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25. ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.' mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59. short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25. conference: end_date: 2019-01-12 location: San Diego, CA, United States name: 'ITCS: Innovations in theoretical Computer Science Conference' start_date: 2019-01-10 date_created: 2020-01-30T09:16:05Z date_published: 2018-12-31T00:00:00Z date_updated: 2021-01-12T08:13:26Z day: '31' ddc: - '000' department: - _id: KrPi doi: 10.4230/LIPICS.ITCS.2019.59 ec_funded: 1 file: - access_level: open_access checksum: 5cebb7f7849a3beda898f697d755dd96 content_type: application/pdf creator: dernst date_created: 2020-02-04T08:17:52Z date_updated: 2020-07-14T12:47:57Z file_id: '7443' file_name: 2018_LIPIcs_Pietrzak.pdf file_size: 822884 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 124' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/194 month: '12' oa: 1 oa_version: Published Version page: 59:1-59:25 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) publication_identifier: isbn: - 978-3-95977-095-8 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Proofs of catalytic space tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2018' ... --- _id: '7458' abstract: - lang: eng text: The coupling between magnetic and electric subsystems in composites of ferromagnetic and ferroelectric phases is a product property that is facilitated by mechanical strain that arises due to magnetostriction and the piezoelectric effect in the constituent phases. Such multiferroic composites are of immense interests for studies on the physics of electromagnetic coupling and for use in a variety of applications. Here, we focus on magneto-electric (ME) coupling in nanocomposites. Particular emphasis is on core-shell particles and coaxial fibers, thin film heterostructures, and planar structures with a variety of mechanical connectivity. A brief review of models that predict strong ME effects in nanostructures is followed by synthesis and characterization. Core-shell particulate composites can be prepared by hydrothermal processes and chemical or deoxyribonucleic acid-assisted assembly. Electrospinning techniques have been utilized to prepare defect free core-shell nanofibers. Core-shell particles and fibers can be assembled into superstructures with the aid of magnetic and electric fields and characterized for possible use in advanced technologies. Chemical-vapor deposition techniques have been shown to be effective for the preparation of heterostructures of ferrites and ferroelectrics. Exotic planar multiferroic structures with potential for enhancing ME coupling strengths are also considered. Scanning probe microscopy techniques are ideal for probing the nature of direct- and converse-ME coupling in individual nanostructures. Magnetoelectric characterization of assemblies of nanocomposites can be done by ME voltage coefficient, magnetic field induced polarization, and magneto-dielectric effects. We conclude with a brief discussion on possible avenues for strengthening the product properties in the nanocomposites. article_number: '061101' article_processing_charge: No article_type: original author: - first_name: Dwight full_name: Viehland, Dwight last_name: Viehland - first_name: Jie Fang full_name: Li, Jie Fang last_name: Li - first_name: Yaodong full_name: Yang, Yaodong last_name: Yang - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Amin full_name: Yourdkhani, Amin last_name: Yourdkhani - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu - first_name: Peng full_name: Zhou, Peng last_name: Zhou - first_name: Tianjin full_name: Zhang, Tianjin last_name: Zhang - first_name: Tianqian full_name: Li, Tianqian last_name: Li - first_name: Arunava full_name: Gupta, Arunava last_name: Gupta - first_name: Maksym full_name: Popov, Maksym last_name: Popov - first_name: Gopalan full_name: Srinivasan, Gopalan last_name: Srinivasan citation: ama: 'Viehland D, Li JF, Yang Y, et al. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 2018;124(6). doi:10.1063/1.5038726' apa: 'Viehland, D., Li, J. F., Yang, Y., Costanzo, T., Yourdkhani, A., Caruntu, G., … Srinivasan, G. (2018). Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. AIP. https://doi.org/10.1063/1.5038726' chicago: 'Viehland, Dwight, Jie Fang Li, Yaodong Yang, Tommaso Costanzo, Amin Yourdkhani, Gabriel Caruntu, Peng Zhou, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics. AIP, 2018. https://doi.org/10.1063/1.5038726.' ieee: 'D. Viehland et al., “Tutorial: Product properties in multiferroic nanocomposites,” Journal of Applied Physics, vol. 124, no. 6. AIP, 2018.' ista: 'Viehland D, Li JF, Yang Y, Costanzo T, Yourdkhani A, Caruntu G, Zhou P, Zhang T, Li T, Gupta A, Popov M, Srinivasan G. 2018. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 124(6), 061101.' mla: 'Viehland, Dwight, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics, vol. 124, no. 6, 061101, AIP, 2018, doi:10.1063/1.5038726.' short: D. Viehland, J.F. Li, Y. Yang, T. Costanzo, A. Yourdkhani, G. Caruntu, P. Zhou, T. Zhang, T. Li, A. Gupta, M. Popov, G. Srinivasan, Journal of Applied Physics 124 (2018). date_created: 2020-02-05T14:18:22Z date_published: 2018-08-10T00:00:00Z date_updated: 2023-02-23T13:08:29Z day: '10' doi: 10.1063/1.5038726 extern: '1' intvolume: ' 124' issue: '6' language: - iso: eng month: '08' oa_version: None publication: Journal of Applied Physics publication_identifier: issn: - 0021-8979 - 1089-7550 publication_status: published publisher: AIP quality_controlled: '1' status: public title: 'Tutorial: Product properties in multiferroic nanocomposites' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2018' ... --- _id: '7717' abstract: - lang: eng text: "Background: DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals.\r\nMethods: We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90 years).\r\nResults: After stringent quality control, we identified 1507 DNA methylation CpG sites (rsCpGs) with statistically significant variation in the rate of change (random slope) of DNA methylation among individuals in a mixed linear model analysis. Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription factors and the Wnt signalling pathway, both of which are related to ageing processes. Furthermore, we investigated the SNP effect on the random slope. We found that 4 out of 1507 rsCpGs had one significant (P < 5 × 10−8/1507) SNP effect and 343 rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide significance (P < 5 × 10−8). Ninety-five percent of the significant (P < 5 × 10−8) SNPs are on different chromosomes from their corresponding probes.