cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10642319
title: IODP Expedition 390C Thin section images

description: Hard rock and sediment thin section images were acquired using either the JRSO-developed Petrographic Image Capture and Archival Tool (PICAT) imager or (rarely) an upright microscope and a digital camera. Sample images are acquired in unpolarized, polarized, and/or cross-polarized light. Image files are presented compressed by hole.
DOI: 10.6084/m9.figshare.17982649
title: Additional file 1 of Construction and validation of a prognostic nomogram for predicting the survival of HIV/AIDS adults who received antiretroviral therapy: a cohort between 2003 and 2019 in Nanjing

description: Additional file 1: Supplementary data. Raw data of HIV/AIDS patients used and analyzed in current study. Note: Variable names and values are described as follows. Infection route (1 = Homosexual transmission, 2 = Heterosexual transmission, 3 = Other transmission); Gender (1 = Male, 2 = Female); Marital status (1 = Unmarried, 2 = Married); Art = time of initiating antiretroviral therapy; TB = tuberculosis (0 = No, 1 = Yes); Continuous diarrhea (0 = No, 1 = Yes); Continuous or intermittent fever (0 = No, 1 = Yes); Shingles (0 = No, 1 = Yes); WHO clinical stage (1 = stage I or II, 2 = stage III, 3 = stage IV); ALT = alanine aminotransferase; AST = aspartate aminotransferase; BMI = body mass index; CD4 = CD4 cell count; WBC = white blood cell; PLT = blood platelet; HB = hemoglobin; CR = creatinine; TG = triglyceride; TC = total cholesterol; FBG = fasting blood glucose; TBIL = total bilirubin; HBV = Hepatitis B Virus (0 = Negative, 1 = Positive); HCV = Hepatitis C Virus (0 = Negative, 1 = Positive); Status = survival status at the last follow-up Status (0 = alive, 1 = dead); End = observation end point.
DOI: 10.5281/zenodo.10642304
title: IODP Expedition 390C Salinity

description: Salinity was measured on interstitial water (IW) samples using an optical refractometer.
DOI: 10.5281/zenodo.10642305
title: IODP Expedition 390C Salinity

description: Salinity was measured on interstitial water (IW) samples using an optical refractometer.
DOI: 10.5281/zenodo.10642298
title: IODP Expedition 390C Portable X-ray fluorescence (p-XRF)

description: Energy-Dispersive X-Ray Fluorescence (ED-XRF) is a rapid, non-destructive technique for determining qualitative and quantitative changes in chemical composition. Aboard the JOIDES Resolution, pXRF is used for measuring points on section halves, rock pieces, and sometimes powders. Spots are typically irradiated at multiple conditions to excite and measure a wide range of elements. The peak intensity changes (we do not provide concentrations) are then used to help recognize and define major chemo-stratigraphic units without the need for destructive sampling.
DOI: 10.5281/zenodo.10642299
title: IODP Expedition 390C Portable X-ray fluorescence (p-XRF)

description: Energy-Dispersive X-Ray Fluorescence (ED-XRF) is a rapid, non-destructive technique for determining qualitative and quantitative changes in chemical composition. Aboard the JOIDES Resolution, pXRF is used for measuring points on section halves, rock pieces, and sometimes powders. Spots are typically irradiated at multiple conditions to excite and measure a wide range of elements. The peak intensity changes (we do not provide concentrations) are then used to help recognize and define major chemo-stratigraphic units without the need for destructive sampling.
DOI: 10.6084/m9.figshare.17982950.v1
title: Additional file 3 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 3: Table S3. The cor-DEGs-DEPs genes with the same or opposite trend.
DOI: 10.6084/m9.figshare.16935645.v1
title: Additional file 2 of Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation

description: Additional file 2: Table S1. KEGG pathway analysis in NAFLD after lifestyle intervention (q &lt; 0.05).
DOI: 10.6084/m9.figshare.17982956.v1
title: Additional file 4 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 4: Table S4. GO terms were highly enriched at both mRNA and protein levels.
DOI: 10.6084/m9.figshare.17982959
title: Additional file 5 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 5: Table S5. KEGG terms were highly enriched at both mRNA and protein levels.
DOI: 10.5281/zenodo.10642308
title: IODP Expedition 390C Section summary

