cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16821748
title: Additional file 3 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 3: Table S3. Species distribution frequency of the BLAST hits based on Nr database.
DOI: 10.5281/zenodo.10581616
title: The Effects of Head-Worn Displays on the Piloting of Small Unmanned Aerial Systems – A Comparative Study of Instruction Methods

description: The dataset atached lists all data collected during our study related to the three dependent variables: 1) Task Completion Time; 2) Accuracy Scores; 3) Cognitive Workload.

Participants of our study are not identifiable by name, only by Participant ID.
DOI: 10.5281/zenodo.10581617
title: The Effects of Head-Worn Displays on the Piloting of Small Unmanned Aerial Systems – A Comparative Study of Instruction Methods

description: The dataset atached lists all data collected during our study related to the three dependent variables: 1) Task Completion Time; 2) Accuracy Scores; 3) Cognitive Workload.

Participants of our study are not identifiable by name, only by Participant ID.
DOI: 10.6084/m9.figshare.16821751
title: Additional file 4 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 4: Table S4. GO classification of the assembled unigenes in R. xanthina f. spontanea. (XLSX 7387 kb)
DOI: 10.6084/m9.figshare.16821757
title: Additional file 6 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 6: Table S6. GO enrichment analysis of DEGs at 4°C vs. 23°C in R. xanthina f. spontanea. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.16821754.v1
title: Additional file 5 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 5: Table S5. KEGG function classification the assembled unigenes in R. xanthina f. spontanea. (XLSX 2156 kb)
DOI: 10.6084/m9.figshare.16821760
title: Additional file 7 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 7: Table S7. GO enrichment analysis of DEGs at -20°C vs. 23°C in R. xanthina f. spontanea. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.8957630.v1
title: Additional file 2: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S2. Differentially expressed genes (DEGs) between the cold treatment and control. FPKM reads per kilobase per million mapped reads. FDR false discovery rate. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.8957633
title: Additional file 3: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S3. Differentially expressed genes (DEGs) encoding protein kinases and DEGs associated with signaling transduction pathway. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8957633.v1
title: Additional file 3: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S3. Differentially expressed genes (DEGs) encoding protein kinases and DEGs associated with signaling transduction pathway. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.16821742
title: Additional file 1 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 1: Table S1. Overview of the sequencing and assembly of the transcriptome.
DOI: 10.6084/m9.figshare.8957657.v1
title: Additional file 7: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S7. Primer information. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8957669.v1
title: Additional file 9: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S9. Transmembrane transport-related genes that were differentially expressed during cold treatment. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.16821745.v1
title: Additional file 2 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 2: Table S2. N50 of transcripts or unigenes from nine samples.
DOI: 10.6084/m9.figshare.21540405
title: Additional file 13 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 13: Supplementary Table 1. The primer sequences in PCR analysis.
DOI: 10.6084/m9.figshare.21540411
title: Additional file 15 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 15: Supplementary Table 3. The results of Univariate Cox regression analysis for pan-cancer.
DOI: 10.6084/m9.figshare.17870341.v1
title: Additional file 1 of Common variants in breast cancer risk loci predispose to distinct tumor subtypes

description: Additional file 1. Figures S1 and S2 and Table S1-S4. This file contains supplementary figures 1-2 and supplementary tables 1-4.
DOI: 10.6084/m9.figshare.16821757.v1
title: Additional file 6 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 6: Table S6. GO enrichment analysis of DEGs at 4°C vs. 23°C in R. xanthina f. spontanea. (XLSX 212 kb)
DOI: 10.6084/m9.figshare.21540411.v1
title: Additional file 15 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 15: Supplementary Table 3. The results of Univariate Cox regression analysis for pan-cancer.
DOI: 10.6084/m9.figshare.16821763
title: Additional file 8 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 8: Table S8. KEGG enrichment analysis of DEGs at 4°C vs. 23°C in R. xanthina f. spontanea. (XLSX 743 kb)
DOI: 10.6084/m9.figshare.16821766
title: Additional file 9 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 9: Table S9. KEGG enrichment analysis of DEGs at -20°C vs. 23°C in R. xanthina f. spontanea. (XLSX 318 kb)
DOI: 10.6084/m9.figshare.16821766.v1
title: Additional file 9 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 9: Table S9. KEGG enrichment analysis of DEGs at -20°C vs. 23°C in R. xanthina f. spontanea. (XLSX 318 kb)
DOI: 10.6084/m9.figshare.14724649.v1
title: Supplementary Files S3 It contains the annotation of full-length ERVs made by LTRharvest/LTRdigest. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.14724667.v1
title: Supplementary Files S6 MaxQuant output and XML file with parameters used for the analysis. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.16821925.v2
title: Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

