cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/53ab08e695503bfbbeaeee637835da0b
title: Fish Food on Floodplain Farm Fields 2019

description: In the winter and spring of 2018-2019, 5,000 acres of agricultural land in Yolo County, California was intentionally flooded. These “dry-side” rice fields, although on the former floodplain of the Sacramento River, are separated from the fish-bearing Sacramento River (the “wet-side”) by high flood levees. Today, levees cut off 95% of the Central Valley’s floodplains from river channels so that Central Valley aquatic ecosystems no longer recruit floodplain the food web resources needed to support robust aquatic food webs, create fish biomass and sustain abundant fish populations. In this experiment we asked whether floodplain food web resources “grown” in intentionally inundated “dry-side” agricultural fields could be exported back to the river via flood drainage infrastructure. If so, we were interested to know whether those resources could improve juvenile salmon foraging success and increase growth rates. In order to test these questions, we caged fish in the floodplain drainage canal, at the location where the floodplain drainage water entered the river and at locations both up- and downstream. We hypothesized that zooplankton abundance and fish growth rates would be elevated at the managed floodplain outfall location, relative to the upstream location. We measured water quality parameters, zooplankton species assemblage and abundance, and juvenile Chinook salmon growth rates with PIT tagged, hatchery-origin fish confined to enclosures at the study locations. The 5,000 acres of managed floodplain was drained over the coarse of 5 weeks in February and March, 2019 at a maximum rate of 1,000 cfs. The Sacramento River flow during the experiment ranged from 20,000-30,000 cfs. Fish growth rates at the floodplain outfall location were up to five times greater than growth rates upstream of the outfall and enclosure fish experienced growth rate benefits at least up to a mile downstream from the managed floodplain outfall. This study demonstrated a management practice that transfers floodplain food web benefits from managed floodplains without anadromous fish access, to the food-scarce Sacramento River ecosystem. Multiple districts across the Sacramento Valley maintain similar water infrastructure to what was used in this pilot action. If incorporated at large scale into water management practices, fish food production on “dry-side” agricultural fields and wildlife refuges could contribute substantial food resources to rearing and out-migrating juvenile salmon populations in the Sacramento River system.
DOI: 10.6073/pasta/4d933b4a4332185a003192e264e294bf
title: Jornada Basin LTER: Wireless substation at NPP G-IBPE site: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data is measured at 10cm, 20 cm, and 30 cm soil depths at the NPP G-IBPE substation located in center of 70m x 70m Jornada LTER NPP G-IBPE site. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured every 30 minutes. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.21062328.v1
title: Additional file 4 of Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues

description: Additional file 4. RNAseq adipose analysis file; DESeq2 analysis results.
DOI: 10.6084/m9.figshare.21062334
title: Additional file 6 of Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues

description: Additional file 6. RNAseq fibroblasts data file; Outliers removed and normalized counts.
DOI: 10.6084/m9.figshare.21062337
title: Additional file 7 of Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues

description: Additional file 7. RNAseq fibroblasts analysis file; DESeq2 analysis results.
DOI: 10.6084/m9.figshare.12673854
title: Additional file 4 of Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes

description: Additional file 4: Table S13. Phenotypic Variance by Decile Raw Data.
DOI: 10.6084/m9.figshare.21062325.v1
title: Additional file 3 of Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues

description: Additional file 3. RNAseq muscle data file; Outliers removed and normalized counts.
DOI: 10.6084/m9.figshare.21062340.v1
title: Additional file 8 of Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues

description: Additional file 8. Proteomics adipose peptide datafile; Normalized LFQ values.
DOI: 10.6084/m9.figshare.12673854.v1
title: Additional file 4 of Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes

description: Additional file 4: Table S13. Phenotypic Variance by Decile Raw Data.
DOI: 10.6084/m9.figshare.21062529
title: DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility

description: The results of associations between single nucleotide polymorphisms (SNPs) of genes in DNA repairing pathway and lung cancer (LC) risk are inconsistent. We applied allele, dominant and recessive models to explore the risk of researched variants to LC in total LC and subgroups by ethnicity or LC subtypes with a cutoff point of <i>p</i> &lt; 0.05. A total of 76,935 cases and 88,649 controls from 192 articles were included. Among the analyzed 40 variants from 20 genes, we found 9 statistically significant variants in overall populations by allele model, including five SNPs (rs1760944, rs9344, rs13181, rs1001581, and rs915927) increasing LC risk (odd ratios [ORs] = 1.10–1.71) and four SNPs (rs1042522, rs3213245, rs11615, and rs238406) decreasing the risk (ORs = 0.75–0.94). We identified rs1042522 and rs13181 as significant variants for LC in three models. Additionally, we identified differential significant SNPs in ethnic and subtype’s analysis with comparison to total population. There are five SNPs in DNA repairing pathway associated with increased LC risk and four others decreased LC risk. Besides, the risky SNPs in different ethnicities and various LC subtypes were partly different, and the contribution of different genotypes to risk alleles were various as well.
DOI: 10.6084/m9.figshare.12143877.v1
title: Additional file 2 of Characterisation of extraembryonic endoderm-like cells from mouse embryonic fibroblasts induced using chemicals alone

description: Additional file 2 : Table S1. Primers used for PCR/qPCR. Table S2. GO analysis of the top 10 upregulated CCs and MFs, and the top 10 downregulated CCs and MFs in ciXEN cells at passage 5 and passage 30 compared to those in MEFs. Table S3. Pathway analysis of the upregulated metabolic pathways in ciXEN cells at passage 5 compared to those in MEFs.
DOI: 10.6084/m9.figshare.20013979
title: The ORF7a protein of SARS-CoV-2 initiates autophagy and limits autophagosome-lysosome fusion via degradation of SNAP29 to promote virus replication

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is closely related to various cellular aspects associated with autophagy. However, how SARS-CoV-2 mediates the subversion of the macroautophagy/autophagy pathway remains largely unclear. In this study, we demonstrate that overexpression of the SARS-CoV-2 ORF7a protein activates LC3-II and leads to the accumulation of autophagosomes in multiple cell lines, while knockdown of the viral <i>ORF7a</i> gene via shRNAs targeting <i>ORF7a</i> sgRNA during SARS-CoV-2 infection decreased autophagy levels. Mechanistically, the ORF7a protein initiates autophagy via the AKT-MTOR-ULK1‐mediated pathway, but ORF7a limits the progression of autophagic flux by activating CASP3 (caspase 3) to cleave the SNAP29 protein at aspartic acid residue 30 (D30), ultimately impairing complete autophagy. Importantly, SARS-CoV-2 infection-induced accumulated autophagosomes promote progeny virus production, whereby ORF7a downregulates SNAP29, ultimately resulting in failure of autophagosome fusion with lysosomes to promote viral replication. Taken together, our study reveals a mechanism by which SARS-CoV-2 utilizes the autophagic machinery to facilitate its own propagation via ORF7a.<b>Abbreviations:</b>
3-MA: 3-methyladenine; ACE2: angiotensin converting enzyme 2; ACTB/β-actin: actin beta; ATG7: autophagy related 7; Baf A1: bafilomycin A<sub>1</sub>; BECN1: beclin 1; CASP3: caspase 3; COVID-19: coronavirus disease 2019; GFP: green fluorescent protein; hpi: hour post-infection; hpt: hour post-transfection; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MERS: Middle East respiratory syndrome; MTOR: mechanistic target of rapamycin kinase; ORF: open reading frame; PARP: poly(ADP-ribose) polymerase; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; shRNAs: short hairpin RNAs; siRNA: small interfering RNA; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TCID<sub>50</sub>: tissue culture infectious dose; TEM: transmission electron microscopy; TUBB, tubulin, beta; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.20013979.v1
title: The ORF7a protein of SARS-CoV-2 initiates autophagy and limits autophagosome-lysosome fusion via degradation of SNAP29 to promote virus replication

