Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations"

Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations", including magnetic fields, number density and average velocities of particles.

opencc-zeroMar 2023View details →

Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution

Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyze the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive – but not significant – trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary "replicates" can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.

opencc-by-4.0Mar 2023View details →

Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements

A library of 50 enhancers, each tested in three different lengths and with two different promoters (300 combinations), was packaged into AAV9 and delivered to newborn mice. Enhancers were selected from the VISTA Enhancer Browser of transgenic reporter data, and included 25 candidates active in the embryonic myocardium and 25 negative control candidates active in embryonic endothelium but not in myocardium. In the heart, AAV9 selectively transduces cardiomyocytes. After collecting ventricles at P28, the reporter transcripts were sequenced, and the frequency of each barcode was compared to its frequency in the viral pool DNA. Here we provide fastq files for each sample, an Excel spreadsheet (MPRA-Metadata.xls) containing annotation, and an Excel spreadsheet (MPRA-counts.xlsx) containing extracted barcode counts for each enhancer, as well as additional annotation and calculated enhancer activity.

opencc-by-4.0Apr 2023View details →

Massively parallel screens to identify splice disruptive variants in human disease genes

Splicing is a critical step in mRNA maturation with roles in gene regulation and proteome diversification. Splice disruptive variants (SDVs) are implicated in diverse human diseases, and 10-33% of exonic variants may disrupt splicing. However, identifying SDVs remains challenging due to the degeneracy and redundancy of the underlying sequence code. Experimental splicing measurements from patient cells or mini-gene assays can detect SDVs but have traditionally been low-throughput.  Massively parallel reporter assays (MPSAs) systematically measure splicing impacts at scale and could clarify variant pathogenicity and inform models of splicing regulation. In this assay, complex barcoded libraries of mutant exons are synthesized, cloned into minigene constructs, and transfected into human cells. Splicing outcomes of each mutation are quantified en masse using targeted RNA-seq of minigene-derived transcripts, and I developed custom python package to process the resulting data. In Chapter 2, I apply this assay to the pituitary transcription factor gene POU1F1 (in collaboration Dr. Sally Camper’s lab). Mutations in POU1F1 cause combined pituitary hormone deficiency (CPHD), a clinically and genetically heterogenous disorder with prevalence ~1:4000. We targeted exon 2, which has two alterative isoforms (alpha and beta) using competing splice acceptors that encode mutually antagonistic proteins. We measured the splicing effects of 1,070 SNVs across the exon and surrounding introns and identified 96 SDVs - 14 of which were synonymous substitutions. Our measurements were concordant with six nearby heterozygous missense and synonymous variants seen in unrelated hypopituitarism patients. This map identifies a putative splice silencer motif that represses the use of the normally lowly expressed beta isoform. In Chapter 3, I apply a MPSA to a critical developmental renal transcription factor gene, WT1 (in collaboration with clinical nephrologist Dr. Jen Lai Yee). Mutations in WT1 are implicated in nephrotic syndrome and sexual differentiation phenotypes. I focus on exon 9 which is alternatively spliced at competing donor sites resulting in two isoforms (KTS+ and KTS-). KTS+ and KTS- are normally expressed in ~2:1 ratio, but perturbation of the ratio can lead to Frasier’s syndrome – a rare nephrotic syndrome. We tested 518 SNVs for splicing defects and identified 8 known Frasier’s Syndrome variants as well as 16 additional variants that similarly lowered the KTS ratio. We also detected 19 variants increasing the KTS ratio - two of which have been observed in patients with sexual differentiation phenotypes. Although MPSAs can measure splicing effects of hundreds of variants simultaneously, the current scale of variant discovery via exome and genome sequencing demands efficient and accurate computational approaches to identify splice disruptive variants genome-wide. To evaluate the state of the art within contemporary splice prediction algorithms, in Chapter 4 I employed the results of five high throughput splicing assays and one literature curated variant set. A unique advantage of MPSAs over typical training and validation datasets is that they avoid bias towards essential splice site variants. I found the latest deep learning tools, SpliceAI and Pangolin, were most concordant with the measured splicing effects. However, all tools showed less agreement with exonic splicing outcomes compared to intronic. Some tools’ predictions, like SpliceAI’s, were sensitive to specified annotation files. Thus, there is still room for improvement within the next generation of splice prediction algorithms which future MPSA studies may facilitate.

