cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6013907
title: RAS-related GTPases <i>DIRAS1</i> and <i>DIRAS2</i> induce autophagic cancer cell death and are required for autophagy in murine ovarian cancer cells

description: Among the 3 GTPases in the DIRAS family, <i>DIRAS3/ARHI</i> is the best characterized. <i>DIRAS3</i> is an imprinted tumor suppressor gene that encodes a 26-kDa GTPase that shares 60% homology to RAS and RAP. DIRAS3 is downregulated in many tumor types, including ovarian cancer, where re-expression inhibits cancer cell growth, reduces motility, promotes tumor dormancy and induces macroautophagy/autophagy. Previously, we demonstrated that DIRAS3 is required for autophagy in human cells. <i>Diras3</i> has been lost from the mouse genome during evolutionary re-arrangement, but murine cells can still undergo autophagy. We have tested whether DIRAS1 and DIRAS2, which are homologs found in both human and murine cells, could serve as surrogates to DIRAS3 in the murine genome affecting autophagy and cancer cell growth. Similar to DIRAS3, these 2 GTPases share 40–50% homology to RAS and RAP, but differ from DIRAS3 primarily in the lengths of their N-terminal extensions. We found that DIRAS1 and DIRAS2 are downregulated in ovarian cancer and are associated with decreased disease-free and overall survival. Re-expression of these genes suppressed growth of human and murine ovarian cancer cells by inducing autophagy-mediated cell death. Mechanistically, DIRAS1 and DIRAS2 induce and regulate autophagy by inhibition of the AKT1-MTOR and RAS-MAPK signaling pathways and modulating nuclear localization of the autophagy-related transcription factors FOXO3/FOXO3A and TFEB. Taken together, these data suggest that DIRAS1 and DIRAS2 likely serve as surrogates in the murine genome for DIRAS3, and may function as a backup system to fine-tune autophagy in humans.
DOI: 10.6073/pasta/aa2b187d45a67cf4cfa82c32a55a5373
title: Luquillo Experimental Forest atmospheric and high and mid elevation weather data.

description: The data archive is here:https://doi.org/10.2737/RDS-2022-0050 please use this DOI when citing this dataset.
 This data publication contains daily means from laser ceilometer data from Sabana, ozone data from Bisley, and meteorological data collected from Bisley and the mountain top station of East Peak, all located on the Luquillo Experimental Forest (El Yunque National Forest) in Puerto Rico. Atmospheric data include: mean cloud observed frequency, mean lowest height cloud (cloud base), mean daytime mixing layer height observed frequency, mean lowest mixing layer height from hours 7am and 7pm only, and mean daytime mixing layer height collected from February 2013 through April 2021. Also included is mean ozone amount collected from April 2008 through early April 2021. The cloud and mixing layer frequency and low values were calculated using the Automated Surface Observing System (ASOS) method employed at airports in the area. Weather data include high elevation East Peak mean northeast wind speed (wind rose quartiles 45° to 90°), mean southeast wind speed (wind rose quartiles 90° to 135°), and mean total wind speed measured from October 2009 through 2020 (and a few months in 2021). Additional weather data collected from January 2008 through mid October 2020 include mid elevation Bisley mean precipitation, mean relative humidity, and mean temperature.
 Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
DOI: 10.6084/m9.figshare.14926897.v1
title: Additional file 1 of The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis

description: Additional file 1.
DOI: 10.6073/pasta/06c21b4b9e33e53fa76fe459273913c4
title: Plant species composition for sensor network array, 2017 - ongoing.

