@unpublished{9435, abstract = {For any given positive integer l, we prove that every plane deformation of a circlewhich preserves the 1/2and 1/ (2l + 1) -rational caustics is trivial i.e. the deformationconsists only of similarities (rescalings and isometries).}, author = {Kaloshin, Vadim and Koudjinan, Edmond}, title = {{Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles}}, year = {2021}, } @inproceedings{9604, abstract = {Generalizing Lee’s inductive argument for counting the cells of higher order Voronoi tessellations in ℝ² to ℝ³, we get precise relations in terms of Morse theoretic quantities for piecewise constant functions on planar arrangements. Specifically, we prove that for a generic set of n ≥ 5 points in ℝ³, the number of regions in the order-k Voronoi tessellation is N_{k-1} - binom(k,2)n + n, for 1 ≤ k ≤ n-1, in which N_{k-1} is the sum of Euler characteristics of these function’s first k-1 sublevel sets. We get similar expressions for the vertices, edges, and polygons of the order-k Voronoi tessellation.}, author = {Biswas, Ranita and Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza}, booktitle = {Leibniz International Proceedings in Informatics}, isbn = {9783959771849}, issn = {18688969}, location = {Online}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Counting cells of order-k voronoi tessellations in ℝ3 with morse theory}}, doi = {10.4230/LIPIcs.SoCG.2021.16}, volume = {189}, year = {2021}, } @inproceedings{9620, abstract = {In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019). We provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.}, author = {Alistarh, Dan-Adrian and Davies, Peter}, booktitle = {Structural Information and Communication Complexity}, isbn = {9783030795269}, issn = {1611-3349}, location = {Wrocław, Poland}, pages = {3--12}, publisher = {Springer Nature}, title = {{Collecting coupons is faster with friends}}, doi = {10.1007/978-3-030-79527-6_1}, volume = {12810}, year = {2021}, } @inproceedings{9826, abstract = {Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices. We propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks.}, author = {Auerbach, Benedikt and Chakraborty, Suvradip and Klein, Karen and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z and Walter, Michael and Yeo, Michelle X}, booktitle = {Topics in Cryptology – CT-RSA 2021}, isbn = {9783030755386}, issn = {16113349}, location = {Virtual Event}, pages = {399--421}, publisher = {Springer Nature}, title = {{Inverse-Sybil attacks in automated contact tracing}}, doi = {10.1007/978-3-030-75539-3_17}, volume = {12704}, year = {2021}, } @inproceedings{9825, abstract = {The dual attack has long been considered a relevant attack on lattice-based cryptographic schemes relying on the hardness of learning with errors (LWE) and its structured variants. As solving LWE corresponds to finding a nearest point on a lattice, one may naturally wonder how efficient this dual approach is for solving more general closest vector problems, such as the classical closest vector problem (CVP), the variants bounded distance decoding (BDD) and approximate CVP, and preprocessing versions of these problems. While primal, sieving-based solutions to these problems (with preprocessing) were recently studied in a series of works on approximate Voronoi cells [Laa16b, DLdW19, Laa20, DLvW20], for the dual attack no such overview exists, especially for problems with preprocessing. With one of the take-away messages of the approximate Voronoi cell line of work being that primal attacks work well for approximate CVP(P) but scale poorly for BDD(P), one may further wonder if the dual attack suffers the same drawbacks, or if it is perhaps a better solution when trying to solve BDD(P). In this work we provide an overview of cost estimates for dual algorithms for solving these “classical” closest lattice vector problems. Heuristically we expect to solve the search version of average-case CVPP in time and space 20.293𝑑+𝑜(𝑑) in the single-target model. The distinguishing version of average-case CVPP, where we wish to distinguish between random targets and targets planted at distance (say) 0.99⋅𝑔𝑑 from the lattice, has the same complexity in the single-target model, but can be solved in time and space 20.195𝑑+𝑜(𝑑) in the multi-target setting, when given a large number of targets from either target distribution. This suggests an inequivalence between distinguishing and searching, as we do not expect a similar improvement in the multi-target setting to hold for search-CVPP. We analyze three slightly different decoders, both for distinguishing and searching, and experimentally obtain concrete cost estimates for the dual attack in dimensions 50 to 80, which confirm our heuristic assumptions, and show that the hidden order terms in the asymptotic estimates are quite small. Our main take-away message is that the dual attack appears to mirror the approximate Voronoi cell line of work – whereas using approximate Voronoi cells works well for approximate CVP(P) but scales poorly for BDD(P), the dual approach scales well for BDD(P) instances but performs poorly on approximate CVP(P).}, author = {Laarhoven, Thijs and Walter, Michael}, booktitle = {Topics in Cryptology – CT-RSA 2021}, isbn = {9783030755386}, issn = {16113349}, location = {Virtual Event}, pages = {478--502}, publisher = {Springer Nature}, title = {{Dual lattice attacks for closest vector problems (with preprocessing)}}, doi = {10.1007/978-3-030-75539-3_20}, volume = {12704}, year = {2021}, } @inproceedings{9823, abstract = {Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that all the outputs are within distance 1 of one another, and each output value lies on a shortest path between two input values. From prior work, it is known that there is no wait-free algorithm among 𝑛≥3 processes for this problem on any cycle of length 𝑐≥4 , by reduction from 2-set agreement (Castañeda et al. 2018). In this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length 𝑐≥4 , via a generalisation of Sperner’s Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs.}, author = {Alistarh, Dan-Adrian and Ellen, Faith and Rybicki, Joel}, booktitle = {Structural Information and Communication Complexity}, isbn = {9783030795269}, issn = {16113349}, location = {Wrocław, Poland}, pages = {87--105}, publisher = {Springer Nature}, title = {{Wait-free approximate agreement on graphs}}, doi = {10.1007/978-3-030-79527-6_6}, volume = {12810}, year = {2021}, } @inproceedings{9824, abstract = {We define a new compact coordinate system in which each integer triplet addresses a voxel in the BCC grid, and we investigate some of its properties. We propose a characterization of 3D discrete analytical planes with their topological features (in the Cartesian and in the new coordinate system) such as the interrelation between the thickness of the plane and the separability constraint we aim to obtain.}, author = {Čomić, Lidija and Zrour, Rita and Largeteau-Skapin, Gaëlle and Biswas, Ranita and Andres, Eric}, booktitle = {Discrete Geometry and Mathematical Morphology}, isbn = {9783030766566}, issn = {16113349}, location = {Uppsala, Sweden}, pages = {152--163}, publisher = {Springer Nature}, title = {{Body centered cubic grid - coordinate system and discrete analytical plane definition}}, doi = {10.1007/978-3-030-76657-3_10}, volume = {12708}, year = {2021}, } @unpublished{9980, abstract = {Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.}, author = {Prehal, Christian and Talian, Sara Drvarič and Vizintin, Alen and Amenitsch, Heinz and Dominko, Robert and Freunberger, Stefan Alexander and Wood, Vanessa}, booktitle = {Research Square}, keywords = {Li2S, Lithium Sulphur Batteries, SAXS, WAXS}, pages = {21}, title = {{Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries}}, doi = {10.21203/rs.3.rs-818607/v1}, year = {2021}, } @article{12584, abstract = {This project explored the integrated use of satellite, ground observations and hydrological distributed models to support water resources assessment and monitoring in High Mountain Asia (HMA). Hydrological data products were generated taking advantage of the synergies of European and Chinese data assets and space-borne observation systems. Energy-budget-based glacier mass balance and hydrological models driven by satellite observations were developed. These models can be applied to describe glacier-melt contribution to river flow. Satellite hydrological data products were used for forcing, calibration, validation and data assimilation in distributed river basin models. A pilot study was carried out on the Red River basin. Multiple hydrological data products were generated using the data collected by Chinese satellites. A new Evapo-Transpiration (ET) dataset from 2000 to 2018 was generated, including plant transpiration, soil evaporation, rainfall interception loss, snow/ice sublimation and open water evaporation. Higher resolution data were used to characterize glaciers and their response to environmental forcing. These studies focused on the Parlung Zangbo Basin, where glacier facies were mapped with GaoFeng (GF), Sentinal-2/Multi-Spectral Imager (S2/MSI) and Landsat8/Operational Land Imager (L8/OLI) data. The geodetic mass balance was estimated between 2000 and 2017 with Zi-Yuan (ZY)-3 Stereo Images and the SRTM DEM. Surface velocity was studied with Landsat5/Thematic Mapper (L5/TM), L8/OLI and S2/MSI data over the period 2013–2019. An updated method was developed to improve the retrieval of glacier albedo by correcting glacier reflectance for anisotropy, and a new dataset on glacier albedo was generated for the period 2001–2020. A detailed glacier energy and mass balance model was developed with the support of field experiments at the Parlung No. 4 Glacier and the 24 K Glacier, both in the Tibetan Plateau. Besides meteorological measurements, the field experiments included glaciological and hydrological measurements. The energy balance model was formulated in terms of enthalpy for easier treatment of water phase transitions. The model was applied to assess the spatial variability in glacier melt. In the Parlung No. 4 Glacier, the accumulated glacier melt was between 1.5 and 2.5 m w.e. in the accumulation zone and between 4.5 and 6.0 m w.e. in the ablation zone, reaching 6.5 m w.e. at the terminus. The seasonality in the glacier mass balance was observed by combining intensive field campaigns with continuous automatic observations. The linkage of the glacier and snowpack mass balance with water resources in a river basin was analyzed in the Chiese (Italy) and Heihe (China) basins by developing and applying integrated hydrological models using satellite retrievals in multiple ways. The model FEST-WEB was calibrated using retrievals of Land Surface Temperature (LST) to map soil hydrological properties. A watershed model was developed by coupling ecohydrological and socioeconomic systems. Integrated modeling is supported by an updated and parallelized data assimilation system. The latter exploits retrievals of brightness temperature (Advanced Microwave Scanning Radiometer, AMSR), LST (Moderate Resolution Imaging Spectroradiometer, MODIS), precipitation (Tropical Rainfall Measuring Mission (TRMM) and FengYun (FY)-2D) and in-situ measurements. In the case study on the Red River Basin, a new algorithm has been applied to disaggregate the SMOS (Soil Moisture and Ocean Salinity) soil moisture retrievals by making use of the correlation between evaporative fraction and soil moisture.