description: Report includes data for individual core sections: coring/drilling depths and recovery, database identifiers for the whole section and section halves, and number of samples taken from the section before and after splitting.
DOI: 10.5281/zenodo.10642309
title: IODP Expedition 390C Section summary

description: Report includes data for individual core sections: coring/drilling depths and recovery, database identifiers for the whole section and section halves, and number of samples taken from the section before and after splitting.
DOI: 10.5281/zenodo.10642312
title: IODP Expedition 390C Magnetic remanence (SRM-longcore)

description: Magnetic remanence was measured on section halves (and rarely on whole-round sections) using a 2G Enterprises 760R cryogenic magnetometer, first as natural remanent magnetization (NRM) and then after demagnetization steps were performed on the samples by alternating field (AF) demagnetizer coils mounted in-line within the instrument.
DOI: 10.5281/zenodo.10642313
title: IODP Expedition 390C Magnetic remanence (SRM-longcore)

description: Magnetic remanence was measured on section halves (and rarely on whole-round sections) using a 2G Enterprises 760R cryogenic magnetometer, first as natural remanent magnetization (NRM) and then after demagnetization steps were performed on the samples by alternating field (AF) demagnetizer coils mounted in-line within the instrument.
DOI: 10.5281/zenodo.10642296
title: IODP Expedition 390C 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.10642297
title: IODP Expedition 390C 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.10642310
title: IODP Expedition 390C Magnetic remanence (spinner)

description: Magnetic remanence was measured on discrete samples by an Agico JR-6A spinner magnetometer, first as natural remanent magnetization (NRM) and then after demagnetization or remagnetization steps were performed on the samples (e.g., alternating field [AF] demagnetization, thermal demagnetization [TD], or isothermal remanent magnetization [IRM]).
DOI: 10.5281/zenodo.10642311
title: IODP Expedition 390C Magnetic remanence (spinner)

description: Magnetic remanence was measured on discrete samples by an Agico JR-6A spinner magnetometer, first as natural remanent magnetization (NRM) and then after demagnetization or remagnetization steps were performed on the samples (e.g., alternating field [AF] demagnetization, thermal demagnetization [TD], or isothermal remanent magnetization [IRM]).
DOI: 10.5517/ccdc.csd.cc2536s9
title: CCDC 1999090: Experimental Crystal Structure Determination

description: Related Article: Yisi Yang, Libo Li, Rui-Biao Lin, Yingxiang Ye, Zizhu Yao, Ling Yang, Fahui Xiang, Shimin Chen, Zhangjing Zhang, Shengchang Xiang, Banglin Chen |2021|Nature Chemistry|13|933|doi:10.1038/s41557-021-00740-z
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10642306
title: IODP Expedition 390C Sample report

description: Report includes detailed information about samples taken for testing: location/depth, type/form factor, test, request number, and database identifier.
DOI: 10.5281/zenodo.10642307
title: IODP Expedition 390C Sample report

description: Report includes detailed information about samples taken for testing: location/depth, type/form factor, test, request number, and database identifier.
DOI: 10.5281/zenodo.10642302
title: IODP Expedition 390C Color reflectance

description: Color reflectance data were measured on section halves using an integration sphere and a UV-VIS spectrophotometer mounted on the Section Half Multisensor Logger (SHMSL). Spectral counts are recorded in the range of 380 to 700 nm, covering the visible spectrum, and binned in ~2 nm bins. Spectral data are reduced from spectra and recorded in tristimulus XYZ values, CieLAB L*a*b* values, and other units.
DOI: 10.5281/zenodo.10642303
title: IODP Expedition 390C Color reflectance

description: Color reflectance data were measured on section halves using an integration sphere and a UV-VIS spectrophotometer mounted on the Section Half Multisensor Logger (SHMSL). Spectral counts are recorded in the range of 380 to 700 nm, covering the visible spectrum, and binned in ~2 nm bins. Spectral data are reduced from spectra and recorded in tristimulus XYZ values, CieLAB L*a*b* values, and other units.
DOI: 10.6084/m9.figshare.21498627
title: Patterns, drivers, and implications of post-fire delayed tree mortality in temperate conifer forests of the western US