description: Above-ground plant species cover was recorded for vegetation plots
 in the sensor network, starting in 2017. Cover was measured annually
 at peak biomass using a 100 point-intercept method.
DOI: 10.6084/m9.figshare.20694188
title: Two ophiolite belts in the East Kunlun Orogenic Belt record evolution from the Proto-Tethys to Paleo-Tethys Oceans

description: As relics of oceanic lithosphere, ophiolites exposed in the East Kunlun region are crucial for deciphering the evolution from the Proto-Tethys to the Paleo-Tethys. Two ophiolite belts have been recognized in the East Kunlun Orogenic Belt: the northern Heishan-Dagele-Qingshuiquan Ophiolite Belt and the southern Muzitag-A’nyemaqen Ophiolite Belt. Most basaltic rocks in the northern ophiolite belt show apparent geochemical features of enriched mid-ocean ridge basalts, with some of suprasubduction zone-type affinity, and probably formed in arc to back-arc settings with ages of 537–406 Ma. Cumulates (wehrlites) and arc-related volcanics in these ophiolite complexes also display a subduction-related signature. However, most basalts in the southern ophiolite belt exhibit characteristics of mid-ocean ridge basalts and plume-related basalts, which are unrelated to subduction zone. The anhydrous troctolite outcrops in the southern belt also support this viewpoint. Statistics of all the available age data for the southern ophiolites indicate two cycles of seafloor spreading or plume activity, which gave rise to two main epochs of magmatic activity at 535–450 Ma and 345–308 Ma, respectively. The northern ophiolite belt recorded the evolution of the Proto-Tethys Ocean from at least the Early Cambrian to the Late Silurian. Based on geochronological and geochemical comparisons, the southern ophiolite belt shows similarities with the ophiolites in the Longmucuo-Shuanghu suture of Qiangtang on the south, which record the closure of Proto-Tethys Ocean and the opening of the Paleo-Tethys Ocean. The spatial and temporal distribution of the two ophiolite belts in the East Kunlun Orogenic Belt reveals the long-lived evolution from the Proto-Tethys to Paleo-Tethys system.
DOI: 10.6084/m9.figshare.14927090.v1
title: Additional file 1 of MCM6 indicates adverse tumor features and poor outcomes and promotes G1/S cell cycle progression in neuroblastoma

description: Additional file 1: Table S1.
DOI: 10.6084/m9.figshare.14927090
title: Additional file 1 of MCM6 indicates adverse tumor features and poor outcomes and promotes G1/S cell cycle progression in neuroblastoma

description: Additional file 1: Table S1.
DOI: 10.6084/m9.figshare.19633800
title: Additional file 2 of Comprehensive evaluation of Chinese peanut mini-mini core collection and QTL mapping for aflatoxin resistance

description: Additional file 2: Table S1. Correlation analysis of three resistances. Table S2. Correlation analysis between three resistances and other traits. Table S3. The information of the 99 accessions which are derived into two sub-groups. Table S4. The distribution of SNPs and Indels. Table S5. The information of candidate genes.
DOI: 10.6084/m9.figshare.19633843
title: Additional file 1 of Transcriptomic profiling of pemphigus lesion infiltrating mononuclear cells reveals a distinct local immune microenvironment and novel lncRNA regulators

description: Additional file 1. Supplementary figures
DOI: 10.6084/m9.figshare.19633852
title: Additional file 4 of Transcriptomic profiling of pemphigus lesion infiltrating mononuclear cells reveals a distinct local immune microenvironment and novel lncRNA regulators

description: Additional file 4. Enrichment results of the brown module
DOI: 10.3886/icpsr06563
title: Physician Responses to Medicare Payment Reductions: Impacts on the Public and Private Sectors, 1988-1991
title: Archival Version

