cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/9fae641495fea570c60f0ad2777344b8
title: Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy

description: Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
DOI: 10.6084/m9.figshare.11896140.v1
title: Additional file 2 of Mutation screening of the USH2A gene reveals two novel pathogenic variants in Chinese patients causing simplex usher syndrome 2

description: Additional file 2: Table S2. variants predicted non-pathogenic in this study.
DOI: 10.17171/2-12-2-1
title: LiVES COstA Digest

description: LiVES Collection of Osteological Anthropometry Digest
DOI: 10.5066/p9kwk13b
title: Piping plover nesting habitat distribution maps for the U.S. Prairie Pothole Region, 2000&amp;ndash;2021

description: These maps were developed to support an effort to understand the spatial characteristics of piping plover (Charadrius melodus) nesting habitats. The maps show the expected nesting habitat distributions and piping plover intensity between 2000 and 2021 in the U.S. Prairie Pothole Region.
DOI: 10.5281/zenodo.7789803
title: Cross-phyla protein annotation by structural prediction and alignment

description: <strong>Background:</strong> Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity, however this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences. <strong>Results:</strong> We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: <strong>Mor</strong>pholog<strong>F</strong>inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in &gt;90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. <strong>Conclusions:</strong> Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.
description: we upload two more tables that contain the yeast and Arabidopsis proteins with similar structures to human proteins, as well as information on whether they are homologs or not.
description: {"references": ["Ruperti, Fabian and Papadopoulos, Nikolaos, et al. (2022). Data related to https://doi.org/10.1101/2022.07.05.498892"]}
DOI: 10.6084/m9.figshare.11896134
title: Additional file 1 of Mutation screening of the USH2A gene reveals two novel pathogenic variants in Chinese patients causing simplex usher syndrome 2

description: Additional file 1: Table S1. Primer information for the USH2A gene exons 2 to 72 sequencing. (XLS 31 kb)
DOI: 10.6084/m9.figshare.11896173
title: Additional file 3 of ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

description: Additional file 3: Table S2. Primer sequences for qPCR and ChIP-qPCR.
DOI: 10.6084/m9.figshare.11896134.v1
title: Additional file 1 of Mutation screening of the USH2A gene reveals two novel pathogenic variants in Chinese patients causing simplex usher syndrome 2

description: Additional file 1: Table S1. Primer information for the USH2A gene exons 2 to 72 sequencing. (XLS 31 kb)
DOI: 10.6084/m9.figshare.11896167.v1
title: Additional file 2 of ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

description: Additional file 2: Table S1. Predicted non-classical functions and cofactor candidates of HMRs. Each row represents a cofactor candidate ranked by adjusted R2.
DOI: 10.6084/m9.figshare.11896173.v1
title: Additional file 3 of ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

description: Additional file 3: Table S2. Primer sequences for qPCR and ChIP-qPCR.
DOI: 10.6084/m9.figshare.11896245
title: Additional file 1 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional fileÂ 1. Peptide information of brain and colon for iTRAQ experiment.
DOI: 10.6084/m9.figshare.11896251.v1
title: Additional file 3 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional file 3: Table S2. Detailed information of differentially expressed proteins in brain of three groups.
DOI: 10.6084/m9.figshare.6653423
title: The effect of shame on anger at others: awareness of the emotion-causing events matters