opencc-zeroApr 2023View details →

Parallel evolution of behaviour, physiology and life history associated with altitudinal shifts in forest type in Heliconius butterflies

Parallel evolution of morphological traits is widely reported, providing evidence for the role of local conditions in driving adaptive divergence. Comparatively, fewer studies have tested for parallelism in behaviour, and it is less clear to what extent heritable behavioural shifts contribute to adaptive divergence. We exploit repeated incipient speciation across altitudinal gradients to explore behaviour and physiology in Heliconius butterflies adapted to high-elevation. We performed common garden experiments with H. chestertonii, a high-altitude specialist from the Colombian Cordillera Occidental, and H. erato venus, a low-elevation proxy for the ancestral population, and compared our results to existing data for an equivalent Ecuadorian taxa-pair. Using broad-scale climatic data, we show that both pairs diverge across similar ecological gradients, confirmed using localised data loggers in the ranges of H. chestertonii and H. e. venus. We further show that H. chestertonii and H. e. venus have divergent activity patterns, attributable to different responses to microclimate, and life histories. Finally, we provide evidence for parallelism in these traits with H. himera and H. e. cyrbia. We propose that this is a result of selection associated with independent colonisations of high-altitude forests, emphasising the importance of heritable behavioural and physiological adaptations during population divergence and speciation.

opencc-by-4.0Apr 2023View details →

'Chaotic micro-comb based parallel ranging' dataset and code

Available data and code for manuscript: "Chaotic micro-comb based parallel ranging" Arxiv version: https://arxiv.org/abs/2112.10241 Execution tested with Matlab 2020b or newer on Windows. Unzip folder to access files. Matlab figures are stored in matlab_figures folder. Raw data are stored in raw_data folder. To obtain plots from figure 2 (arXiv manuscript) execute Hilbert_freq_noise_analysis.m file. To process raw dat for figures 3,4 utilize sequential_analysis.m script. To plot point clouds of the processed data (\raw_data\fig3\analyzed_data) utilize plot_point_cloud_rmcw.m script. Comment/uncomment to change parameters for velocity/distance measurements (chess/wheel). Contact anton.lukashchuk@epfl.ch if problems with matlab code arise.  All matlab code remains under copyright by the authors: Anton Lukashchuk, Johann Riemensberger. The code is provided solely to be used to reproduce the figures of the aforementioned paper.

opencc-by-4.0Apr 2023View details →

Chaotic microcomb inertia-free parallel ranging dataset and code

Available data and code for manuscript: "Chaotic microcomb inertia-free parallel ranging" Arxiv version: https://arxiv.org/abs/2212.14275 Execution tested with Matlab 2020b or newer on Windows. Unzip folder to access files. Matlab figures are stored in matlab_figures folder. For figure 2 execute feed_forward_tuning_analysis.m file Change tuning rate (row 23) for appropriate values (25, 50, 100 Hz). For figure 3 execute sequential_analysis_findpeaks.m and vipa_point_cloud.m files. Raw data are stored in raw_data folder. Contact anton.lukashchuk@epfl.ch if problems with matlab code arise.  All matlab code remains under copyright by the authors: Anton Lukashchuk. The code is provided solely to be used to reproduce the figures of the aforementioned paper.

opencc-by-4.0May 2023View details →

Parallel Bilby O4 Review Data

The result files from the parallel-bilby O4 review. Review page here: https://git.ligo.org/lscsoft/parallel_bilby/-/wikis/O4-Review Review repo here: https://git.ligo.org/avi.vajpeyi/pbilby_o4_review

opencc-by-4.0May 2023View details →

Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification"

Data needed to reproduce the figures of <a href="https://arxiv.org/abs/2305.05881">https://arxiv.org/abs/2305.05881</a> and a simple code example of a quantum-convex-classical neural network used to train a sine versus cosine classification problem.

opencc-by-4.0Jul 2023View details →

Parallel and shared glosses to the first book of the Etymologiae [edge and node tables]

