@misc{14705, abstract = {Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.}, author = {Elkrewi, Marwan N}, keywords = {sex chromosome evolution, genome assembly, dosage compensation}, publisher = {Institute of Science and Technology Austria}, title = {{Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation"}}, doi = {10.15479/AT:ISTA:14705}, year = {2024}, } @misc{15108, abstract = {in the research article "Efficiency and resilience of cooperation in asymmetric social dilemmas" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina). We used different implementations for the case of two and three players, both described below.}, author = {Hübner, Valentin and Kleshnina, Maria}, publisher = {Zenodo}, title = {{Computer code for "Efficiency and resilience of cooperation in asymmetric social dilemmas"}}, doi = {10.5281/ZENODO.10639167}, year = {2024}, } @misc{13275, abstract = {We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.}, author = {Rammelmüller, Lukas and Huber, David and Volosniev, Artem}, publisher = {SciPost Foundation}, title = {{Codebase release 1.0 for FermiFCI}}, doi = {10.21468/scipostphyscodeb.12-r1.0}, year = {2023}, } @misc{12820, abstract = {Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. This data repository contains NMR data presented in the associated manuscript}, author = {Schanda, Paul}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR"}}, doi = {10.15479/AT:ISTA:12820}, year = {2023}, } @misc{13124, abstract = {This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.}, author = {Redchenko, Elena and Poshakinskiy, Alexander and Sett, Riya and Zemlicka, Martin and Poddubny, Alexander and Fink, Johannes M}, publisher = {Zenodo}, title = {{Tunable directional photon scattering from a pair of superconducting qubits}}, doi = {10.5281/ZENODO.7858567}, year = {2023}, } @misc{13122, abstract = {Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1}, author = {Sahu, Rishabh}, publisher = {Zenodo}, title = {{Entangling microwaves with light}}, doi = {10.5281/ZENODO.7789417}, year = {2023}, } @misc{12945, abstract = {basic data for use in code for experimental data analysis for manuscript under revision: Dynamic pathogen detection and social feedback shape collective hygiene in ants Casillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S}, author = {Cremer, Sylvia}, keywords = {collective behavior, host-pathogen interactions, social immunity, epidemiology, social insects, probabilistic modeling}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: "Dynamic pathogen detection and social feedback shape collective hygiene in ants" }}, doi = {10.15479/AT:ISTA:12945}, year = {2023}, } @misc{14279, abstract = {The zip file includes source data used in the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript. A sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. 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 "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration"}}, doi = {10.5281/ZENODO.8133960}, year = {2023}, } @misc{12370, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. }, author = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.15479/AT:ISTA:12370}, year = {2023}, } @misc{12949, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, }