@misc{14494, abstract = {We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023). Buri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841}, author = {Buri, Pascal and Fatichi, Simone and Shaw, Thomas and Miles, Evan and McCarthy, Michael and Fyffe, Catriona Louise and Fugger, Stefan and Ren, Shaoting and Kneib, Marin and Jouberton, Achille and Steiner, Jakob and Fujita, Koji and Pellicciotti, Francesca}, publisher = {Zenodo}, title = {{Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"}}, doi = {10.5281/ZENODO.8402426}, year = {2023}, } @misc{12869, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. }, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for: A stochastic cellular automaton model of culture formation}}, doi = {10.15479/AT:ISTA:12869}, year = {2023}, } @misc{14523, abstract = {see Readme file}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James and Souslov, Anton}, publisher = {Zenodo}, title = {{SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1}}, doi = {10.5281/ZENODO.8329143}, year = {2023}, } @misc{14579, abstract = {This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science. }, author = {Wetzel, William}, publisher = {Zenodo}, title = {{HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0}}, doi = {10.5281/ZENODO.8133117}, year = {2023}, } @misc{14562, abstract = {Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. }, author = {Schur, Florian KM}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning"}}, doi = {10.15479/AT:ISTA:14562}, year = {2023}, } @misc{14472, abstract = {Data related to the following paper: "Stress granules plug and stabilize damaged endolysosomal membranes" (https://doi.org/10.1038/s41586-023-06726-w) Abstract: Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.}, author = {Vanhille-Campos, Christian Eduardo and Šarić, Anđela}, publisher = {Institute of Science and Technology Austria}, title = {{Stress granules plug and stabilize damaged endolysosomal membranes}}, doi = {10.15479/AT:ISTA:14472}, year = {2023}, } @misc{14616, abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.}, author = {Toups, Melissa A and Vicoso, Beatriz}, publisher = {Dryad}, title = {{The X chromosome of insects likely predates the origin of Class Insecta}}, doi = {10.5061/DRYAD.HX3FFBGKT}, year = {2023}, } @misc{14617, abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.}, author = {Toups, Melissa A and Vicoso, Beatriz}, publisher = {Zenodo}, title = {{The X chromosome of insects likely predates the origin of Class Insecta}}, doi = {10.5281/ZENODO.8138705}, year = {2023}, } @misc{14619, abstract = {Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).}, author = {Cheng, Bingqing}, publisher = {Zenodo}, title = {{BingqingCheng/solubility: V1.0}}, doi = {10.5281/ZENODO.8398094}, year = {2023}, } @misc{12693, abstract = {See Readme File for further information.}, author = {Cremer, Sylvia}, publisher = {Institute of Science and Technology Austria}, title = {{Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males }}, doi = {10.15479/AT:ISTA:12693}, year = {2023}, } @misc{13336, author = {Kleshnina, Maria}, publisher = {Zenodo}, title = {{kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games}}, doi = {10.5281/ZENODO.8059564}, year = {2023}, } @misc{12933, abstract = {Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".}, author = {Puixeu Sala, Gemma}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}}, doi = {10.15479/AT:ISTA:12933}, year = {2023}, } @misc{12817, abstract = {3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.}, author = {Danzl, Johann G}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for the publication "Dense 4D nanoscale reconstruction of living brain tissue"}}, doi = {10.15479/AT:ISTA:12817}, year = {2023}, } @misc{14892, abstract = {Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.}, author = {Feitosa Tomé, Douglas}, publisher = {Zenodo}, title = {{douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation}}, doi = {10.5281/ZENODO.10251087}, year = {2023}, } @misc{14919, abstract = {GLACIER METEOROLOGICAL DATA SWISS ALPS -2022 }, author = {Shaw, Thomas and Buri, Pascal and McCarthy, Michael and Miles, Evan and Pellicciotti, Francesca}, publisher = {Zenodo}, title = {{Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer}}, doi = {10.5281/ZENODO.8277285}, year = {2023}, } @misc{12497, abstract = {Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.