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is closely related to various cellular aspects associated with autophagy. However, how SARS-CoV-2 mediates the subversion of the macroautophagy/autophagy pathway remains largely unclear. In this study, we demonstrate that overexpression of the SARS-CoV-2 ORF7a protein activates LC3-II and leads to the accumulation of autophagosomes in multiple cell lines, while knockdown of the viral <i>ORF7a</i> gene via shRNAs targeting <i>ORF7a</i> sgRNA during SARS-CoV-2 infection decreased autophagy levels. Mechanistically, the ORF7a protein initiates autophagy via the AKT-MTOR-ULK1‐mediated pathway, but ORF7a limits the progression of autophagic flux by activating CASP3 (caspase 3) to cleave the SNAP29 protein at aspartic acid residue 30 (D30), ultimately impairing complete autophagy. Importantly, SARS-CoV-2 infection-induced accumulated autophagosomes promote progeny virus production, whereby ORF7a downregulates SNAP29, ultimately resulting in failure of autophagosome fusion with lysosomes to promote viral replication. Taken together, our study reveals a mechanism by which SARS-CoV-2 utilizes the autophagic machinery to facilitate its own propagation via ORF7a.<b>Abbreviations:</b>
3-MA: 3-methyladenine; ACE2: angiotensin converting enzyme 2; ACTB/β-actin: actin beta; ATG7: autophagy related 7; Baf A1: bafilomycin A<sub>1</sub>; BECN1: beclin 1; CASP3: caspase 3; COVID-19: coronavirus disease 2019; GFP: green fluorescent protein; hpi: hour post-infection; hpt: hour post-transfection; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MERS: Middle East respiratory syndrome; MTOR: mechanistic target of rapamycin kinase; ORF: open reading frame; PARP: poly(ADP-ribose) polymerase; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; shRNAs: short hairpin RNAs; siRNA: small interfering RNA; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TCID<sub>50</sub>: tissue culture infectious dose; TEM: transmission electron microscopy; TUBB, tubulin, beta; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.8479982
title: MOESM5 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 5: Table S7. Biological functions enriched in 597 up-regulated genes with decreased H3K4me2 levels in 701Ri-1-5.
DOI: 10.6084/m9.figshare.19608939
title: LncRNA growth arrest specific transcript 5 inhibits the growth of pituitary neuroendocrine tumors via miR-27a-5p/cylindromatosis axis

description: The long noncoding RNA growth arrest-specific transcript 5 (GAS5) has been reported to function as a suppressor in many cancers. However, the role and mechanism of lncRNA GAS5 in pituitary neuroendocrine tumors (PitNETs) remain unclear. Here, we found that lncRNA GAS5 and cylindromatosis (CYLD) expression was downregulated in invasive PitNET tissues and was negatively correlated with miR-27a-5p expression. LncRNA GAS5 overexpression inhibited proliferation of PitNETs cell line MMQ and GH3 cells and induced cell apoptosis, simultaneously, inhibited miR-27a-5p expression and increased CYLD expression. Moreover, miR-27a-5p mimic significantly decreased the luciferase activities of lncRNA GAS5 and CYLD luciferase reporter vector and downregulated CYLD expression, while miR-27a-5p inhibitor increased the expression of CYLD in MMQ and GH3 cells. Furthermore, RNA-immunoprecipitation assay revealed the direct binding between lncRNA GAS5 and miR-27a-5p. Additionally, miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on MMQ and GH3 cell proliferation. In vivo lncRNA GAS5 overexpression inhibited GH3 cell tumor growth, while miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on GH3 cell tumor growth. These results suggest that lncRNA GAS5 acts as an endogenous sponge by binding miR-27a-5p to increase the expression of its target gene CYLD, thereby inhibits PitNETs cell proliferation and tumor growth.
DOI: 10.6084/m9.figshare.19608939.v1
title: LncRNA growth arrest specific transcript 5 inhibits the growth of pituitary neuroendocrine tumors via miR-27a-5p/cylindromatosis axis