description: Dataset includes the classified post-fire delayed tree mortality maps, the supporting imagery classification accuracy assessment data, supporting analysis databases and R code used for data summary, analysis, and figure generation.
DOI: 10.6084/m9.figshare.17982757
title: Additional file 2 of MiR-30c-5p loss-induced PELI1 accumulation regulates cell proliferation and migration via activating PI3K/AKT pathway in papillary thyroid carcinoma

description: Additional file 2: The co-expressed genes that were associated with PI3K-AKT pathway.
DOI: 10.6084/m9.figshare.17982751.v1
title: Additional file 1 of MiR-30c-5p loss-induced PELI1 accumulation regulates cell proliferation and migration via activating PI3K/AKT pathway in papillary thyroid carcinoma

description: Additional file 1: Genes derived from TCGA THCA databases, whose pearson correlation coefficient value with PELI1 are &gt;0.5.
DOI: 10.5281/zenodo.10642300
title: IODP Expedition 390C 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.10642301
title: IODP Expedition 390C 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.10642292
title: IODP Expedition 390C Laser height profile (section half)

description: Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.
DOI: 10.5281/zenodo.10642293
title: IODP Expedition 390C Laser height profile (section half)

description: Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.
DOI: 10.6084/m9.figshare.6974093
title: SNP data from Neurospora intermedia

description: This dataset contains a VCF file with SNPs from 21 <i>Neurospora intermedia</i> and 5 <i>N. metzenbergii</i> strains mapped to the genome assembly of <i>N. intermedia</i> strain 8807.<br>SNPs are generated from raw paired-end reads which have been deposited to the Sequence Read Archive 
(SRA) in BioProjects PRJNA486257 
(http://www.ncbi.nlm.nih.gov/bioproject/486257).<br>See Svedberg et al., (2018) "Convergent evolution of complex 
genomic rearrangements in two fungal meiotic drive elements" for further
 information: https://www.nature.com/articles/s41467-018-06562-x (DOI:10.1038/s41467-018-06562-x)Supplementary Table 11 contains Illumina sequencing statistics.<br><br>Full list of strains: 10411, 1785, 1786, 1787, 1795, 1832, 1938, 2316, 2365, 3194, 5119, 5124, 6249, 6263, 6595, 6795, 7402, 7426, 7427, 7429, 8761, 8767, 8769, 8793, 8853, P4149<br><br>All strains are referred to by their ID numbers at the Fungal Genetics Stock Center (www.fgsc.net), where they also can be ordered.<br>The reference genome of strain 8807 was released with the paper: <br>
 Sun et al. (2017). Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma. Nature Communications <i>8</i>, 1140. (https://www.nature.com/articles/s41467-017-01317-6)It can be downloaded here:<br>Sun,
 Yu; Svedberg, Jesper; Hiltunen, Markus; Corcoran, Pádraic; Johannesson,
 Hanna (2017): High-quality Neurospora tetrasperma genome assemblies. 
figshare. Dataset.https://figshare.com/articles/High-quality_Neurospora_tetrasperma_genome_assemblies/5327515<br>
DOI: 10.6084/m9.figshare.17982947.v1
title: Additional file 2 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 2: Table S2. The differentially expressed proteins (DEPs) were expressed between the model and control groups.
DOI: 10.6084/m9.figshare.17982941
title: Additional file 1 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 1: Table S1. The differentially expressed genes (DEGs) were expressed between the model and control groups.
DOI: 10.6084/m9.figshare.17982941.v1
title: Additional file 1 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 1: Table S1. The differentially expressed genes (DEGs) were expressed between the model and control groups.
DOI: 10.6084/m9.figshare.7498403
title: Average PSD for different samples

description: The PSD distribution of four samples is listed.
DOI: 10.6084/m9.figshare.17982950
title: Additional file 3 of Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