description: Numerous studies have found that shame increases individuals’ anger at others. However, according to recent theories about the social function of shame and anger at others, it is possible that shame controls individuals’ anger at others in specific conditions. We replicated previous findings that shame increased individuals’ anger at others’ unfairness, when others were not aware of the individual’s experience of shameful events. We also found for the first time that shame controlled or even decreased individuals’ anger at others’ unfairness, when others were aware of the individual’s experience of shameful events. The results were consistent when shame was induced by either a recall paradigm or an imagination paradigm, and in either the ultimatum game or the dictator game. This suggests that shame strategically controls individuals’ anger at others to demonstrate that they are willing to benefit others, when facing the risk of social exclusion. Our findings highlight the interpersonal function of shame and deepen the understanding of the relationship between shame and anger at others.
DOI: 10.6084/m9.figshare.11896245.v1
title: Additional file 1 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional fileÂ 1. Peptide information of brain and colon for iTRAQ experiment.
DOI: 10.6084/m9.figshare.11896320.v1
title: Additional file 13 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 13: Table S11. Summary of F. graminearum and S. cerevisiae BLASTp results using predicted top regulators. Only significant hits are listed (E-value &lt;1e-5).
DOI: 10.6084/m9.figshare.11896323
title: Additional file 14 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 14: Table S12. Phenotype association analysis for each module.
DOI: 10.6084/m9.figshare.11896323.v1
title: Additional file 14 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 14: Table S12. Phenotype association analysis for each module.
DOI: 10.6084/m9.figshare.11896326
title: Additional file 15 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 15: Table S13. Regulatory networks compartmentalization analysis using Fisherâ€™s exact test. FS: F. graminearum-specific; Core: Conserved genome. Mix: not enriched.
DOI: 10.6084/m9.figshare.11896329
title: Additional file 16 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 16: Table S14. Comparing the TRNs with previous F. graminearum GRNs [21].
DOI: 10.6084/m9.figshare.11896314
title: Additional file 11 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 11: Table S9. Gene annotation enrichment of each module in 55 main functional categories (P value &lt;â€‰0.05).
DOI: 10.6084/m9.figshare.11896329.v1
title: Additional file 16 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 16: Table S14. Comparing the TRNs with previous F. graminearum GRNs [21].
DOI: 10.6084/m9.figshare.11896335
title: Additional file 1 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 1: Table S1. Gene expression data sets used to predict module networks of F. graminearum in this work.
DOI: 10.6084/m9.figshare.13467935.v1
title: Additional file 1 of Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure

description: Additional file 1 The file includes the performance measures of competitive methods on the RBP-24 dataset. The AUC values of using DeepRKE- and without RNA secondary structure sequence, as well as the AUC values using DeepRKE- without RNA secondary structure and distributed representation of sequences.
DOI: 10.6084/m9.figshare.11896167
title: Additional file 2 of ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

description: Additional file 2: Table S1. Predicted non-classical functions and cofactor candidates of HMRs. Each row represents a cofactor candidate ranked by adjusted R2.
DOI: 10.6084/m9.figshare.11896314.v1
title: Additional file 11 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 11: Table S9. Gene annotation enrichment of each module in 55 main functional categories (P value &lt;â€‰0.05).
DOI: 10.6084/m9.figshare.11896374
title: Additional file 7 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 7: Table S6. Summary of 49 regulatory modules, including information on the number of target genes, the top regulators, and the top four enriched Gene Ontology terms (P value &lt;â€‰0.05).
DOI: 10.6084/m9.figshare.11896248
title: Additional file 2 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional file 2: Table S1. Detailed information of differentially expressed proteins in colon of three groups.
DOI: 10.6084/m9.figshare.11896317
title: Additional file 12 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 12: Table S10. Consensus functional terms associated with GO enrichment and enriched TF binding sites for module target genes.
DOI: 10.6084/m9.figshare.11896371
title: Additional file 6 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 6: Table S5. Lists of target genes in each module.
DOI: 10.6084/m9.figshare.11896374.v1
title: Additional file 7 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 7: Table S6. Summary of 49 regulatory modules, including information on the number of target genes, the top regulators, and the top four enriched Gene Ontology terms (P value &lt;â€‰0.05).
DOI: 10.6084/m9.figshare.11896251
title: Additional file 3 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional file 3: Table S2. Detailed information of differentially expressed proteins in brain of three groups.
DOI: 10.6084/m9.figshare.6653423.v1
title: The effect of shame on anger at others: awareness of the emotion-causing events matters

