cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6973241
title: Additional file 3: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 for 16 or 3Â h (XLS 259 kb)
DOI: 10.6084/m9.figshare.6973031
title: Additional file 2: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Modules significantly (pâ &lt;â 0.05) correlated with characteristic components in tea. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5400559.v1
title: Sequential Design for Functional Calibration of Computer Models

description: The calibration of computer models using physical experimental data has received a compelling interest in the last decade. Recently, multiple works have addressed the functional calibration of computer models, where the calibration parameters are functions of the observable inputs rather than taking a set of fixed values as traditionally treated in the literature. While much of the recent work on functional calibration was focused on estimation, the issue of sequential design for functional calibration still presents itself as an open question. Addressing the sequential design issue is thus the focus of this article. We investigate different sequential design approaches and show that the simple separate design approach has its merit in practical use when designing for functional calibration. Analysis is carried out on multiple simulated and real-world examples.
DOI: 10.6084/m9.figshare.6973031.v1
title: Additional file 2: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Modules significantly (pâ &lt;â 0.05) correlated with characteristic components in tea. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6973268.v1
title: Additional file 4: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S4. DEPs in comparison KJ201-Piz-t/KJ201-NPB. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6973190.v1
title: Additional file 1: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S1. GWAS reports that included in the current study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6973208
title: Additional file 3: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S3. Significant terms of the Gene Ontology, Pathway, and Disease enrichment of 38 CCT-associated genes (FDRâ &lt;â 0.05). (XLSX 55 kb)
DOI: 10.6084/m9.figshare.6973226
title: Additional file 2: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 or vehicle for 16Â h. (XLS 273 kb)
DOI: 10.6084/m9.figshare.6973334
title: Additional file 3: of Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize

description: Table S2. Root trait data of the RIL population at the three time points. (XLSX 135 kb)
DOI: 10.6084/m9.figshare.6973334.v1
title: Additional file 3: of Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize

description: Table S2. Root trait data of the RIL population at the three time points. (XLSX 135 kb)
DOI: 10.6084/m9.figshare.6449138.v1
title: Additional file 1: of Genomic predictions combining SNP markers and copy number variations in Nellore cattle

description: Table S1. Detail information of the CNVs detected with high confidence. (XLSX 37 kb)
DOI: 10.5525/gla.researchdata.1598
title: Cysteine post-translational modifications regulate protein interactions of caveolin-3

description: This data set contains data used to form the basis of a scientific publication.
Microsoft Excel files contain quantitative data from analysis of images of western immunoblots
Microsoft Powerpoint files contain original uncropped images of western immunoblots
DOI: 10.6084/m9.figshare.19556145
title: Additional file 1 of The m6A demethylase ALKBH5 promotes tumor progression by inhibiting RIG-I expression and interferon alpha production through the IKKε/TBK1/IRF3 pathway in head and neck squamous cell carcinoma

description: Additional file 1: Supplementary Table S1. The primers and sequences used in this study.
DOI: 10.6084/m9.figshare.19556148.v1
title: Additional file 2 of The m6A demethylase ALKBH5 promotes tumor progression by inhibiting RIG-I expression and interferon alpha production through the IKKε/TBK1/IRF3 pathway in head and neck squamous cell carcinoma

description: Additional file 2: Supplementary Table S2. The differentially expressed genes with upregulation of mRNA/methylation after sequencing.
DOI: 10.6084/m9.figshare.19556145.v1
title: Additional file 1 of The m6A demethylase ALKBH5 promotes tumor progression by inhibiting RIG-I expression and interferon alpha production through the IKKε/TBK1/IRF3 pathway in head and neck squamous cell carcinoma

description: Additional file 1: Supplementary Table S1. The primers and sequences used in this study.
DOI: 10.6084/m9.figshare.19556148
title: Additional file 2 of The m6A demethylase ALKBH5 promotes tumor progression by inhibiting RIG-I expression and interferon alpha production through the IKKε/TBK1/IRF3 pathway in head and neck squamous cell carcinoma

