cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11956479
title: Identification of the differentially expressed protein biomarkers in rat blood plasma in response to gamma irradiation

description: <b>Purpose:</b> Simple, rapid and high-throughput dose assessment is critical for clinical diagnosis, treatment and emergency intervention in a large-scale radiological accident. The goal of this study is to screen and identify new ionizing radiation-responsive protein biomarkers in rat plasma. <b>Materials and methods:</b> Sprague-Dawley rats were exposed to single doses of 0, 1, 3, 5 Gy of Cobalt-60 γ-rays total body irradiation at a dose rate of 1 Gy/min. The tandem mass tag labeling (TMT) combined with liquid chromatography mass spectrometry (LC-MS/MS) approach was used to screen the differentially expressed proteins in rat plasma collected at 1, 3, 5 and 7 days post-irradiation. Bioinformatics analysis was conducted to explore the biological functions of these proteins. The expression levels of candidate radiation-sensitive protein biomarkers were confirmed using enzyme-linked immune-sorbent assay (ELISA). <b>Results:</b> A total of 503 differentially expressed proteins were identified. Most of these proteins were implicated in immune response, phagocytosis and signal transduction following ionizing radiation. Five up-regulated proteins including alpha-2-macroglobulin (A2m), chromogranin-A (CHGA), glutathione pertidase 3 (GPX3), clusterin (Clu) and ceruloplasmin (Cp) were selected for ELISA analysis. It was found that the expression levels of A2m, CHGA and GPX3 protein were increased in a dose-dependent manner at 1, 3 and 5 days after irradiation. <b>Conclusion:</b> Proteomics analysis revealed radiation-induced differentially expressed proteins in rat plasma. Our results suggested that A2m, CHGA, GPX3 protein expressions alterations in rat plasma may have potential as biomarkers to evaluate radiation exposure.
DOI: 10.6084/m9.figshare.11956479.v1
title: Identification of the differentially expressed protein biomarkers in rat blood plasma in response to gamma irradiation

description: <b>Purpose:</b> Simple, rapid and high-throughput dose assessment is critical for clinical diagnosis, treatment and emergency intervention in a large-scale radiological accident. The goal of this study is to screen and identify new ionizing radiation-responsive protein biomarkers in rat plasma. <b>Materials and methods:</b> Sprague-Dawley rats were exposed to single doses of 0, 1, 3, 5 Gy of Cobalt-60 γ-rays total body irradiation at a dose rate of 1 Gy/min. The tandem mass tag labeling (TMT) combined with liquid chromatography mass spectrometry (LC-MS/MS) approach was used to screen the differentially expressed proteins in rat plasma collected at 1, 3, 5 and 7 days post-irradiation. Bioinformatics analysis was conducted to explore the biological functions of these proteins. The expression levels of candidate radiation-sensitive protein biomarkers were confirmed using enzyme-linked immune-sorbent assay (ELISA). <b>Results:</b> A total of 503 differentially expressed proteins were identified. Most of these proteins were implicated in immune response, phagocytosis and signal transduction following ionizing radiation. Five up-regulated proteins including alpha-2-macroglobulin (A2m), chromogranin-A (CHGA), glutathione pertidase 3 (GPX3), clusterin (Clu) and ceruloplasmin (Cp) were selected for ELISA analysis. It was found that the expression levels of A2m, CHGA and GPX3 protein were increased in a dose-dependent manner at 1, 3 and 5 days after irradiation. <b>Conclusion:</b> Proteomics analysis revealed radiation-induced differentially expressed proteins in rat plasma. Our results suggested that A2m, CHGA, GPX3 protein expressions alterations in rat plasma may have potential as biomarkers to evaluate radiation exposure.
DOI: 10.6084/m9.figshare.14053627
title: Additional file 1 of Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus

description: Additional file 1: Table S1 Gene numbers in the subfamilies of ABC transporter in the genomes of Papilio xuthus, other 31 insects, other five arthropods and human. Table S2. Details of the 56 ABC transporters identified in the genome of Papilio xuthus. Table S3. Details of the Rab families identified in the genome of Papilio xuthus and Bombyx mori. Table S4. The target of the CRISPR-edited locus and primer for genotyping sequences. Table S5. Mutation rate among different individual mutants and their mutated clones across different target sites. Table S6. The information of RNA sequencing and data for samples. Table S7. The mapping information of RNA reads for all samples. Table S8. The mutations in the target regions from transcriptomics data. Table S9. Differentially expressed genes (DEGs) between the mutants of five edited genes (brown, ok, scarlet, white, lightoid) and their wild-types. Table S10. Summary on functions of five genes experimentally verified in this study and previously published.
DOI: 10.6084/m9.figshare.14053627.v1
title: Additional file 1 of Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus

description: Additional file 1: Table S1 Gene numbers in the subfamilies of ABC transporter in the genomes of Papilio xuthus, other 31 insects, other five arthropods and human. Table S2. Details of the 56 ABC transporters identified in the genome of Papilio xuthus. Table S3. Details of the Rab families identified in the genome of Papilio xuthus and Bombyx mori. Table S4. The target of the CRISPR-edited locus and primer for genotyping sequences. Table S5. Mutation rate among different individual mutants and their mutated clones across different target sites. Table S6. The information of RNA sequencing and data for samples. Table S7. The mapping information of RNA reads for all samples. Table S8. The mutations in the target regions from transcriptomics data. Table S9. Differentially expressed genes (DEGs) between the mutants of five edited genes (brown, ok, scarlet, white, lightoid) and their wild-types. Table S10. Summary on functions of five genes experimentally verified in this study and previously published.
DOI: 10.6084/m9.figshare.11956515
title: Hierarchical sparse functional principal component analysis for multistage multivariate profile data

description: Modern manufacturing systems typically involve multiple production stages, the real-time status of which can be tracked continuously using sensor networks that generate a large number of profiles associated with all process variables at all stages. The analysis of the collective behavior of the multistage multivariate profile data is essential for understanding the variance patterns of the entire manufacturing process. For this purpose, two major challenges regarding the high data dimensionality and low model interpretability have to be well addressed. This article proposes integrating Multivariate Functional Principal Component Analysis (MFPCA) with a three-level structured sparsity idea to develop a novel Hierarchical Sparse MFPCA (HSMFPCA), in which the stage-wise, profile-wise and element-wise sparsity are jointly investigated to clearly identify the informative stages and variables in each eigenvector. In this way, the derived principal components would be more interpretable. The proposed HSMFPCA employs the regression-type reformulation of the PCA and the reparameterization of the entries of eigenvectors, and enjoys an efficient optimization algorithm in high-dimensional settings. The extensive simulations and a real example study verify the superiority of the proposed HSMFPCA with respect to the estimation accuracy and interpretation clarity of the derived eigenvectors.
DOI: 10.6084/m9.figshare.11956515.v1
title: Hierarchical Sparse Functional Principal Component Analysis for Multistage Multivariate Profile Data

description: Modern manufacturing systems typically involve multiple production stages, the real-time status of which can be tracked continuously nowadays by the widely deployed sensor networks that generate a large number of profiles associated with all process variables at all stages. The analysis of the collective behavior of these multistage multivariate profile data is essential for understanding the variance patterns of the entire manufacturing process. For this purpose, two major challenges regarding the high data dimensionality and low model interpretability have to be well addressed. This paper proposes integrating the multivariate functional principal component analysis (MFPCA) with a three-level structured sparsity idea to develop a novel hierarchical sparse MFPCA (HSMFPCA), in which the stage-wise, profile-wise and element-wise sparsity are jointly investigated to clearly identify the informative stages and variables in each eigenvector. In this way, the derived principal components would be more interpretable. The proposed HSMFPCA employs the regression-type reformulation of the PCA and the reparameterization of the entries of eigenvectors, and enjoys an efficient optimization algorithm in high-dimensional settings. The extensive simulations and a real example study verify the superiority of the proposed HSMFPCA with respect to the estimation accuracy and interpretation clarity of the derived eigenvectors. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.6713666
title: LncRNA H19-elevated LIN28B promotes lung cancer progression through sequestering miR-196b