description: Additional file 3: Table S3. The cor-DEGs-DEPs genes with the same or opposite trend.
DOI: 10.6084/m9.figshare.6449843
title: Stereotactic body radiation therapy (SBRT) improves local control and overall survival compared to conventionally fractionated radiation for stage I non-small cell lung cancer (NSCLC)

description: <b>Background:</b> Stereotactic body radiotherapy (SBRT) has been adopted as the standard of care for inoperable early-stage non-small cell lung cancer (NSCLC), with local control rates consistently &gt;90%. However, data directly comparing the outcomes of SBRT with those of conventionally fractionated radiotherapy (CONV) is lacking. <b>Material and methods:</b> Between 1990 and 2013, 497 patients (525 lesions) with early-stage NSCLC (T1-T2N0M0) were treated with CONV (<i>n</i> = 127) or SBRT (<i>n</i> = 398). In this retrospective analysis, five endpoints were compared, with and without adjusting for clinical and dosimetric factors. Competing risks analysis was performed to estimate and compare the cumulative incidence of local failure (LF), nodal failure (NF), distant failure (DF) and disease progression. Overall survival (OS) was estimated by the Kaplan–Meier method and compared by the Cox regression model. Propensity score (PS) matched analysis was performed based on seven patient and clinical variables: age, gender, Karnofsky performance status (KPS), histology, T stage, biologically equivalent dose (BED), and history of smoking. <b>Results:</b> The median dose delivered for CONV was 75.6 Gy in 1.8–2.0 Gy fractions (range 60–90 Gy; median BED = 89.20 Gy) and for SBRT 48 Gy in four fractions (45–60 Gy in three to five fractions; median BED = 105.60 Gy). Median follow-up was 24.4 months, and 3-year LF rates were 34.1% with CONV and 13.6% with SBRT (<i>p</i> &lt; .001). Three-year OS rates were 38.9 and 53.1%, respectively (<i>p</i> = .018). PS matching showed a significant improvement of OS (<i>p</i> = .0497) for SBRT. T stage was the only variable correlating with all five endpoints. <b>Conclusion:</b> SBRT compared to CONV is associated with improved LF rates and OS. Our data supports the continued use and expansion of SBRT as the standard of care treatment for inoperable early-stage NSCLC.
DOI: 10.6084/m9.figshare.7498403.v1
title: Average PSD for different samples

description: The PSD distribution of four samples is listed.
DOI: 10.6084/m9.figshare.24278927
title: Matrix density regulates adipocyte phenotype

description: Alterations of the extracellular matrix contribute to adipose tissue dysfunction in metabolic disease. We studied the role of matrix density in regulating human adipocyte phenotype in a tunable hydrogel culture system. Lipid accumulation was maximal in intermediate hydrogel density of 5 weight %, relative to 3% and 10%. Adipogenesis and lipid and oxidative metabolic gene pathways were enriched in adipocytes in 5% relative to 3% hydrogels, while fibrotic gene pathways were enriched in 3% hydrogels. These data demonstrate that the intermediate density matrix promotes a more adipogenic, less fibrotic adipocyte phenotype geared towards increased lipid and aerobic metabolism. These observations contribute to a growing literature describing the role of matrix density in regulating adipose tissue function.
DOI: 10.6084/m9.figshare.24278927.v1
title: Matrix density regulates adipocyte phenotype

description: Alterations of the extracellular matrix contribute to adipose tissue dysfunction in metabolic disease. We studied the role of matrix density in regulating human adipocyte phenotype in a tunable hydrogel culture system. Lipid accumulation was maximal in intermediate hydrogel density of 5 weight %, relative to 3% and 10%. Adipogenesis and lipid and oxidative metabolic gene pathways were enriched in adipocytes in 5% relative to 3% hydrogels, while fibrotic gene pathways were enriched in 3% hydrogels. These data demonstrate that the intermediate density matrix promotes a more adipogenic, less fibrotic adipocyte phenotype geared towards increased lipid and aerobic metabolism. These observations contribute to a growing literature describing the role of matrix density in regulating adipose tissue function.
DOI: 10.6084/m9.figshare.16935570.v1
title: Additional file 1 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 1: Table S1. Univariate Cox regression analysis of rhomboid family genes in cancers from TCGA database.
DOI: 10.6084/m9.figshare.6449843.v1
title: Stereotactic body radiation therapy (SBRT) improves local control and overall survival compared to conventionally fractionated radiation for stage I non-small cell lung cancer (NSCLC)