}, author = {Menenti, Massimo and Li, Xin and Jia, Li and Yang, Kun and Pellicciotti, Francesca and Mancini, Marco and Shi, Jiancheng and Escorihuela, Maria José and Zheng, Chaolei and Chen, Qiting and Lu, Jing and Zhou, Jie and Hu, Guangcheng and Ren, Shaoting and Zhang, Jing and Liu, Qinhuo and Qiu, Yubao and Huang, Chunlin and Zhou, Ji and Han, Xujun and Pan, Xiaoduo and Li, Hongyi and Wu, Yerong and Ding, Baohong and Yang, Wei and Buri, Pascal and McCarthy, Michael J. and Miles, Evan S. and Shaw, Thomas E. and Ma, Chunfeng and Zhou, Yanzhao and Corbari, Chiara and Li, Rui and Zhao, Tianjie and Stefan, Vivien and Gao, Qi and Zhang, Jingxiao and Xie, Qiuxia and Wang, Ning and Sun, Yibo and Mo, Xinyu and Jia, Junru and Jouberton, Achille Pierre and Kneib, Marin and Fugger, Stefan and Paciolla, Nicola and Paolini, Giovanni}, issn = {2072-4292}, journal = {Remote Sensing}, keywords = {General Earth and Planetary Sciences}, number = {24}, publisher = {MDPI}, title = {{Multi-source hydrological data products to monitor High Asian river basins and regional water security}}, doi = {10.3390/rs13245122}, volume = {13}, year = {2021}, } @article{12590, abstract = {Ice cliffs play a key role in the mass balance of debris-covered glaciers, but assessing their importance is limited by a lack of datasets on their distribution and evolution at scales larger than an individual glacier. These datasets are often derived using operator-biased and time-consuming manual delineation approaches, despite the recent emergence of semi-automatic mapping methods. These methods have used elevation or multispectral data, but the varying slope and mixed spectral signal of these dynamic features makes the transferability of these approaches particularly challenging. We develop three semi-automated and objective new approaches, based on the Spectral Curvature and Linear Spectral Unmixing of multispectral images, to map these features at a glacier to regional scale. The transferability of each method is assessed by applying it to three sites in the Himalaya, where debris-covered glaciers are widespread, with varying lithologic, glaciological and climatic settings, and encompassing different periods of the melt season. We develop the new methods keeping in mind the wide range of remote sensing platforms currently in use, and focus in particular on two products: we apply the three approaches at each site to near-contemporaneous atmospherically-corrected Pléiades (2 m resolution) and Sentinel-2 (10 m resolution) images and assess the effects of spatial and spectral resolution on the results. We find that the Spectral Curvature method works best for the high spatial resolution, four band Pléaides images, while a modification of the Linear Spectral Unmixing using the scaling factor of the unmixing is best for the coarser spatial resolution, but additional spectral information of Sentinel-2 products. In both cases ice cliffs are mapped with a Dice coefficient higher than 0.48. Comparison of the Pléiades results with other existing methods shows that the Spectral Curvature approach performs better and is more robust than any other existing automated or semi-automated approaches. Both methods outline a high number of small, sometimes shallow-sloping and thinly debris-covered ice patches that differ from our traditional understanding of cliffs but may have non-negligible impact on the mass balance of debris-covered glaciers. Overall these results pave the way for large scale efforts of ice cliff mapping that can enable inclusion of these features in debris-covered glacier melt models, as well as allow the generation of multiple datasets to study processes of cliff formation, evolution and decline.}, author = {Kneib, M. and Miles, E.S. and Jola, S. and Buri, P. and Herreid, S. and Bhattacharya, A. and Watson, C.S. and Bolch, T. and Quincey, D. and Pellicciotti, Francesca}, issn = {0034-4257}, journal = {Remote Sensing of Environment}, keywords = {Computers in Earth Sciences, Geology, Soil Science}, number = {2}, publisher = {Elsevier}, title = {{Mapping ice cliffs on debris-covered glaciers using multispectral satellite images}}, doi = {10.1016/j.rse.2020.112201}, volume = {253}, year = {2021}, } @article{12591, abstract = {Glacier albedo determines the net shortwave radiation absorbed at the glacier surface and plays a crucial role in glacier energy and mass balance. Remote sensing techniques are efficient means to retrieve glacier surface albedo over large and inaccessible areas and to study its variability. However, corrections of anisotropic reflectance of glacier surface have been established for specific shortwave bands only, such as Landsat 5 Thematic Mapper (L5/TM) band 2 and band 4, which is a major limitation of current retrievals of glacier broadband albedo. In this study, we calibrated and evaluated four anisotropy correction models for glacier snow and ice, applicable to visible, near-infrared and shortwave-infrared wavelengths using airborne datasets of Bidirectional Reflectance Distribution Function (BRDF). We then tested the ability of the best-performing anisotropy correction model, referred to from here on as the ‘updated model’, to retrieve albedo from L5/TM, Landsat 8 Operational Land Imager (L8/OLI) and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and evaluated these results with field measurements collected on eight glaciers around the world. Our results show that the updated model: (1) can accurately estimate anisotropic factors of reflectance for snow and ice surfaces; (2) generally performs better than prior approaches for L8/OLI albedo retrieval but is not appropriate for L5/TM; (3) generally retrieves MODIS albedo better than the MODIS standard albedo product (MCD43A3) in both absolute values and glacier albedo temporal evolution, i.e., exhibiting both fewer gaps and better agreement with field observations. As the updated model enables anisotropy correction of a maximum of 10 multispectral bands and is implemented in Google Earth Engine (GEE), it is promising for observing and analyzing glacier albedo at large spatial scales.}, author = {Ren, Shaoting and Miles, Evan S. and Jia, Li and Menenti, Massimo and Kneib, Marin and Buri, Pascal and McCarthy, Michael J. and Shaw, Thomas E. and Yang, Wei and Pellicciotti, Francesca}, issn = {2072-4292}, journal = {Remote Sensing}, number = {9}, publisher = {MDPI}, title = {{Anisotropy parameterization development and evaluation for glacier surface albedo retrieval from satellite observations}}, doi = {10.3390/rs13091714}, volume = {13}, year = {2021}, } @article{12589, abstract = {Near-surface air temperature (Ta) is highly important for modelling glacier ablation, though its spatio-temporal variability over melting glaciers still remains largely unknown. We present a new dataset of distributed Ta for three glaciers of different size in the south-east Tibetan Plateau during two monsoon-dominated summer seasons. We compare on-glacier Ta to ambient Ta extrapolated from several local off-glacier stations. We parameterise the along-flowline sensitivity of Ta on these glaciers to changes in off-glacier temperatures (referred to as “temperature sensitivity”) and present the results in the context of available distributed on-glacier datasets around the world. Temperature sensitivity decreases rapidly up to 2000–3000 m along the down-glacier flowline distance. Beyond this distance, both the Ta on the Tibetan glaciers and global glacier datasets show little additional cooling relative to the off-glacier temperature. In general, Ta on small glaciers (with flowline distances <1000 m) is highly sensitive to temperature changes outside the glacier boundary layer. The climatology of a given region can influence the general magnitude of this temperature sensitivity, though no strong relationships are found between along-flowline temperature sensitivity and mean summer temperatures or precipitation. The terminus of some glaciers is affected by other warm-air processes that increase temperature sensitivity (such as divergent boundary layer flow, warm up-valley winds or debris/valley heating effects) which are evident only beyond ∼70 % of the total glacier flowline distance. Our results therefore suggest a strong role of local effects in modulating temperature sensitivity close to the glacier terminus, although further work is still required to explain the variability of these effects for different glaciers.}, author = {Shaw, Thomas E. and Yang, Wei and Ayala, Álvaro and Bravo, Claudio and Zhao, Chuanxi and Pellicciotti, Francesca}, issn = {1994-0424}, journal = {The Cryosphere}, keywords = {Earth-Surface Processes, Water Science and Technology}, number = {2}, pages = {595--614}, publisher = {Copernicus Publications}, title = {{Distributed summer air temperatures across mountain glaciers in the south-east Tibetan Plateau: Temperature sensitivity and comparison with existing glacier datasets}}, doi = {10.5194/tc-15-595-2021}, volume = {15}, year = {2021}, } @article{12586, abstract = {Ice cliffs are common on debris-covered glaciers and have relatively high melt rates due to their direct exposure to incoming radiation. Previous studies have shown that their number and relative area can change considerably from year to year, but this variability has not been explored, in part because available cliff observations are irregular. Here, we systematically mapped and tracked ice cliffs across four debris-covered glaciers in High Mountain Asia for every late ablation season from 2009 to 2019 using high-resolution multi-spectral satellite imagery. We then quantified the processes occurring at the feature scale to train a stochastic birth-death model to represent the cliff population dynamics. Our results show that while the cliff relative area can change by up to 20% from year to year, the natural long-term variability is constrained, thus defining a glacier-specific cliff carrying capacity. In a subsequent step, the inclusion of external drivers related to climate, glacier dynamics, and hydrology highlights the influence of these variables on the cliff population dynamics, which is usually not a direct one due to the complexity and interdependence of the processes taking place at the glacier surface. In some extreme cases (here, a glacier surge), these external drivers may lead to a reorganization of the cliffs at the glacier surface and a change in the natural variability. These results have implications for the melt of debris-covered glaciers, in addition to showing the high rate of changes at their surface and highlighting some of the links between cliff population and glacier state.}, author = {Kneib, M. and Miles, E. S. and Buri, P. and Molnar, P. and McCarthy, M. and Fugger, S. and Pellicciotti, Francesca}, issn = {2169-9003}, journal = {Journal of Geophysical Research: Earth Surface}, keywords = {Earth-Surface Processes, Geophysics}, number = {10}, publisher = {American Geophysical Union}, title = {{Interannual dynamics of ice cliff populations on debris‐covered glaciers from remote sensing observations and stochastic modeling}}, doi = {10.1029/2021jf006179}, volume = {126}, year = {2021}, } @article{12587, abstract = {Surface energy-balance models are commonly used in conjunction with satellite thermal imagery to estimate supraglacial debris thickness. Removing the need for local meteorological data in the debris thickness estimation workflow could improve the versatility and spatiotemporal application of debris thickness estimation. We evaluate the use of regional reanalysis data to derive debris thickness for two mountain glaciers using a surface energy-balance model. Results forced using ERA-5 agree with AWS-derived estimates to within 0.01 ± 0.05 m for Miage Glacier, Italy, and 0.01 ± 0.02 m for Khumbu Glacier, Nepal. ERA-5 data were then used to estimate spatiotemporal changes in debris thickness over a ~20-year period for Miage Glacier, Khumbu Glacier and Haut Glacier d'Arolla, Switzerland. We observe significant increases in debris thickness at the terminus for Haut Glacier d'Arolla and at the margins of the expanding debris cover at all glaciers. While simulated debris thickness was underestimated compared to point measurements in areas of thick debris, our approach can reconstruct glacier-scale debris thickness distribution and its temporal evolution over multiple decades. We find significant changes in debris thickness over areas of thin debris, areas susceptible to high ablation rates, where current knowledge of debris evolution is limited.}, author = {Stewart, Rebecca L. and Westoby, Matthew and Pellicciotti, Francesca and Rowan, Ann and Swift, Darrel and Brock, Benjamin and Woodward, John}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {262}, pages = {366--384}, publisher = {Cambridge University Press}, title = {{Using climate reanalysis data in conjunction with multi-temporal satellite thermal imagery to derive supraglacial debris thickness changes from energy-balance modelling}}, doi = {10.1017/jog.2020.111}, volume = {67}, year = {2021}, } @article{12585, abstract = {Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.}, author = {Miles, Evan and McCarthy, Michael and Dehecq, Amaury and Kneib, Marin and Fugger, Stefan and Pellicciotti, Francesca}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Health and sustainability of glaciers in High Mountain Asia}}, doi = {10.1038/s41467-021-23073-4}, volume = {12}, year = {2021}, } @article{12588, abstract = {The thinning patterns of debris-covered glaciers in High Mountain Asia are not well understood. Here we calculate the effect of supraglacial ice cliffs on the mass balance of all glaciers in a Himalayan catchment, using a process-based ice cliff melt model. We show that ice cliffs are responsible for higher than expected thinning rates of debris-covered glacier tongues, leading to an underestimation of their ice mass loss of 17% ± 4% in the catchment if not considered. We also show that cliffs do enhance melt where other processes would suppress it, that is, at high elevations, or where debris is thick, and that they contribute relatively more to glacier mass loss if oriented north. Our approach provides a key contribution to our understanding of the mass losses of debris-covered glaciers, and a new quantification of their catchment wide melt and mass balance.}, author = {Buri, Pascal and Miles, Evan S. and Steiner, Jakob F. and Ragettli, Silvan and Pellicciotti, Francesca}, issn = {1944-8007}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {6}, publisher = {American Geophysical Union}, title = {{Supraglacial ice cliffs can substantially increase the mass loss of debris‐covered glaciers}}, doi = {10.1029/2020gl092150}, volume = {48}, year = {2021}, } @article{12583, abstract = {Peruvian glaciers are important contributors to dry season runoff for agriculture and hydropower, but they are at risk of disappearing due to climate change. We applied a physically based, energy balance melt model at five on-glacier sites within the Peruvian Cordilleras Blanca and Vilcanota. Net shortwave radiation dominates the energy balance, and despite this flux being higher in the dry season, melt rates are lower due to losses from net longwave radiation and the latent heat flux. The sensible heat flux is a relatively small contributor to melt energy. At three of the sites the wet season snowpack was discontinuous, forming and melting within a daily to weekly timescale, and resulting in highly variable melt rates closely related to precipitation dynamics. Cold air temperatures due to a strong La Niña year at Shallap Glacier (Cordillera Blanca) resulted in a continuous wet season snowpack, significantly reducing wet season ablation. Sublimation was most important at the highest site in the accumulation zone of the Quelccaya Ice Cap (Cordillera Vilcanota), accounting for 81% of ablation, compared to 2%–4% for the other sites. Air temperature and precipitation inputs were perturbed to investigate the climate sensitivity of the five glaciers. At the lower sites warmer air temperatures resulted in a switch from snowfall to rain, so that ablation was increased via the decrease in albedo and increase in net shortwave radiation. At the top of Quelccaya Ice Cap warming caused melting to replace sublimation so that ablation increased nonlinearly with air temperature.}, author = {Fyffe, Catriona L. and Potter, Emily and Fugger, Stefan and Orr, Andrew and Fatichi, Simone and Loarte, Edwin and Medina, Katy and Hellström, Robert Å. and Bernat, Maud and Aubry‐Wake, Caroline and Gurgiser, Wolfgang and Perry, L. Baker and Suarez, Wilson and Quincey, Duncan J. and Pellicciotti, Francesca}, issn = {2169-8996}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Geophysics}, number = {23}, publisher = {American Geophysical Union}, title = {{The energy and mass balance of Peruvian Glaciers}}, doi = {10.1029/2021jd034911}, volume = {126}, year = {2021}, } @inproceedings{12767, abstract = {Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound. This work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization.}, author = {Bansal, Suguman and Chatterjee, Krishnendu and Vardi, Moshe Y.}, booktitle = {27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783030720155}, issn = {1611-3349}, location = {Luxembourg City, Luxembourg}, pages = {20--37}, publisher = {Springer Nature}, title = {{On satisficing in quantitative games}}, doi = {10.1007/978-3-030-72016-2}, volume = {12651}, year = {2021}, } @unpublished{10011, abstract = {We propose a new weak solution concept for (two-phase) mean curvature flow which enjoys both (unconditional) existence and (weak-strong) uniqueness properties. These solutions are evolving varifolds, just as in Brakke's formulation, but are coupled to the phase volumes by a simple transport equation. First, we show that, in the exact same setup as in Ilmanen's proof [J. Differential Geom. 38, 417-461, (1993)], any limit point of solutions to the Allen-Cahn equation is a varifold solution in our sense. Second, we prove that any calibrated flow in the sense of Fischer et al. [arXiv:2003.05478] - and hence any classical solution to mean curvature flow - is unique in the class of our new varifold solutions. This is in sharp contrast to the case of Brakke flows, which a priori may disappear at any given time and are therefore fatally non-unique. Finally, we propose an extension of the solution concept to the multi-phase case which is at least guaranteed to satisfy a weak-strong uniqueness principle.}, author = {Hensel, Sebastian and Laux, Tim}, booktitle = {arXiv}, keywords = {Mean curvature flow, gradient flows, varifolds, weak solutions, weak-strong uniqueness, calibrated geometry, gradient-flow calibrations}, title = {{A new varifold solution concept for mean curvature flow: Convergence of the Allen-Cahn equation and weak-strong uniqueness}}, doi = {10.48550/arXiv.2109.04233}, year = {2021}, } @unpublished{9230, abstract = {We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate. It is shown that the deterministic level of the maximum interpolates smoothly between the ones of log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from 3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of log-correlated variables with time-dependent variance and rate occur. A key ingredient of the proof is a precise upper tail tightness estimate for the maximum of the model on intervals of size one, that includes a Gaussian correction. This correction is expected to be present for the Riemann zeta function and pertains to the question of the correct order of the maximum of the zeta function in large intervals.}, author = {Arguin, Louis-Pierre and Dubach, Guillaume and Hartung, Lisa}, booktitle = {arXiv}, title = {{Maxima of a random model of the Riemann zeta function over intervals of varying length}}, doi = {10.48550/arXiv.2103.04817}, year = {2021}, } @unpublished{9281, abstract = {We comment on two formal proofs of Fermat's sum of two squares theorem, written using the Mathematical Components libraries of the Coq proof assistant. The first one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's recent new proof relying on partition-theoretic arguments. Both formal proofs rely on a general property of involutions of finite sets, of independent interest. The proof technique consists for the most part of automating recurrent tasks (such as case distinctions and computations on natural numbers) via ad hoc tactics.