cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7943200
title: Deep Reinforcement Learning Enables Better Bias Control in Benchmark for Virtual Screening

description: This compressed file contains all datasets made for the validation of MUBDsyn.

datasets_int_val: 17 cases in this folder are derived from MUBD for GPCRs. MUBDreal was made by MUBD-DecoyMaker2.0 and MUBDsyn was made by MUBD-DecoyMakersyn.
datasets_ext_val_classical_VS: Five cases in this folder are derived from the shared cases of MUV and DUD-E. The active sets of MUV were taken as the input to make corresponding MUBD datasets. Files in SBVS are raw molecular docking results by smina.
datasets_ext_val_SI_classical_VS: DeepCoy and TocoDecoy were used to make the datasets corresponding to the same five cases above. The data of DeepCoy was directly retrieved from DeepCoy resources at OPIG while topology decoys of TocoDecoy_9W were made based on the scripts provided at TocoDecoy GitHub Repository. Files in SBVS are raw molecular docking results by smina.
datasets_ext_val_ML_VS: Ten cases in this folder are derived from NRLiSt-BDB. Corresponding MUBD datasets were made as described above.
All these datasets can be used for the reproduction of validation performed in the manuscript or to benchmark various virtual screening methods.
DOI: 10.6084/m9.figshare.7654193.v1
title: Additional file 1: of Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken

description: Table S1. Detailed information of primers used in this study. Table S2. All novel circRNAs detected in granulosa cells. Table S3. Flank intron length statistics. Table S4. Differentially expressed circRNAs (Fold change &gt;â 2, q-value &lt;â 0.05) in different granulosa cells. Table S5. Gene ontology for host genes of differential expressed circRNAs. Table S6. KEGG pathway for host genes of all differentially expressed circRNAs in three granulosa cells stage. Table S7. Overlapped prediction genes by TargetScan and miRDB. Table S8. Gene ontology of predicted target genes based on circRALGPS2. Table S9. KEGG pathway of predicted target genes based on circRALGPS2. (XLSX 1280 kb)
DOI: 10.6084/m9.figshare.9751490
title: MOESM2 of Function and mechanism of long non-coding RNA Gm21284 in the development of hippocampal cholinergic neurons

description: Additional file 2. The Statement of RiboBio.
DOI: 10.6084/m9.figshare.9751490.v1
title: MOESM2 of Function and mechanism of long non-coding RNA Gm21284 in the development of hippocampal cholinergic neurons

description: Additional file 2. The Statement of RiboBio.
DOI: 10.6084/m9.figshare.14994232
title: Dynamic changes of plasma extracellular vesicle long RNAs during perioperative period of colorectal cancer

description: Extracellular vesicles (EVs) long RNAs (exLRs) have been shown to be indicators for the diagnosis and prognosis of colorectal cancer (CRC); however, the dynamic changes of exLRs during perioperative period and their cellular sources in CRC remains largely unknown. In this study, exLR sequencing (exLR-seq) was performed on plasma samples from three CRC patients at four time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T3]). Bioinformatics approaches were used to investigate the profile and biofunctions of exLRs and their cellular sources. Greater than 12,000 mRNAs and 2,000 lncRNAs were reliably detected in each exLR-seq sample. Compared with T0, there were 110 differentially expressed genes (DEGs) in T1, 60 DEGs in T2, and 50 DEGs in T3. A total of 11 DEGs were found at all three time points and were related to membrane potential. In addition, compared to T0, 22 differentially expressed lncRNAs (DELRs) were found in T1, 19 DELRs in T2, and 38 DELRs in T3. Moreover, only three DELRs were detected at all three time points. Interestingly, EVs from CD8 + T cells, CD4+ memory T cells and NK cells decreased after surgery and the absolute quantity of EVs from immune cells were reduced as well. In summary, this study was the first to characterize the dynamic changes of exLRs during perioperative period and the cellular sources. These findings established the foundation for further studies involving the effects of these dynamically changed exLRs on CRC.
DOI: 10.6084/m9.figshare.14994232.v1
title: Dynamic changes of plasma extracellular vesicle long RNAs during perioperative period of colorectal cancer