description: <b>Background:</b> Stereotactic body radiotherapy (SBRT) has been adopted as the standard of care for inoperable early-stage non-small cell lung cancer (NSCLC), with local control rates consistently &gt;90%. However, data directly comparing the outcomes of SBRT with those of conventionally fractionated radiotherapy (CONV) is lacking. <b>Material and methods:</b> Between 1990 and 2013, 497 patients (525 lesions) with early-stage NSCLC (T1-T2N0M0) were treated with CONV (<i>n</i> = 127) or SBRT (<i>n</i> = 398). In this retrospective analysis, five endpoints were compared, with and without adjusting for clinical and dosimetric factors. Competing risks analysis was performed to estimate and compare the cumulative incidence of local failure (LF), nodal failure (NF), distant failure (DF) and disease progression. Overall survival (OS) was estimated by the Kaplan–Meier method and compared by the Cox regression model. Propensity score (PS) matched analysis was performed based on seven patient and clinical variables: age, gender, Karnofsky performance status (KPS), histology, T stage, biologically equivalent dose (BED), and history of smoking. <b>Results:</b> The median dose delivered for CONV was 75.6 Gy in 1.8–2.0 Gy fractions (range 60–90 Gy; median BED = 89.20 Gy) and for SBRT 48 Gy in four fractions (45–60 Gy in three to five fractions; median BED = 105.60 Gy). Median follow-up was 24.4 months, and 3-year LF rates were 34.1% with CONV and 13.6% with SBRT (<i>p</i> &lt; .001). Three-year OS rates were 38.9 and 53.1%, respectively (<i>p</i> = .018). PS matching showed a significant improvement of OS (<i>p</i> = .0497) for SBRT. T stage was the only variable correlating with all five endpoints. <b>Conclusion:</b> SBRT compared to CONV is associated with improved LF rates and OS. Our data supports the continued use and expansion of SBRT as the standard of care treatment for inoperable early-stage NSCLC.
DOI: 10.6084/m9.figshare.16935645
title: Additional file 2 of Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation

description: Additional file 2: Table S1. KEGG pathway analysis in NAFLD after lifestyle intervention (q &lt; 0.05).
DOI: 10.5281/zenodo.10651030
title: Dataset for doi: https://doi.org/10.1016/j.ajcnut.2024.01.012
title: Dietary patterns and their associations with sociodemographic and lifestyle factors in adult survivors of childhood cancer: a cross sectional study

description: Dataset for manuscript tables and figures.
DOI: 10.5281/zenodo.10651031
title: Dataset for doi: https://doi.org/10.1016/j.ajcnut.2024.01.012
title: Dietary patterns and their associations with sociodemographic and lifestyle factors in adult survivors of childhood cancer: a cross sectional study

description: Dataset for manuscript tables and figures.
DOI: 10.6084/m9.figshare.16935585
title: Additional file 6 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 6: Table S2. Correlation between RHBDF2 level and different modules in WGCNA.
DOI: 10.6084/m9.figshare.16935585.v1
title: Additional file 6 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 6: Table S2. Correlation between RHBDF2 level and different modules in WGCNA.
DOI: 10.6084/m9.figshare.16935564
title: Additional file 12 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 12: Table S4. Significant enrichment pathways and functions both in WGCNA and GSEA.
DOI: 10.6084/m9.figshare.16935564.v1
title: Additional file 12 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 12: Table S4. Significant enrichment pathways and functions both in WGCNA and GSEA.
DOI: 10.6084/m9.figshare.16935588.v1
title: Additional file 7 of RHBDF2 gene functions are correlated to facilitated renal clear cell carcinoma progression

description: Additional file 7: Table S3. Hub genes of red, green and orange modules in WGCNA.