This record contains the node table and the edge table for plotting and analyzing the co-occurrence network of glossed manuscripts transmitting the first book of the Etymologiae of Isidore of Seville. This data is used in: Evina Stein. ‘Parallel Glosses, Shared Glosses, and Gloss Clustering: Can Network-Based Approach Help Us to Understand Organic Corpora of Glosses?’, Journal of Historical Network Research 9 (2023), 36-116. Abstract: Glossing was an important element of medieval western manuscript culture. However, glosses are notoriously difficult to analyze because of their triviality, fluid nature, heterogeneity of origin, complex transmission histories, and anonymity. Traditional scholarly approaches such as close reading and the genealogical method often do not produce satisfactory results, especially in the case of gloss corpora that are highly organic, i.e., display the traits listed above to a significant degree. This article outlines a method for analyzing the organic corpora of glosses based on their treatment as networks. The theoretical model for the proposed method is the co-occurrence network, a network model in which relationships between entities (nodes) are established based on certain shared properties or constituent elements (edges). In the case of corpora of glosses, glossed manuscripts are assumed as nodes, and the glosses that specific manuscripts have in common constitute the edges between them. Since gloss parallelism can arise through different processes, including randomness, the article describes two strategies that reduce such noise so that the transmission of glosses can be effectively examined. The method is demonstrated on a representative corpus – the early medieval glosses to the first book of the Etymologiae of Isidore of Seville.

opencc-zeroDec 2022View details →

Data from: Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments

Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.

opencc-by-3.0-usJun 2023View details →

Data for publication "Aerodynamic interactions of drops on parallel fibers"

A collection of the data and scripts used to produce figures and derive conclusions for: "Aerodynamic interactions of drops on parallel fibers." The DOI number for this paper is 10.1038/s41567-023-02159-4. It is available at the following URL: <a href="https://www.nature.com/articles/s41567-023-02159-4">https://www.nature.com/articles/s41567-023-02159-4</a>. Please see Repo_Contents.pdf for details.

opencc-by-4.0Sep 2023View details →

Lysozyme-in-water 1us full-atom GROMACS simulation for MDAnalysis parallelization benchmark

I'm using trajectory and topology for an 1us run generated according to <a href="http://www.mdtutorials.com/gmx/lysozyme/index.html">lysozyme in water</a> tutorial and used later in <a href="https://www.nature.com/articles/s41598-023-32459-x">this</a> publication (charged HIS trajectory). A full-atom <code>xtc</code> trajectory containing 25690 atoms in total (see topology for more detail). Associated benchmark and its description can be found <a href="https://gist.github.com/marinegor/17558d1685cd2f24a6de65aa99cf5c9e">here</a>.

opencc-by-4.0Sep 2023View details →

Isoacridone dyes with parallel reactivity from both singlet and triplet excited states for biphotonic catalysis and upconversion

Raw data of the publication in Chem. Sci. titled "Isoacridone dyes with parallel reactivity from both singlet and triplet excited states for biphotonic catalysis and upconversion"

opencc-zeroOct 2023View details →

Data from: Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird genus Motacilla: one species, the White Wagtail (M. alba), shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (African Pied Wagtail M. aguimp + Mekong Wagtail M. samveasnae and Japanese Wagtail M. grandis + White-browed Wagtail M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a "complete evidence" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.

closedIPD-NOFeb 2026View details →

A Multi-Center, Randomized, Double Masked, Parallel-Group, Vehicle-Controlled, Clinical Study to Assess the Safety and Efficacy of Reproxalap Ophthalmic Solution in Subjects With Dry Eye Disease

ClinicalTrials.gov study NCT03404115. IPD Sharing: NO. Countries: 1. Publications: 1.

American Ginseng to Improve HIV-Associated Fatigue: A Randomized, Placebo-Controlled, Parallel Design, Multiple-Dose Clinical Trial

ClinicalTrials.gov study NCT01500096. IPD Sharing: Not stated. Countries: 1. Publications: 2.

A Randomized, Double-Blind, Parallel-Group, Placebo-Controlled, Fixed Dose Study Evaluating the Efficacy and Safety of Orvepitant in Subjects With Major Depressive Disorder

ClinicalTrials.gov study NCT00880399. IPD Sharing: Not stated. Countries: 2. Publications: 1.

24-Week, Multicenter, Randomized, Parallel-group, Open-label, Active Controlled Phase IV Study to Assess the Efficacy, Safety and Tolerability of Saxagliptin Compared With Acarbose When in Combination

ClinicalTrials.gov study NCT02243176. IPD Sharing: Not stated. Countries: 1. Publications: 1.

A Parallel Group Comparison of the Efficacy and Safety of Degarelix at Two Different Dosing Regimens in Patients With Prostate Cancer

ClinicalTrials.gov study NCT00116779. IPD Sharing: Not stated. Countries: 2. Publications: 1.