description: Extracellular vesicles (EVs) long RNAs (exLRs) have been shown to be indicators for the diagnosis and prognosis of colorectal cancer (CRC); however, the dynamic changes of exLRs during perioperative period and their cellular sources in CRC remains largely unknown. In this study, exLR sequencing (exLR-seq) was performed on plasma samples from three CRC patients at four time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T3]). Bioinformatics approaches were used to investigate the profile and biofunctions of exLRs and their cellular sources. Greater than 12,000 mRNAs and 2,000 lncRNAs were reliably detected in each exLR-seq sample. Compared with T0, there were 110 differentially expressed genes (DEGs) in T1, 60 DEGs in T2, and 50 DEGs in T3. A total of 11 DEGs were found at all three time points and were related to membrane potential. In addition, compared to T0, 22 differentially expressed lncRNAs (DELRs) were found in T1, 19 DELRs in T2, and 38 DELRs in T3. Moreover, only three DELRs were detected at all three time points. Interestingly, EVs from CD8 + T cells, CD4+ memory T cells and NK cells decreased after surgery and the absolute quantity of EVs from immune cells were reduced as well. In summary, this study was the first to characterize the dynamic changes of exLRs during perioperative period and the cellular sources. These findings established the foundation for further studies involving the effects of these dynamically changed exLRs on CRC.
DOI: 10.6084/m9.figshare.20236127.v1
title: Additional file 1 of Integrative analysis of miRNA and mRNA profiles reveals that gga-miR-106-5p inhibits adipogenesis by targeting the KLF15 gene in chickens

description: Additional file 1: Table S1. Primers used in this study. Table S2. Clustering of differentially expressed miRNA expression profiles in chicken abdominal adipocytes at different stages of differentiation. Table S3. Differentially expressed genes during the adipogenic differentiation of chicken abdominal preadipocytes. Table S4. Functional enrichment analysis of all differentially expressed mRNAs in chicken abdominal adipocytes at different stages of differentiation. Table S5. All targets of differentially expressed miRNAs and functional enrichment analysis of differentially expressed targets. Table S6. Regulatory network analysis of differentially expressed miRNAs and differentially expressed transcriptional factors. Table S7. Potential target genes of the KLF15 transcriptional factor. Table S8. Putative chicken KLF15 motif in the promoters of representative genes related to cell proliferation and lipogenesis.
DOI: 10.34740/kaggle/dsv/7636872
title: ⏳ endoflife.date database (duckdb)
DOI: 10.6084/m9.figshare.9751610
title: Vaginal microbiome 16S sequencing for PCOS

description: This is the original 16S rRNA gene sequencing fastq files for the paper titled as "The vaginal microbiome among female with polycystic ovarian syndrome: a case control study".<br>
DOI: 10.6084/m9.figshare.24955985
title: Additional file 2 of Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

description: Supplementary Material 2: Table S1 QTLs for PGC and their position in the substitution segments in SSSLs. Table S2 Substitution segments carrying QTLs for PGC in pyramiding lines. Table S3 The phenotypes of rice chalkiness in 1QLs to 4QLs. Table S4 Additive effects of QTL combinations on PGC in 1QLs to 4QLs. Table S5 Epistatic effects of QTL combinations on PGC in pyramiding lines. Table S6 Average temperatures of 30 days after rice flowering in different cropping seasons
DOI: 10.6084/m9.figshare.24955985.v1
title: Additional file 2 of Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

description: Supplementary Material 2: Table S1 QTLs for PGC and their position in the substitution segments in SSSLs. Table S2 Substitution segments carrying QTLs for PGC in pyramiding lines. Table S3 The phenotypes of rice chalkiness in 1QLs to 4QLs. Table S4 Additive effects of QTL combinations on PGC in 1QLs to 4QLs. Table S5 Epistatic effects of QTL combinations on PGC in pyramiding lines. Table S6 Average temperatures of 30 days after rice flowering in different cropping seasons
DOI: 10.6084/m9.figshare.14994232.v2
title: Dynamic changes of plasma extracellular vesicle long RNAs during perioperative period of colorectal cancer