description: LncRNA H19 is involved in the development of multiple cancers. Here, we firstly provide new evidence that H19 can induce LIN28B, a conserved RNA binding protein, to accelerate lung cancer growth through sponging miR-196b. Abundance in LIN28B was observed in clinical lung cancer samples. A positive link was observed between H19 and LIN28B in clinical lung cancer samples. In lung cancer cells, H19 was capable of increasing LIN28B expression. Mechanistically, miR-196b directly targeted LIN28B to inhibit LIN28B expression. H19 was capable of promoting LIN28B expression through sequestering miR-196b. Functionally, H19-increased LIN28B conferred the cell proliferation of lung cancer. Our finding indicates that H19 depresses miR-196b to elevate LIN28B, resulting in accelerating cell proliferation in lung cancer.
DOI: 10.6084/m9.figshare.6713666.v1
title: LncRNA H19-elevated LIN28B promotes lung cancer progression through sequestering miR-196b

description: LncRNA H19 is involved in the development of multiple cancers. Here, we firstly provide new evidence that H19 can induce LIN28B, a conserved RNA binding protein, to accelerate lung cancer growth through sponging miR-196b. Abundance in LIN28B was observed in clinical lung cancer samples. A positive link was observed between H19 and LIN28B in clinical lung cancer samples. In lung cancer cells, H19 was capable of increasing LIN28B expression. Mechanistically, miR-196b directly targeted LIN28B to inhibit LIN28B expression. H19 was capable of promoting LIN28B expression through sequestering miR-196b. Functionally, H19-increased LIN28B conferred the cell proliferation of lung cancer. Our finding indicates that H19 depresses miR-196b to elevate LIN28B, resulting in accelerating cell proliferation in lung cancer.
DOI: 10.6084/m9.figshare.14053798
title: Additional file 7 of Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition

description: Additional file 7: Table S7. Genes involving in plant hormone signal transduction and pigments metabolism.
DOI: 10.6084/m9.figshare.14053798.v1
title: Additional file 7 of Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition

description: Additional file 7: Table S7. Genes involving in plant hormone signal transduction and pigments metabolism.
DOI: 10.6084/m9.figshare.15102375
title: The Expression and Survival Significance of Glucose Transporter-1 in Pancreatic Cancer: Meta-Analysis, Bioinformatics Analysis and Retrospective Study

description: To explore the expression profile and prognostic relevance of GLUT-1 in pancreatic cancer, a meta-analysis, bioinformatics analysis based on Gene Expression Omnibus (GEO), Oncomine dataset and The Cancer Genome Atlas (TCGA) database, and immunohistochemistry in tumor and normal tissue from 88 pancreatic ductal adenocarcinoma (PDAC) patients were performed. GLUT-1 was significantly overexpressed in pancreatic cancer but it could not be a significant biomarker for prognosis. TNM stage and pathological grade could be biomarker of poor prognosis of patients with pancreatic cancer.
DOI: 10.6084/m9.figshare.15102375.v1
title: The Expression and Survival Significance of Glucose Transporter-1 in Pancreatic Cancer: Meta-Analysis, Bioinformatics Analysis and Retrospective Study

description: To explore the expression profile and prognostic relevance of GLUT-1 in pancreatic cancer, a meta-analysis, bioinformatics analysis based on Gene Expression Omnibus (GEO), Oncomine dataset and The Cancer Genome Atlas (TCGA) database, and immunohistochemistry in tumor and normal tissue from 88 pancreatic ductal adenocarcinoma (PDAC) patients were performed. GLUT-1 was significantly overexpressed in pancreatic cancer but it could not be a significant biomarker for prognosis. TNM stage and pathological grade could be biomarker of poor prognosis of patients with pancreatic cancer.
DOI: 10.6084/m9.figshare.7762370
title: Additional file 1: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: Estimates of the dates for the segmental duplication events of the BZL gene pairs in soybean. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7762370.v1
title: Additional file 1: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: Estimates of the dates for the segmental duplication events of the BZL gene pairs in soybean. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7762385
title: Additional file 4: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: ChIP data reveal genes potentially regulated by the GmBZL3 transcription factor in soybean. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7762385.v1
title: Additional file 4: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: ChIP data reveal genes potentially regulated by the GmBZL3 transcription factor in soybean. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7762394
title: Additional file 6: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: Identification of nonsynonymous SNPs and deletions in the GmBZL3 gene from 106 soybean resequencing datasets (Valliyodan et al. 2016). Highlighted text showing SNPs and nonsynonymous mutations. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7762394.v1
title: Additional file 6: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: Identification of nonsynonymous SNPs and deletions in the GmBZL3 gene from 106 soybean resequencing datasets (Valliyodan et al. 2016). Highlighted text showing SNPs and nonsynonymous mutations. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7762397
title: Additional file 7: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: The list of primers used in qRT-PCR and ChIP-qPCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7762397.v1
title: Additional file 7: of GmBZL3 acts as a major BR signaling regulator through crosstalk with multiple pathways in Glycine max