description: The purpose of this study was to investigate the effects on
physician behavior of decreases in Medicare payment rates for surgical
procedures. The study examined the volume of services provided, billed
charges, and the selection of diagnostic or therapeutic alternative
procedures, or clinically unrelated procedures, for Medicare and
privately-insured patients. Also studied were the proportion of
physician income derived from Medicare and the profitability of
procedures as they related to the volume of services provided. This
data collection comprises observations for 21 surgical procedure groups
in the specialty areas of general surgery, gastroenterology, orthopedic
surgery, ophthalmology, urology, gynecological surgery, thoracic
surgery, and cardiology, from up to 187 hospitals and for up to 15
quarters. Efforts were made to include high volume and expensive
procedures. Excluded were radiology, pathology, or other lab
procedures, and procedures that had experienced erratic changes in
volume due to changes in technology or changes in national standards.
Also included in this collection are hospital characteristics and
county-level data pertaining to number of hospital beds, per capita
income, licensed practical nurse and registered nurse wages, doctors
per 1000 population, and health maintenance organization enrollees per
1000 population.
description: Convenience sample representing 3.7 percent of the universe.
description: Datasets: 
DS0: Study-Level Files
DS1: Raw Data
DS2: Data in SAS Transport Format
description: All United States hospitals.
description: The SAS transport file (Part 2) was written using
the SAS XPORT engine.
DOI: 10.3886/icpsr06563.v1
title: Physician Responses to Medicare Payment Reductions: Impacts on the Public and Private Sectors, 1988-1991
title: Version 1

description: The purpose of this study was to investigate the effects on physician behavior of decreases in Medicare payment rates for surgical procedures. The study examined the volume of services provided, billed charges, and the selection of diagnostic or therapeutic alternative procedures, or clinically unrelated procedures, for Medicare and privately-insured patients. Also studied were the proportion of physician income derived from Medicare and the profitability of procedures as they related to the volume of services provided. This data collection comprises observations for 21 surgical procedure groups in the specialty areas of general surgery, gastroenterology, orthopedic surgery, ophthalmology, urology, gynecological surgery, thoracic surgery, and cardiology, from up to 187 hospitals and for up to 15 quarters. Efforts were made to include high volume and expensive procedures. Excluded were radiology, pathology, or other lab procedures, and procedures that had experienced erratic changes in volume due to changes in technology or changes in national standards. Also included in this collection are hospital characteristics and county-level data pertaining to number of hospital beds, per capita income, licensed practical nurse and registered nurse wages, doctors per 1000 population, and health maintenance organization enrollees per 1000 population.
description: Datasets: 
 
 DS0: Study-Level Files 
 DS1: Raw Data 
 DS2: Data in SAS Transport Format
description: (1) The SAS transport file (Part 2) was written using the SAS XPORT engine.
description: All United States hospitals.
description: Convenience sample representing 3.7 percent of the universe.
DOI: 10.3886/icpsr06563.v2
title: Physician Responses to Medicare Payment Reductions: Impacts on the Public and Private Sectors, 1988-1991
title: Version 2

description: The purpose of this study was to investigate the effects on
physician behavior of decreases in Medicare payment rates for surgical
procedures. The study examined the volume of services provided, billed
charges, and the selection of diagnostic or therapeutic alternative
procedures, or clinically unrelated procedures, for Medicare and
privately-insured patients. Also studied were the proportion of
physician income derived from Medicare and the profitability of
procedures as they related to the volume of services provided. This
data collection comprises observations for 21 surgical procedure groups
in the specialty areas of general surgery, gastroenterology, orthopedic
surgery, ophthalmology, urology, gynecological surgery, thoracic
surgery, and cardiology, from up to 187 hospitals and for up to 15
quarters. Efforts were made to include high volume and expensive
procedures. Excluded were radiology, pathology, or other lab
procedures, and procedures that had experienced erratic changes in
volume due to changes in technology or changes in national standards.
Also included in this collection are hospital characteristics and
county-level data pertaining to number of hospital beds, per capita
income, licensed practical nurse and registered nurse wages, doctors
per 1000 population, and health maintenance organization enrollees per
1000 population.
description: Convenience sample representing 3.7 percent of the universe.
description: Datasets: 
DS0: Study-Level Files
DS1: Raw Data
DS2: Data in SAS Transport Format
description: All United States hospitals.
description: The SAS transport file (Part 2) was written using
the SAS XPORT engine.
DOI: 10.6084/m9.figshare.19633854.v1
title: Additional file 4 of Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC)

description: Additional file 4: Table S3. Differentially expressed genes induced by Lsm12 knockdown.
DOI: 10.6073/pasta/bec4409fc5222822e43c48ed0cbc9514
title: Northeastern Puerto Rico open-canopy and under-canopy temperature and moisture data on an elevational gradient

