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Fig. 13 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters
Fig. 13. Two unrelated small Brazilian snakes that are similar to Eutrachelophis spp. in nuchal markings and in having 15 dorsal scale rows, but they differ from each other and from Eutrachelophis spp. in fundamental hemipenial and maxillary characters. Color-pattern similarities in these and a few other small snakes include an anterior band or spots (first arrow), followed by paired spots or a fused pale crossbar (second arrow) that is medially constricted like the fused ocelli in some specimens of Eutrachelophis (compare with figs. 2 and 4). A, B. Amnesteophis melanauchen (Jan), a Brazilian
Fig. 33 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters
Fig. 33. Xenodon suspectus Cope. Dorsal and ventral views of the six additional American Museum specimens of X. suspectus, gathered in the 1920s by Harvey Bassler. A. AMNH R-52244, Contamana, Río Ucayali (Loreto); B–E. All from Río Itaya, near Iquitos (in Loreto); B. AMNH R-53636; C. AMNH R-
Fig. 32 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters
Fig. 32. Xenodon suspectus Cope in dorsal and ventral view. AMNH R-52175, an adult male from Chanchamayo, (Junín), Peru; hemipenis from this specimen shown in figure 20.
FIG. 3 in On the specific identification of subfossil Cryptoprocta (Mammalia, Carnivora) from Madagascar
FIG. 3. — Dorsal views of the cranium of a recently collected Cryptoprocta ferox Bennett, 1833 (above) and the neotype subfossil C. spelea Grandidier, 1902 (MNHN 1977.755). The specimen of C. ferox (AMNH 188213) collected at Manakara in 1931 is amongst some of the larger modern individuals of this species measured during the course of this study. Scale bar: 10 cm.
FIG. 5 in On the specific identification of subfossil Cryptoprocta (Mammalia, Carnivora) from Madagascar
FIG. 5. — Lateral views of the cranium of a recently collected Cryptoprocta ferox Bennett, 1833 (above) and the neotype subfossil C. spelea Grandidier, 1902 (MNHN 1977.755). The specimen of C. ferox (AMNH 188213) collected at Manakara in 1931 is amongst some of the larger modern individuals of this species measured during the course of this study. Scale bar: 10 cm.
FIG. 2 in On the specific identification of subfossil Cryptoprocta (Mammalia, Carnivora) from Madagascar
FIG. 2. — Bivariate plots of humerus and tibia measurements of modern (black) and subfossil (white) specimens of Cryptoprocta Bennett, 1833. The two bones were chosen for illustration because they represent cases of good separation (humerus) and the bone with the smallest differences (tibia) between modern and the subfossil sample.
FIG. 4 in On the specific identification of subfossil Cryptoprocta (Mammalia, Carnivora) from Madagascar
FIG. 4. — Ventral views of the cranium of a recently collected Cryptoprocta ferox Bennett, 1833 (above) and the neotype subfossil C. spelea Grandidier, 1902 (MNHN 1977.755). The specimen of C. ferox (AMNH 188213) collected at Manakara in 1931 is amongst some of the larger modern individuals of this species measured during the course of this study. Scale bar: 10 cm.
FIG. 1 in On the specific identification of subfossil Cryptoprocta (Mammalia, Carnivora) from Madagascar
FIG. 1. — Frequency distributions of dental measurements of modern (black) and subfossil (gray) specimens of Cryptoprocta Bennett, 1833.
Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1
<p>Supplementary Data files to accompany manuscript by Harding et al "Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1"</p> <ul> <li>Supplementary Data 1 - Multiple sequence alignment for HTT used for Consurf analysis</li> <li>Supplementary Data 2 - Multiple sequence alignment for HAP40 used for Consurf analysis</li> <li>Supplementary Data 3 - Apo HTT cryo-EM map </li> <li>Supplementary Data 4 - HTT-HAP40 Q23 regularised SAXS profile</li> <li>Supplementary Data 5 - HTT-HAP40 Q54 regularised SAXS profile</li> <li>Supplementary Data 6 - HTT-HAP40 Δexon 1 regularised SAXS profile</li> <li>Supplementary Data 7 - XL-MS data</li> <li>Supplementary Data 8 - HTT-HAP40 ensemble weightings</li> <li>Supplementary Data 9 - HTT-HAP40 Q23 ensemble models</li> <li>Supplementary Data 10 - HTT-HAP40 Q54 ensemble models</li> <li>Supplementary Data 11 - HTT-HAP40 Δexon 1 ensemble models</li> </ul>
Research data supporting: "Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly"
<p>This repository contains the set of data shown in the paper "<em>Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly</em>", published on <em>ACS Nano</em> (DOI: 10.1021/acsnano.1c0500).</p> <p>All the input data needed to run the simulations and get the results are organized in 5 different folders:</p> <ul> <li> <p><code>1-MinimlisticCGModel/</code></p> <p>in this folder there are the Gromacs and PLUMED input files for reproducing the minimalistic coarse-grained model shown in the article.</p> </li> <li> <p><code>2-AAandFineCGModels/</code></p> <p>the folder contains the atomistic (<code>monomerAA/</code>) and the coarse-grained Martini "wet" (<code>monomerGCWet/</code>) input files for modelling the Original monomer with one carboxyl group. The coarse-grained Martini "dry" (<code>monomerCGDry/</code>) model is reported for the Original monomer at the three different charged states.</p> </li> <li> <p><code>3-UnbiasedMD/</code></p> <p>this folder includes the Gromacs input files needed to reproduce the Unbiased simulations as shown in the article.</p> </li> <li> <p><code>4-MetaD/</code></p> <p>this folder incorporates the Gromacs and PLUMED input files necessary to reproduce both the Infrequent CG Metadynamics simulations (<code>InfrequentMetaD/</code>) and the Multiple-walker CG Metadynamics simulations (<code>MultipleWalkerMetaD/</code>)</p> </li> <li> <p><code>5-InSilico/</code></p> <p>in this folder all the files used to run the simulations about the exoliation experiments (<code>Original/</code>, <code>Type-1/</code>, <code>Type-2/</code>, <code>Type-3/</code>, <code>Type-4/</code>) are reported. Every subfolder contains all input files for the three different charged monomers (<code>Olig1-/</code>, <code>Olig2-/</code>, <code>Olig3-/</code>).</p> </li> </ul>
Data from: Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection
<p>Floral scent is a key mediator in plant–pollinator interactions; however, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. We recorded 289 scent compounds in deceptive moth fly-pollinated <i>Arum maculatum </i>from various populations north vs. south of the Alps, the highest number so far reported in a single plant species. Scent and fruit set differed between regions, and some, but not all differences in scent could be explained by differential phenotypic selection in northern vs. southern populations. Our study is the first to provide evidence that phenotypic selection is involved in shaping geographic patterns of floral scent in deceptive plants. The hyperdiverse scent of <i>A. maculatum</i> might result from the plant's imitation of various brood substrates of its pollinators.</p>
Source data for "Conformer-specific polar cycloaddition of dibromobutadiene with trapped propene ions"
<p>Experimental primary data and calculated molecular structures for the publication "Conformer-specific polar cycloaddition of dibromobutadiene with trapped propene ions” </p>
Data related to research article: Towards mouse genetic-specific RNA-sequencing read mapping
<p>This dataset contains data related to the research article: "Towards mouse genetic-specific RNA-sequencing read mapping".</p>
Dataset for "Di-synaptic specificity of serial information flow for conditioned fear"
<p>Dataset for the publication "Di-synaptic specificity of serial information flow for conditioned fear"</p>
Age-specific effects of deletions: Implications for ageing theories
