cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24891116.v1
title: A Kernel Measure of Dissimilarity between <i>M</i> Distributions

description: Given M≥2 distributions defined on a general measurable space, we introduce a nonparametric (kernel) measure of multi-sample dissimilarity (KMD)—a parameter that quantifies the difference between the <i>M</i> distributions. The population KMD, which takes values between 0 and 1, is 0 if and only if all the <i>M</i> distributions are the same, and 1 if and only if all the distributions are mutually singular. Moreover, KMD possesses many properties commonly associated with <i>f</i>-divergences such as the data processing inequality and invariance under bijective transformations. The sample estimate of KMD, based on independent observations from the <i>M</i> distributions, can be computed in near linear time (up to logarithmic factors) using <i>k</i>-nearest neighbor graphs (for k≥1 fixed). We develop an easily implementable test for the equality of <i>M</i> distributions based on the sample KMD that is consistent against all alternatives where at least two distributions are not equal. We prove central limit theorems for the sample KMD, and provide a complete characterization of the asymptotic power of the test, as well as its detection threshold. The usefulness of our measure is demonstrated via real and synthetic data examples; our method is also implemented in an R package. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19220905
title: Additional file 2 of Computational identification of clonal cells in single-cell CRISPR screens

description: Additional file 2.
DOI: 10.6084/m9.figshare.12819091
title: Additional file 2 of Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression

description: Additional file 2: Supplementary Table S2. Genomic variants targeted for deep sequencing.
DOI: 10.6084/m9.figshare.8113973
title: Additional file 1: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

description: Primers used for MAS during CSSLs development. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.17026931
title: Role of Rho guanine nucleotide exchange factors in non-small cell lung cancer

description: Conventionally, Rho guanine nucleotide exchange factors (GEFs) are known activators of Rho guanosine triphosphatases (GTPases) that promote tumorigenesis. However, the role of Rho GEFs in non-small cell lung cancer (NSCLC) remains largely unknown. Through the screening of 81 Rho GEFs for their expression profiles and correlations with survival, four of them were identified with strong significance for predicting the prognosis of NSCLC patients. The four Rho GEFs, namely ABR, PREX1, DOCK2 and DOCK4, were downregulated in NSCLC tissues compared to normal tissues. The downregulation of ABR, PREX1, DOCK2 and DOCK4, which can be attributfed to promoter methylation, is correlated with poor prognosis. The underexpression of the four key Rho GEFs might be related to the upregulation of MYC signaling and DNA repair pathways, leading to carcinogenesis and poor prognosis. Moreover, overexpression of ABR was shown to have a tumor-suppressive effect in PC9 and H1703 cells. In conclusion, the data reveal the unprecedented role of ABR as tumor suppressor in NSCLC. The previously unnoticed functions of Rho GEFs in NSCLC will inspire researchers to investigate the distinct roles of Rho GEFs in cancers, in order to provide critical strategies in clinical practice.
DOI: 10.6084/m9.figshare.19634863.v1
title: Additional file 1 of Identifying causal genes for stroke via integrating the proteome and transcriptome from brain and blood