description: Numerous studies have found that shame increases individuals’ anger at others. However, according to recent theories about the social function of shame and anger at others, it is possible that shame controls individuals’ anger at others in specific conditions. We replicated previous findings that shame increased individuals’ anger at others’ unfairness, when others were not aware of the individual’s experience of shameful events. We also found for the first time that shame controlled or even decreased individuals’ anger at others’ unfairness, when others were aware of the individual’s experience of shameful events. The results were consistent when shame was induced by either a recall paradigm or an imagination paradigm, and in either the ultimatum game or the dictator game. This suggests that shame strategically controls individuals’ anger at others to demonstrate that they are willing to benefit others, when facing the risk of social exclusion. Our findings highlight the interpersonal function of shame and deepen the understanding of the relationship between shame and anger at others.
DOI: 10.6084/m9.figshare.11896308.v1
title: Additional file 10 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 10: Table S8. Summary of transcription factor binding site (TFBS) enrichment and conservation analysis for each module using MEME and Tomtom.
DOI: 10.6084/m9.figshare.11896308
title: Additional file 10 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 10: Table S8. Summary of transcription factor binding site (TFBS) enrichment and conservation analysis for each module using MEME and Tomtom.
DOI: 10.6084/m9.figshare.11896320
title: Additional file 13 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 13: Table S11. Summary of F. graminearum and S. cerevisiae BLASTp results using predicted top regulators. Only significant hits are listed (E-value &lt;1e-5).
DOI: 10.6084/m9.figshare.11896248.v1
title: Additional file 2 of Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

description: Additional file 2: Table S1. Detailed information of differentially expressed proteins in colon of three groups.
DOI: 10.6084/m9.figshare.11896326.v1
title: Additional file 15 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 15: Table S13. Regulatory networks compartmentalization analysis using Fisherâ€™s exact test. FS: F. graminearum-specific; Core: Conserved genome. Mix: not enriched.
DOI: 10.6084/m9.figshare.11896335.v1
title: Additional file 1 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 1: Table S1. Gene expression data sets used to predict module networks of F. graminearum in this work.
DOI: 10.6084/m9.figshare.6653435
title: Geochemistry of peridotites from the Yap Trench, Western Pacific: implications for subduction zone mantle evolution

description: This study examines the major and trace elements of peridotites from the Yap Trench in the western Pacific to investigate mantle evolution beneath a subduction zone. Major element results show that the peridotites are low in Al<sub>2</sub>O<sub>3</sub> (0.31–0.65 wt.%) and CaO (0.04–0.07 wt.%) contents and high in Mg# (Mg/(Mg+Fe)) (0.91–0.92) and have spinels with Cr# (Cr/(Cr+Al)) higher than 0.6 (0.61–0.73). Trace element results show that the peridotites have extremely low heavy rare earth element (HREE) contents compared with abyssal peridotites but have U-shaped chondrite-normalized rare earth element (REE) patterns. The degree of mantle melting estimated based on the major elements, HREEs, and spinel Cr# range from 19% to 25%, indicating that the Yap Trench peridotites may be residues of melting associated with the presence of water in the mantle source. In addition to light rare earth element (LREE) enrichment, the peridotites are characterized by high contents of highly incompatible elements, positive U and Sr anomalies, negative Ti anomalies, and high Zr/Hf ratios. The correlations between these elements and both the degree of serpentinization and high field strength element (HFSE) contents suggest that fluid alteration alone cannot account for the enrichment of the peridotites and that at least the enrichment of LREEs was likely caused by melt–mantle interaction. Comparison between the peridotites and the depletion trend defined by the primitive mantle (PM) and the depleted mantle (DM) suggests that the Yap Trench mantle was modified by subduction-related melt characterized by high contents of incompatible elements, high Zr/Hf ratios, and low HFSE contents. Hydrous melting may have been enhanced by tectonic erosion of the subducting Caroline Plate with complex tectonic morphostructures at the earliest stages of subduction initiation.
DOI: 10.6084/m9.figshare.6653435.v1
title: Geochemistry of peridotites from the Yap Trench, Western Pacific: implications for subduction zone mantle evolution

