--- _id: '943' abstract: - lang: eng text: Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation. article_processing_charge: No author: - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Yoji full_name: Tabata, Yoji last_name: Tabata - first_name: Nathalie full_name: Brandenberg, Nathalie last_name: Brandenberg - first_name: Matthias full_name: Lutolf, Matthias last_name: Lutolf - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias last_name: Bollenbach - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887 apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887 chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887. ieee: M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017. ista: Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383. mla: Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887. short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383. date_created: 2018-12-11T11:49:20Z date_published: 2017-06-30T00:00:00Z date_updated: 2023-09-26T15:38:05Z day: '30' department: - _id: AnKi - _id: GaTk doi: 10.1126/science.aam5887 ec_funded: 1 external_id: isi: - '000404351500036' pmid: - '28663499' intvolume: ' 356' isi: 1 issue: '6345' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/ month: '06' oa: 1 oa_version: Submitted Version page: 1379 - 1383 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2524F500-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '201439' name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6474' quality_controlled: '1' scopus_import: '1' status: public title: Decoding of position in the developing neural tube from antiparallel morphogen gradients type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 356 year: '2017' ... --- _id: '944' abstract: - lang: eng text: The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms. acknowledged_ssus: - _id: Bio - _id: PreCl article_processing_charge: No author: - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter orcid: 0000-0002-7903-3010 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Guanxi full_name: Xiao, Guanxi last_name: Xiao - first_name: Olga full_name: Klezovitch, Olga last_name: Klezovitch - first_name: Valeri full_name: Vasioukhin, Valeri last_name: Vasioukhin - first_name: Troy full_name: Ghashghaei, Troy last_name: Ghashghaei - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012 apa: Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012 chicago: Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012. ieee: R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017. ista: Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3. mla: Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012. short: R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3. date_created: 2018-12-11T11:49:20Z date_published: 2017-05-03T00:00:00Z date_updated: 2023-09-26T15:37:02Z day: '03' department: - _id: SiHi - _id: MaJö doi: 10.1016/j.neuron.2017.04.012 ec_funded: 1 external_id: isi: - '000400466700011' intvolume: ' 94' isi: 1 issue: '3' language: - iso: eng month: '05' oa_version: None page: 517 - 533.e3 project: - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 25D7962E-B435-11E9-9278-68D0E5697425 grant_number: RGP0053/2014 name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level publication: Neuron publication_identifier: issn: - '08966273' publication_status: published publisher: Cell Press publist_id: '6473' quality_controlled: '1' scopus_import: '1' status: public title: Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 94 year: '2017' ... --- _id: '942' abstract: - lang: eng text: 'A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. ' article_processing_charge: No author: - first_name: Xuan full_name: Le, Xuan last_name: Le - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: David full_name: Lo, David last_name: Lo - first_name: Claire full_name: Le Goues, Claire last_name: Le Goues - first_name: Willem full_name: Visser, Willem last_name: Visser citation: ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309' apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309' chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.' ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.' ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.' mla: 'Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.' short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604. conference: end_date: 2017-09-08 location: Paderborn, Germany name: 'FSE: Foundations of Software Engineering' start_date: 2017-09-04 date_created: 2018-12-11T11:49:19Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-26T15:38:36Z day: '01' department: - _id: ToHe doi: 10.1145/3106237.3106309 external_id: isi: - '000414279300055' isi: 1 language: - iso: eng month: '09' oa_version: None page: 593 - 604 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-145035105-8 publication_status: published publisher: ACM publist_id: '6477' quality_controlled: '1' scopus_import: '1' status: public title: 'S3: Syntax- and semantic-guided repair synthesis via programming by examples' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: F130154 year: '2017' ... --- _id: '939' abstract: - lang: eng text: We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding. article_number: '033905' article_processing_charge: No author: - first_name: Bikashkali full_name: Midya, Bikashkali id: 456187FC-F248-11E8-B48F-1D18A9856A87 last_name: Midya - first_name: Vladimir full_name: Konotop, Vladimir