<p><span>Evolution of ageing requires mutations with late-life deleterious effects. Classic theories assume these mutations either have neutral (Mutation Accumulation) or beneficial (Antagonistic Pleiotropy) effects early in life, but it is also possible that they start out as mildly harmful and gradually become more deleterious with age. Despite a wealth of studies on the genetics of ageing, we still have a poor understanding of how common mutations with age-specific effects are and what ageing theory they support. To advance our knowledge on this topic we measure a set of genomic deletions for their heterozygous effects on juvenile performance, fecundity at three ages, and adult survival. Most deletions have age-specific effects, and these are commonly harmful late in life. Many of the deletions assayed here would thus contribute to ageing if present in a population. Taking only age-specific fecundity into account, some deletions support Antagonistic Pleiotropy, but the majority of them better fit a scenario where their negative effects on fecundity become progressively worse with age. Most deletions have a negative effect on juvenile performance, a fact which strengthens the conclusion that deletions primarily contribute to ageing through negative effects that amplify with age.</span></p>
Data from: Species-specific traits mediate avian demographic responses under past climate change
<p>Anticipating species' responses to environmental change is a<span> pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the traits which mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life-history traits associated with changes in effective population size (<em>N<sub>e</sub></em>) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing survival, reproduction, and dispersal processes on long-term demographic responses to climate change and highlight traits most likely to influence population responses to ongoing climate warming.</span></p>
Supporting information for: Age-specific sensitivity analysis of stable, stochastic and transient growth for stage-classified populations
<p>The study associated with this dataset proposes a way of performing age-specific sensitivity analysis of stable, stochastic and transient growth for stage-classified populations. Here, you find simulation code in R to produce figures in the manuscript and matrices reporting demographic data upon which code computations are performed.</p>
Paternal condition affects offspring reproduction and life history in a sex-specific manner in Drosophila melanogaster
<p>Nongenetic parental effects can contribute to the adaptation of species to changing environments by circumventing some of the limitations of genetic inheritance. A clearer understanding of the influence of nongenetic inheritance and its potentially sex-specific responses in daughters and sons is needed to better predict the evolutionary trajectories of species. However, whereas nongenetic maternal effects have long been recognized and widely studied, comparatively little is known about corresponding paternal effects. Here, by following 30 isogenic lines of <em>Drosophila</em> <em>melanogaster</em> across two generations, each reared under two dietary regimes in each generation, we tested how protein restriction during larval development of the fathers affects the fitness and health of their daughters and sons. We then quantified genetic and non-genetic paternal, and direct environmental, effects across multiple axes of offspring fitness. Daughters and sons responded differently to their father's developmental history. While isolines differed in mean trait values, their specific responses to protein restriction generally varied little. The sex- and trait-specific responses to paternal effects emphasize the complexity of inter-generational parental effects, which raise important questions about their mode of transmission and adaptive value, including the potential for conflict between the sexes.</p>
Extended data: Tissue-specific multi-omics analysis of atrial fibrillation
<p>Summary statistics and result repository for the publication Tissue-specific multi-omics analysis of atrial fibrillation:</p> <p>Assum, I., Krause, J., Scheinhardt, M.O. <em>et al.</em> Tissue-specific multi-omics analysis of atrial fibrillation. <em>Nat Commun </em><strong>13, </strong>441 (2022). https://doi.org/10.1038/s41467-022-27953-1</p> <p>For the related source code, see https://doi.org/https://doi.org/10.5281/zenodo.5094276 or https://github.com/heiniglab/symatrial.</p> <p>Ines Assum<sup>1,2,†</sup>, Julia Krause<sup>3,4,†</sup>, Markus O. Scheinhardt<sup>5</sup>, Christian Müller<sup>3,4</sup>, Elke Hammer<sup>6,7</sup>, Christin S. Börschel<sup>4,8</sup>, Uwe Vöker<sup>6,7</sup>, Lenard Conradi<sup>9</sup>, Bastiaan Geelhoed<sup>4,8,10</sup>, Tanja Zeller<sup>3,4,</sup>*, Renate B. Schnabel<sup>4,8,</sup>*, Matthias Heinig<sup>1,2,11,</sup>*</p> <p><sup>† </sup>,* These authors contributed equally.</p> <p><sup> 1</sup> Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.<br> <sup> 2</sup> Department of Informatics, Technical University Munich, München, Germany.<br> <sup> 3</sup> University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup> 4</sup> Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany.<br> <sup> 5</sup> Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany.<br> <sup> 6</sup> Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.<br> <sup> 7</sup> Partner site Greifswald, DZHK (German Center for Cardiovascular Research), Greifswald, Germany.<br> <sup> 8</sup> Department of Cardiology, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup> 9</sup> Department of Cardiovascular Surgery, University Heart and Vascular Center Hamburg, Hamburg, Germany.<br> <sup>10 </sup>Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.<br> <sup>11</sup>Partner site Munich, DZHK (German Center for Cardiovascular Research), Munich, Germany.</p> <p> </p> <p>ABSTRACT:</p> <p>Genome-wide association studies (GWAS) for atrial fibrillation (AF) have uncovered numerous disease-associated variants. Their underlying molecular mechanisms, especially consequences for mRNA and protein expression remain largely elusive. Thus, refined multi-omics approaches are needed for deciphering the underlying molecular networks. Here, we integrate genomics, transcriptomics, and proteomics of human atrial tissue in a cross-sectional study to identify widespread effects of genetic variants on both transcript (cis-eQTL) and protein (cis-pQTL) abundance. We further establish a novel targeted transQTL approach based on polygenic risk scores to determine candidates for AF core genes. Using this approach, we identify two trans-eQTLs and five trans-pQTLs for AF GWAS hits, and elucidate the role of the transcription factor NKX2-5 as a link between the GWAS SNP rs9481842 and AF. Altogether, we present an integrative multi-omics method to uncover trans-acting networks in small datasets and provide a rich resource of atrial tissue-specific regulatory variants for transcript and protein levels for cardiovascular disease gene prioritization.</p> <p>This version contains a reference file identifying effect alleles for all QTL results and adds additional genotype and allele frequency information for all QTL SNPs. </p> <p>TABLE OF CONTENTS:</p> <ul> <li>Reference for effect alleles<br> <em>map_AFHRI_B_effect_alleles.txt</em></li> <li>Reference for genotype and allele frequencies (derived using PLINK) <ul> <li><em>genotype_allele_frequencies_eQTL_SNPs.txt</em></li> <li><em>genotype_allele_frequencies_pQTL_SNPs.txt</em></li> <li><em>genotype_allele_frequencies_resQTL_SNPs.txt</em></li> </ul> </li> <li>Single-omic <em>cis</em>-QTL results <ul> <li><em>cis</em>-eQTLs (all pairs, incl. LD clump info)<br> <em>eQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-pQTLs (all pairs, incl. LD clump info)<br> <em>pQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-res eQTLs (all pairs, incl. LD clump info)<br> <em>res_eQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-res pQTLs (all pairs, incl. LD clump info)<br> <em>res_pQTL_right_atrial_appendage_allpairs_clump.txt</em></li> <li><em>cis</em>-ratioQTLs (all pairs, incl. LD clump info)<br> <em>ratioQTL_right_atrial_appendage_allpairs_clump.txt</em></li> </ul> </li> <li>Functional <em>cis</em>-QTL categories and eQTL/pQTL overlap: <ul> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with a significant eQTL and pQTL (FDR<0.05)<br> <em>Fig2a_source_data_Shared_eQTL_pQTL_clump.txt</em></li> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with a significant eQTL but no pQTL (FDR<0.05)<br> <em>Fig2b_source_data_Independent_eQTL_clump.txt</em></li> <li>All eQTLs, pQTLs, res eQTLs, res pQTLs and ratioQTLs for all SNP-gene pairs with no eQTL but a significant pQTL (FDR<0.05)<br> <em>Fig2c_source_data_Independent_pQTL_clump.txt</em><span> </span></li> </ul> </li> <li>QTS rankings and enrichment results <ul> <li>eQTS rankings and enrichments<br> <em>TableS6_source_data_eQTS_ranking.txt<br> TableS7_source_data_eQTS_GSEA_results.txt</em></li> <li>pQTS rankings and enrichments<br> <em>TableS8_source_data_pQTS_ranking.txt<br> TableS9_source_data_pQTS_GSEA_results.txt</em></li> </ul> </li> <li><em>Trans</em>-QTLs<br> all tested pairs including <em>trans</em>-pQTLs for <em>trans</em>-eQTLs and <em>trans</em>-eQTLs for <em>trans</em>-pQTLs<br> <em>Table2_source_data_Trans-QTL_results.txt</em></li> </ul> <p> </p>
Data from: Specific leaf area is lower on ultramafic than on neighbouring non-ultramafic soils
<p>These are datasets in csv format for ultramafic and non-ultramafic sampling sites where specific leaf area (SLA) was collected in five climatically diverse regions: Puerto Rico (tropical wet), Costa Rica (tropical dry), South Africa (subtropical), California and Lesbos (both with Mediterranean climate). The datasets include plant species level mean SLA values, regional coordinates, regional climate data, bioclimatic variables for individual sites, and a joined dataset that includes site level coordinates and climate variables. The R script to reproduce all analyses and figures is also included.</p>
ScienceDex guides
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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.