}, author = {Dubach, Guillaume and Mühlböck, Fabian}, booktitle = {arXiv}, title = {{Formal verification of Zagier's one-sentence proof}}, doi = {10.48550/arXiv.2103.11389}, year = {2021}, } @unpublished{10579, abstract = {We consider a totally asymmetric simple exclusion process (TASEP) consisting of particles on a lattice that require binding by a "token" to move. Using a combination of theory and simulations, we address the following questions: (i) How token binding kinetics affects the current-density relation; (ii) How the current-density relation depends on the scarcity of tokens; (iii) How tokens propagate the effects of the locally-imposed disorder (such a slow site) over the entire lattice; (iv) How a shared pool of tokens couples concurrent TASEPs running on multiple lattices; (v) How our results translate to TASEPs with open boundaries that exchange particles with the reservoir. Since real particle motion (including in systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.}, author = {Kavcic, Bor and Tkačik, Gašper}, booktitle = {arXiv}, title = {{Token-driven totally asymmetric simple exclusion process}}, doi = {10.48550/arXiv.2112.13558}, year = {2021}, } @article{10806, abstract = {Ligands are a fundamental part of nanocrystals. They control and direct nanocrystal syntheses and provide colloidal stability. Bound ligands also affect the nanocrystals’ chemical reactivity and electronic structure. Surface chemistry is thus crucial to understand nanocrystal properties and functionality. Here, we investigate the synthesis of metal oxide nanocrystals (CeO2-x, ZnO, and NiO) from metal nitrate precursors, in the presence of oleylamine ligands. Surprisingly, the nanocrystals are capped exclusively with a fatty acid instead of oleylamine. Analysis of the reaction mixtures with nuclear magnetic resonance spectroscopy revealed several reaction byproducts and intermediates that are common to the decomposition of Ce, Zn, Ni, and Zr nitrate precursors. Our evidence supports the oxidation of alkylamine and formation of a carboxylic acid, thus unraveling this counterintuitive surface chemistry.}, author = {Calcabrini, Mariano and Van den Eynden, Dietger and Sanchez Ribot, Sergi and Pokratath, Rohan and Llorca, Jordi and De Roo, Jonathan and Ibáñez, Maria}, issn = {2691-3704}, journal = {JACS Au}, keywords = {general medicine}, number = {11}, pages = {1898--1903}, publisher = {American Chemical Society}, title = {{Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate}}, doi = {10.1021/jacsau.1c00349}, volume = {1}, year = {2021}, } @article{12187, abstract = {Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations.}, author = {Long, Jincheng and Walker, James and She, Wenjing and Aldridge, Billy and Gao, Hongbo and Deans, Samuel and Vickers, Martin and Feng, Xiaoqi}, issn = {0036-8075}, journal = {Science}, keywords = {Multidisciplinary}, number = {6550}, publisher = {American Association for the Advancement of Science (AAAS)}, title = {{Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis}}, doi = {10.1126/science.abh0556}, volume = {373}, year = {2021}, } @article{12186, abstract = {Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.}, author = {Ding, Pingtao and Sakai, Toshiyuki and Krishna Shrestha, Ram and Manosalva Perez, Nicolas and Guo, Wenbin and Ngou, Bruno Pok Man and He, Shengbo and Liu, Chang and Feng, Xiaoqi and Zhang, Runxuan and Vandepoele, Klaas and MacLean, Dan and Jones, Jonathan D G}, issn = {0022-0957}, journal = {Journal of Experimental Botany}, keywords = {Plant Science, Physiology}, number = {22}, pages = {7927--7941}, publisher = {Oxford University Press}, title = {{Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors}}, doi = {10.1093/jxb/erab373}, volume = {72}, year = {2021}, } @article{9698, abstract = {Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.}, author = {Keith, John A. and Valentin Vassilev-Galindo, Valentin and Cheng, Bingqing and Chmiela, Stefan and Gastegger, Michael and Müller, Klaus-Robert and Tkatchenko, Alexandre}, issn = {1520-6890}, journal = {Chemical Reviews}, number = {16}, pages = {9816--9872}, publisher = {American Chemical Society}, title = {{Combining machine learning and computational chemistry for predictive insights into chemical systems}}, doi = {10.1021/acs.chemrev.1c00107}, volume = {121}, year = {2021}, } @article{12309, abstract = {Take a rational elliptic curve defined by the equation y2=x3+ax in minimal form and consider the sequence Bn of the denominators of the abscissas of the iterate of a non-torsion point. We show that B5m has a primitive divisor for every m. Then, we show how to generalize this method to the terms of the form Bmp with p a prime congruent to 1 modulo 4.}, author = {Verzobio, Matteo}, issn = {0065-1036}, journal = {Acta Arithmetica}, keywords = {Algebra and Number Theory}, number = {2}, pages = {129--168}, publisher = {Institute of Mathematics, Polish Academy of Sciences}, title = {{Primitive divisors of elliptic divisibility sequences for elliptic curves with j=1728}}, doi = {10.4064/aa191016-30-7}, volume = {198}, year = {2021}, } @article{12308, abstract = {Let P and Q be two points on an elliptic curve defined over a number field K. For α∈End(E), define Bα to be the OK-integral ideal generated by the denominator of x(α(P)+Q). Let O be a subring of End(E), that is a Dedekind domain. We will study the sequence {Bα}α∈O. We will show that, for all but finitely many α∈O, the ideal Bα has a primitive divisor when P is a non-torsion point and there exist two endomorphisms g≠0 and f so that f(P)=g(Q). This is a generalization of previous results on elliptic divisibility sequences.}, author = {Verzobio, Matteo}, issn = {2522-0160}, journal = {Research in Number Theory}, keywords = {Algebra and Number Theory}, number = {2}, publisher = {Springer Nature}, title = {{Primitive divisors of sequences associated to elliptic curves with complex multiplication}}, doi = {10.1007/s40993-021-00267-9}, volume = {7}, year = {2021}, } @inproceedings{12909, author = {Schlögl, Alois and Elefante, Stefano and Hornoiu, Andrei and Stadlbauer, Stephan}, booktitle = {ASHPC21 – Austrian-Slovenian HPC Meeting 2021}, isbn = {978-961-6980-77-7}, location = {Virtual}, pages = {5}, publisher = {University of Ljubljana}, title = {{Managing software on a heterogenous HPC cluster}}, doi = {10.3359/2021hpc}, year = {2021}, } @inproceedings{11458, abstract = {The increasing computational requirements of deep neural networks (DNNs) have led to significant interest in obtaining DNN models that are sparse, yet accurate. Recent work has investigated the even harder case of sparse training, where the DNN weights are, for as much as possible, already sparse to reduce computational costs during training. Existing sparse training methods are often empirical and can have lower accuracy relative to the dense baseline. In this paper, we present a general approach called Alternating Compressed/DeCompressed (AC/DC) training of DNNs, demonstrate convergence for a variant of the algorithm, and show that AC/DC outperforms existing sparse training methods in accuracy at similar computational budgets; at high sparsity levels, AC/DC even outperforms existing methods that rely on accurate pre-trained dense models. An important property of AC/DC is that it allows co-training of dense and sparse models, yielding accurate sparse–dense model pairs at the end of the training process. This is useful in practice, where compressed variants may be desirable for deployment in resource-constrained settings without re-doing the entire training flow, and also provides us with insights into the accuracy gap between dense and compressed models. The code is available at: https://github.com/IST-DASLab/ACDC.}, author = {Peste, Elena-Alexandra and Iofinova, Eugenia B and Vladu, Adrian and Alistarh, Dan-Adrian}, booktitle = {35th Conference on Neural Information Processing Systems}, isbn = {9781713845393}, issn = {1049-5258}, location = {Virtual, Online}, pages = {8557--8570}, publisher = {Curran Associates}, title = {{AC/DC: Alternating Compressed/DeCompressed training of deep neural networks}}, volume = {34}, year = {2021}, } @article{10585, abstract = {Recently it was shown that anyons on the two-sphere naturally arise from a system of molecular impurities exchanging angular momentum with a many-particle bath (Phys. Rev. Lett. 126, 015301 (2021)). Here we further advance this approach and rigorously demonstrate that in the experimentally realized regime the lowest spectrum of two linear molecules immersed in superfluid helium corresponds to the spectrum of two anyons on the sphere. We develop the formalism within the framework of the recently experimentally observed angulon quasiparticle}, author = {Brooks, Morris and Lemeshko, Mikhail and Lundholm, Douglas and Yakaboylu, Enderalp}, issn = {2218-2004}, journal = {Atoms}, keywords = {anyons, quasiparticles, Quantum Hall Effect, topological states of matter}, number = {4}, publisher = {MDPI}, title = {{Emergence of anyons on the two-sphere in molecular impurities}}, doi = {10.3390/atoms9040106}, volume = {9}, year = {2021}, } @inproceedings{13147, abstract = {We investigate fast and communication-efficient algorithms for the classic problem of minimizing a sum of strongly convex and smooth functions that are distributed among n different nodes, which can communicate using a limited number of bits. Most previous communication-efficient approaches for this problem are limited to first-order optimization, and therefore have \emph{linear} dependence on the condition number in their communication complexity. We show that this dependence is not inherent: communication-efficient methods can in fact have sublinear dependence on the condition number. For this, we design and analyze the first communication-efficient distributed variants of preconditioned gradient descent for Generalized Linear Models, and for Newton’s method. Our results rely on a new technique for quantizing both the preconditioner and the descent direction at each step of the algorithms, while controlling their convergence rate. We also validate our findings experimentally, showing faster convergence and reduced communication relative to previous methods.}, author = {Alimisis, Foivos and Davies, Peter and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {196--206}, publisher = {ML Research Press}, title = {{Communication-efficient distributed optimization with quantized preconditioners}}, volume = {139}, year = {2021}, } @inproceedings{13146, abstract = {A recent line of work has analyzed the theoretical properties of deep neural networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue of the NTK has been related to the memorization capacity, the global convergence of gradient descent algorithms and the generalization of deep nets. However, existing results either provide bounds in the two-layer setting or assume that the spectrum of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper, we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU nets, both in the limiting case of infinite widths and for finite widths. In the finite-width setting, the network architectures we consider are fairly general: we require the existence of a wide layer with roughly order of N neurons, N being the number of data samples; and the scaling of the remaining layer widths is arbitrary (up to logarithmic factors). To obtain our results, we analyze various quantities of independent interest: we give lower bounds on the smallest singular value of hidden feature matrices, and upper bounds on the Lipschitz constant of input-output feature maps.