description: Additional file 1: Supplementary Tables 1–32.
DOI: 10.6084/m9.figshare.11784144
title: Additional file 10 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 10: Information on primers used for qRT-PCR verification of differential gene expression. A Microsoft Excel file containing a single worksheet “Primers qRT-PCR Assay”. This table provides information on the design of qRT-PCR primers for 20 chicken genes. The Roslin Institute Gallus gallus (RIGG) oligo ID number, NCBI Entrez Gene ID, gene symbol, gene description, and the 5′-3′ sequence for forward and reverse primers used for qRT-PCR analysis are provided. Although four “invariant genes” were included, only two genes were acceptable by qBase software for use in normalization of qRT-PCR expression levels.
DOI: 10.6084/m9.figshare.11784144.v1
title: Additional file 10 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 10: Information on primers used for qRT-PCR verification of differential gene expression. A Microsoft Excel file containing a single worksheet “Primers qRT-PCR Assay”. This table provides information on the design of qRT-PCR primers for 20 chicken genes. The Roslin Institute Gallus gallus (RIGG) oligo ID number, NCBI Entrez Gene ID, gene symbol, gene description, and the 5′-3′ sequence for forward and reverse primers used for qRT-PCR analysis are provided. Although four “invariant genes” were included, only two genes were acceptable by qBase software for use in normalization of qRT-PCR expression levels.
DOI: 10.6084/m9.figshare.11784150
title: Additional file 1 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 1: K-means clusters identified from four pairwise contrasts of fasting and refeeding conditions. A Microsoft Excel file containing two worksheets named: “K-means clusters_FDR adj P≤0.05” and “Plots of K-Means Clusters (C0-C9)”. The first worksheet provides an annotated list of the 196 DEGs assigned to 10 clusters (C0-C9) of functionally-related hepatic genes. Information is provided on each DEG including the RIGG oligo ID, gene symbol, gene description, log2 fold-change (FC) of pairwise contrasts of fasting (C1 and C2) and refeeding (C3 and C4) conditions, and the cluster number. The second worksheet contains a PowerPoint figure composed of 10 K-Means Clusters that differentially respond to fasting and refeeding conditions.
DOI: 10.6084/m9.figshare.11784150.v1
title: Additional file 1 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 1: K-means clusters identified from four pairwise contrasts of fasting and refeeding conditions. A Microsoft Excel file containing two worksheets named: “K-means clusters_FDR adj P≤0.05” and “Plots of K-Means Clusters (C0-C9)”. The first worksheet provides an annotated list of the 196 DEGs assigned to 10 clusters (C0-C9) of functionally-related hepatic genes. Information is provided on each DEG including the RIGG oligo ID, gene symbol, gene description, log2 fold-change (FC) of pairwise contrasts of fasting (C1 and C2) and refeeding (C3 and C4) conditions, and the cluster number. The second worksheet contains a PowerPoint figure composed of 10 K-Means Clusters that differentially respond to fasting and refeeding conditions.
DOI: 10.6084/m9.figshare.11784159
title: Additional file 2 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 2: Comparison of DEGs identified by microarray analysis versus “Analysis Ready” (AR)-DEGs accepted by IPA. A Microsoft Excel file containing a single worksheet “ IPA rejection of DEGs”. This worksheet list the number of chicken DEGs (FDR adj. P ≤ 0.05) identified by microarray analysis and the number of “Analysis Ready” (AR)-DEGs recognized by the Ingenuity Knowledge Base and used for Ingenuity Pathway Analysis (IPA). On average, 22.5% of the chicken microarray DEGs identified with a valid RefSeq ID were rejected by IPA.
DOI: 10.6084/m9.figshare.11784159.v1
title: Additional file 2 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 2: Comparison of DEGs identified by microarray analysis versus “Analysis Ready” (AR)-DEGs accepted by IPA. A Microsoft Excel file containing a single worksheet “ IPA rejection of DEGs”. This worksheet list the number of chicken DEGs (FDR adj. P ≤ 0.05) identified by microarray analysis and the number of “Analysis Ready” (AR)-DEGs recognized by the Ingenuity Knowledge Base and used for Ingenuity Pathway Analysis (IPA). On average, 22.5% of the chicken microarray DEGs identified with a valid RefSeq ID were rejected by IPA.
DOI: 10.6084/m9.figshare.11784162
title: Additional file 1 of A microcarrier-based spheroid 3D invasion assay to monitor dynamic cell movement in extracellular matrix

description: Additional file 1. Homemade macros to quantify migrating cell areas of each distance range in Fiji.
DOI: 10.6084/m9.figshare.11784162.v1
title: Additional file 1 of A microcarrier-based spheroid 3D invasion assay to monitor dynamic cell movement in extracellular matrix

description: Additional file 1. Homemade macros to quantify migrating cell areas of each distance range in Fiji.
DOI: 10.6084/m9.figshare.11784165
title: Additional file 3 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 3: Lists of DEGs from five meaningful pairwise contrasts of fasting and refeeding conditions. A Microsoft Excel file containing five worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) identified from pairwise contrasts. Each worksheet provides a list of AR-DEGs identified by pairwise treatment contrasts including the gene symbol, Entrez gene name, log2 expression ratio, and gene/protein ID number.
DOI: 10.6084/m9.figshare.11784165.v1
title: Additional file 3 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 3: Lists of DEGs from five meaningful pairwise contrasts of fasting and refeeding conditions. A Microsoft Excel file containing five worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) identified from pairwise contrasts. Each worksheet provides a list of AR-DEGs identified by pairwise treatment contrasts including the gene symbol, Entrez gene name, log2 expression ratio, and gene/protein ID number.
DOI: 10.6084/m9.figshare.11784168
title: Additional file 4 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 4: Over-represented canonical and functional pathways identified by IPA in the D2FED48h vs D2FAST48h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.11784168.v1
title: Additional file 4 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 4: Over-represented canonical and functional pathways identified by IPA in the D2FED48h vs D2FAST48h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.11784174
title: Additional file 5 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 5: Over-represented canonical and functional pathways identified by IPA in the D2FAST48h vs D3REFED24h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped by IPA to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.11784174.v1
title: Additional file 5 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 5: Over-represented canonical and functional pathways identified by IPA in the D2FAST48h vs D3REFED24h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped by IPA to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.11784180
title: Additional file 6 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 6: Over-represented canonical and functional pathways identified by IPA in the D2FAST48h vs D4REFED48h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.11784180.v1
title: Additional file 6 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 6: Over-represented canonical and functional pathways identified by IPA in the D2FAST48h vs D4REFED48h contrast. A Microsoft Excel file containing eight worksheets of AR-DEGs (FDR adjusted P ≤ 0.05) mapped to over-represented canonical and functional pathways. Each worksheet provides the gene symbol, Entrez gene name, log2 ratio, cellular location and type of gene.
DOI: 10.6084/m9.figshare.23304887.v1
title: Additional file 9 of Targeting CXCR4 abrogates resistance to trastuzumab by blocking cell cycle progression and synergizes with docetaxel in breast cancer treatment