description: Extracellular vesicles (EVs) long RNAs (exLRs) have been shown to be indicators for the diagnosis and prognosis of colorectal cancer (CRC); however, the dynamic changes of exLRs during perioperative period and their cellular sources in CRC remains largely unknown. In this study, exLR sequencing (exLR-seq) was performed on plasma samples from three CRC patients at four time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T3]). Bioinformatics approaches were used to investigate the profile and biofunctions of exLRs and their cellular sources. Greater than 12,000 mRNAs and 2,000 lncRNAs were reliably detected in each exLR-seq sample. Compared with T0, there were 110 differentially expressed genes (DEGs) in T1, 60 DEGs in T2, and 50 DEGs in T3. A total of 11 DEGs were found at all three time points and were related to membrane potential. In addition, compared to T0, 22 differentially expressed lncRNAs (DELRs) were found in T1, 19 DELRs in T2, and 38 DELRs in T3. Moreover, only three DELRs were detected at all three time points. Interestingly, EVs from CD8 + T cells, CD4+ memory T cells and NK cells decreased after surgery and the absolute quantity of EVs from immune cells were reduced as well. In summary, this study was the first to characterize the dynamic changes of exLRs during perioperative period and the cellular sources. These findings established the foundation for further studies involving the effects of these dynamically changed exLRs on CRC.
DOI: 10.6084/m9.figshare.14994232.v3
title: Dynamic changes of plasma extracellular vesicle long RNAs during perioperative period of colorectal cancer

description: Extracellular vesicles (EVs) long RNAs (exLRs) have been shown to be indicators for the diagnosis and prognosis of colorectal cancer (CRC); however, the dynamic changes of exLRs during perioperative period and their cellular sources in CRC remains largely unknown. In this study, exLR sequencing (exLR-seq) was performed on plasma samples from three CRC patients at four time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T3]). Bioinformatics approaches were used to investigate the profile and biofunctions of exLRs and their cellular sources. Greater than 12,000 mRNAs and 2,000 lncRNAs were reliably detected in each exLR-seq sample. Compared with T0, there were 110 differentially expressed genes (DEGs) in T1, 60 DEGs in T2, and 50 DEGs in T3. A total of 11 DEGs were found at all three time points and were related to membrane potential. In addition, compared to T0, 22 differentially expressed lncRNAs (DELRs) were found in T1, 19 DELRs in T2, and 38 DELRs in T3. Moreover, only three DELRs were detected at all three time points. Interestingly, EVs from CD8 + T cells, CD4+ memory T cells and NK cells decreased after surgery and the absolute quantity of EVs from immune cells were reduced as well. In summary, this study was the first to characterize the dynamic changes of exLRs during perioperative period and the cellular sources. These findings established the foundation for further studies involving the effects of these dynamically changed exLRs on CRC.
DOI: 10.6084/m9.figshare.7654319
title: Additional file 8: of Physiological and iTRAQ-based proteomic analyses reveal the function of exogenous Îł-aminobutyric acid (GABA) in improving tea plant (Camellia sinensis L.) tolerance at cold temperature

description: Table S8, S9 & S10: Sequences of all unique peptides matched to each identified proteins. (ZIP 1383 kb)
DOI: 10.6084/m9.figshare.14994268.v1
title: Azilsartan protects against hyperglycemia-induced hyperpermeability of the blood-brain barrier

description: Diabetes mellitus (DM) is a complex metabolic disease with significant neurological complications and is reported to be closely related to the blood-brain barrier (BBB) disruption. Azilsartan is an antagonist of the Angiotensin II receptor developed for the treatment of hypertension, and it has been recently reported to have neuroprotective effects. The present study aims to investigate the protective effect of Azilsartan against hyperglycemia-induced BBB disruption and its underlying mechanism. Male db/db mice were treated with Azilsartan (20 μg/day) for 10 consecutive days. Compared to the control group, increased BBB permeability, suppressed occludin expression, excessive release of inflammatory factors, and downregulation of krüppel-like factor 2 (KLF2) were observed in diabetic mice, all of which were dramatically reversed by Azilsartan treatment. In the <i>in vitro</i> experiments, elevated endothelial permeability and decreased expression of occludin and KLF2 were observed in high glucose-challenged endothelial cells, which were significantly alleviated by Azilsartan. Lastly, the silencing of KLF2 abolished the protective effects of Azilsartan against the high glucose-induced expression of occludin and endothelial monolayer permeability in bEnd.3 brain endothelial cells. Based on these observations, we concluded that Azilsartan protected against hyperglycemia-induced hyperpermeability of BBB via the KLF2/occludin axis.
DOI: 10.6084/m9.figshare.14994268
title: Azilsartan protects against hyperglycemia-induced hyperpermeability of the blood-brain barrier