description: The list of primers used in qRT-PCR and ChIP-qPCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.21393895
title: Additional file 3 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

description: Additional file 2. Clinicopathological Data for 40 TNBC.
DOI: 10.6084/m9.figshare.21393895.v1
title: Additional file 3 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

description: Additional file 2. Clinicopathological Data for 40 TNBC.
DOI: 10.6084/m9.figshare.21393898
title: Additional file 4 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

description: Additional file 3. Digital raw data.
DOI: 10.6084/m9.figshare.21393898.v1
title: Additional file 4 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

description: Additional file 3. Digital raw data.
DOI: 10.6084/m9.figshare.21393903
title: Additional file 5 of Role of a lipid metabolism-related lncRNA signature in risk stratification and immune microenvironment for colon cancer

description: Additional file 5: Table S2. The enriched pathways of the Cluster 1 and 2.
DOI: 10.6084/m9.figshare.21393903.v1
title: Additional file 5 of Role of a lipid metabolism-related lncRNA signature in risk stratification and immune microenvironment for colon cancer

description: Additional file 5: Table S2. The enriched pathways of the Cluster 1 and 2.
DOI: 10.5281/zenodo.10698564
title: Data for "A hippocampus-accumbens code guides goal-directed appetitive behavior"

description: This dataset represents the source data for the manuscript "A hippocampus-accumbens code guides goal-directed appetitive behavior" by Barnstedt, Mocellin, and Remy. All files are saved as dataframes with pandas (v1.4.3, using 'blosc' compression for H5).

It contains the following files:






ArchT.feather

Dataframe containing all source behavioural data for mice expressing ArchT in NAc-projecting dHPC neurons. 10 mice in ArchT/EYFP groups are tested for 8 days on a head-fixed spatial reward learning task. 100 Hz temporal resolution.


behaviour.h5
Dataframe containing all source behavioural data accompanying calcium imaging, collected from analogue signals and camera signals, downsampled to 15/30 Hz to match imaging temporal resolution.


C.h5
Deconvolved calcium signals from 5372 dHPC pyramidal neurons recorded at 15/30 Hz in Thy1-GCaMP6s mice. Data collected with two-photon imaging and extracted using CaImAn.


ChR.feather
Dataframe containing all source behavioural data for mice expressing ChR2 in dHPC axons in NAc. 7 mice in ChR2/EYFP groups are tested over several days while naive and during a head-fixed spatial reward learning task. 75 Hz temporal resolution.


comps.feather
Dataframe containing one row per neuron, showing diverse neuronal features.


psth_ds.feather
Dataframe with peri-stimulus time histograms of calcium activity around lick onsets.


S.h5
Deconvolved calcium events from 5372 dHPC pyramidal neurons recorded at 15/30 Hz in Thy1-GCaMP6s mice. Data collected with two-photon imaging and extracted using CaImAn.


success_comreward.feather
Dataframe showing successful behavioural trials with percentage of dHPC-/dHPC-->NAc neurons with place field centers near the reward zone.


training.feather
Dataframe containing all source behavioural data without calcium imaging, collected from analogue signals and camera signals, collected at 25/75 Hz from 18 mice.
DOI: 10.5281/zenodo.10698565
title: Data for "A hippocampus-accumbens code guides goal-directed appetitive behavior"

description: This dataset represents the source data for the manuscript "A hippocampus-accumbens code guides goal-directed appetitive behavior" by Barnstedt, Mocellin, and Remy. All files are saved as dataframes with pandas (v1.4.3, using 'blosc' compression for H5).