description: Additional file 2: Supplementary Table S2. The differentially expressed genes with upregulation of mRNA/methylation after sequencing.
DOI: 10.6084/m9.figshare.6973268
title: Additional file 4: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S4. DEPs in comparison KJ201-Piz-t/KJ201-NPB. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6973274.v1
title: Additional file 2: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: Reference collection excel file with meta-data. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.11692788
title: MOESM1 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 1: Table S1. Identified proteins from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.11692788.v1
title: MOESM1 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 1: Table S1. Identified proteins from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.11692791
title: MOESM2 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 2: Table S2. consistent presence / absence expression protein profile.
DOI: 10.6084/m9.figshare.11692791.v1
title: MOESM2 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 2: Table S2. consistent presence / absence expression protein profile.
DOI: 10.6084/m9.figshare.11692797
title: MOESM4 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 4: Table S4. Identified lipid classes from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.11692797.v1
title: MOESM4 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 4: Table S4. Identified lipid classes from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.11692794
title: MOESM3 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 3: Table S3. Identified lipid species from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.11692794.v1
title: MOESM3 of Proteomic and lipidomic analysis of exosomes derived from ovarian cancer cells and ovarian surface epithelial cells

description: Additional file 3: Table S3. Identified lipid species from two ovarian cell lines derived exosomes.
DOI: 10.6084/m9.figshare.6973307.v1
title: Additional file 6: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S5. GO and KEGG analyses of DEPs in comparison KJ201-Piz-t/KJ201-NPB. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6973310.v1
title: Additional file 4: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: Results of validation test. (CSV 2265 kb)
DOI: 10.6084/m9.figshare.6973313
title: Additional file 2: of Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize

description: Table S1. Root trait data of the parental lines at the three time points. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6973325.v1
title: Additional file 5: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: BioProject and PubMLST Ids for genome assemblies used in reference collection. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.13787743
title: Additional file 1 of Targeting dopamine receptor D2 as a novel therapeutic strategy in endometrial cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.20604828
title: Testing Biased Randomization Assumptions and Quantifying Imperfect Matching and Residual Confounding in Matched Observational Studies

description: One central goal of design of observational studies is to embed nonexperimental data into an approximate randomized controlled trial using statistical matching. Despite empirical researchers’ best intention and effort to create high-quality matched samples, residual imbalance due to observed covariates not being well matched often persists. Although statistical tests have been developed to test the randomization assumption and its implications, few provide a means to quantify the level of residual confounding due to observed covariates not being well matched in matched samples. In this article, we develop two generic classes of exact statistical tests for a biased randomization assumption. One important by-product of our testing framework is a quantity called <i>residual sensitivity value</i> (RSV), which provides a means to quantify the level of residual confounding due to imperfect matching of observed covariates in a matched sample. We advocate taking into account RSV in the downstream primary analysis. The proposed methodology is illustrated by re-examining a famous observational study concerning the effect of right heart catheterization (RHC) in the initial care of critically ill patients. Code implementing the method can be found in the supplementary materials.
DOI: 10.6084/m9.figshare.20604828.v1
title: Testing Biased Randomization Assumptions and Quantifying Imperfect Matching and Residual Confounding in Matched Observational Studies

description: One central goal of design of observational studies is to embed nonexperimental data into an approximate randomized controlled trial using statistical matching. Despite empirical researchers’ best intention and effort to create high-quality matched samples, residual imbalance due to observed covariates not being well matched often persists. Although statistical tests have been developed to test the randomization assumption and its implications, few provide a means to quantify the level of residual confounding due to observed covariates not being well matched in matched samples. In this article, we develop two generic classes of exact statistical tests for a biased randomization assumption. One important by-product of our testing framework is a quantity called <i>residual sensitivity value</i> (RSV), which provides a means to quantify the level of residual confounding due to imperfect matching of observed covariates in a matched sample. We advocate taking into account RSV in the downstream primary analysis. The proposed methodology is illustrated by re-examining a famous observational study concerning the effect of right heart catheterization (RHC) in the initial care of critically ill patients. Code implementing the method can be found in the supplementary materials.
DOI: 10.6084/m9.figshare.6449138
title: Additional file 1: of Genomic predictions combining SNP markers and copy number variations in Nellore cattle