description: Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis were performed and co-expression and competing endogenous RNAs (ceRNA) networks were constructed. We identified that four circRNAs that were differentially expressed specifically in β cells exposed to palmitic acid, whereas four circRNAs were differentially expressed specifically in β cells exposed to stearic acid. Seven circRNAs were differentially co-expressed in palmitic acid- and stearic acid-treated β cells. In pathway exploration, we identified the core protein Solute carrier family 2 member 2 (SLc2a2), which is mainly involved in insulin resistance, maturity onset diabetes of the young and type 2 diabetes. The expressions of key circRNAs in β-TC6 cells were validated by Real time quantitative PCR, with a consistent result in high-throughput sequencing. The findings aid our understanding of the mechanisms governing the difference between palmitic acid- and stearic acid-induced β cell dysfunction and provide potential therapeutic targets for developing treatments against long-term high fat diet-induced β cell injury. <b>Abbreviations:</b> Acvr1c: Activin A receptor, type 1C; CeRNA, Competing endogenous RNAs; circRNA, circular RNA; DEcircRNA: Differentially Expressed circular RNA; DEmiRNA: Differentially Expressed microRNA; DEmRNA: Differentially Expressed mRNA; GO: Gene Ontology; HPDHigh Palmitic acid Diet; HSD: High Stearic acid Diet; KEGG: Kyoto Encyclopedia of Genes and Genomes; miRNA: microRNA; ncRNAs: non-coding RNAs; qPCR: Real time quantitative PCRS; FAs: Saturated Fatty Acids; SLc2a2: Solute carrier family 2 member 2; T2D: Type 2 Diabetes
DOI: 10.6084/m9.figshare.8957627.v1
title: Additional file 1: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S1. KEGG mapping of the Magnolia wufengensis unigenes. (XLSX 206 kb)
DOI: 10.6084/m9.figshare.8957642
title: Additional file 4: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S4. Differentially expressed transcription factors (TFs) in response to cold treatment of Magnolia wufengensis leaves. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.14724664.v1
title: Supplementary Files S2 It contains the annotation of full-length ERVs made by RetroTector. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.8957642.v1
title: Additional file 4: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S4. Differentially expressed transcription factors (TFs) in response to cold treatment of Magnolia wufengensis leaves. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.21540408.v1
title: Additional file 14 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 14: Supplementary Table 2. The results of expression differences for pan-cancer analysis.
DOI: 10.6084/m9.figshare.21540405.v1
title: Additional file 13 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 13: Supplementary Table 1. The primer sequences in PCR analysis.
DOI: 10.6084/m9.figshare.6860396.v1
title: Structure-based prediction of West Nile virus-human protein-protein interactions

description: In recent years, West Nile virus (WNV) has posed a great threat to global human health due to its explosive spread. Studying the protein-protein interactions (PPIs) between WNV and human is beneficial for understanding the pathogenesis of WNV and the immune response mechanism of human against WNV infection at the molecular level. In this study, we identified the human target proteins which interact with WNV based on protein structure similarity, and then the interacting pairs were filtered by the subcellular co-localization information. As a result, a network of 3,346 interactions was constructed, involving 6 WNV proteins and 1970 human target proteins. To our knowledge, this is the first predicted interactome for WNV-human. By analyzing the topological properties and evolution rates of the human target proteins, it was demonstrated that these proteins tend to be the central and bottleneck proteins in the human PPI network and are more conserved than the non-target ones. Triplet analysis showed that the target proteins are adjacent to each other in the human PPI network, suggesting that these proteins may have similar biological functions. Further, the functional enrichment analysis indicated that the target proteins are mainly involved in virus process, transcription regulation, cell adhesion and so on. In addition, the common and specific targets were identified and compared based on the networks between WNV-human and Dengue virus II (DENV2)-human. Finally, by combining topological features and existing drug target information, we identified 30 potential anti-WNV human targets, among which 11 ones were reported to be associated with WNV infection.
DOI: 10.6084/m9.figshare.8957651.v1
title: Additional file 6: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S6. Differently-expressed genes involved in photosynthesis in response to cold treatment of Magnolia wufengensis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.19967697
title: Spatio-temporal process monitoring using exponentially weighted spatial LASSO

description: Spatio-temporal process monitoring (STPM) has received a considerable attention recently due to its broad applications in environment monitoring, disease surveillance, streaming image processing, and more. Because spatio-temporal data often have complicated structure, including latent spatio-temporal data correlation, complex spatio-temporal mean structure, and nonparametric data distribution, STPM is a challenging research problem. In practice, if a spatio-temporal process has a distributional shift (e.g., mean shift) started at a specific time point, then the spatial locations with the shift are usually clustered in small regions. This kind of spatial feature of the shift has not been considered in the existing STPM literature yet. In this paper, we develop a new STPM method that takes into account the spatial feature of the shift in its construction. The new method combines the ideas of exponentially weighted moving average in the temporal domain for online process monitoring and spatial LASSO in the spatial domain for accommodating the spatial feature of a future shift. It can also accommodate the complicated spatio-temporal data structure well. Both simulation studies and a real-data application show that it can provide a reliable and effective tool for different STPM applications.
DOI: 10.6084/m9.figshare.13151778.v1
title: Additional file 1 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 1: Table S1. Genetic diversity, Fst and gene flow in Chinese landraces (CL) and modern Chinese cultivars (MCC) in ten wheat agro-ecological zones.
DOI: 10.6084/m9.figshare.8957627
title: Additional file 1: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S1. KEGG mapping of the Magnolia wufengensis unigenes. (XLSX 206 kb)
DOI: 10.6084/m9.figshare.13151778
title: Additional file 1 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 1: Table S1. Genetic diversity, Fst and gene flow in Chinese landraces (CL) and modern Chinese cultivars (MCC) in ten wheat agro-ecological zones.
DOI: 10.5281/zenodo.10624918
title: Data from: Can permanent grassland soils with elevated organic carbon buffer negative effects of more persistent precipitation regimes on forage grass performance?

description: This dataset relatest to the published article "Can permanent grassland soils with elevated organic carbon buffer negative effects of more persistent precipitation regimes on forage grass performance?" in Science Of The Total Environment (see https://doi.org/10.1016/j.scitotenv.2024.170623).
DOI: 10.5281/zenodo.10624919
title: Data from: Can permanent grassland soils with elevated organic carbon buffer negative effects of more persistent precipitation regimes on forage grass performance?

description: This dataset relatest to the published article "Can permanent grassland soils with elevated organic carbon buffer negative effects of more persistent precipitation regimes on forage grass performance?" in Science Of The Total Environment (see https://doi.org/10.1016/j.scitotenv.2024.170623).
DOI: 10.6084/m9.figshare.13152174
title: Additional file 6 of Insights into the mechanism of Arnebia euchroma on leukemia via network pharmacology approach

description: Additional file 6. Table S4. Weighted component-important target interactions.
DOI: 10.6084/m9.figshare.13152196
title: Additional file 5 of Genetic architecture of cardiometabolic risks in people living with HIV

description: Additional file 5: Table S7. List of variants significantly associated with lipid levels in African Americans in the CNICS HIV cohort (p &lt; E-5), non-significant in Willer et al. [31] (p &gt; 0.05) and with no overlap between 99% confidence intervals for the beta coefficients between CNICS and Willer et al.
DOI: 10.6084/m9.figshare.8957651
title: Additional file 6: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S6. Differently-expressed genes involved in photosynthesis in response to cold treatment of Magnolia wufengensis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8957657
title: Additional file 7: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S7. Primer information. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8957663.v1
title: Additional file 8: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S8. Differentially expressed genes (DEGs) associated with membrane components. (XLSX 14 kb)