}, author = {Nguyen, Quynh and Mondelli, Marco and Montufar, Guido}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {8119--8129}, publisher = {ML Research Press}, title = {{Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks}}, volume = {139}, year = {2021}, } @inproceedings{10665, abstract = {Formal verification of neural networks is an active topic of research, and recent advances have significantly increased the size of the networks that verification tools can handle. However, most methods are designed for verification of an idealized model of the actual network which works over real arithmetic and ignores rounding imprecisions. This idealization is in stark contrast to network quantization, which is a technique that trades numerical precision for computational efficiency and is, therefore, often applied in practice. Neglecting rounding errors of such low-bit quantized neural networks has been shown to lead to wrong conclusions about the network’s correctness. Thus, the desired approach for verifying quantized neural networks would be one that takes these rounding errors into account. In this paper, we show that verifying the bitexact implementation of quantized neural networks with bitvector specifications is PSPACE-hard, even though verifying idealized real-valued networks and satisfiability of bit-vector specifications alone are each in NP. Furthermore, we explore several practical heuristics toward closing the complexity gap between idealized and bit-exact verification. In particular, we propose three techniques for making SMT-based verification of quantized neural networks more scalable. Our experiments demonstrate that our proposed methods allow a speedup of up to three orders of magnitude over existing approaches.}, author = {Henzinger, Thomas A and Lechner, Mathias and Zikelic, Dorde}, booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence}, isbn = {978-1-57735-866-4}, issn = {2374-3468}, location = {Virtual}, number = {5A}, pages = {3787--3795}, publisher = {AAAI Press}, title = {{Scalable verification of quantized neural networks}}, volume = {35}, year = {2021}, } @inproceedings{10667, abstract = {Bayesian neural networks (BNNs) place distributions over the weights of a neural network to model uncertainty in the data and the network's prediction. We consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with infinite time horizon systems. Compared to the existing sampling-based approaches, which are inapplicable to the infinite time horizon setting, we train a separate deterministic neural network that serves as an infinite time horizon safety certificate. In particular, we show that the certificate network guarantees the safety of the system over a subset of the BNN weight posterior's support. Our method first computes a safe weight set and then alters the BNN's weight posterior to reject samples outside this set. Moreover, we show how to extend our approach to a safe-exploration reinforcement learning setting, in order to avoid unsafe trajectories during the training of the policy. We evaluate our approach on a series of reinforcement learning benchmarks, including non-Lyapunovian safety specifications.}, author = {Lechner, Mathias and Žikelić, Ðorđe and Chatterjee, Krishnendu and Henzinger, Thomas A}, booktitle = {35th Conference on Neural Information Processing Systems}, location = {Virtual}, title = {{Infinite time horizon safety of Bayesian neural networks}}, doi = {10.48550/arXiv.2111.03165}, year = {2021}, } @article{13358, abstract = {DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA-based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non-photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine-based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA-based devices and nanomaterials.}, author = {Ryssy, Joonas and Natarajan, Ashwin K. and Wang, Jinhua and Lehtonen, Arttu J. and Nguyen, Minh‐Kha and Klajn, Rafal and Kuzyk, Anton}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {11}, pages = {5859--5863}, publisher = {Wiley}, title = {{Light‐responsive dynamic DNA‐origami‐based plasmonic assemblies}}, doi = {10.1002/anie.202014963}, volume = {60}, year = {2021}, } @inbook{13360, abstract = {Inorganic nanoparticles (NPs) exhibit a wide range of fascinating physicochemical properties, many of which can be controlled by modulating the NP–NP coupling. Controlling the self-assembly of NPs using light has traditionally been achieved by functionalizing their surfaces with monolayers of photoswitchable molecules, which can be reversibly isomerized between two or more states upon exposure to different wavelengths of light. NPs whose assembly can be controlled by light in a reversible fashion can find interesting applications. The chapter deals with systems comprising mixtures of non-photoswitchable NPs and small-molecule photoacids and photobases. Examples of light-controlled self-assembly of NPs hitherto reported have been categorized into six distinct approaches. These are: functionalizing NPs with monolayers of photoswitchable molecules, light-controlled adsorption/desorption of photoswitchable molecules onto NPs, and light-induced electron transfer between the particle's inorganic core and the NP-bound ligands.}, author = {Bian, Tong and Chu, Zonglin and Klajn, Rafal}, booktitle = {Out‐of‐Equilibrium (Supra)molecular Systems and Materials}, editor = {Giuseppone, Nicolas and Walther, Andreas}, isbn = {9783527346158}, pages = {241--273}, publisher = {Wiley}, title = {{Controlling Self‐Assembly of Nanoparticles Using Light}}, doi = {10.1002/9783527821990.ch9}, year = {2021}, } @article{13357, abstract = {Coulombic interactions can be used to assemble charged nanoparticles into higher-order structures, but the process requires oppositely charged partners that are similarly sized. The ability to mediate the assembly of such charged nanoparticles using structurally simple small molecules would greatly facilitate the fabrication of nanostructured materials and harnessing their applications in catalysis, sensing and photonics. Here we show that small molecules with as few as three electric charges can effectively induce attractive interactions between oppositely charged nanoparticles in water. These interactions can guide the assembly of charged nanoparticles into colloidal crystals of a quality previously only thought to result from their co-crystallization with oppositely charged nanoparticles of a similar size. Transient nanoparticle assemblies can be generated using positively charged nanoparticles and multiply charged anions that are enzymatically hydrolysed into mono- and/or dianions. Our findings demonstrate an approach for the facile fabrication, manipulation and further investigation of static and dynamic nanostructured materials in aqueous environments.}, author = {Bian, Tong and Gardin, Andrea and Gemen, Julius and Houben, Lothar and Perego, Claudio and Lee, Byeongdu and Elad, Nadav and Chu, Zonglin and Pavan, Giovanni M. and Klajn, Rafal}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemical Engineering, General Chemistry}, number = {10}, pages = {940--949}, publisher = {Springer Nature}, title = {{Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures}}, doi = {10.1038/s41557-021-00752-9}, volume = {13}, year = {2021}, } @misc{13072, abstract = {CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits)}, author = {McCartney, Daniel L and Hillary, Robert F and Conole, Eleanor LS and Trejo Banos, Daniel and Gadd, Danni A and Walker, Rosie M and Nangle, Cliff and Flaig, Robin and Campbell, Archie and Murray, Alison D and Munoz Maniega, Susana and del C Valdes-Hernandez, Maria and Harris, Mathew A and Bastin, Mark E and Wardlaw, Joanna M and Harris, Sarah E and Porteous, David J and Tucker-Drob, Elliot M and McIntosh, Andrew M and Evans, Kathryn L and Deary, Ian J and Cox, Simon R and Robinson, Matthew Richard and Marioni, Riccardo E}, publisher = {Zenodo}, title = {{Blood-based epigenome-wide analyses of cognitive abilities}}, doi = {10.5281/ZENODO.5794028}, year = {2021}, } @misc{13068, abstract = {Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".}, author = {Randriamanantsoa, Samuel and Papargyriou, Aristeidis and Maurer, Carlo and Peschke, Katja and Schuster, Maximilian and Zecchin, Giulia and Steiger, Katja and Öllinger, Rupert and Saur, Dieter and Scheel, Christina and Rad, Roland and Hannezo, Edouard B and Reichert, Maximilian and Bausch, Andreas R.}, publisher = {Zenodo}, title = {{Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids}}, doi = {10.5281/ZENODO.5148117}, year = {2021}, } @article{7551, abstract = {Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.}, author = {Fredes Tolorza, Felipe A and Silva Sifuentes, Maria A and Koppensteiner, Peter and Kobayashi, Kenta and Jösch, Maximilian A and Shigemoto, Ryuichi}, journal = {Current Biology}, number = {1}, pages = {P25--38.E5}, publisher = {Elsevier}, title = {{Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation}}, doi = {10.1016/j.cub.2020.09.074}, volume = {31}, year = {2021}, } @article{7463, abstract = {Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.}, author = {Lombardi, Fabrizio and Shriki, Oren and Herrmann, Hans J and de Arcangelis, Lucilla}, issn = {1872-8286}, journal = {Neurocomputing}, pages = {657--666}, publisher = {Elsevier}, title = {{Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches}}, doi = {10.1016/j.neucom.2020.05.126}, volume = {461}, year = {2021}, } @misc{6995, abstract = {Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.}, author = {Samarasinghe, Ranmal A. and Miranda, Osvaldo and Buth, Jessie E. and Mitchell, Simon and Ferando, Isabella and Watanabe, Momoko and Kurdian, Arinnae and Golshani, Peyman and Plath, Kathrin and Lowry, William E. and Parent, Jack M. and Mody, Istvan and Novitch, Bennett G.}, issn = {1546-1726}, pages = {32}, publisher = {Springer Nature}, title = {{Identification of neural oscillations and epileptiform changes in human brain organoids}}, doi = {10.1038/s41593-021-00906-5}, volume = {24}, year = {2021}, } @article{6965, abstract = {The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.}, author = {Rychlewicz, Kamil P}, issn = {1469-2120}, journal = {Bulletin of the London Mathematical Society}, number = {2}, pages = {560--574}, publisher = {Wiley}, title = {{The positivity of local equivariant Hirzebruch class for toric varieties}}, doi = {10.1112/blms.12442}, volume = {53}, year = {2021}, } @article{8253, abstract = {Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks.}, author = {Zenke, Friedemann and Vogels, Tim P}, issn = {1530-888X}, journal = {Neural Computation}, number = {4}, pages = {899--925}, publisher = {MIT Press}, title = {{The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks}}, doi = {10.1162/neco_a_01367}, volume = {33}, year = {2021}, } @article{8198, abstract = {We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.}, author = {Diringer, Asaf A. and Gulden, Tobias}, issn = {24699969}, journal = {Physical Review B}, number = {21}, publisher = {American Physical Society}, title = {{Impact of drive harmonics on the stability of Floquet many-body localization}}, doi = {10.1103/PhysRevB.103.214204}, volume = {103}, year = {2021}, } @article{8373, abstract = {It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.}, author = {Pitrik, József and Virosztek, Daniel}, issn = {0024-3795}, journal = {Linear Algebra and its Applications}, keywords = {Kubo-Ando mean, weighted multivariate mean, barycenter}, pages = {203--217}, publisher = {Elsevier}, title = {{A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means}}, doi = {10.1016/j.laa.2020.09.007}, volume = {609}, year = {2021}, } @article{8317, abstract = {When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.}, author = {Aichholzer, Oswin and Akitaya, Hugo A. and Cheung, Kenneth C. and Demaine, Erik D. and Demaine, Martin L. and Fekete, Sándor P. and Kleist, Linda and Kostitsyna, Irina and Löffler, Maarten and Masárová, Zuzana and Mundilova, Klara and Schmidt, Christiane}, issn = {09257721}, journal = {Computational Geometry: Theory and Applications}, publisher = {Elsevier}, title = {{Folding polyominoes with holes into a cube}}, doi = {10.1016/j.comgeo.2020.101700}, volume = {93}, year = {2021}, } @article{7685, abstract = {We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.}, author = {Boccato, Chiara}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {1}, publisher = {World Scientific}, title = {{The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime}}, doi = {10.1142/S0129055X20600065}, volume = {33}, year = {2021}, } @article{8582, abstract = {Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear. Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains. Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane. This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.}, author = {Li, Hongjiang and von Wangenheim, Daniel and Zhang, Xixi and Tan, Shutang and Darwish-Miranda, Nasser and Naramoto, Satoshi and Wabnik, Krzysztof T and de Rycke, Riet and Kaufmann, Walter and Gütl, Daniel J and Tejos, Ricardo and Grones, Peter and Ke, Meiyu and Chen, Xu and Dettmer, Jan and Friml, Jiří}, issn = {14698137}, journal = {New Phytologist}, number = {1}, pages = {351--369}, publisher = {Wiley}, title = {{Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana}}, doi = {10.1111/nph.16887}, volume = {229}, year = {2021}, } @article{8546, abstract = {Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors.}, author = {Zhang, Tingting and Liu, Tengyuan and Mora, Natalia and Guegan, Justine and Bertrand, Mathilde and Contreras, Ximena and Hansen, Andi H and Streicher, Carmen and Anderle, Marica and Danda, Natasha and Tiberi, Luca and Hippenmeyer, Simon and Hassan, Bassem A.}, issn = { 22111247}, journal = {Cell Reports}, number = {10}, publisher = {Elsevier}, title = {{Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum}}, doi = {10.1016/j.celrep.2021.109208}, volume = {35}, year = {2021}, } @article{8430, abstract = {While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.}, author = {Ojavee, Sven E and Kousathanas, Athanasios and Trejo Banos, Daniel and Orliac, Etienne J and Patxot, Marion and Lall, Kristi and Magi, Reedik and Fischer, Krista and Kutalik, Zoltan and Robinson, Matthew Richard}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Research}, title = {{Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis}}, doi = {10.1038/s41467-021-22538-w}, volume = {12}, year = {2021}, } @article{8602, abstract = {Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.}, author = {Boocock, Daniel R and Hino, Naoya and Ruzickova, Natalia and Hirashima, Tsuyoshi and Hannezo, Edouard B}, issn = {17452481}, journal = {Nature Physics}, pages = {267--274}, publisher = {Springer Nature}, title = {{Theory of mechanochemical patterning and optimal migration in cell monolayers}}, doi = {10.1038/s41567-020-01037-7}, volume = {17}, year = {2021}, } @article{8603, abstract = {We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem.}, author = {Frank, Rupert and Seiringer, Robert}, issn = {10970312}, journal = {Communications on Pure and Applied Mathematics}, number = {3}, pages = {544--588}, publisher = {Wiley}, title = {{Quantum corrections to the Pekar asymptotics of a strongly coupled polaron}}, doi = {10.1002/cpa.21944}, volume = {74}, year = {2021}, } @article{8606, abstract = {The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance, and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the upregulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots.}, author = {He, P and Zhang, Yuzhou and Li, H and Fu, X and Shang, H and Zou, C and Friml, Jiří and Xiao, G}, issn = {1467-7644}, journal = {Plant Biotechnology Journal}, number = {3}, pages = {548--562}, publisher = {Wiley}, title = {{GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton}}, doi = {10.1111/pbi.13484}, volume = {19}, year = {2021}, } @article{8708, abstract = {The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.}, author = {Simon, Alexis and Fraisse, Christelle and El Ayari, Tahani and Liautard‐Haag, Cathy and Strelkov, Petr and Welch, John J and Bierne, Nicolas}, issn = {14209101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {208--223}, publisher = {Wiley}, title = {{How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels}}, doi = {10.1111/jeb.13709}, volume = {34}, year = {2021}, } @article{8723, abstract = {Deep learning at scale is dominated by communication time. Distributing samples across nodes usually yields the best performance, but poses scaling challenges due to global information dissemination and load imbalance across uneven sample lengths. State-of-the-art decentralized optimizers mitigate the problem, but require more iterations to achieve the same accuracy as their globally-communicating counterparts. We present Wait-Avoiding Group Model Averaging (WAGMA) SGD, a wait-avoiding stochastic optimizer that reduces global communication via subgroup weight exchange. The key insight is a combination of algorithmic changes to the averaging scheme and the use of a group allreduce operation. We prove the convergence of WAGMA-SGD, and empirically show that it retains convergence rates similar to Allreduce-SGD. For evaluation, we train ResNet-50 on ImageNet; Transformer for machine translation; and deep reinforcement learning for navigation at scale. Compared with state-of-the-art decentralized SGD variants, WAGMA-SGD significantly improves training throughput (e.g., 2.1× on 1,024 GPUs for reinforcement learning), and achieves the fastest time-to-solution (e.g., the highest score using the shortest training time for Transformer).}, author = {Li, Shigang and Tal Ben-Nun, Tal Ben-Nun and Nadiradze, Giorgi and Girolamo, Salvatore Di and Dryden, Nikoli and Alistarh, Dan-Adrian and Hoefler, Torsten}, issn = {10459219}, journal = {IEEE Transactions on Parallel and Distributed Systems}, number = {7}, publisher = {IEEE}, title = {{Breaking (global) barriers in parallel stochastic optimization with wait-avoiding group averaging}}, doi = {10.1109/TPDS.2020.3040606}, volume = {32}, year = {2021}, } @article{8743, abstract = {Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.}, author = {Salces-Castellano, Antonia and Stankowski, Sean and Arribas, Paula and Patino, Jairo and Karger, Dirk N. and Butlin, Roger and Emerson, Brent C.}, issn = {1558-5646}, journal = {Evolution}, number = {2}, pages = {231--244}, publisher = {Wiley}, title = {{Long-term cloud forest response to climate warming revealed by insect speciation history}}, doi = {10.1111/evo.14111}, volume = {75}, year = {2021}, } @article{8673, abstract = {In RuCl3, inelastic neutron scattering and Raman spectroscopy reveal a continuum of non-spin-wave excitations that persists to high temperature, suggesting the presence of a spin liquid state on a honeycomb lattice. In the context of the Kitaev model, finite magnetic fields introduce interactions between the elementary excitations, and thus the effects of high magnetic fields that are comparable to the spin-exchange energy scale must be explored. Here, we report measurements of the magnetotropic coefficient—the thermodynamic coefficient associated with magnetic anisotropy—over a wide range of magnetic fields and temperatures. We find that magnetic field and temperature compete to determine the magnetic response in a way that is independent of the large intrinsic exchange-interaction energy. This emergent scale-invariant magnetic anisotropy provides evidence for a high degree of exchange frustration that favours the formation of a spin liquid state in RuCl3.}, author = {Modic, Kimberly A and McDonald, Ross D. and Ruff, J.P.C. and Bachmann, Maja D. and Lai, You and Palmstrom, Johanna C. and Graf, David and Chan, Mun K. and Balakirev, F.F. and Betts, J.B. and Boebinger, G.S. and Schmidt, Marcus and Lawler, Michael J. and Sokolov, D.A. and Moll, Philip J.W. and Ramshaw, B.J. and Shekhter, Arkady}, issn = {17452481}, journal = {Nature Physics}, pages = {240--244}, publisher = {Springer Nature}, title = {{Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields}}, doi = {10.1038/s41567-020-1028-0}, volume = {17}, year = {2021}, } @article{8757, abstract = {Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test.