}, author = {Becker, Lea Marie and Schanda, Paul}, keywords = {aromatic side chains, isotopic labeling, protein dynamics, ring flips, spin relaxation}, publisher = {Institute of Science and Technology Austria}, title = {{Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues}}, doi = {10.15479/AT:ISTA:12497}, year = {2023}, } @misc{13126, abstract = {Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.}, author = {Danzl, Johann G}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for the publication "Imaging brain tissue architecture across millimeter to nanometer scales"}}, doi = {10.15479/AT:ISTA:13126}, year = {2023}, } @misc{13116, abstract = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. }, author = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin}, publisher = {Institute of Science and Technology Austria}, title = {{Chiral and nematic phases of flexible active filaments}}, doi = {10.15479/AT:ISTA:13116}, year = {2023}, } @misc{14614, abstract = {Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.}, author = {Lasne, Clementine and Elkrewi, Marwan N}, keywords = {Panorpa, scorpionfly, genome, transcriptome}, publisher = {Institute of Science and Technology Austria}, title = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}}, doi = {10.15479/AT:ISTA:14614}, year = {2023}, } @misc{15027, abstract = {This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).}, author = {Curk, Samo}, publisher = {Figshare}, title = {{aggregation_data}}, year = {2023}, } @misc{14991, abstract = {This repository contains the data, scripts, WRF codes and files required to reproduce the results of the manuscript "Assessing Memory in Convection Schemes Using Idealized Tests" submitted to the Journal of Advances in Modeling Earth Systems (JAMES).}, author = {Hwong, Yi-Ling and Colin, Maxime and Aglas, Philipp and Muller, Caroline J and Sherwood, Steven C.}, publisher = {Zenodo}, title = {{Data-assessing memory in convection schemes using idealized tests}}, doi = {10.5281/ZENODO.7757041}, year = {2023}, } @misc{14990, abstract = {The software artefact to evaluate the approximation of stationary distributions implementation.}, author = {Meggendorfer, Tobias}, publisher = {Zenodo}, title = {{Artefact for: Correct Approximation of Stationary Distributions}}, doi = {10.5281/ZENODO.7548214}, year = {2023}, } @misc{14995, abstract = {Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation.}, author = {Koval, Nikita and Fedorov, Alexander and Sokolova, Maria and Tsitelov, Dmitry and Alistarh, Dan-Adrian}, publisher = {Zenodo}, title = {{Lincheck: A practical framework for testing concurrent data structures on JVM}}, doi = {10.5281/ZENODO.7877757}, year = {2023}, } @misc{14994, abstract = {This resource contains the artifacts for reproducing the experimental results presented in the paper titled "A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties" that has been submitted in CAV 2023.}, author = {Majumdar, Rupak and Mallik, Kaushik and Rychlicki, Mateusz and Schmuck, Anne-Kathrin and Soudjani, Sadegh}, publisher = {Zenodo}, title = {{A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties}}, doi = {10.5281/ZENODO.7877790}, year = {2023}, } @misc{15035, abstract = {This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties With Prefix Transducers accepted at RV'23, and give further pointers to implementation of prefix transducers. It has two parts: a pre-compiled docker image and sources that one can use to compile (locally or in docker) the software and run the experiments.}, author = {Chalupa, Marek and Henzinger, Thomas A}, publisher = {Zenodo}, title = {{Monitoring hyperproperties with prefix transducers}}, doi = {10.5281/ZENODO.8191723}, year = {2023}, } @misc{14812, abstract = {This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode}, author = {Stankowski, Sean}, publisher = {Zenodo}, title = {{Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails}}, doi = {10.5281/ZENODO.8318995}, year = {2023}, } @misc{13173, abstract = {GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.