description: The long noncoding RNA growth arrest-specific transcript 5 (GAS5) has been reported to function as a suppressor in many cancers. However, the role and mechanism of lncRNA GAS5 in pituitary neuroendocrine tumors (PitNETs) remain unclear. Here, we found that lncRNA GAS5 and cylindromatosis (CYLD) expression was downregulated in invasive PitNET tissues and was negatively correlated with miR-27a-5p expression. LncRNA GAS5 overexpression inhibited proliferation of PitNETs cell line MMQ and GH3 cells and induced cell apoptosis, simultaneously, inhibited miR-27a-5p expression and increased CYLD expression. Moreover, miR-27a-5p mimic significantly decreased the luciferase activities of lncRNA GAS5 and CYLD luciferase reporter vector and downregulated CYLD expression, while miR-27a-5p inhibitor increased the expression of CYLD in MMQ and GH3 cells. Furthermore, RNA-immunoprecipitation assay revealed the direct binding between lncRNA GAS5 and miR-27a-5p. Additionally, miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on MMQ and GH3 cell proliferation. In vivo lncRNA GAS5 overexpression inhibited GH3 cell tumor growth, while miR-27a-5p mimic or silenced CYLD attenuated the effect of lncRNA GAS5 on GH3 cell tumor growth. These results suggest that lncRNA GAS5 acts as an endogenous sponge by binding miR-27a-5p to increase the expression of its target gene CYLD, thereby inhibits PitNETs cell proliferation and tumor growth.
DOI: 10.6084/m9.figshare.8479976
title: MOESM3 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 3: Table S3. Biological functions enriched in the up- and down-regulated genes in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.6084/m9.figshare.8479979
title: MOESM4 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 4: Table S6. Peaks and genes with decreased levels of H3K4me2 or H3K4me3 to more than 1.5-fold in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.6084/m9.figshare.8479979.v1
title: MOESM4 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 4: Table S6. Peaks and genes with decreased levels of H3K4me2 or H3K4me3 to more than 1.5-fold in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.6084/m9.figshare.8479982.v1
title: MOESM5 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 5: Table S7. Biological functions enriched in 597 up-regulated genes with decreased H3K4me2 levels in 701Ri-1-5.
DOI: 10.17630/aa042eff-5b55-4096-991f-e92cf4f51375
title: Data underpinning "Isothiourea-catalysed enantioselective Michael addition of N-heterocyclic pronucleophiles to α,β-unsaturated aryl esters"
DOI: 10.6084/m9.figshare.8479976.v1
title: MOESM3 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 3: Table S3. Biological functions enriched in the up- and down-regulated genes in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.25549/usctheses-c40-389330
title: Trends in the Alaskan bottom-trawl fishery from 1993-2015: a GIS-based spatiotemporal analysis [pdf]
DOI: 10.6084/m9.figshare.13192515.v1
title: Additional file 1 of Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity

description: Additional file 1: Supplementary Tables S1-S8.
DOI: 10.5066/p1pkezoj
title: High-resolution airborne magnetic and radiometric survey of the Republic Graben, Okanogan and Kettle metamorphic core complexes, Kootenay Arc and surrounding regions, Northeastern Washington

