cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19228253
title: Circ_0025033 deficiency suppresses paclitaxel resistance and malignant development of paclitaxel-resistant ovarian cancer cells by modulating the miR-532-3p/FOXM1 network

description: Ovarian cancer (OC) is the main cause of cancer-related death in women, and drug resistance is a leading cause of treatment failure. Recently, the involvement of circular RNAs (circRNAs) in cancer progression has become an area of increased investigation. The objective of this study is to uncover the function and regulatory mechanism of circ_0025033 in paclitaxel (PTX)-resistant OC cells. The expression of circ_0025033, FOXM1 and miR-532-3p was investigated using quantitative real-time polymerase chain reaction (qRT-PCR), and the protein expression of FOXM1 was quantified by western blot. Cell biological functions, including cell viability, migration/invasion and apoptosis, were explored using 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assays, transwell assays and flow cytometry assays. The interaction between miR-532-3p and circ_0025033 or FOXM1 predicted by bioinformatics analysis was validated by pull-down assay and dual-luciferase reporter assay. Exosomes were isolated to determine the further function of circ_0025033. Circ_0025033 and FOXM1 were highly expressed, while miR-532-3p was poorly expressed in OC tissues and cells, and the expression pattern was greater in PTX-resistant OC cells. Circ_0025033 knockdown lessened PTX resistance, suppressed migration/invasion and promoted apoptosis of PTX-resistant cells. With respect to mechanism, circ_0025033 upregulated the expression of FOXM1 by targeting miR-532-3p, and circ_0025033 knockdown blocked the malignant activities of PTX-resistant OC cells by enriching miR-532-3p and suppressing FOXM1. Exosomes derived from PTX-resistant cells with circ_0025033 knockdown also could repress the malignant actions of PTX-resistant OC cells. Circ_0025033 downregulation impaired PTX resistance and malignant activities of PTX-resistant OC cells by regulating the miR-532-3p/FOXM1 network.
DOI: 10.6084/m9.figshare.19228253.v1
title: Circ_0025033 deficiency suppresses paclitaxel resistance and malignant development of paclitaxel-resistant ovarian cancer cells by modulating the miR-532-3p/FOXM1 network

description: Ovarian cancer (OC) is the main cause of cancer-related death in women, and drug resistance is a leading cause of treatment failure. Recently, the involvement of circular RNAs (circRNAs) in cancer progression has become an area of increased investigation. The objective of this study is to uncover the function and regulatory mechanism of circ_0025033 in paclitaxel (PTX)-resistant OC cells. The expression of circ_0025033, FOXM1 and miR-532-3p was investigated using quantitative real-time polymerase chain reaction (qRT-PCR), and the protein expression of FOXM1 was quantified by western blot. Cell biological functions, including cell viability, migration/invasion and apoptosis, were explored using 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assays, transwell assays and flow cytometry assays. The interaction between miR-532-3p and circ_0025033 or FOXM1 predicted by bioinformatics analysis was validated by pull-down assay and dual-luciferase reporter assay. Exosomes were isolated to determine the further function of circ_0025033. Circ_0025033 and FOXM1 were highly expressed, while miR-532-3p was poorly expressed in OC tissues and cells, and the expression pattern was greater in PTX-resistant OC cells. Circ_0025033 knockdown lessened PTX resistance, suppressed migration/invasion and promoted apoptosis of PTX-resistant cells. With respect to mechanism, circ_0025033 upregulated the expression of FOXM1 by targeting miR-532-3p, and circ_0025033 knockdown blocked the malignant activities of PTX-resistant OC cells by enriching miR-532-3p and suppressing FOXM1. Exosomes derived from PTX-resistant cells with circ_0025033 knockdown also could repress the malignant actions of PTX-resistant OC cells. Circ_0025033 downregulation impaired PTX resistance and malignant activities of PTX-resistant OC cells by regulating the miR-532-3p/FOXM1 network.
DOI: 10.5281/zenodo.10672830
title: IODP Expedition 393 RGB channels (calculated from core photos)

description: Red, green, and blue pixel data were extracted from Section Half Imaging Logger (SHIL) linescan images, typically binned at 0.5 cm resolution using the central 2 cm of the image.
DOI: 10.5281/zenodo.10672831
title: IODP Expedition 393 RGB channels (calculated from core photos)

description: Red, green, and blue pixel data were extracted from Section Half Imaging Logger (SHIL) linescan images, typically binned at 0.5 cm resolution using the central 2 cm of the image.
DOI: 10.6084/m9.figshare.14509590
title: Additional file 3 of Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