description: Additional file 9. Table S1: Antibodies used for RPPA and western blot.
DOI: 10.6084/m9.figshare.11784189
title: Additional file 8 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 8: Pearson’s Correlation Analysis of gene expression levels of 10 DEGs determined by genome microarray and verified by qRT-PCR analyses. A Microsoft Excel file containing the average normalized expression level (log2 ratio) of 10 DEGs as determined by both microarray analysis and qRT-PCR analysis. The Pearson’s correlation coefficient (r = 0.970; P ≤ 0.01, 8 degrees of freedom) indicates a highly significant correlation between gene expression levels obtained from both microarray and qRT-PCR analyses.
DOI: 10.6084/m9.figshare.11784189.v1
title: Additional file 8 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 8: Pearson’s Correlation Analysis of gene expression levels of 10 DEGs determined by genome microarray and verified by qRT-PCR analyses. A Microsoft Excel file containing the average normalized expression level (log2 ratio) of 10 DEGs as determined by both microarray analysis and qRT-PCR analysis. The Pearson’s correlation coefficient (r = 0.970; P ≤ 0.01, 8 degrees of freedom) indicates a highly significant correlation between gene expression levels obtained from both microarray and qRT-PCR analyses.
DOI: 10.6084/m9.figshare.11784195
title: Additional file 9 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 9: Microarray reference RNA hybridization design. A Microsoft Excel file containing a single worksheet “20.7 K Array Hybridization Design”. A total of 50 Arizona 20.7 K Chicken Oligo Arrays (NCBI GEO Platform # GPL6049) were used in a reference RNA hybridization design. Each biological sample (liver RNA sample) was labelled with Alexa Flour® 555 (green) dye. An aliquot of the pooled reference RNA sample was labelled with Alexa Flour® 647 (red) dye and these were hybridized together on one of the 20.7 K oligo microarrays. The 50 microarrays were assigned to 10 fasting-refeeding treatment groups with five biological replicates (liver RNA from five cockerels). A balanced block design was used for hybridization of 10 microarrays across 5 consecutive days, where one liver RNA sample represented each of the 10 treatment groups on each hybridization day (10 arrays/day).
DOI: 10.6084/m9.figshare.11784195.v1
title: Additional file 9 of Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

description: Additional file 9: Microarray reference RNA hybridization design. A Microsoft Excel file containing a single worksheet “20.7 K Array Hybridization Design”. A total of 50 Arizona 20.7 K Chicken Oligo Arrays (NCBI GEO Platform # GPL6049) were used in a reference RNA hybridization design. Each biological sample (liver RNA sample) was labelled with Alexa Flour® 555 (green) dye. An aliquot of the pooled reference RNA sample was labelled with Alexa Flour® 647 (red) dye and these were hybridized together on one of the 20.7 K oligo microarrays. The 50 microarrays were assigned to 10 fasting-refeeding treatment groups with five biological replicates (liver RNA from five cockerels). A balanced block design was used for hybridization of 10 microarrays across 5 consecutive days, where one liver RNA sample represented each of the 10 treatment groups on each hybridization day (10 arrays/day).
DOI: 10.6084/m9.figshare.12819205.v1
title: Additional file 5 of Identification of volatile active components in Acori Tatarinowii Rhizome essential oil from different regions in China by C6 glioma cells

description: Additional file 5. The original rPCR data of ATEO bioactivity.
DOI: 10.6084/m9.figshare.23304887
title: Additional file 9 of Targeting CXCR4 abrogates resistance to trastuzumab by blocking cell cycle progression and synergizes with docetaxel in breast cancer treatment