It contains the following files:






ArchT.feather

Dataframe containing all source behavioural data for mice expressing ArchT in NAc-projecting dHPC neurons. 10 mice in ArchT/EYFP groups are tested for 8 days on a head-fixed spatial reward learning task. 100 Hz temporal resolution.


behaviour.h5
Dataframe containing all source behavioural data accompanying calcium imaging, collected from analogue signals and camera signals, downsampled to 15/30 Hz to match imaging temporal resolution.


C.h5
Deconvolved calcium signals from 5372 dHPC pyramidal neurons recorded at 15/30 Hz in Thy1-GCaMP6s mice. Data collected with two-photon imaging and extracted using CaImAn.


ChR.feather
Dataframe containing all source behavioural data for mice expressing ChR2 in dHPC axons in NAc. 7 mice in ChR2/EYFP groups are tested over several days while naive and during a head-fixed spatial reward learning task. 75 Hz temporal resolution.


comps.feather
Dataframe containing one row per neuron, showing diverse neuronal features.


psth_ds.feather
Dataframe with peri-stimulus time histograms of calcium activity around lick onsets.


S.h5
Deconvolved calcium events from 5372 dHPC pyramidal neurons recorded at 15/30 Hz in Thy1-GCaMP6s mice. Data collected with two-photon imaging and extracted using CaImAn.


success_comreward.feather
Dataframe showing successful behavioural trials with percentage of dHPC-/dHPC-->NAc neurons with place field centers near the reward zone.


training.feather
Dataframe containing all source behavioural data without calcium imaging, collected from analogue signals and camera signals, collected at 25/75 Hz from 18 mice.
DOI: 10.6084/m9.figshare.21393919
title: Additional file 1 of Clinical implications of circulating tumor DNA in predicting the outcome of diffuse large B cell lymphoma patients receiving first-line therapy

description: Additional file 1: Table S1. Gene list of Onco-LymScan panel. Table S2. Overview of patient characteristics. Table S3. Demographic of patient characteristics. Table S4. Sequencing quality data of tumor gDNA samples. Table S5. Sequencing quality data of cfDNA samples. Table S6. Univariate Cox proportional hazard regression survival analysis including pretreatment ctDNA levels and other clinical indices.
DOI: 10.6084/m9.figshare.21393919.v1
title: Additional file 1 of Clinical implications of circulating tumor DNA in predicting the outcome of diffuse large B cell lymphoma patients receiving first-line therapy

description: Additional file 1: Table S1. Gene list of Onco-LymScan panel. Table S2. Overview of patient characteristics. Table S3. Demographic of patient characteristics. Table S4. Sequencing quality data of tumor gDNA samples. Table S5. Sequencing quality data of cfDNA samples. Table S6. Univariate Cox proportional hazard regression survival analysis including pretreatment ctDNA levels and other clinical indices.
DOI: 10.6084/m9.figshare.8286782
title: MOESM1 of Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa

description: Additional file 1: Table S1. Primer sequences for quantitative RT-PCR analysis of candidate proteins. Table S2. DEPs identified in autotetraploid B. rapa. Table S3. The identified 204 DEPs with correlated DEGs in autotetraploid B. rapa. Table S4. The identified 358 DEPs with no change in the transcript level in autotetraploid B. rapa.
DOI: 10.6084/m9.figshare.8286782.v1
title: MOESM1 of Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa

description: Additional file 1: Table S1. Primer sequences for quantitative RT-PCR analysis of candidate proteins. Table S2. DEPs identified in autotetraploid B. rapa. Table S3. The identified 204 DEPs with correlated DEGs in autotetraploid B. rapa. Table S4. The identified 358 DEPs with no change in the transcript level in autotetraploid B. rapa.
DOI: 10.6084/m9.figshare.15102528
title: Additional file 3 of Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

description: Additional file 3: Table S2-2. Differentially methylated sites on mRNAs
DOI: 10.6084/m9.figshare.15102528.v1
title: Additional file 3 of Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

description: Additional file 3: Table S2-2. Differentially methylated sites on mRNAs