description: Diabetes mellitus (DM) is a complex metabolic disease with significant neurological complications and is reported to be closely related to the blood-brain barrier (BBB) disruption. Azilsartan is an antagonist of the Angiotensin II receptor developed for the treatment of hypertension, and it has been recently reported to have neuroprotective effects. The present study aims to investigate the protective effect of Azilsartan against hyperglycemia-induced BBB disruption and its underlying mechanism. Male db/db mice were treated with Azilsartan (20 μg/day) for 10 consecutive days. Compared to the control group, increased BBB permeability, suppressed occludin expression, excessive release of inflammatory factors, and downregulation of krüppel-like factor 2 (KLF2) were observed in diabetic mice, all of which were dramatically reversed by Azilsartan treatment. In the <i>in vitro</i> experiments, elevated endothelial permeability and decreased expression of occludin and KLF2 were observed in high glucose-challenged endothelial cells, which were significantly alleviated by Azilsartan. Lastly, the silencing of KLF2 abolished the protective effects of Azilsartan against the high glucose-induced expression of occludin and endothelial monolayer permeability in bEnd.3 brain endothelial cells. Based on these observations, we concluded that Azilsartan protected against hyperglycemia-induced hyperpermeability of BBB via the KLF2/occludin axis.
DOI: 10.6084/m9.figshare.7130603
title: SI kinematics data.xlsx

description: Body and wing kinematics
DOI: 10.6084/m9.figshare.14995000
title: The evolution of hydrochemical and isotopic signatures from precipitation, surface water to groundwater in a typical karst watershed, Central Texas, USA

description: The Upper Cibolo Creek (UCC) karst watershed in Central Texas, USA, represents a portion of the drainage area that supplies water to the recharge zone for the Edwards Aquifer. However, the surface water–groundwater interactions along the UCC are not well quantified, and the hydraulic interactions are important for water budget and water quality of the aquifer. In this study, we investigated the evolution of hydrochemical and isotopic signatures (<i>δ</i><sup>18</sup>O, <i>δ</i><sup>2</sup>H and <i>d</i>-excess) from precipitation, surface water to groundwater in the UCC watershed from 2017 to 2019, and investigated surface water–groundwater interactions using samples from 14 creeks/spring sites. Factor analysis for the observed parameters demonstrates that changes in water hydrochemistry are primarily controlled by human activity, precipitation input, and water–rock interaction. Hierarchical clustering analysis of temporal isotope variations confirms that significant surface water–groundwater interactions occur in the UCC watershed. We identified relationships between nitrate concentrations at creek/spring sites and land-use conditions, and nitrate input sources were determined utilizing the dual-isotope analyses (<i>δ</i><sup>15</sup>N and <i>δ</i><sup>18</sup>O) of nitrate. This study provides capacity for a more precise assessment of water resources and water quality in Central Texas.
DOI: 10.6084/m9.figshare.7130774
title: Male and Female Mice Uranium Tissue ICP/MS and Water Intake Data. Following a 60-day Drinking Water Exposure to 5 and 50 ppm Uranium (uranyl acetate).

description: Male and Female C57BL/6J Mice, Tissue Uranium ICP/MS and Water intake data for mice exposed to uranium for 60-days (uranyl acetate).Bolt AM. et. al. Title of Manuscript: Minimal uranium accumulation in lymphoid tissues following an oral 60-day uranyl acetate exposure in male and female C57BL/6J mice. PLos One. 2018

PONE-D-18-22528R1<br>

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DOI: 10.6084/m9.figshare.19189413
title: Characterization and pathogenicity of a novel avian nephritis virus isolated in China