description: The Republic survey consists of high-resolution aeromagnetic and radiometric data designed to image the subsurface geology and structure of a large portion of northeastern Washington. These data are intended for rigorous modeling and interpretation of the geology and structure in this region and will be used to evaluate the potential for undiscovered resources and will contribute to USGS and Washington DNR-related mineral and geothermal resource assessments of the region. This release includes aeromagnetic and aeroradiometric data collected via low-altitude helicopter flown over northeastern Washington State, centered over the town of Republic, Washington. The data were acquired between September 26, 2022 and August 21, 2023 by Precision Geosurveys, Inc. of Langley, British Columbia and processed by EDCON-PRJ, Inc. of Lakewood, Colorado, contracted by the U.S. Geological Survey and funded through the Earth Mapping Resources Initiative (EarthMRI). The survey includes gridded data from target altitude of 80-100 meters above ground level, subject to aircraft climb and descent limitations. Primary transverse flight lines were flown in the east-west direction and spaced 200 meters apart. Tie lines were flown in the north-south direction and spaced 2000 meters apart. Additionally, the survey includes two transect lines flown down the Similkameen and Okanogan Valleys where local topography was too extreme to maintain an ideal drape surface. A total of 94,506 line kilometers of data were collected over an area of 16,885 square kilometers. Survey procedures are described in detail in the document “WA Republic Mag RAD D22 Project Report_report.pdf” available in this data release. The Republic aeromagnetic and aeroradiometric survey was collected over steep and highly variable terrain, thus the terrain clearance should be considered carefully when modeling and interpreting magnetic and radiometric data. This data release includes .csv file databases for the main survey and transect data collections, derivative magnetic and radiometric data in map view in .grd and .tiff file format, and shapefiles of the transect lines along the Similkameen and Okanogan Valleys.
DOI: 10.5281/zenodo.10419650
title: Patrocinio F1 Valencia
DOI: 10.5281/zenodo.10419649
title: Patrocinio F1 Valencia
DOI: 10.25549/usctheses-ouc11259429
title: Microsoft Word - Carolina Durling. Third Draft  BL EDITS .docx
DOI: 10.2908/isoc_bde15b_h
title: Broadband and connectivity - households
title: Accès à large bande et connectivité - ménages
title: Breitband und Konnektivität - Haushalte
DOI: 10.5281/zenodo.10636291
title: melanotaenia_australis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10636292
title: melanotaenia_australis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.8480087.v1
title: Additional file 3: of lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA

description: Table S1. mRNA genes highly correlated with each lncRNA DE gene for TCGA HNSC tumor vs normal. (XLS 26 kb)
DOI: 10.6084/m9.figshare.8479970
title: MOESM2 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 2: Table S2. Genes up- and down-regulated by more than 1.5-fold in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.6084/m9.figshare.8479970.v1
title: MOESM2 of H3K4me2 functions as a repressive epigenetic mark in plants

description: Additional file 2: Table S2. Genes up- and down-regulated by more than 1.5-fold in 701Ri-1-5 mutant compared to in the wild-type NIP.
DOI: 10.6084/m9.figshare.8480087
title: Additional file 3: of lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA

description: Table S1. mRNA genes highly correlated with each lncRNA DE gene for TCGA HNSC tumor vs normal. (XLS 26 kb)
DOI: 10.17630/c9e0cf42-a23c-44f5-abb8-4ff3b5451a75
title: High-Triplet-Energy Bipolar Host Materials Based on Phosphine Oxide Derivatives for Efficient Sky- Blue Thermally Activated Delayed Fluorescence Organic Light-Emitting Diodes with Reduced Roll-off (dataset)
DOI: 10.6084/m9.figshare.12673911.v1
title: Additional file 5 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

description: Additional file 5: Table S3. Summary statistics produced by QUAST for SPAdes de novo assemblies of VK01, VK02 and VK08 from shotgun data.
DOI: 10.6084/m9.figshare.12673902
title: Additional file 2 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

description: Additional file 2: Table S1. Details of the libraries generated from the Mütter Museum vaccination kits and vaccinia virus mapping statistics.
DOI: 10.6084/m9.figshare.12673911
title: Additional file 5 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

description: Additional file 5: Table S3. Summary statistics produced by QUAST for SPAdes de novo assemblies of VK01, VK02 and VK08 from shotgun data.
DOI: 10.6084/m9.figshare.12673923
title: Additional file 9 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

description: Additional file 9: Table S4. OPXV genomes used for comparison in the phylogenetic analyses.
DOI: 10.6084/m9.figshare.12673881
title: Additional file 12 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

description: Additional file 12: Table S5. OPXV genomes used for bait design.