description: The data archive is here:https://doi.org/10.2737/RDS-2022-0051 please use this DOI when citing this dataset.
 This data publication contains monthly means of temperature and moisture data collected from August 2006 through September 2021 from 22 locations along an elevational gradient, from 0 to 1045 meters, in Northeastern Puerto Rico. The higher elevational data are in the Luquillo Experimental Forest (El Yunque National Forest). Five kinds of data are included: air temperature and precipitation measured in the open (not under canopy) at 20 locations, air temperature and soil temperature both measured under the canopy at all 22 locations, and soil moisture under the canopy at 4 locations. Two locations have 3 sites each, measured in different canopy types at the same location. The other 20 locations have one site each, making a total of 26 measurement sites. Data are provided as monthly averages at each site.
 Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
DOI: 10.6084/m9.figshare.19633848
title: Additional file 2 of Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC)

description: Additional file 2: Table S1. Differentially expressed genes identified in the animal model of OSCC tumorigenesis.
DOI: 10.6084/m9.figshare.9160088.v1
title: <i>De novo</i> and comparative transcriptome analysis of genetic male sterile and fertile lines in radish <i>(</i><i>Raphanus sativus)</i>

description: In radish, male sterility studies mainly focus on cytoplasmic male sterility (CMS) while genetic male sterility (GMS) has received less attention. To explore global gene expression profiles and identify genes associated with GMS, we performed de novo and comparative transcriptome analyses of flower buds from a GMS line and maintainer (fertile) line. Our study produced approximately 700 million paired-end reads, which were assembled into 115,284 unigenes with an average length of 1,196 bp and N50 of 1,729 bp. These unigenes were extensively annotated, with nearly 60% of them having homologs in the databases and 50% assigned with Gene Ontology (GO) terms. A total of 3,390 differentially expressed genes (DEGs) between the GMS line and the maintainer line were identified, with 2,645 down-regulated and 745 up-regulated in the GMS line. GO analyses showed biological processes related to plant reproductive development such as gametophyte development, pollen wall assembly, pollen development and pollen exine formation, as well as those related to cell wall development such as cell wall oganization and cell wall biogenesis, were significantly different in these two lines. The transcriptome assembly and comparative transcriptome analysis provides novel insights into the GMS in radishfacilitating the application of GMS in radish hybrid breeding. <b>Abbreviation:</b> 136S, the male sterile line in this article; 136F, the corresponding maintainer line(fertile); AGL, AGAMOUS-LIKE gene; CMS, cytoplasmic male sterility while; COG, Clusters of Orthologous Groups; DEGs, differentially expressed genes, FPKM, Fragments Per Kilobase of transcript per Million mapped reads; GMS, genetic male sterility; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes, NPGs, non-pollen genes
DOI: 10.6084/m9.figshare.7587335
title: Additional file 1: of Multi-omics integration reveals molecular networks and regulators of psoriasis

description: Table S1. Transcriptome, DNA methylome, and GWAS studies included in the study. Table S2. Knowledge-based artificial pathways from published GWAS studies and large-scale meta-profiling of diverse collections of gene expression data sets. Table S3. Differential coexpression modules in psoriasis. Table S4. Gene signatures in the psoriasis transcriptomic study. Table S5. MSEA results in GWAS. Table S6. MSEA results in EWAS. Table S7. Common Pathways between GWAS and EWAS. Table S8. GWAS/EWAS-unique supersets and key driver analysis. Table S9. Key driver analysis of Common supersets in psoriasis skin and blood networks. Table S10. In silico mining of the key driver genes using bioinformatics tools. Table S11. Gene expression perturbations of key driver subnetwork in lesional skin tissue in psoriasis patients. (ZIP 358 kb)
DOI: 10.6084/m9.figshare.7587335.v1
title: Additional file 1: of Multi-omics integration reveals molecular networks and regulators of psoriasis