description: This study examines the major and trace elements of peridotites from the Yap Trench in the western Pacific to investigate mantle evolution beneath a subduction zone. Major element results show that the peridotites are low in Al<sub>2</sub>O<sub>3</sub> (0.31–0.65 wt.%) and CaO (0.04–0.07 wt.%) contents and high in Mg# (Mg/(Mg+Fe)) (0.91–0.92) and have spinels with Cr# (Cr/(Cr+Al)) higher than 0.6 (0.61–0.73). Trace element results show that the peridotites have extremely low heavy rare earth element (HREE) contents compared with abyssal peridotites but have U-shaped chondrite-normalized rare earth element (REE) patterns. The degree of mantle melting estimated based on the major elements, HREEs, and spinel Cr# range from 19% to 25%, indicating that the Yap Trench peridotites may be residues of melting associated with the presence of water in the mantle source. In addition to light rare earth element (LREE) enrichment, the peridotites are characterized by high contents of highly incompatible elements, positive U and Sr anomalies, negative Ti anomalies, and high Zr/Hf ratios. The correlations between these elements and both the degree of serpentinization and high field strength element (HFSE) contents suggest that fluid alteration alone cannot account for the enrichment of the peridotites and that at least the enrichment of LREEs was likely caused by melt–mantle interaction. Comparison between the peridotites and the depletion trend defined by the primitive mantle (PM) and the depleted mantle (DM) suggests that the Yap Trench mantle was modified by subduction-related melt characterized by high contents of incompatible elements, high Zr/Hf ratios, and low HFSE contents. Hydrous melting may have been enhanced by tectonic erosion of the subducting Caroline Plate with complex tectonic morphostructures at the earliest stages of subduction initiation.
DOI: 10.6084/m9.figshare.13469131.v1
title: Ropivacaine inhibits the proliferation and migration of colorectal cancer cells through ITGB1

description: To study whether ropivacaine inhibits the proliferation and migration of colon cancer cells through ITGB1 (Integrin beta-1). First, the effect of ropivacaine on cell proliferation and migration was detected by MTT and Transwell. DAPI staining, annexin V staining and Western blot were used to detect the expression of apoptosis-related proteins to investigate the effect of ropivacaine on cell apoptosis. Using bioinformatics software to predict the potential drug targets of ropivacaine. RT-PCR, Western blot and immunofluorescence verify the distribution and expression of the drug target ITGB1, and detect its downstream-related proteins to further prove that ropivacaine affects colon cancer cells by acting on ITGB1 protein. 1. Ropivacaine significantly inhibited the proliferation of colon cancer cells and promoted their apoptosis 2. Ropivacaine could interact with ITGB1 protein, and inhibited the expression of ITGB1 protein in colon cancer cells, thereby affecting its downstream signaling pathway. Ropivacaine regulates the function of colon cancer cells by targeting the expression of ITGB1 protein and affecting the activation of its downstream signaling pathways. <b>Abbreviation:</b> Integrin beta-1 (ITGB1); 3-(45)-dimethylthiahiazo (-z-y1)-35-di- phenytetrazoliumromide (MTT); 4. 6-diamimo-2-phenyl indole (DAPI); Reverse transcrption PCR (RT-PCR); Colorectal cancer (CRC); Local anesthetics (LA); voltage-gated sodium channel (VGSC); dulbecco s modifed eade medium (DMEM); propidium iodide (PI); dodecyl sulf ate, sodium salt-Polyacrylamide gel electrophoresis (SDS-PAGE); Polyvinylidene Fluoride (PVDF); BCL2 associated X (Bax); Focal Adhesion Kinase (FAK); extracellular signal-regulated kmase (ERK); alpha serme threcnime-proteim kinase (AKT); Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Tris-buffered salme with 0.1% Tween 20 (TBST); Similarty ensemble approach (SEA)