description: Additional file 9. Table S1: Antibodies used for RPPA and western blot.
DOI: 10.6084/m9.figshare.12819205
title: Additional file 5 of Identification of volatile active components in Acori Tatarinowii Rhizome essential oil from different regions in China by C6 glioma cells

description: Additional file 5. The original rPCR data of ATEO bioactivity.
DOI: 10.6084/m9.figshare.25219268
title: Bonner Ferguson Data for JCST manuscript 2024.xlsx

description: We sought to determine if there are any differences in changes of student attitudes before and after 3.5-week and 7-week condensed flipped Organic Chemistry I courses using the Attitude toward the Subject of Chemistry Inventory Version 2 (ASCIv2). We also compared student performance for both course lengths as measured by exam and overall course grades. The results indicate that student attitudes started and remained more negative in a 3.5-week course than the 7-week course, even though exam and course grade averages are not significantly different between the formats.
DOI: 10.6084/m9.figshare.25219268.v1
title: Bonner Ferguson Data for JCST manuscript 2024.xlsx

description: We sought to determine if there are any differences in changes of student attitudes before and after 3.5-week and 7-week condensed flipped Organic Chemistry I courses using the Attitude toward the Subject of Chemistry Inventory Version 2 (ASCIv2). We also compared student performance for both course lengths as measured by exam and overall course grades. The results indicate that student attitudes started and remained more negative in a 3.5-week course than the 7-week course, even though exam and course grade averages are not significantly different between the formats.
DOI: 10.6084/m9.figshare.14889475.v1
title: Additional file 2 of The underlying molecular mechanisms and prognostic factors of RNA binding protein in colorectal cancer: a study based on multiple online databases

description: Additional file 2. The abnormally expressed RBPs and RBPs related to CRC survival.
DOI: 10.6084/m9.figshare.23819920
title: Additional file 1 of SUMOylation of AnxA6 facilitates EGFR-PKCα complex formation to suppress epithelial cancer growth

description: Additional file 1.
DOI: 10.6084/m9.figshare.10735652
title: A global database of Paired Resorption Efficiency of Nitrogen and Phosphorus (PRENP, Version 1.0)

description: We complied a global database of Paired Resorption Efficiency of
Nitrogen and Phosphorus (PRENP, Version 1.0) in leaves of terrestrial plants
based on literature surveyed via Web of Science (http://isiknowledge.com),
Google Scholar (https://scholar.google.com) and the China National Knowledge
Infrastructure (http://www.cnki.net). The key words ‘nitrogen resorption’ and
‘phosphorus resorption’ were used to search published studies of leaf NRE and PRE.
Data were included only when NRE and PRE were measured simultaneously. To avoid misattributing natural nutrient limitation due to anthropogenic
disturbances, we excluded data for intensively managed ecosystems (e.g.,
agroforest, fertilized plantations, sown pastures, croplands and urban
forests). Overall, our database includes observations of leaf NRE
and PRE across 171 sites. For each site, we first averaged values of NRE (NRE<sub>dom</sub>) and
PRE (PRE<sub>dom</sub>) for all reported dominant species, respectively. If
data on several forest stands or grassland plots were reported at the same site,
NRE<sub>dom</sub> and PRE<sub>dom</sub> were averaged before computing NRE<sub>dom</sub>/PRE<sub>dom</sub>.
Site-averaged NRE<sub>dom</sub>/PRE<sub>dom </sub>was then calculated as an indicator
of relative nutrient limitation. Please find more information in the Nature Geoscience paper by Du et al. Author's permission is required to use the dataset.
DOI: 10.6084/m9.figshare.11784345
title: Additional file 3 of Zhenqing recipe attenuates non-alcoholic fatty liver disease by regulating the SIK1/CRTC2 signaling in experimental diabetic rats

description: Additional file 3. Uncropped western blots.
DOI: 10.6084/m9.figshare.11784345.v1
title: Additional file 3 of Zhenqing recipe attenuates non-alcoholic fatty liver disease by regulating the SIK1/CRTC2 signaling in experimental diabetic rats

description: Additional file 3. Uncropped western blots.
DOI: 10.6084/m9.figshare.11784360
title: Additional file 1 of Multi-dimensional omics characterization in glioblastoma identifies the purity-associated pattern and prognostic gene signatures

description: Additional file 1: Table S1. The purity values in TCGA-GBM cohort. Table S2. Cox proportional hazards model in TCGA-GBM cohort. Table S3. Differentially expressed genes between tumor and normal samples. Table S4. Expression of Immune checkpoint molecules before and after purity adjustment. Table S5. Differentially mutated gene frequency in oncogenic signaling pathways.