}, author = {Shigemoto, Ryuichi}, keywords = {medial habenula, GABAB receptor, vesicle release, Flash and Freeze, Flash and Freeze-fracture}, publisher = {Institute of Science and Technology Austria}, title = {{Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals}}, doi = {10.15479/AT:ISTA:13173}, year = {2023}, } @misc{11686, abstract = {Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes.}, author = {Turelli, Michael and Barton, Nicholas H}, keywords = {Biological sciences}, publisher = {Dryad}, title = {{Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control}}, doi = {10.25338/B81931}, year = {2022}, } @misc{10833, abstract = {Detailed information about the data set see "dataset description.txt" file.}, author = {Hasler, Roger and Reiner-Rozman, Ciril and Fossati, Stefan and Aspermair, Patrik and Dostalek, Jakub and Lee, Seungho and Ibáñez, Maria and Bintinger, Johannes and Knoll, Wolfgang}, publisher = {Zenodo}, title = {{Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device}}, doi = {10.5281/ZENODO.5500360}, year = {2022}, } @misc{13076, abstract = {The source code for replicating experiments presented in the paper. The implementation of the designed priority schedulers can be found in Galois-2.2.1/include/Galois/WorkList/: StealingMultiQueue.h is the StealingMultiQueue. MQOptimized/ contains MQ Optimized variants. We provide images that contain all the dependencies and datasets. Images can be pulled from npostnikova/mq-based-schedulers repository, or downloaded from Zenodo. See readme for more detail.}, author = {Postnikova, Anastasiia and Koval, Nikita and Nadiradze, Giorgi and Alistarh, Dan-Adrian}, publisher = {Zenodo}, title = {{Multi-queues can be state-of-the-art priority schedulers}}, doi = {10.5281/ZENODO.5733408}, year = {2022}, } @misc{11695, abstract = {Data underlying the figures in the publication "The chemistry of Cu3N and Cu3PdN nanocrystals" }, author = {Parvizian, Mahsa and Duran Balsa, Alejandra and Pokratath, Rohan and Kalha, Curran and Lee, Seungho and Van den Eynden, Dietger and Ibáñez, Maria and Regoutz, Anna and De Roo, Jonathan}, publisher = {Zenodo}, title = {{Data for "The chemistry of Cu3N and Cu3PdN nanocrystals"}}, doi = {10.5281/ZENODO.6542908}, year = {2022}, } @misc{11711, abstract = {Codes and data for reproducing the results of N. B. Budanur and B. Hof "An autonomous compartmental model for accelerating epidemics"}, author = {Budanur, Nazmi B}, publisher = {Zenodo}, title = {{burakbudanur/autoacc-public}}, doi = {10.5281/ZENODO.6802720}, year = {2022}, } @misc{13064, abstract = {Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.}, author = {Orliac, Etienne and Trejo Banos, Daniel and Ojavee, Sven and Läll, Kristi and Mägi, Reedik and Visscher, Peter and Robinson, Matthew Richard}, publisher = {Dryad}, title = {{Improving genome-wide association discovery and genomic prediction accuracy in biobank data}}, doi = {10.5061/DRYAD.GTHT76HMZ}, year = {2022}, } @misc{12339, abstract = {Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales.}, author = {Tomanek, Isabella and Guet, Calin C}, publisher = {Dryad}, title = {{Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose}}, doi = {10.5061/dryad.rfj6q57ds}, year = {2022}, } @misc{13066, abstract = {Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.}, author = {Koch, Eva and Ravinet, Mark and Westram, Anja M and Jonannesson, Kerstin and Butlin, Roger}, publisher = {Dryad}, title = {{Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution}}, doi = {10.5061/DRYAD.M905QFV4B}, year = {2022}, } @misc{14520, abstract = {This dataset comprises all data shown in the figures of the submitted article "Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request.}, author = {Zemlicka, Martin and Redchenko, Elena and Peruzzo, Matilda and Hassani, Farid and Trioni, Andrea and Barzanjeh, Shabir and Fink, Johannes M}, publisher = {Zenodo}, title = {{Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses}}, doi = {10.5281/ZENODO.8408897}, year = {2022}, } @misc{10934, abstract = {FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. }, author = {Radler, Philipp}, keywords = {Bacterial cell division, in vitro reconstitution, FtsZ, FtsN, FtsA}, publisher = {Institute of Science and Technology Austria}, title = {{In vitro reconstitution of Escherichia coli divisome activation}}, doi = {10.15479/AT:ISTA:10934}, year = {2022}, } @misc{11542, author = {Schulz, Rouven}, publisher = {Institute of Science and Technology Austria}, title = {{Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)}}, doi = {10.15479/AT:ISTA:11542}, year = {2022}, } @misc{12522, abstract = {This .zip File contains the transport data, the codes for the data analysis, the microscopy analysis and the codes for the theoretical simulations for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks" by M. Valentini, et. al. The transport data are saved with hdf5 file format. The files can be open with the log browser of Labber.