description: Additional file 2. Supplementary Dataset 1. Dataset for environmental data and barcodes/categories used in this study. File in excel format containing multiple tabs. Tables for the soil series from the CL and SL sites (tab 1); soil physiochemical properties (tab 2); monthly weather conditions for each site during the sampling points (tab 3); overall sequencing metadata (barcodes, categories; tab 4), pH and % gravimetric moisture for bulk soil during sampling T1 for both sites (tab 5); metadata for samples/libraries used for comparison of primers (V1V2 vs V9, tab 6).
DOI: 10.6084/m9.figshare.14509590.v1
title: Additional file 3 of Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

description: Additional file 2. Supplementary Dataset 1. Dataset for environmental data and barcodes/categories used in this study. File in excel format containing multiple tabs. Tables for the soil series from the CL and SL sites (tab 1); soil physiochemical properties (tab 2); monthly weather conditions for each site during the sampling points (tab 3); overall sequencing metadata (barcodes, categories; tab 4), pH and % gravimetric moisture for bulk soil during sampling T1 for both sites (tab 5); metadata for samples/libraries used for comparison of primers (V1V2 vs V9, tab 6).
DOI: 10.6084/m9.figshare.14509686
title: Additional file 2 of Tandem fecal microbiota transplantation cycles in an allogeneic hematopoietic stem cell transplant recipient targeting carbapenem-resistant Enterobacteriaceae colonization: a case report and literature review

description: Additional file 2: Table S1. Protocol of donor screening in MedBiome. IBD inflammatory bowel disease, IBS irritable bowel syndrome, GI gastrointestinal, CRP C- reactive protein, ESR erythrocyte sedimentation rate, HIV human immunodeficiency virus.
DOI: 10.6084/m9.figshare.14509686.v1
title: Additional file 2 of Tandem fecal microbiota transplantation cycles in an allogeneic hematopoietic stem cell transplant recipient targeting carbapenem-resistant Enterobacteriaceae colonization: a case report and literature review

description: Additional file 2: Table S1. Protocol of donor screening in MedBiome. IBD inflammatory bowel disease, IBS irritable bowel syndrome, GI gastrointestinal, CRP C- reactive protein, ESR erythrocyte sedimentation rate, HIV human immunodeficiency virus.
DOI: 10.6084/m9.figshare.24995484
title: Additional file 1 of Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.)

description: Additional file 1.
DOI: 10.6084/m9.figshare.24995484.v1
title: Additional file 1 of Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.)

description: Additional file 1.
DOI: 10.6084/m9.figshare.24995501
title: Additional file 1 of ADAM8 silencing suppresses the migration and invasion of fibroblast-like synoviocytes via FSCN1/MAPK cascade in osteoarthritis

description: Additional file 1: Table S1. siRNA sequences of rat genes. Table S2. Primers used in qRT-PCR. Figure S1. qRT-PCR analysis of the mRNA expression levels of TULP2, DNAH6, CTRC, HIPK4, BEX1, CPA2, ARG2, BIN2A, MYCN and GNAL in FLSs after intervention with IL-1β. *P&lt;0.05; **P&lt;0.01. Figure S2. MAPK inhibitor Adezmapimod inhibited invasion, migration and inflammatory expression of IL-1β-stimulated FLSs. (A) CCK-8 results showing cytotoxicity of Adezmapimod on FLSs. (B) Western blot and quantitative analysis of P-JNK/JNK, P-ERK/ERK and P-P38/P38 in IL-1β-stimulated FLSs after treatment with Adezmapimod. (C, F) Wound healing assays and quantitative analysis of the migration ability of FLSs. (D, G) Transwell assays and quantitative analysis of the migration ability of FLSs. (E, H) Transwell assays and quantitative analysis of the invasion ability of FLSs with different concentrations of IL-1βin IL-1β-stimulated FLSs after treatment with Adezmapimod. (I) Western blot and quantitative analysis of IL-6, TNF-α and COX2 in IL-1β-stimulated FLSs after treatment with Adezmapimod. Scale bar = 200 µm. *P&lt;0.05; **P&lt;0.01. Figure S3. The GSEA analysis revealed that the MAPK signaling pathway was significantly enriched in FLSs after treatment with IL-1β. Figure S4. Western blot and quantitative analysis of P-JNK/JNK, P-ERK/ERK and P-P38/P38 in FLSs after treatment with BDP13176. ns, non-significant, **P&lt;0.01.
DOI: 10.6084/m9.figshare.24995501.v1
title: Additional file 1 of ADAM8 silencing suppresses the migration and invasion of fibroblast-like synoviocytes via FSCN1/MAPK cascade in osteoarthritis

description: Additional file 1: Table S1. siRNA sequences of rat genes. Table S2. Primers used in qRT-PCR. Figure S1. qRT-PCR analysis of the mRNA expression levels of TULP2, DNAH6, CTRC, HIPK4, BEX1, CPA2, ARG2, BIN2A, MYCN and GNAL in FLSs after intervention with IL-1β. *P&lt;0.05; **P&lt;0.01. Figure S2. MAPK inhibitor Adezmapimod inhibited invasion, migration and inflammatory expression of IL-1β-stimulated FLSs. (A) CCK-8 results showing cytotoxicity of Adezmapimod on FLSs. (B) Western blot and quantitative analysis of P-JNK/JNK, P-ERK/ERK and P-P38/P38 in IL-1β-stimulated FLSs after treatment with Adezmapimod. (C, F) Wound healing assays and quantitative analysis of the migration ability of FLSs. (D, G) Transwell assays and quantitative analysis of the migration ability of FLSs. (E, H) Transwell assays and quantitative analysis of the invasion ability of FLSs with different concentrations of IL-1βin IL-1β-stimulated FLSs after treatment with Adezmapimod. (I) Western blot and quantitative analysis of IL-6, TNF-α and COX2 in IL-1β-stimulated FLSs after treatment with Adezmapimod. Scale bar = 200 µm. *P&lt;0.05; **P&lt;0.01. Figure S3. The GSEA analysis revealed that the MAPK signaling pathway was significantly enriched in FLSs after treatment with IL-1β. Figure S4. Western blot and quantitative analysis of P-JNK/JNK, P-ERK/ERK and P-P38/P38 in FLSs after treatment with BDP13176. ns, non-significant, **P&lt;0.01.
DOI: 10.6084/m9.figshare.12412616
title: Differentiation proliferative capacity of skeletal muscle satellite cells from Dapulian and Landrace pigs

description: Previously, we found there were significant differences in the development of skeletal muscle, myofiber characteristics between Chinese pig breed Dapulian and Landrace. Furthermore, the development of skeletal muscle is related to the proliferation of satellite cells (SCs). Thus, our aim was to compare the differences of proliferative abilities and expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace in this study. We isolated skeletal muscle SCs with collagenase digestion from the longissimus dorsi muscles of 1-day-old male Dapulian and Landrace piglets. After successful culture of SCs <i>in vitro</i>, proliferative capacity was estimated at different time points. Meanwhile, the expression of key genes related to SCs proliferation was detected by qRT-PCR and western blotting. Proliferation results showed a significantly greater number of viable SCs from Dapulian pigs compared to that from Landrace pigs at 72–120 h of culture (<i>p</i> &lt; .05). The mRNA expression of <i>MYOD</i>, <i>MYF5</i> and <i>MYOG</i> in SCs from Dapulian pigs was higher (<i>p</i> &lt; .05) compared with Landrace pigs. Whereas the mRNA levels of <i>MSTN, MTOR</i>, <i>S6K</i>, <i>EIF4E</i> and <i>4EBP1</i> were significantly lower in SCs from Dapulian than those from Landrace (<i>p</i> &lt; .05). Protein levels of MSTN, S6K, MTOR and EIF4E were consistent with corresponding mRNA expression. In summary, these findings indicated that SCs isolated from the two breeds exhibit different proliferative capacities, and the proliferative potential of SCs from Dapulian pigs was greater than those from Landrace pigs.HighlightsThere were significant differences in the development of skeletal muscle, myofibre number and myofibre size between Chinese indigenous pig breed Dapulian and commercial pig breed Landrace.The proliferative capacity of satellite cells (SCs) from Dapulian pigs was greater than that from Landrace pigs.The expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace was different.
 There were significant differences in the development of skeletal muscle, myofibre number and myofibre size between Chinese indigenous pig breed Dapulian and commercial pig breed Landrace. The proliferative capacity of satellite cells (SCs) from Dapulian pigs was greater than that from Landrace pigs. The expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace was different.
DOI: 10.6084/m9.figshare.12412616.v1
title: Differentiation proliferative capacity of skeletal muscle satellite cells from Dapulian and Landrace pigs

description: Previously, we found there were significant differences in the development of skeletal muscle, myofiber characteristics between Chinese pig breed Dapulian and Landrace. Furthermore, the development of skeletal muscle is related to the proliferation of satellite cells (SCs). Thus, our aim was to compare the differences of proliferative abilities and expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace in this study. We isolated skeletal muscle SCs with collagenase digestion from the longissimus dorsi muscles of 1-day-old male Dapulian and Landrace piglets. After successful culture of SCs <i>in vitro</i>, proliferative capacity was estimated at different time points. Meanwhile, the expression of key genes related to SCs proliferation was detected by qRT-PCR and western blotting. Proliferation results showed a significantly greater number of viable SCs from Dapulian pigs compared to that from Landrace pigs at 72–120 h of culture (<i>p</i> &lt; .05). The mRNA expression of <i>MYOD</i>, <i>MYF5</i> and <i>MYOG</i> in SCs from Dapulian pigs was higher (<i>p</i> &lt; .05) compared with Landrace pigs. Whereas the mRNA levels of <i>MSTN, MTOR</i>, <i>S6K</i>, <i>EIF4E</i> and <i>4EBP1</i> were significantly lower in SCs from Dapulian than those from Landrace (<i>p</i> &lt; .05). Protein levels of MSTN, S6K, MTOR and EIF4E were consistent with corresponding mRNA expression. In summary, these findings indicated that SCs isolated from the two breeds exhibit different proliferative capacities, and the proliferative potential of SCs from Dapulian pigs was greater than those from Landrace pigs.HighlightsThere were significant differences in the development of skeletal muscle, myofibre number and myofibre size between Chinese indigenous pig breed Dapulian and commercial pig breed Landrace.The proliferative capacity of satellite cells (SCs) from Dapulian pigs was greater than that from Landrace pigs.The expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace was different.
 There were significant differences in the development of skeletal muscle, myofibre number and myofibre size between Chinese indigenous pig breed Dapulian and commercial pig breed Landrace. The proliferative capacity of satellite cells (SCs) from Dapulian pigs was greater than that from Landrace pigs. The expression of key genes related to proliferation between the SCs isolated from Dapulian and Landrace was different.
DOI: 10.6084/m9.figshare.14509753.v1
title: Additional file 1 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 1: Table S1. The co-expression result of autophagy-related lncRNAs and autophagy genes.
DOI: 10.6084/m9.figshare.14509756
title: Additional file 2 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 2: Table S2. The 39 strong prognostic autophagy-related lncRNAs were identified by univariate Cox regression analysis and product-limit method.
DOI: 10.6084/m9.figshare.14509756.v1
title: Additional file 2 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 2: Table S2. The 39 strong prognostic autophagy-related lncRNAs were identified by univariate Cox regression analysis and product-limit method.
DOI: 10.6084/m9.figshare.14509759
title: Additional file 3 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 3: Table S3. The 3580 genes have co-expression with 7 prognostic autophagy-related lncRNAs.
DOI: 10.6084/m9.figshare.14509753
title: Additional file 1 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 1: Table S1. The co-expression result of autophagy-related lncRNAs and autophagy genes.
DOI: 10.6084/m9.figshare.14509759.v1
title: Additional file 3 of The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma

description: Additional file 3: Table S3. The 3580 genes have co-expression with 7 prognostic autophagy-related lncRNAs.
DOI: 10.5281/zenodo.10672828
title: IODP Expedition 393 P-wave velocity logger (whole round)

description: P-wave velocity data were measured on whole-round sections on the Whole-Round Multisensor Logger (WRMSL) using pairs of piezoelectric transducers mounted on a caliper system. Measurements may be affected by degassing of pore fluid and microfracturing during core recovery. Report includes P-wave velocity in x-y plane and distance and traveltime between transducers.
DOI: 10.5281/zenodo.10672829
title: IODP Expedition 393 P-wave velocity logger (whole round)

description: P-wave velocity data were measured on whole-round sections on the Whole-Round Multisensor Logger (WRMSL) using pairs of piezoelectric transducers mounted on a caliper system. Measurements may be affected by degassing of pore fluid and microfracturing during core recovery. Report includes P-wave velocity in x-y plane and distance and traveltime between transducers.
DOI: 10.6084/m9.figshare.5596894
title: Variation in trophic cascade strength is triggered by top-down process in an ant-wasp-fig system

description: R code and Original data for:<b>Figure
2:</b> Number of
wasps from branches with weaver ants or without ants in the cool-dry (A),
hot-dry (B), and rainy (C) seasons. Species composition is shown on the top of bar
plot for each season, left pie (with ants), right pie (ants excluded). Syconia
in the cool-dry season in ant exclusion treatments were all aborted. Linear
mixed-effects models were fitted, with the number of fig wasps as the response
variable, with treatment (trees with or without <i>Oecophylla smaragdina</i> ) as the fixed factor, tree as a random
factor. * (<i>P</i> &lt; 0.05), ** (<i>P </i>&lt; 0.01), *** (<i>P </i>&lt;
0.001), NS = not significant. CF = <i>Ceratosolen fusciceps</i>;
SM = <i>Sycophaga</i><i> mayri</i>; ST = <i>S. testacea</i>; SA = <i>S.
agraensis</i>; AS = <i>Apocrypta </i>sp.; AW = <i>A. westwoodi</i>. Columns and bars
show mean ± SD. # represent pollinating fig wasp. Numbers under the pie
represent replications of syconium sampled.<b>Figure
3: </b>Number of seed from branches with weaver ants or
ants excluded in cool-dry, hot-dry, and rainy seasons. * (<i>P</i> &lt; 0.05), *** (<i>P </i>&lt;
0.001). Numbers in the box represent replications of syconium sampled.<b></b><b>Figure 4:</b> Mean (±SD) interaction strength (A) of
weaver ant, <i>Oecophyla smaragdina</i>, on
the gall making fig wasp, <i>Sycophagus</i><i> mayri</i>,
and the strength of the trophic cascade (B) in different seasons. * (<i>P</i> &lt; 0.05), *** (<i>P </i>&lt; 0.001).<b> </b>Numbers
in the brackets represent replications of with ants/ant exclusion branchlets
pairs.<b>Figure 5: </b>Box plot of the number of weaver ant nests (A),
number of weaver ants foraging in fig-bearing branchlets (B), foundress number (C), and oviposition
scars of non-pollinating fig wasps (D) in the fruits of <i>Ficus racemosa </i>after receptive stage of <i>Ficus racemosa </i>in different seasons. Different letters represent
significant differences between each season, pairwise comparisons
conducted using Tukey and Kramer test. Each circle represents a data
point.







<b>Figure 6: </b>Number (mean ± SD) of weaver ants, <i>Oecophyla smaragdina </i>(A), pollinating
fig wasp activity, <i>Ceratosolen fusciceps </i>(B), and gall making fig wasp, <i>Sycophagus</i> <i>mayri </i>activity (C) from 6:00
to 20:00 in different seasons. Symbols represent means and drop lines show the
standard deviation. Different letters represent significant differences between
each season, significance derived using nonparametric rank-based analysis of
longitudinal data with ANOVA-type statistics (ATS).<br>
DOI: 10.6084/m9.figshare.24995556
title: Additional file 1 of Identification of sulfur metabolism-related gene signature in osteoarthritis and TM9SF2’s sustenance effect on M2 macrophages' phagocytic activity

description: Additional file 1. Table 1. Gene lists for analysis.
DOI: 10.6084/m9.figshare.24995556.v1
title: Additional file 1 of Identification of sulfur metabolism-related gene signature in osteoarthritis and TM9SF2’s sustenance effect on M2 macrophages' phagocytic activity

description: Additional file 1. Table 1. Gene lists for analysis.
DOI: 10.5281/zenodo.10672826
title: IODP Expedition 393 P-wave velocity caliper (section/discrete)

description: P-wave velocity data were measured on undisturbed section halves (JRSO-defined x-axis) and/or discrete cube and cylinder samples (x, y, or z-axis) using pairs of piezoelectric transducers mounted on a caliper system. Report includes P-wave velocity in x, y, and/or z-direction, caliper separation, traveltime between transucers, and first arrival picks.
DOI: 10.5281/zenodo.10672827
title: IODP Expedition 393 P-wave velocity caliper (section/discrete)

description: P-wave velocity data were measured on undisturbed section halves (JRSO-defined x-axis) and/or discrete cube and cylinder samples (x, y, or z-axis) using pairs of piezoelectric transducers mounted on a caliper system. Report includes P-wave velocity in x, y, and/or z-direction, caliper separation, traveltime between transucers, and first arrival picks.
DOI: 10.6084/m9.figshare.16606932
title: Additional file 4 of Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice

description: Additional file 3. Microbiome OTU
DOI: 10.6084/m9.figshare.12936974
title: Virtual screening of approved clinic drugs with main protease (3CL<sup>pro</sup>) reveals potential inhibitory effects on SARS-CoV-2

description: 3CL<sup>pro</sup> is the main protease of the novel coronavirus (SARS-CoV-2) responsible for their intracellular duplication. Based on virtual screening technology and molecular dynamics simulation, we found 23 approved clinical drugs such as Viomycin, Capastat, Carfilzomib and Saquinavir, which showed high affinity with the 3CL<sup>pro</sup> active sites. These findings showed that there were potential drugs that inhibit SARS-Cov-2's 3CL<sup>pro</sup> in the current clinical drug library, and these drugs can be further tested or chemically modified for the treatment of COVID-19. Communicated by Ramaswamy H. Sarma