description: Table S1. Detail information of the CNVs detected with high confidence. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6973514.v1
title: Additional file 3: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a Sequencing and mapping statistics of MN and WSC NOVA CLIP. b Sequencing and mapping statistics of MN and WSC NOVA CLIP. c mm9 coordinates and genomic annotation of WSC NOVA CLIP peaks. d List of known NOVA targets harboring WSC NOVA CLIP peaks. e List of known NOVA targets harboring MN NOVA CLIP peaks. f GO enrichment of known MN versus WSC NOVA targets. g Transcripts with enriched NOVA CLIP signals in MNs compared to WSC. h Transcripts with depleted NOVA CLIP signals in MNs compared to WSC. (XLSX 13044 kb)
DOI: 10.6084/m9.figshare.6973523.v1
title: Additional file 4: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a Differential analysis results for all intronic joint peaks. b Differential analysis results for all intronic joint peaks. (XLSX 14058 kb)
DOI: 10.6084/m9.figshare.6973538
title: Additional file 5: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a Transcript regions differentially spliced between MNs and WSC. b For the nine exons with over- or under-represented MN NOVA binding sites in regulatory â hotspotsâ , correlation between observed and predicted dI between MNs and WSC. (XLSX 365 kb)
DOI: 10.6084/m9.figshare.6449258.v1
title: Additional file 6: of RNA sequencing-based longitudinal transcriptomic profiling gives novel insights into the disease mechanism of generalized pustular psoriasis

description: Table S4. List of DEGs enriched in canonical pathways by IPA analysis. (XLS 198Â kb)
DOI: 10.5066/p93vw8gx
title: Organic and inorganic constituents in surface water and native and non-native fish and frog health data collected from streams, impoundments and wetlands in the New Jersey Pinelands, 2017-2020 (ver. 1.1, August 2022)

description: The data presented include concentrations of 122 organic, 23 inorganic constituents, and estrogenicity in water collected from 13 off-stream non-point source sites (natural and created wetlands) and eight on-stream point source sites (streams and impoundments) in the New Jersey Pinelands, 2017-2020. Native and non-native fish health data collected from the on-stream sites as well as native frog data collected from the off-stream sites are also included. For the on-stream point-source component, we analyzed water chemistry, hormone activity, and collected native and non-native fish from two locations upstream and one downstream from two municipal wastewater treatment plants (six total sites) and from two minimally impacted locations to serve as reference conditions. For the off-stream non-point source component, we analyzed water chemistry, hormone activity, and collected Green Frogs (Lithobates clamitans) from eight stormwater basins and ponds embedded in altered landscapes and five ponds surrounded by forest land to serve as reference sites. Animals were assessed histologically for measures of endocrine disruption and surface water was analyzed for hormone activity and known or suspected endocrine disrupting compounds (EDCs) including hormones, phytoestrogens, waste indicator compounds and some metals.
DOI: 10.6084/m9.figshare.14724652
title: Supplementary Files S1 It contains the RepeatMasker annotation of the six avian genomes. 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.14724655
title: Supplementary Files S5 Output of the WhatGene pipeline for paradise crow, chicken, zebra finch and emu. 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.19556337
title: Additional file 4 of Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system

description: Additional file 4. Statistics analysis example in R language.
DOI: 10.6084/m9.figshare.19556331
title: Additional file 2 of Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system

description: Additional file 2. Gene enrichment analysis dataset.
DOI: 10.6084/m9.figshare.19556346.v1
title: Additional file 6 of Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system

description: Additional file 6. Original dataset for analysis.
DOI: 10.6084/m9.figshare.19556346
title: Additional file 6 of Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system

description: Additional file 6. Original dataset for analysis.
DOI: 10.15468/dl.dekwuy
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polemannia simplicior Hilliard & B.L.Burtt"
 ]
}

 The dataset includes 82 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074680-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bnyb5g
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plagiostachys strobilifera (Baker) Ridl."
 ]
}

 The dataset includes 101 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074682-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9sa9z9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus spirei Beille"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074683-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kr6j2v
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pimpinella hastata C.B.Clarke"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074684-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7s43u
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plectranthus praetermissus Codd"
 ]
}

 The dataset includes 18 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074685-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebtcmz
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlomoides koraiensis (Nakai) Kamelin & Makhm."
 ]
}

 The dataset includes 73 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074686-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.