description: Avian nephritis virus infections of chicken flocks cause enteric and kidney disease, uneven growth, and runting stunting syndrome, leading to economic losses in the poultry industry. In this study, one ANV strain, designated as AH202017, was isolated from a diseased broiler flock in Anhui province, China, in 2020. Virus production in LMH cell culture was confirmed by real-time RT–PCR and immunofluorescence assay. The complete genome sequencing analysis indicated that AH202017 shares 77.5–85.5% identity with 12 reference strains in GenBank. Phylogenetic analysis of the capsid protein revealed that AH202017 is more closely related to VIC-6a/Australia/2014 belonging to ANV genotype 2. However, the phylogenetic tree, based on the ORF1a protein and ORF1b protein, indicated that AH202017 manifests a close relationship with GXJL815/China/2017 belonging to genotype 8. In infection experiments, four infected chickens showed depression and one chicken died at 6 days post-infection, corresponding to 5% mortality. The virus was shed daily in the faeces of infected chickens, and was found distributed in multiple organs. Macroscopic and microscopic lesions in the kidneys were observed. This is the first paper that describes the genomic characteristics and pathogenicity of a novel ANV strain in China.
RESEARCH HIGHLIGHTSA novel ANV strain was isolated for the first time from diseased broilers in China.The ANV strain caused nephritis and 5% mortality rate in 1-day-old SPF chickens. A novel ANV strain was isolated for the first time from diseased broilers in China. The ANV strain caused nephritis and 5% mortality rate in 1-day-old SPF chickens.
DOI: 10.6084/m9.figshare.23383886
title: Prokaryotic expression of the V protein of the peste des petits ruminants virus and development of an indirect ELISA

description: In this study, we recombinantly expressed the V protein of the peste des petits ruminants virus (PPRV) and evaluated its diagnostic value for PPRV infection using an indirect ELISA (i-ELISA). The optimal concentration of the coated antigen of V protein was 15 ng/well at a serum dilution of 1:400, and the optimal positive threshold value was 0.233. A cross-reactivity assay showed that the V protein-based i-ELISA was specific to PPRV with consistent reproducibility and showed a specificity of 82.6% and a sensitivity of 100% with a virus neutralization test. Using the recombinant V protein as an antigen in ELISA is useful for seroepidemiological studies of PPRV infections.
DOI: 10.6084/m9.figshare.23383886.v1
title: Prokaryotic expression of the V protein of the peste des petits ruminants virus and development of an indirect ELISA

description: In this study, we recombinantly expressed the V protein of the peste des petits ruminants virus (PPRV) and evaluated its diagnostic value for PPRV infection using an indirect ELISA (i-ELISA). The optimal concentration of the coated antigen of V protein was 15 ng/well at a serum dilution of 1:400, and the optimal positive threshold value was 0.233. A cross-reactivity assay showed that the V protein-based i-ELISA was specific to PPRV with consistent reproducibility and showed a specificity of 82.6% and a sensitivity of 100% with a virus neutralization test. Using the recombinant V protein as an antigen in ELISA is useful for seroepidemiological studies of PPRV infections.
DOI: 10.6084/m9.figshare.22335328
title: NMR analyses of ALIX-CHMP4 interactions and CHMP4 conformtation and dynamics

description: Figure 4A: 1H/15N chemical shift perturbation profiles of 100 μM 15N/2H-labeled Bro1 on addition of 300 μM unlabeled CHMP4 constructs; CHMP4C(121–233, S191C) and CHMP4B(121–224,S184C).
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Figure 4C: 1H/15N and 13C’/15N chemical shift perturbation profiles of 150 μM 15N/13C-labeled PRD(703–800)Strep in the presence of 450 μM unlabeled CHMP4 constructs. 
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Figure 5F: Evidence of transient long-range interactions in CHMP4C paralog using experimental PRE profiles (shown as paramagnetic-labeled vs. diamagnetic-labeled 1H/15N cross-peak height ratios) of 15N-labeled CHMP4C(121–233,G154C) and CHMP4C(121–233,M165C).
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Figure 6A and 6B: The reduction in 1H/15N cross-peak heights of 150 μM 15N-labeled (A) CHMP4C(121–233,S191C) and (B) CHMP4B(121–224,S184C) as a function of increasing amount of unlabeled Bro1.<br>
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Figure 6C and 6D: The perturbations in 1H/15N chemical shifts of 150 μM 15N-labeled (C) CHMP4C(121–233,S191C) and (D) CHMP4B(121–224,S184C) as a function of increasing amount of unlabeled PRD(703–800)Strep.<br>
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Figure 6I, 6J, and 6K: The reduction in 1H/15N cross-peak heights of 30 μM 15N/2H-labeled (I) (CHMP4C121–233,S191C), (J) CHMP4B(121–224,S184C), and (K) CHMP4C(121–224,S184C, I225A, L228A, W231A) in the presence of 90 μM unlabeled ALIX(1–868,P801G)Strep.