}, author = {Valentini, Marco and San-Jose, Pablo and Arbiol, Jordi and Marti-Sanchez, Sara and Botifoll, Marc}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks"}}, doi = {10.15479/AT:ISTA:12102}, year = {2022}, } @misc{11321, abstract = {Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. }, author = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H}, publisher = {Institute of Science and Technology Austria}, title = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}}, doi = {10.15479/at:ista:11321}, year = {2022}, } @misc{11653, abstract = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.}, author = {Elkrewi, Marwan N}, publisher = {Institute of Science and Technology Austria}, title = {{Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"}}, doi = {10.15479/AT:ISTA:11653}, year = {2022}, } @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}, } @misc{12987, abstract = {Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.}, author = {Koch, Eva and Morales, Hernán E. and Larsson, Jenny and Westram, Anja M and Faria, Rui and Lemmon, Alan R. and Lemmon, E. Moriarty and Johannesson, Kerstin and Butlin, Roger K.}, publisher = {Dryad}, title = {{Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis}}, doi = {10.5061/DRYAD.ZGMSBCCB4}, year = {2021}, } @misc{13080, abstract = {Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org)) We upload a pdf with extended data sets, and the raw data for these extended datasets as well.}, author = {Puglia, Denise and Martinez, Esteban and Menard, Gerbold and Pöschl, Andreas and Gronin, Sergei and Gardner, Geoffrey and Kallaher, Ray and Manfra, Michael and Marcus, Charles and Higginbotham, Andrew P and Casparis, Lucas}, publisher = {Zenodo}, title = {{Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire}}, doi = {10.5281/ZENODO.4592435}, year = {2021}, } @misc{13057, abstract = {This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request.}, author = {Peruzzo, Matilda and Hassani, Farid and Szep, Grisha and Trioni, Andrea and Redchenko, Elena and Zemlicka, Martin and Fink, Johannes M}, publisher = {Zenodo}, title = {{Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction}}, doi = {10.5281/ZENODO.5592103}, year = {2021}, } @misc{13061, abstract = {Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.}, author = {Casillas Perez, Barbara E and Pull, Christopher and Naiser, Filip and Naderlinger, Elisabeth and Matas, Jiri and Cremer, Sylvia}, publisher = {Dryad}, title = {{Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies}}, doi = {10.5061/DRYAD.7PVMCVDTJ}, year = {2021}, } @misc{13069, abstract = {To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.}, author = {Chauve, Laetitia and Hodge, Francesca and Murdoch, Sharlene and Masoudzadeh, Fatemah and Mann, Harry-Jack and Lopez-Clavijo, Andrea and Okkenhaug, Hanneke and West, Greg and Sousa, Bebiana C. and Segonds-Pichon, Anne and Li, Cheryl and Wingett, Steven and Kienberger, Hermine and Kleigrewe, Karin and de Bono, Mario and Wakelam, Michael and Casanueva, Olivia}, publisher = {Zenodo}, title = {{Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans}}, doi = {10.5281/ZENODO.5519410}, year = {2021}, } @misc{13058, abstract = {The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.}, author = {Ucar, Mehmet C}, publisher = {Zenodo}, title = {{Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance"}}, doi = {10.5281/ZENODO.5257160}, year = {2021}, } @misc{13062, abstract = {This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.}, author = {Szep, Eniko and Sachdeva, Himani and Barton, Nicholas H}, publisher = {Dryad}, title = {{Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model}}, doi = {10.5061/DRYAD.8GTHT76P1}, year = {2021}, }