last_name: Konotop citation: ama: 'Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905' apa: 'Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905' chicago: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.' ieee: 'B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.' ista: 'Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.' mla: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.' short: B. Midya, V. Konotop, Physical Review Letters 119 (2017). date_created: 2018-12-11T11:49:18Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-09-26T15:39:46Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevLett.119.033905 ec_funded: 1 external_id: isi: - '000405718200012' intvolume: ' 119' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: 'https://arxiv.org/abs/1706.04085 ' month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6481' quality_controlled: '1' scopus_import: '1' status: public title: 'Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 119 year: '2017' ... --- _id: '9853' abstract: - lang: eng text: Egg laying rates and infection loads of C. obscurior queens article_processing_charge: No author: - first_name: Julia full_name: Giehr, Julia last_name: Giehr - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Raw data from ant queens increase their reproductive efforts after pathogen infection. 2017. doi:10.6084/m9.figshare.5117788.v1 apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Raw data from ant queens increase their reproductive efforts after pathogen infection. The Royal Society. https://doi.org/10.6084/m9.figshare.5117788.v1 chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5117788.v1. ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Raw data from ant queens increase their reproductive efforts after pathogen infection.” The Royal Society, 2017. ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Raw data from ant queens increase their reproductive efforts after pathogen infection, The Royal Society, 10.6084/m9.figshare.5117788.v1. mla: Giehr, Julia, et al. Raw Data from Ant Queens Increase Their Reproductive Efforts after Pathogen Infection. The Royal Society, 2017, doi:10.6084/m9.figshare.5117788.v1. short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, (2017). date_created: 2021-08-10T06:57:57Z date_published: 2017-06-19T00:00:00Z date_updated: 2023-09-26T15:45:47Z day: '19' department: - _id: SyCr doi: 10.6084/m9.figshare.5117788.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5117788.v1 month: '06' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '914' relation: used_in_publication status: public status: public title: Raw data from ant queens increase their reproductive efforts after pathogen infection type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '822' abstract: - lang: eng text: 'Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. ' article_processing_charge: No author: - first_name: Marjon full_name: De Vos, Marjon id: 3111FFAC-F248-11E8-B48F-1D18A9856A87 last_name: De Vos - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Alan full_name: Mcnally, Alan last_name: Mcnally - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114 apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114 chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114. ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017. ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671. mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114. short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671. date_created: 2018-12-11T11:48:41Z date_published: 2017-10-03T00:00:00Z date_updated: 2023-09-26T16:18:48Z day: '03' department: - _id: ToBo doi: 10.1073/pnas.1713372114 ec_funded: 1 external_id: isi: - '000412130500061' pmid: - '28923953' intvolume: ' 114' isi: 1 issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/ month: '10' oa: 1 oa_version: Submitted Version page: 10666 - 10671 pmid: 1 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '6827' quality_controlled: '1' scopus_import: '1' status: public title: Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 114 year: '2017' ... --- _id: '833' abstract: - lang: eng text: We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams. alternative_title: - LNCS article_processing_charge: No author: - first_name: Teresa full_name: Heiss, Teresa id: 4879BB4E-F248-11E8-B48F-1D18A9856A87 last_name: Heiss orcid: 0000-0002-1780-2689 - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:10.1007/978-3-319-64689-3_32' apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32' chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32. ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.' ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.' mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32. short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409. conference: end_date: 2017-08-24 location: Ystad, Sweden name: 'CAIP: Computer Analysis of Images and Patterns' start_date: 2017-08-22 date_created: 2018-12-11T11:48:45Z date_published: 2017-07-28T00:00:00Z date_updated: 2023-09-26T16:10:03Z day: '28' department: - _id: HeEd doi: 10.1007/978-3-319-64689-3_32 editor: - first_name: Michael full_name: Felsberg, Michael last_name: Felsberg - first_name: Anders full_name: Heyden, Anders last_name: Heyden - first_name: Norbert full_name: Krüger, Norbert last_name: Krüger external_id: isi: - '000432085900032' intvolume: ' 10424' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.02045 month: '07' oa: 1 oa_version: Submitted Version page: 397 - 409 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6815' quality_controlled: '1' scopus_import: '1' status: public title: Streaming algorithm for Euler characteristic curves of multidimensional images type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10424 year: '2017' ... --- _id: '805' abstract: - lang: eng text: During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2). article_processing_charge: No author: - first_name: Sabrina full_name: Pfurr, Sabrina last_name: Pfurr - first_name: Yu full_name: Chu, Yu last_name: Chu - first_name: Christian full_name: Bohrer, Christian last_name: Bohrer - first_name: Franziska full_name: Greulich, Franziska last_name: Greulich - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Könül full_name: Mammadzada, Könül last_name: Mammadzada - first_name: Miriam full_name: Hils, Miriam last_name: Hils - first_name: Sebastian full_name: Arnold, Sebastian last_name: Arnold - first_name: Verdon full_name: Taylor, Verdon last_name: Taylor - first_name: Kristina full_name: Schachtrup, Kristina last_name: Schachtrup - first_name: N Henriette full_name: Uhlenhaut, N Henriette last_name: Uhlenhaut - first_name: Christian full_name: Schachtrup, Christian last_name: Schachtrup citation: ama: Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 2017;144:3917-3931. doi:10.1242/dev.145698 apa: Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. Company of Biologists. https://doi.org/10.1242/dev.145698 chicago: Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.145698. ieee: S. Pfurr et al., “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” Development, vol. 144. Company of Biologists, pp. 3917–3931, 2017. ista: Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931. mla: Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” Development, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:10.1242/dev.145698. short: S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931. date_created: 2018-12-11T11:48:36Z date_published: 2017-10-31T00:00:00Z date_updated: 2023-09-26T16:20:09Z day: '31' department: - _id: SiHi doi: 10.1242/dev.145698 external_id: isi: - '000414025600007' intvolume: ' 144' isi: 1 language: - iso: eng month: '10' oa_version: None page: 3917 - 3931 publication: Development publication_status: published publisher: Company of Biologists publist_id: '6846' quality_controlled: '1' scopus_import: '1' status: public title: The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 144 year: '2017' ... --- _id: '834' abstract: - lang: eng text: 'Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.' acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover, and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915) article_number: '104201' article_processing_charge: No author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Papic full_name: Zlatko, Papic last_name: Zlatko - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin citation: ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201 apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201 chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201. ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10. American Physical Society, 2017. ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201. mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201. short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:48:45Z date_published: 2017-09-06T00:00:00Z date_updated: 2023-09-26T15:51:54Z day: '06' department: - _id: MaSe doi: 10.1103/PhysRevB.96.104201 external_id: isi: - '000409429300004' intvolume: ' 96' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.02389 month: '09' oa: 1 oa_version: Submitted Version publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6814' quality_controlled: '1' scopus_import: '1' status: public title: Thouless energy and multifractality across the many-body localization transition type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '823' abstract: - lang: eng text: The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region. article_number: '093404' article_processing_charge: No author: - first_name: Simona full_name: Colabrese, Simona last_name: Colabrese - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Luca full_name: Leuzzi, Luca last_name: Leuzzi - first_name: Enzo full_name: Marinari, Enzo last_name: Marinari citation: ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3' apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3' chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.' ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.' ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.' mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.' short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).' date_created: 2018-12-11T11:48:41Z date_published: 2017-09-26T00:00:00Z date_updated: 2023-09-26T16:18:12Z day: '26' department: - _id: GaTk doi: 10.1088/1742-5468/aa85c3 ec_funded: 1 external_id: isi: - '000411842900001' intvolume: ' 2017' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.06303 month: '09' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: issn: - '17425468' publication_status: published publisher: IOPscience publist_id: '6826' quality_controlled: '1' scopus_import: '1' status: public title: Phase transitions in integer linear problems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2017 year: '2017' ...