description: Table S1. Transcriptome, DNA methylome, and GWAS studies included in the study. Table S2. Knowledge-based artificial pathways from published GWAS studies and large-scale meta-profiling of diverse collections of gene expression data sets. Table S3. Differential coexpression modules in psoriasis. Table S4. Gene signatures in the psoriasis transcriptomic study. Table S5. MSEA results in GWAS. Table S6. MSEA results in EWAS. Table S7. Common Pathways between GWAS and EWAS. Table S8. GWAS/EWAS-unique supersets and key driver analysis. Table S9. Key driver analysis of Common supersets in psoriasis skin and blood networks. Table S10. In silico mining of the key driver genes using bioinformatics tools. Table S11. Gene expression perturbations of key driver subnetwork in lesional skin tissue in psoriasis patients. (ZIP 358 kb)
DOI: 10.6084/m9.figshare.7587500
title: Additional file 2: of Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome

description: Detailed annotation of the retained 129 variants. ACMG standards were used for variant classification, and the OMIM database was used for priority analysis of the phenotype matching. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.19633848.v1
title: Additional file 2 of Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC)

description: Additional file 2: Table S1. Differentially expressed genes identified in the animal model of OSCC tumorigenesis.
DOI: 10.6084/m9.figshare.22791722.v1
title: Bioinformatics Identification and Validation of Aging‑Related Molecular Subtype and Prognostic Signature in Sarcoma

description: Aging could regulate many biological processes in malignancies by regulating cell senescence. Consensus cluster analysis was conducted to differentiate TCGA sarcoma cases. LASSO cox regression analysis was performed to construct an aging-related prognostic signature. We identified two categories of TCGA-sarcoma with significant difference in prognosis, immune infiltration and chemotherapy and targeted therapy. Moreover, an aging-related prognostic signature was constructed for sarcoma, which had a good performance in predicting the 3-year and 5-year overall survival of sarcoma patients. We also identified a lncRNA MALAT1/miR-508-3p/CCNA2 regulatory axis for sarcoma. This stratification could provide more evidence for estimating prognosis and immunotherapy of sarcoma.
DOI: 10.6084/m9.figshare.7587500.v1
title: Additional file 2: of Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome

description: Detailed annotation of the retained 129 variants. ACMG standards were used for variant classification, and the OMIM database was used for priority analysis of the phenotype matching. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.19633857.v1
title: Additional file 5 of Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC)

description: Additional file 5: Table S4. Alternative splicing of genes induced by Lsm12 knockdown.
DOI: 10.6084/m9.figshare.7587566.v1
title: Additional file 11: of Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium

description: Data S8. Characteristic transcription factor genes list between comparison groups. (XLS 46 kb)
DOI: 10.6084/m9.figshare.20170465
title: Evidence for selection on SARS-CoV-2 RNA translation revealed by the evolutionary dynamics of mutations in UTRs and CDSs

description: RNA translation is the rate-limiting step when cells synthesize proteins. Elevating translation efficiency (TE) is intuitively beneficial. Particularly, when viruses invade host cells, how to compete with endogenous RNAs for efficient translation is a major issue to be resolved. We collected millions of worldwide SARS-CoV-2 sequences during the past year and traced the dynamics of allele frequency of every mutation. We defined adaptive and deleterious mutations according to the rise and fall of their frequencies along time. For 5ʹUTR and synonymous mutations in SARS-CoV-2, the selection on TE is evident near start codons. Adaptive mutations generally decrease GC content while deleterious mutations increase GC content. This trend fades away with increasing distance to start codons. Mutations decreasing GC content near start codons would unravel the complex RNA structure and facilitate translation initiation, which are beneficial to SARS-CoV-2, and vice versa. During this evolutionary arms race between human and virus, SARS-CoV-2 tries to improve its <i>cis</i> elements to compete with host RNAs for rapid translation.
DOI: 10.6084/m9.figshare.7587470
title: Additional file 1: of Risk factors associated with mortality in neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) and clinical implications

description: Original data used for statistical analyses. (XLS 41 kb)