}, author = {Bozelos, Panagiotis and Vogels, Tim P}, issn = {14710048}, journal = {Nature Reviews Neuroscience}, number = {1}, pages = {1--2}, publisher = {Springer Nature}, title = {{Talking science, online}}, doi = {10.1038/s41583-020-00408-6}, volume = {22}, year = {2021}, } @article{8793, abstract = {We study optimal election sequences for repeatedly selecting a (very) small group of leaders among a set of participants (players) with publicly known unique ids. In every time slot, every player has to select exactly one player that it considers to be the current leader, oblivious to the selection of the other players, but with the overarching goal of maximizing a given parameterized global (“social”) payoff function in the limit. We consider a quite generic model, where the local payoff achieved by a given player depends, weighted by some arbitrary but fixed real parameter, on the number of different leaders chosen in a round, the number of players that choose the given player as the leader, and whether the chosen leader has changed w.r.t. the previous round or not. The social payoff can be the maximum, average or minimum local payoff of the players. Possible applications include quite diverse examples such as rotating coordinator-based distributed algorithms and long-haul formation flying of social birds. Depending on the weights and the particular social payoff, optimal sequences can be very different, from simple round-robin where all players chose the same leader alternatingly every time slot to very exotic patterns, where a small group of leaders (at most 2) is elected in every time slot. Moreover, we study the question if and when a single player would not benefit w.r.t. its local payoff when deviating from the given optimal sequence, i.e., when our optimal sequences are Nash equilibria in the restricted strategy space of oblivious strategies. As this is the case for many parameterizations of our model, our results reveal that no punishment is needed to make it rational for the players to optimize the social payoff.}, author = {Zeiner, Martin and Schmid, Ulrich and Chatterjee, Krishnendu}, issn = {0166218X}, journal = {Discrete Applied Mathematics}, number = {1}, pages = {392--415}, publisher = {Elsevier}, title = {{Optimal strategies for selecting coordinators}}, doi = {10.1016/j.dam.2020.10.022}, volume = {289}, year = {2021}, } @article{8816, abstract = {Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail.}, author = {Runkel, Ingo and Szegedy, Lorant}, issn = {14320916}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {83–117}, publisher = {Springer Nature}, title = {{Area-dependent quantum field theory}}, doi = {10.1007/s00220-020-03902-1}, volume = {381}, year = {2021}, } @article{8818, abstract = {The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis.}, author = {Ramirez Villegas, Juan F and Besserve, Michel and Murayama, Yusuke and Evrard, Henry C. and Oeltermann, Axel and Logothetis, Nikos K.}, issn = {14764687}, journal = {Nature}, number = {7840}, pages = {96--102}, publisher = {Springer Nature}, title = {{Coupling of hippocampal theta and ripples with pontogeniculooccipital waves}}, doi = {10.1038/s41586-020-2914-4}, volume = {589}, year = {2021}, } @article{8773, abstract = {Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell.}, author = {Brown, Adam and Romanov, Anna}, issn = {1088-6826}, journal = {Proceedings of the American Mathematical Society}, keywords = {Applied Mathematics, General Mathematics}, number = {1}, pages = {37--52}, publisher = {American Mathematical Society}, title = {{Contravariant forms on Whittaker modules}}, doi = {10.1090/proc/15205}, volume = {149}, year = {2021}, } @article{8792, abstract = {This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system.}, author = {Marveggio, Alice and Schimperna, Giulio}, issn = {10902732}, journal = {Journal of Differential Equations}, number = {2}, pages = {924--970}, publisher = {Elsevier}, title = {{On a non-isothermal Cahn-Hilliard model based on a microforce balance}}, doi = {10.1016/j.jde.2020.10.030}, volume = {274}, year = {2021}, } @article{8912, abstract = {For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures, and overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance.}, author = {Sarac, Naci E and Altun, Ömer Faruk and Atam, Kamil Tolga and Karahoda, Sertac and Kaya, Kamer and Yenigün, Hüsnü}, issn = {09574174}, journal = {Expert Systems with Applications}, number = {4}, publisher = {Elsevier}, title = {{Boosting expensive synchronizing heuristics}}, doi = {10.1016/j.eswa.2020.114203}, volume = {167}, year = {2021}, } @article{8928, abstract = {Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.}, author = {Arnoux, Stéphanie and Fraisse, Christelle and Sauvage, Christopher}, issn = {14209101}, journal = {Journal of Evolutionary Biology}, number = {2}, pages = {270--283}, publisher = {Wiley}, title = {{Genomic inference of complex domestication histories in three Solanaceae species}}, doi = {10.1111/jeb.13723}, volume = {34}, year = {2021}, } @article{8992, abstract = {The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.}, author = {Tan, Shutang and Luschnig, Christian and Friml, Jiří}, issn = {17529867}, journal = {Molecular Plant}, number = {1}, pages = {151--165}, publisher = {Elsevier}, title = {{Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling}}, doi = {10.1016/j.molp.2020.11.004}, volume = {14}, year = {2021}, } @article{8988, abstract = {The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.}, author = {Düllberg, Christian F and Auer, Albert and Canigova, Nikola and Loibl, Katrin and Loose, Martin}, issn = {10916490}, journal = {PNAS}, number = {1}, publisher = {National Academy of Sciences}, title = {{In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1}}, doi = {10.1073/pnas.2010054118}, volume = {118}, year = {2021}, } @article{8927, abstract = {The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.}, author = {Nardo, Alexander D. and Schneeweiss-Gleixner, Mathias and Bakail, May M and Dixon, Emmanuel D. and Lax, Sigurd F. and Trauner, Michael}, issn = {14783231}, journal = {Liver International}, number = {1}, pages = {20--32}, publisher = {Wiley}, title = {{Pathophysiological mechanisms of liver injury in COVID-19}}, doi = {10.1111/liv.14730}, volume = {41}, year = {2021}, } @article{13356, abstract = {Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.}, author = {Bian, Tong and Klajn, Rafal}, issn = {1749-6632}, journal = {Annals of the New York Academy of Sciences}, keywords = {History and Philosophy of Science, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {1}, pages = {191--201}, publisher = {Wiley}, title = {{Morphology control in crystalline nanoparticle–polymer aggregates}}, doi = {10.1111/nyas.14674}, volume = {1505}, year = {2021}, } @article{13359, abstract = {Dissipative self-assembly is ubiquitous in nature, where it gives rise to complex structures and functions such as self-healing, homeostasis, and camouflage. These phenomena are enabled by the continuous conversion of energy stored in chemical fuels, such as ATP. Over the past decade, an increasing number of synthetic chemically driven systems have been reported that mimic the features of their natural counterparts. At the same time, it has been shown that dissipative self-assembly can also be fueled by light; these optically fueled systems have been developed in parallel to the chemically fueled ones. In this perspective, we critically compare these two classes of systems. Despite the complementarity and fundamental differences between these two modes of dissipative self-assembly, our analysis reveals that multiple analogies exist between chemically and light-fueled systems. We hope that these considerations will facilitate further development of the field of dissipative self-assembly.}, author = {Weißenfels, Maren and Gemen, Julius and Klajn, Rafal}, issn = {2451-9294}, journal = {Chem}, keywords = {Materials Chemistry, Biochemistry (medical), General Chemical Engineering, Environmental Chemistry, Biochemistry, General Chemistry}, number = {1}, pages = {23--37}, publisher = {Elsevier}, title = {{Dissipative self-assembly: Fueling with chemicals versus light}}, doi = {10.1016/j.chempr.2020.11.025}, volume = {7}, year = {2021}, } @article{8966, abstract = {During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.}, author = {Schauer, Alexandra and Heisenberg, Carl-Philipp J}, issn = {0012-1606}, journal = {Developmental Biology}, keywords = {Developmental Biology, Cell Biology, Molecular Biology}, pages = {71--81}, publisher = {Elsevier}, title = {{Reassembling gastrulation}}, doi = {10.1016/j.ydbio.2020.12.014}, volume = {474}, year = {2021}, } @article{8993, abstract = {N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.}, author = {Abas, Lindy and Kolb, Martina and Stadlmann, Johannes and Janacek, Dorina P. and Lukic, Kristina and Schwechheimer, Claus and Sazanov, Leonid A and Mach, Lukas and Friml, Jiří and Hammes, Ulrich Z.}, issn = {10916490}, journal = {PNAS}, number = {1}, publisher = {National Academy of Sciences}, title = {{Naphthylphthalamic acid associates with and inhibits PIN auxin transporters}}, doi = {10.1073/pnas.2020857118}, volume = {118}, year = {2021}, } @article{8999, abstract = {In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. }, author = {Avila, Kerstin and Hof, Björn}, issn = {1099-4300}, journal = {Entropy}, number = {1}, publisher = {MDPI}, title = {{Second-order phase transition in counter-rotating taylor-couette flow experiment}}, doi = {10.3390/e23010058}, volume = {23}, year = {2021}, } @article{9005, abstract = {Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field.}, author = {Brooks, Morris and Lemeshko, Mikhail and Lundholm, D. and Yakaboylu, Enderalp}, issn = {10797114}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Molecular impurities as a realization of anyons on the two-sphere}}, doi = {10.1103/PhysRevLett.126.015301}, volume = {126}, year = {2021}, } @article{9009, abstract = {Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane.}, author = {Grosser, Joshua A. and Maes, Margaret E and Nickells, Robert W.}, issn = {1573-675X}, journal = {Apoptosis}, number = {2}, pages = {132--145}, publisher = {Springer Nature}, title = {{Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis}}, doi = {10.1007/s10495-020-01654-w}, volume = {26}, year = {2021}, } @article{9038, abstract = {Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. }, author = {Aguilar-Merino, Patricia and Álvarez-Pérez, Gonzalo and Taboada-Gutiérrez, Javier and Duan, Jiahua and Prieto Gonzalez, Ivan and Álvarez-Prado, Luis Manuel and Nikitin, Alexey Y. and Martín-Sánchez, Javier and Alonso-González, Pablo}, issn = {20794991}, journal = {Nanomaterials}, number = {1}, publisher = {MDPI}, title = {{Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal}}, doi = {10.3390/nano11010120}, volume = {11}, year = {2021}, } @article{9020, abstract = {We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. }, author = {Gulden, Tobias and Kamenev, Alex}, issn = {1099-4300}, journal = {Entropy}, number = {1}, publisher = {MDPI}, title = {{Dynamics of ion channels via non-hermitian quantum mechanics}}, doi = {10.3390/e23010125}, volume = {23}, year = {2021}, } @article{9037, abstract = {We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak 𝜀 ‐net theorem in Banach spaces of type 𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.}, author = {Ivanov, Grigory}, issn = {14692120}, journal = {Bulletin of the London Mathematical Society}, number = {2}, pages = {631--641}, publisher = {London Mathematical Society}, title = {{No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p}}, doi = {10.1112/blms.12449}, volume = {53}, year = {2021}, } @article{9046, author = {Römhild, Roderich and Andersson, Dan I.