\r\nConclusions: We identified CpG sites that have variability in the rate of change of DNA methylation between individuals, and our results suggest a genetic basis of this variation. Genes around these CpG sites have been reported to be involved in the ageing process." article_number: '75' article_processing_charge: No article_type: original author: - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: Riccardo E full_name: Marioni, Riccardo E last_name: Marioni - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jon full_name: Higham, Jon last_name: Higham - first_name: Duncan full_name: Sproul, Duncan last_name: Sproul - first_name: Naomi R full_name: Wray, Naomi R last_name: Wray - first_name: Ian J full_name: Deary, Ian J last_name: Deary - first_name: Allan F full_name: McRae, Allan F last_name: McRae - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: ama: Zhang Q, Marioni RE, Robinson MR, et al. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 2018;10(1). doi:10.1186/s13073-018-0585-7 apa: Zhang, Q., Marioni, R. E., Robinson, M. R., Higham, J., Sproul, D., Wray, N. R., … Visscher, P. M. (2018). Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-018-0585-7 chicago: Zhang, Qian, Riccardo E Marioni, Matthew Richard Robinson, Jon Higham, Duncan Sproul, Naomi R Wray, Ian J Deary, Allan F McRae, and Peter M Visscher. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine. Springer Nature, 2018. https://doi.org/10.1186/s13073-018-0585-7. ieee: Q. Zhang et al., “Genotype effects contribute to variation in longitudinal methylome patterns in older people,” Genome Medicine, vol. 10, no. 1. Springer Nature, 2018. ista: Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae AF, Visscher PM. 2018. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 10(1), 75. mla: Zhang, Qian, et al. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine, vol. 10, no. 1, 75, Springer Nature, 2018, doi:10.1186/s13073-018-0585-7. short: Q. Zhang, R.E. Marioni, M.R. Robinson, J. Higham, D. Sproul, N.R. Wray, I.J. Deary, A.F. McRae, P.M. Visscher, Genome Medicine 10 (2018). date_created: 2020-04-30T10:42:50Z date_published: 2018-10-22T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '22' doi: 10.1186/s13073-018-0585-7 extern: '1' intvolume: ' 10' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s13073-018-0585-7 month: '10' oa: 1 oa_version: Published Version publication: Genome Medicine publication_identifier: issn: - 1756-994X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Genotype effects contribute to variation in longitudinal methylome patterns in older people type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '7718' abstract: - lang: eng text: Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores. article_processing_charge: No article_type: original author: - first_name: Serena full_name: Tucci, Serena last_name: Tucci - first_name: Samuel H. full_name: Vohr, Samuel H. last_name: Vohr - first_name: Rajiv C. full_name: McCoy, Rajiv C. last_name: McCoy - first_name: Benjamin full_name: Vernot, Benjamin last_name: Vernot - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Chiara full_name: Barbieri, Chiara last_name: Barbieri - first_name: Brad J. full_name: Nelson, Brad J. last_name: Nelson - first_name: Wenqing full_name: Fu, Wenqing last_name: Fu - first_name: Gludhug A. full_name: Purnomo, Gludhug A. last_name: Purnomo - first_name: Herawati full_name: Sudoyo, Herawati last_name: Sudoyo - first_name: Evan E. full_name: Eichler, Evan E. last_name: Eichler - first_name: Guido full_name: Barbujani, Guido last_name: Barbujani - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Joshua M. full_name: Akey, Joshua M. last_name: Akey - first_name: Richard E. full_name: Green, Richard E. last_name: Green citation: ama: Tucci S, Vohr SH, McCoy RC, et al. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 2018;361(6401):511-516. doi:10.1126/science.aar8486 apa: Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., … Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aar8486 chicago: Tucci, Serena, Samuel H. Vohr, Rajiv C. McCoy, Benjamin Vernot, Matthew Richard Robinson, Chiara Barbieri, Brad J. Nelson, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aar8486. ieee: S. Tucci et al., “Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia,” Science, vol. 361, no. 6401. American Association for the Advancement of Science, pp. 511–516, 2018. ista: Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 361(6401), 511–516. mla: Tucci, Serena, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science, vol. 361, no. 6401, American Association for the Advancement of Science, 2018, pp. 511–16, doi:10.1126/science.aar8486. short: S. Tucci, S.H. Vohr, R.C. McCoy, B. Vernot, M.R. Robinson, C. Barbieri, B.J. Nelson, W. Fu, G.A. Purnomo, H. Sudoyo, E.E. Eichler, G. Barbujani, P.M. Visscher, J.M. Akey, R.E. Green, Science 361 (2018) 511–516. date_created: 2020-04-30T10:43:24Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '03' doi: 10.1126/science.aar8486 extern: '1' external_id: pmid: - '30072539' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 511-516 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7712' abstract: - lang: eng text: 'Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait.' article_number: '5407' article_processing_charge: No article_type: original author: - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 2018;9. doi:10.1038/s41467-018-07862-y apa: Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y chicago: Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y. ieee: C. X. Yap et al., “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407. mla: Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer Nature, 2018, doi:10.1038/s41467-018-07862-y. short: C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:19Z date_published: 2018-12-20T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '20' doi: 10.1038/s41467-018-07862-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-07862-y month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Dissection of genetic variation and evidence for pleiotropy in male pattern baldness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7716' abstract: - lang: eng text: Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait. article_number: '989' article_processing_charge: No article_type: original author: - first_name: Robert M. full_name: Maier, Robert M. last_name: Maier - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Sang Hong full_name: Lee, Sang Hong last_name: Lee - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Douglas M. full_name: Ruderfer, Douglas M. last_name: Ruderfer - first_name: Eli A. full_name: Stahl, Eli A. last_name: Stahl - first_name: Stephan full_name: Ripke, Stephan last_name: Ripke - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 2018;9. doi:10.1038/s41467-017-02769-6 apa: Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02769-6 chicago: Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6. ieee: R. M. Maier et al., “Improving genetic prediction by leveraging genetic correlations among human diseases and traits,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 9, 989. mla: Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications, vol. 9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6. short: R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl, S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications 9 (2018). date_created: 2020-04-30T10:42:29Z date_published: 2018-03-07T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '07' doi: 10.1038/s41467-017-02769-6 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02769-6 month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Improving genetic prediction by leveraging genetic correlations among human diseases and traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7715' abstract: - lang: eng text: Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes. article_processing_charge: No article_type: original author: - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Matthew C. full_name: Keller, Matthew C. last_name: Keller - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Yuanhao full_name: Yang, Yuanhao last_name: Yang - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jacob full_name: Gratten, Jacob last_name: Gratten - first_name: Patrick full_name: Turley, Patrick last_name: Turley - first_name: David full_name: Cesarini, David last_name: Cesarini - first_name: Daniel J. full_name: Benjamin, Daniel J. last_name: Benjamin - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Michael E. full_name: Goddard, Michael E. last_name: Goddard - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3 apa: Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3 chicago: Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper, Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018. https://doi.org/10.1038/s41562-018-0476-3. ieee: L. Yengo et al., “Imprint of assortative mating on the human genome,” Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018. ista: Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. 2018. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2(12), 948–954. mla: Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3. short: L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski, J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J. Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954. date_created: 2020-04-30T10:42:12Z date_published: 2018-11-26T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '26' doi: 10.1038/s41562-018-0476-3 extern: '1' intvolume: ' 2' issue: '12' language: - iso: eng month: '11' oa_version: None page: 948-954 publication: Nature Human Behaviour publication_identifier: issn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Imprint of assortative mating on the human genome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '7714' abstract: - lang: eng text: Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer’s disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative). article_number: '224' article_processing_charge: No article_type: original author: - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Futao full_name: Zhang, Futao last_name: Zhang - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Robert full_name: Maier, Robert last_name: Maier - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John J. full_name: McGrath, John J. last_name: McGrath - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 2018;9. doi:10.1038/s41467-017-02317-2 apa: Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang, J. (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2 chicago: Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2. ieee: Z. Zhu et al., “Causal associations between risk factors and common diseases inferred from GWAS summary data,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 9, 224. mla: Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer Nature, 2018, doi:10.1038/s41467-017-02317-2. short: Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson, J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:55Z date_published: 2018-01-15T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '15' doi: 10.1038/s41467-017-02317-2 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02317-2 month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Causal associations between risk factors and common diseases inferred from GWAS summary data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7713' abstract: - lang: eng text: There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations. article_number: '1865' article_processing_charge: No article_type: original author: - first_name: Jing full_name: Guo, Jing last_name: Guo - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y apa: Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J. (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y chicago: Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y. ieee: J. Guo et al., “Global genetic differentiation of complex traits shaped by natural selection in humans,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 9, 1865. mla: Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer Nature, 2018, doi:10.1038/s41467-018-04191-y. short: J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson, P.M. Visscher, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:36Z date_published: 2018-05-14T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '14' doi: 10.1038/s41467-018-04191-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-04191-y month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Global genetic differentiation of complex traits shaped by natural selection in humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7721' abstract: - lang: eng text: 'The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.' article_processing_charge: No article_type: original author: - first_name: R. M. full_name: Maier, R. M. last_name: Maier - first_name: P. M. full_name: Visscher, P. M. last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: N. R. full_name: Wray, N. R. last_name: Wray citation: ama: 'Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 2018;48(7):1055-1067. doi:10.1017/s0033291717002318' apa: 'Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018). Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318' chicago: 'Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318.' ieee: 'R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity: A review of methods and tools for psychiatric genetics research,” Psychological Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.' ista: 'Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 48(7), 1055–1067.' mla: 'Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no. 7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.' short: R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine 48 (2018) 1055–1067. date_created: 2020-04-30T10:44:35Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:15:05Z day: '01' doi: 10.1017/s0033291717002318 extern: '1' intvolume: ' 48' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/s0033291717002318 month: '05' oa: 1 oa_version: Published Version page: 1055-1067 publication: Psychological Medicine publication_identifier: issn: - 0033-2917 - 1469-8978 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: 'Embracing polygenicity: A review of methods and tools for psychiatric genetics research' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2018' ... --- _id: '7723' abstract: - lang: eng text: Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects. article_processing_charge: No article_type: original author: - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360 apa: Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360 chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360. ieee: L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018. ista: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408. mla: Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360. short: L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408. date_created: 2020-04-30T10:45:19Z date_published: 2018-04-01T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '01' doi: 10.1534/genetics.117.300360 extern: '1' intvolume: ' 208' issue: '4' language: - iso: eng month: '04' oa_version: None page: 1397-1408 publication: Genetics publication_identifier: issn: - 0016-6731 - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 208 year: '2018' ... --- _id: '7722' abstract: - lang: eng text: We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits. article_processing_charge: No article_type: original author: - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Ronald full_name: de Vlaming, Ronald last_name: de Vlaming - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Angli full_name: Xue, Angli last_name: Xue - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Allan F. full_name: McRae, Allan F. last_name: McRae - first_name: Joseph E. full_name: Powell, Joseph E. last_name: Powell - first_name: Grant W. full_name: Montgomery, Grant W. last_name: Montgomery - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Greg full_name: Gibson, Greg last_name: Gibson - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4 apa: Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4 chicago: Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4. ieee: J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018. ista: Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753. mla: Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4. short: J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753. date_created: 2020-04-30T10:44:57Z date_published: 2018-04-16T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '16' doi: 10.1038/s41588-018-0101-4 extern: '1' intvolume: ' 50' issue: '5' language: - iso: eng month: '04' oa_version: None page: 746-753 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Signatures of negative selection in the genetic architecture of human complex traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2018' ... --- _id: '7724' abstract: - lang: eng text: Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species. article_processing_charge: No article_type: original author: - first_name: Jaleal S. full_name: Sanjak, Jaleal S. last_name: Sanjak - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Kevin R. full_name: Thornton, Kevin R. last_name: Thornton - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114 apa: Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114 chicago: Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114. ieee: J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018. ista: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156. mla: Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114. short: J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156. date_created: 2020-04-30T10:45:43Z date_published: 2018-01-02T00:00:00Z date_updated: 2021-01-12T08:15:07Z day: '02' doi: 10.1073/pnas.1707227114 extern: '1' intvolume: ' 115' issue: '1' language: - iso: eng month: '01' oa_version: None page: 151-156 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1073/pnas.1806837115 status: public title: Evidence of directional and stabilizing selection in contemporary humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '7754' abstract: - lang: eng text: Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex. article_number: '4348' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner - first_name: Katharina full_name: Ribbeck, Katharina last_name: Ribbeck citation: ama: Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5 apa: Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5 chicago: Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5. ieee: C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348. mla: Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5. short: C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018). date_created: 2020-04-30T11:38:01Z date_published: 2018-10-19T00:00:00Z date_updated: 2021-01-12T08:15:18Z day: '19' doi: 10.1038/s41467-018-06851-5 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-06851-5 month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Enhanced diffusion by binding to the crosslinks of a polymer gel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ...