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Data for: On the identification of hypoxic regions in subject-specific cerebral vasculature by combined CFD/MRI
<p>A long-time exposure to lack of oxygen (hypoxia) in some regions of the cerebrovascular system is believed to be one of the causes of cerebral neurological disease. Performing {\em in vivo} studies on the human brain is complicated and can be highly risky for patients. In the present study, we show how a combination of Magnetic Resonance Imaging (MRI) and Computational Fluid Dynamics (CFD) can provide a non-invasive alternative for studying blood flow and transport of oxygen within the cerebral vasculature. We perform computer simulations of oxygen mass transfer in the subject-specific geometry of the Circle of Willis. The computational domain and boundary conditions are based on 4D flow MRI measurements. Two different oxygen mass transfer models are considered: passive (where oxygen is treated as a dilute chemical species in plasma) and active (where oxygen is bonded to hemoglobin) models. We show that neglecting hemoglobin transport results in a significant underestimation of the arterial wall-mass transfer of oxygen. We identified the hypoxic regions along the arterial walls by introducing the critical thresholds that are obtained by comparison of the estimated range of Damk\"{o}hler number ($Da\subset\langle9;57\rangle$) with the local Sherwood number. Finally, we recommend additional validations of the combined MRI/CFD approach proposed here for larger groups of subject- or patient-specific brain vasculature systems.</p>
dmurraystoker/OGC-biomass: Long-term comparison of invertebrate communities in a blackwater river reveals taxon-specific biomass change
<p>Data, metadata, and R code for "Long-term comparison of invertebrate communities in a blackwater river reveals taxon-specific biomass change."</p> <p>Abstract</p> <p>1. Around the world, researchers are reporting declines in insect fauna. Though uncommonly evaluated in high-profile studies of insect declines, the community context of population trends can facilitate interpretation of the causes and consequences of such losses. Here, we aimed to explore the shifts in a well-studied invertebrate community of a blackwater river and identify potential catalysts of such change.</p> <p>2. We compared the density, biomass, and community structure of freshwater invertebrate assemblages separated by more than 30 years in the Ogeechee River, in the southeastern US, and found biomass declines. We also evaluated long-term trends in river discharge, water temperature, and precipitation.</p> <p>3. Overall, the biomass in the 2010s was approximately 60% of the total in the 1980s. Community analyses indicated that this decline was driven by reduced densities of large-bodied, filter-feeding insects, particularly Hydropsychidae caddisflies (Trichoptera). Conversely, predators and small-bodied primary consumers increased in density, though their contributions to overall biomass were minimal and their increased density was not sufficient to compensate for biomass declines. Seasonal shifts in both invertebrate populations and environmental parameters were evident, especially when focusing on discharge and dissolved organic carbon.</p> <p>4. Through a combination of direct analysis and the use of established research on the metabolic dynamics of the study site, we determined that the overall decline of freshwater invertebrate biomass may be driven by climate-related changes in flood dynamics: seasonal flooding that facilitates delivery of floodplain carbon to filter-feeding consumers has decreased over several decades. Water temperature had also increased and has likely had effects on the invertebrate assemblages.</p> <p>5. Whole-community evaluations such as this one, in contrast to single-taxon and abundance-based studies, provide critical information to elucidate the dynamics of freshwater impairment and insect loss in the Anthropocene.</p>
Cytoscape files - Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation
<p>Cytoscape files of pathway enrichment analyses and PPI mapping associated with manuscript https://www.nature.com/articles/s41467-023-39241-7</p> <p><strong>Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics</strong> <strong>identify cancer-specific mechanisms of stress adaptation </strong></p> <p>Anna Rodina<sup>1,11</sup>, Chao Xu<sup>1,11</sup>, Chander S. Digwal<sup>1,11</sup>, Suhasini Joshi<sup>1,11</sup>, Anand R. Santhaseela<sup>1</sup>, Sadik Bay<sup>1</sup>, Swathi Merugu<sup>1</sup>, Aftab Alam<sup>1</sup>, Pengrong Yan<sup>1</sup>, Chenghua Yang<sup>1,12</sup>, Tanaya Roychowdhury<sup>1</sup>, Palak Panchal<sup>1</sup>, Liza Shrestha<sup>1</sup>, Yanlong Kang<sup>1</sup>, Sahil Sharma<sup>1</sup>, Yogita Patel<sup>2</sup>, Justina Almadovar<sup>1</sup>, Adriana Corben<sup>3,13</sup>, Mary Alpaugh<sup>1,14</sup>, Shanu Modi<sup>4</sup>, Monica L. Guzman<sup>5</sup>, Teng Fei<sup>6</sup>, Tony Taldone<sup>1</sup>, Stephen D. Ginsberg<sup>7,8</sup>, Hediye Erdjument-Bromage<sup>9</sup>, Thomas A. Neubert<sup>9</sup>, Katia Manova-Todorova<sup>10</sup>, Jason C. Young<sup>2</sup>,<strong> </strong>Meng-Fu Bryan Tsou<sup>10</sup><strong>, </strong>Tai Wang<sup>1,*</sup>, Gabriela Chiosis<sup>1,4,*</sup></p> <p><strong>Abstract </strong></p> <p>Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of first-in-class chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based ‘omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks. </p>
Figure 4 in Vocal repertoire and group-specific signature in the Smooth-billed Ani, Crotophaga ani Linnaeus, 1758 (Cuculiformes, Aves)
Figure 4. Boxplots (median and quartiles) of acoustic parameters of the similar vocalizations of Charqueada and Guararema groups of Smooth-billed Ani. Vocalizations:"Ahnee","Whine", "Pre-flight", "Flight" and "Vigil". Acoustic parameters: DUR = duration; MPF = maximum peak frequency; MFF = maximum fundamental frequency; MIF = minimum frequency; MAF = maximum frequency.
Figure 3 in Vocal repertoire and group-specific signature in the Smooth-billed Ani, Crotophaga ani Linnaeus, 1758 (Cuculiformes, Aves)
Figure 3. Spectrograms of the ten types of vocalizations of the Smooth-billed Ani: "Ahnee" (A), "Whine" (B, C, D, E, F and G), "Pre-flight" (H), "Shout" (I), "Flight" (J and K), "Hoot" (L), "Grunt" (M), "Ee-oo-ee" (N), "Vigil" (O),"INR" (P and Q).
Figure 1 in Vocal repertoire and group-specific signature in the Smooth-billed Ani, Crotophaga ani Linnaeus, 1758 (Cuculiformes, Aves)
Figure 1. Location of the studied groups of Smooth-billed Ani in the municipality of Alegre, ES, Brazil.
Trans-specific polymorphism and the convergent evolution of supertypes in MHC class II genes in Darters (Etheostoma)
<p>Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans-specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study we used deep-sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.</p>
Large-scale survey of excitatory synapses reveals sublamina-specific and asymmetric synapse disassembly patterns in a neurodegenerative circuit
<p>Dataset associated with the manuscript titled "<strong>Large-scale survey of excitatory synapses reveals sublamina-specific and asymmetric synapse disassembly patterns in a neurodegenerative circuit"</strong></p>
Artifacts for the IEEE Internet of Things Journal Publication: Specification-based Symbolic Execution for Stateful Network Protocol Implementations in the IoT
<p>Artifacts for the evaluation of the publication <em>Specification-based Symbolic Execution for Stateful Network Protocol Implementations in the IoT </em>which will be published in the IEEE Internet of Things journal. More information is available in the provided README.md file.</p>
Combined in vitro and cell-based selection display method producing specific binders against IL-9 receptor in high yields
<p>The FEBS Journal FJ-22-0728</p> <p>Combined in vitro and cell-based selection display method producing specific binders against IL-9 receptor in high yields</p> <p>Maroš Huličiak, Lada Biedermanová, Daniel Berdár, Štěpán Herynek, Lucie Kolářová,<br> Jakub Tomala, Pavel Mikulecký, and Bohdan Schneider</p> <p><em>Institute of Biotechnology of the Czech Academy of Sciences,<br> Průmyslová 595, 252 50 Vestec, Czech Republic</em></p> <p>Correspondence: Bohdan Schneider, Institute of Biotechnology of the Czech Academy of Sciences,<br> BIOCEV, CZ-252 50 Vestec, Czech Republic,<br> Tel: +420 728 303 566, e-mail: bohdan.schneider@ibt.cas.cz</p> <p>Abstract</p> <p>We combined cell-free ribosome display and cell-based yeast display selection to build specific protein binders to the extracellular domain of the human interleukin 9 receptor alpha (IL-9Rα). The target, IL-9Rα, is the receptor involved in the signaling pathway of IL-9, a pro-inflammatory cytokine medically important for its involvement in respiratory diseases. The successive use of modified protocols of ribosome and yeast displays allowed us to combine their strengths - the virtually infinite selection power of ribosome display and the production of (mostly) properly folded and soluble proteins in yeast display. The described experimental protocol is optimized to produce binders highly specific to the target, including selectivity to common proteins such as BSA, and proteins potentially competing for the binder such as receptors of other cytokines. The binders were trained from DNA libraries of two protein scaffolds called 57aBi and 57bBi developed in our laboratory. We show that the described unconventional combination of ribosome and yeast displays is effective in developing selective small protein binders to the medically relevant molecular target.</p>
Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"
<p>Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available <a href="https://doi.org/10.1101/2022.08.15.503960">here</a>)</p> <p><strong>Analysis of AP-MS data</strong>: analysis.zip</p> <p>Contains the following scripts as well as their outputs:</p> <ul> <li>01_preparation.R R script for filtering and processing our mass spec data.</li> <li>02_diffbinding.R R script for differential analysis followed by gene set enrichment.</li> <li>03_funcstats.R R script for statistical analysis over different ontology terms.</li> <li>04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03.</li> <li>05_1_random_walks.py Python script for performing random walks for specific functional terms.</li> <li>05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1.</li> </ul> <p>The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD035399">entry</a>.</p> <p>Interactive visualization of the results of most of this analysis is available on <a href="https://github.com/PhilippJunk/kras_apms_vis">GitHub </a>as a Shiny app.</p> <p> </p> <p><strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip</p> <p>Contains the following script, as well as its output:</p> <ul> <li>01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances.</li> </ul> <p>The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD039404">entry</a>.</p>
Sex-specific paternal age effects on offspring quality in Drosophila melanogaster
<p>Advanced paternal age has been repeatedly shown to modulate offspring quality via male- and/or female-driven processes, and there are theoretical reasons to expect that some of these effects can be sex-specific. For example, sex allocation theory predicts that, when mated with low-condition males, mothers should invest more in their daughters compared to their sons. This is because male fitness is generally more condition-dependent and more variable than female fitness, which makes it less risky to invest in female offspring. Here, we explore whether paternal age can affect the quality and quantity of offspring in a sex-specific way using Drosophila melanogaster as model organism. In order to understand the contribution of male-driven processes on paternal age effects, we also measured the seminal vesicle size of young and older males and explored its relationship with reproductive success and offspring quality. Older males had lower competitive reproductive success, as expected, but there was no difference between the offspring sex ratio of young and older males. However, we found that paternal age caused an increase in offspring quality (i.e., offspring weight), and that this increase was more marked in daughters than sons. We discuss different male- and female-driven processes that may explain such sex-specific paternal age effects.</p>
Data for: Male-specific nocturnal song functions similar to day song in a diurnal bird species
<p class="MsoNormal">Historically, birdsong research has been biased towards song of male birds at dawn and during the day, even though some diurnal birds sing at night. To address this gap, we studied how song in the willie wagtail, <em>Rhipidura leucophrys</em>—a diurnal species with prolific male-specific nocturnal song during the breeding season—varies with time of day, breeding status, and simulated intrusions. <span>We recorded male nocturnal and dawn song over three breeding seasons and examined how this related to fertile and non-fertile breeding stages of females. To test whether song functions for territory defence, we simulated territorial intrusion experimentally in both sexes with daytime and nighttime playback of male and female song. To test whether nocturnal song could function for mate guarding or post-pairing mate attraction, we describe the mating system of willie wagtails using molecular genetic methods. We showed that both nocturnal and daytime song of male willie wagtails has roles in mate attraction and territory defence, while daytime song by females functioned primarily for territorial defence. </span>Males increased song behaviour during fertile periods of resident females, suggesting possible roles in mate stimulation and mate guarding. <span>Males and females responded similarly to simulated daytime intrusions and no differences were seen in male responses dependent on the time of day.</span> We found 10%-14% of offspring were fathered by extra-pair males, suggesting song may also function for mate guarding and post-pairing mate attraction<span>.</span><span> In a species with small repertoires and simple songs like the willie wagtail, differences between males in overall song output achieved through nocturnal singing may be important in mate attraction and territory defence.</span></p>
Frozen feather and motif files for Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue.
<p>Frozen feather and motif files for manuscript "Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue" by Espinoza DA, et al. Data was downloaded from cisTarget database from aertslab.org.</p>
Raw Data for the article: Analysis of the Specific Immune Response after the Third Dose of mRNA COVID-19 Vaccines in Organ Transplant Recipients: Possible Spike-S1 Reactive IgA Signature in Protection from SARS-CoV-2 Infection
<p><strong>Background:</strong> Several studies have indicated that anti-SARS-CoV-2 mRNA vaccinations are less effective in inducing robust immune responses among solid organ transplant recipients (SOTRs) compared with the immunocompetent. The third dose of vaccine in SOTRs showed promising results of immunogenicity, even though clinical studies have suggested that immunocompromised subjects are less likely to build a protective immune response against SARS-CoV-2 resulting in lower vaccine efficacy for the prevention of severe COVID-19. <strong>Methods:</strong> Serological IgG and IgA were analyzed through CLIA or ELISA, respectively, while Spike-specific T cells were detected by ELISpot assay after the second and third dose of vaccine in 43 SOTRs. <strong>Results:</strong> The third dose induced an improvement in antibody response against SARS-CoV-2. We also reported a strong correlation between specific humoral and cellular responses after the third dose, even though we did not see significant changes in the magnitude of the SARS-CoV-2-specific T cell response. SOTRs who contracted the SARS-CoV-2 infection after the third dose, despite eliciting a positive IgG response, failed to mount an anti-Spike-S1 IgA response, both after the third dose and after SARS-CoV-2 infection. <strong>Conclusions:</strong> We can conclude that serum IgA detection can be helpful, along with IgG detection, for the evaluation of vaccine efficacy, principally in fragile subjects at high risk of infection.</p>
Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions - Simulation dataset
<p>Simulation data related to the article:</p> <p>Liekkinen, J., Olzynska, A., Cwiklik, L., Bernardino de la Serna, J., Vattulainen, I., & Javanainen, M. Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions. <em>bioRxiv</em>, pp.2022-12. (Pre-print available at https://doi.org/10.1101/2022.12.12.520108)</p> <p> </p> <p>DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated in non-equilibrium conditions. The monolayer is compressed or expanded at a constant rate at different temperatures. Surfactant proteins SP-B and SP-C are included in the monolayers for comparison. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.</p> <p>All trajectories are simulated for 5000 ns with Gromacs 5.1.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index (.ndx) files are also included. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/</p> <p>[1] DOI: 10.1021/jp101759q</p> <p>[2] DOI: 10.1021/jz501780a</p> <p>[3] DOI: 10.1016/j.softx.2015.06.001</p>
Code Review of Build System Specifications: Prevalence, Purposes, Patterns, and Perceptions (Replication Package)
<p>Online appendix for "Code Review of Build System Specifications: Prevalence, Purposes, Patterns, and Perceptions", in the Proceedings of the International Conference on Software Engineering (ICSE), 2023. </p>
Data sources and code for: "Species-specific acclimation capacity of key traits explains global vertical distributions of seagrass species"
<p>Minguito-Frutos_etal_2023_Data1.xlsx contains the data for analyzing the relationship between plant size and seagrass growth reproductive strategy and the species-specific vertical distribution of seagrasses. </p> <p>Minguito-Frutos_etal_2023_Data2.xlsx contains the data for the meta-analityc approach studying the relationship between the vertical distribution of seagrass species and the plasticity of their traits (physiological, morphological, structural and growth). </p> <p>Scripts_Minguito_Frutos_etal_2023_GEB_Ref.GEB-2022-0592.R contains the R reproducible code to run all the analyses carried out in this study. </p>
Using standardized fish-specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities
<p>1. Biodiversity inventories and monitoring techniques for marine fishes often overlook small (<5cm), bottom-associated ('cryptobenthic') fishes, and few standardized, comparative assessments of cryptobenthic fish communities exist. We sought to develop a standardized, quantitative survey method for cryptobenthic fishes that permits their sampling across a variety of habitats and conditions.</p> <p>2. Fish-specific autonomous reef monitoring structures (FARMS) are designed to sample cryptobenthic fishes using a suite of accessible and affordable materials. To generate a variety of microhabitats, FARMS consist of three layers of stacked PVC pipes in three different sizes, as well as a bottom and top level of loose PVC-pipe fragments in a mesh basket. We deployed FARMS across a variety of habitats, including coral reefs, seagrass beds, oyster reefs, mangroves, and soft-bottom habitats across six locations (Hawai'i, Texas, Panama, Saudi Arabia, Brazil, and Curaçao).</p> <p>3. From shallow estuaries to coral reefs beyond 100 m depth, FARMS attracted distinct communities of native cryptobenthic fishes with strong site or habitat specificity. Comparing the FARMS to communities sampled with alternative methods (enclosed clove-oil stations on coral reefs in Panama and oyster sampling units on oyster reefs in Texas) suggests that FARMS yield a subset of cryptobenthic species representative of those present on local coral and oyster reefs. While FARMS yield fewer individuals per sample and are restricted to cryptobenthic species, they are efficient sampling devices relative to the sampled area.</p> <p>4. We demonstrate that FARMS represent a useful tool for standardized collections of cryptobenthic fishes. While natural substrata are bound to yield more mature communities with a larger number of individuals and wider range of specialist species, the potential to deploy and retrieve FARMS in turbid environments, beyond regular SCUBA depth, and where fish collections using anesthetics or ichthyocides are forbidden suggests that they are a valuable complementary technique to survey fishes in aquatic ecosystems. Deploying FARMS in locations and habitats where cryptobenthic fish communities have not been studied in detail may yield many valuable specimens of unknown or poorly known species.</p>
datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range
<p>datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.