}, issn = {15537374}, journal = {PLoS Pathogens}, number = {1}, publisher = {Public Library of Science}, title = {{Mechanisms and therapeutic potential of collateral sensitivity to antibiotics}}, doi = {10.1371/journal.ppat.1009172}, volume = {17}, year = {2021}, } @article{9047, abstract = {This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.}, author = {Mondelli, Marco and Hashemi, Seyyed Ali and Cioffi, John M. and Goldsmith, Andrea}, issn = {15582248}, journal = {IEEE Transactions on Wireless Communications}, number = {1}, pages = {18--27}, publisher = {IEEE}, title = {{Sublinear latency for simplified successive cancellation decoding of polar codes}}, doi = {10.1109/TWC.2020.3022922}, volume = {20}, year = {2021}, } @article{9036, abstract = {In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.}, author = {Virosztek, Daniel}, issn = {0001-8708}, journal = {Advances in Mathematics}, keywords = {General Mathematics}, number = {3}, publisher = {Elsevier}, title = {{The metric property of the quantum Jensen-Shannon divergence}}, doi = {10.1016/j.aim.2021.107595}, volume = {380}, year = {2021}, } @article{9101, abstract = {Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.}, author = {Reber, Stephan A. and Oh, Jinook and Janisch, Judith and Stevenson, Colin and Foggett, Shaun and Wilkinson, Anna}, issn = {14359456}, journal = {Animal Cognition}, number = {4}, pages = {753--764}, publisher = {Springer Nature}, title = {{Early life differences in behavioral predispositions in two Alligatoridae species}}, doi = {10.1007/s10071-020-01461-5}, volume = {24}, year = {2021}, } @article{9100, abstract = {Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.}, author = {Faria, Rui and Johannesson, Kerstin and Stankowski, Sean}, issn = {14209101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {4--15}, publisher = {Wiley}, title = {{Speciation in marine environments: Diving under the surface}}, doi = {10.1111/jeb.13756}, volume = {34}, year = {2021}, } @article{9093, abstract = {We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation.}, author = {Marchukov, Oleksandr and Volosniev, Artem}, issn = {2542-4653}, journal = {SciPost Physics}, number = {2}, publisher = {SciPost Foundation}, title = {{Shape of a sound wave in a weakly-perturbed Bose gas}}, doi = {10.21468/scipostphys.10.2.025}, volume = {10}, year = {2021}, } @article{8689, abstract = {This paper continues the discussion started in [CK19] concerning Arnold's legacy on classical KAM theory and (some of) its modern developments. We prove a detailed and explicit `global' Arnold's KAM Theorem, which yields, in particular, the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian system to an integrable system on a closed, nowhere dense, positive measure subset of the phase space. Detailed measure estimates on the Kolmogorov's set are provided in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded) set times the d-torus and (B) a domain with C2 boundary times the d-torus. All constants are explicitly given.}, author = {Chierchia, Luigi and Koudjinan, Edmond}, issn = {1560-3547}, journal = {Regular and Chaotic Dynamics}, keywords = {Nearly{integrable Hamiltonian systems, perturbation theory, KAM Theory, Arnold's scheme, Kolmogorov's set, primary invariant tori, Lagrangian tori, measure estimates, small divisors, integrability on nowhere dense sets, Diophantine frequencies.}, number = {1}, pages = {61--88}, publisher = {Springer Nature}, title = {{V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates}}, doi = {10.1134/S1560354721010044}, volume = {26}, year = {2021}, } @article{9099, abstract = {We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations.}, author = {Srivastava, Tanya K}, issn = {14208938}, journal = {Archiv der Mathematik}, number = {5}, pages = {515--527}, publisher = {Springer Nature}, title = {{Lifting automorphisms on Abelian varieties as derived autoequivalences}}, doi = {10.1007/s00013-020-01564-y}, volume = {116}, year = {2021}, } @article{9098, abstract = {We study properties of the volume of projections of the n-dimensional cross-polytope $\crosp^n = \{ x \in \R^n \mid |x_1| + \dots + |x_n| \leqslant 1\}.$ We prove that the projection of $\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3. We obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.}, author = {Ivanov, Grigory}, issn = {0012365X}, journal = {Discrete Mathematics}, number = {5}, publisher = {Elsevier}, title = {{On the volume of projections of the cross-polytope}}, doi = {10.1016/j.disc.2021.112312}, volume = {344}, year = {2021}, } @article{9188, abstract = {Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.}, author = {Pauler, Florian and Hudson, Quanah and Laukoter, Susanne and Hippenmeyer, Simon}, issn = {0197-0186}, journal = {Neurochemistry International}, keywords = {Cell Biology, Cellular and Molecular Neuroscience}, number = {5}, publisher = {Elsevier}, title = {{Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond}}, doi = {10.1016/j.neuint.2021.104986}, volume = {145}, year = {2021}, } @article{9158, abstract = {While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.}, author = {De Nicola, Stefano}, issn = {1742-5468}, journal = {Journal of Statistical Mechanics: Theory and Experiment}, keywords = {Statistics, Probability and Uncertainty, Statistics and Probability, Statistical and Nonlinear Physics}, number = {1}, publisher = {IOP Publishing}, title = {{Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation}}, doi = {10.1088/1742-5468/abc7c7}, volume = {2021}, year = {2021}, } @article{9118, abstract = {Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors.}, author = {Calcabrini, Mariano and Genc, Aziz and Liu, Yu and Kleinhanns, Tobias and Lee, Seungho and Dirin, Dmitry N. and Akkerman, Quinten A. and Kovalenko, Maksym V. and Arbiol, Jordi and Ibáñez, Maria}, issn = {2380-8195}, journal = {ACS Energy Letters}, number = {2}, pages = {581--587}, publisher = {American Chemical Society}, title = {{Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites}}, doi = {10.1021/acsenergylett.0c02448}, volume = {6}, year = {2021}, } @article{9168, abstract = {Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.}, author = {Fraisse, Christelle and Sachdeva, Himani}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Genetics Society of America}, title = {{The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes}}, doi = {10.1093/genetics/iyaa025}, volume = {217}, year = {2021}, } @article{9113, abstract = {“Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions.}, author = {Manzoor Bhat, Zahid Manzoor and Thimmappa, Ravikumar and Dargily, Neethu Christudas and Raafik, Abdul and Kottaichamy, Alagar Raja and Devendrachari, Mruthyunjayachari Chattanahalli and Itagi, Mahesh and Makri Nimbegondi Kotresh, Harish and Freunberger, Stefan Alexander and Ottakam Thotiyl, Musthafa }, issn = {2168-0485}, journal = {ACS Sustainable Chemistry and Engineering}, number = {8}, pages = {3104--3111}, publisher = {American Chemical Society}, title = {{Ambient condition alcohol reforming to hydrogen with electricity output}}, doi = {10.1021/acssuschemeng.0c07547}, volume = {9}, year = {2021}, } @article{9119, abstract = {We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.}, author = {Fraisse, Christelle and Popovic, Iva and Mazoyer, Clément and Spataro, Bruno and Delmotte, Stéphane and Romiguier, Jonathan and Loire, Étienne and Simon, Alexis and Galtier, Nicolas and Duret, Laurent and Bierne, Nicolas and Vekemans, Xavier and Roux, Camille}, issn = {17550998}, journal = {Molecular Ecology Resources}, pages = {2629--2644}, publisher = {Wiley}, title = {{DILS: Demographic inferences with linked selection by using ABC}}, doi = {10.1111/1755-0998.13323}, volume = {21}, year = {2021}, } @article{9173, abstract = {We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem.}, author = {Srivastava, Tanya K}, issn = {0007-4497}, journal = {Bulletin des Sciences Mathematiques}, number = {03}, publisher = {Elsevier}, title = {{Pathologies of the Hilbert scheme of points of a supersingular Enriques surface}}, doi = {10.1016/j.bulsci.2021.102957}, volume = {167}, year = {2021}, } @inproceedings{9200, abstract = {Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.}, author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian}, booktitle = {HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control}, isbn = {9781450383394}, keywords = {hybrid automaton, membership, system identification}, location = {Nashville, TN, United States}, pages = {2102.12734}, publisher = {Association for Computing Machinery}, title = {{Synthesis of hybrid automata with affine dynamics from time-series data}}, doi = {10.1145/3447928.3456704}, year = {2021}, } @article{9205, abstract = {Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.}, author = {Kampjut, Domen and Steiner, Julia and Sazanov, Leonid A}, issn = {25890042}, journal = {iScience}, number = {3}, publisher = {Elsevier}, title = {{Cryo-EM grid optimization for membrane proteins}}, doi = {10.1016/j.isci.2021.102139}, volume = {24}, year = {2021}, } @article{9207, abstract = {In this paper we experimentally study the transitional range of Reynolds numbers in plane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures triggered by a strong impulsive jet and the large-scale flow generated around these structures. We present a detailed investigation of the large-scale flow and show how its amplitude depends on Reynolds number and amplitude perturbation. In addition, we characterize the initial dynamics of the localized turbulent spot, which includes the coupling between the small and large scales, as well as the dependence of the advection speed on the large-scale flow generated around the spot. Finally, we provide the first experimental measurements of the large-scale flow around an oblique turbulent band.}, author = {Klotz, Lukasz and Pavlenko, A. M. and Wesfreid, J. E.}, issn = {1469-7645}, journal = {Journal of Fluid Mechanics}, publisher = {Cambridge University Press}, title = {{Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow}}, doi = {10.1017/jfm.2020.1089}, volume = {912}, year = {2021}, } @article{9206, abstract = {The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. }, author = {Cadavid, Doris and Wei, Kaya and Liu, Yu and Zhang, Yu and Li, Mengyao and Genç, Aziz and Berestok, Taisiia and Ibáñez, Maria and Shavel, Alexey and Nolas, George S. and Cabot, Andreu}, issn = {1996-1944}, journal = {Materials}, number = {4}, publisher = {MDPI}, title = {{Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks}}, doi = {10.3390/ma14040853}, volume = {14}, year = {2021}, }