cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5492383
title: Knockdown of REGγ inhibits the proliferation and migration and promotes the apoptosis of multiple myeloma cells by downregulating NF-κB signal pathway

description: <b>Objectives:</b> This study aimed to evaluate the effects of REGγ knockdown on the proliferation, apoptosis and migration of multiple myeloma (MM) cells, and reveal the potential regulatory mechanisms. <b>Methods:</b> The expression of REGγ on myeloma cells of 28 MM patients was detected by Western blot. shRNA-REGγ-1 and shRNA-REGγ-2 were constructed to downregulate REGγ in RPMI-8226 cells. The proliferation, apoptosis and migration of transfected cells were analyzed by Cell Counting Kit 8 (CCK8), flow cytometry and transwell chamber, respectively. The expression of phosphorylated p65 (p-p65), p65, NF-kappa-B inhibitor ε (IkBε), matrix metalloproteinase 2 (MMP2), B-cell lymphoma xL (Bcl-xL) and X-linked inhibitor of apoptosis protein (XIAP) in transfected cells was detected by Western blot. Using cycloheximide (CHX), the half-life period of IkBε was detected by Western blot. <b>Results:</b> The expression of REGγ was positive in myeloma cells. The proliferation and migration of RPMI-8226 cells were significantly inhibited by shRNA-REGγ-1/shRNA-REGγ-2, while the apoptosis rates were significantly increased (<i>p</i> &lt; 0.05). The expression of p-p65 and IkBε was significantly reduced in RPMI-8226 cells transfected with shRNA-REGγ-1/shRNA-REGγ-2. The degradation of IkBε was significantly lower in RPMI-8226 cells transfected with shRNA-REGγ-1 than the control (longer half-life period). Besides, the expression of MMP2, Bcl-xL and XIAP in RPMI-8226 cells was significantly inhibited by shRNA-REGγ-1/shRNA-REGγ-2. <b>Discussion:</b> Knockdown of REGγ may inhibit the proliferation and migration, and promote the apoptosis of RPMI-8226 cells possibly by downregulating NF-κB signal pathway.
DOI: 10.6084/m9.figshare.12819091.v1
title: Additional file 2 of Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression

description: Additional file 2: Supplementary Table S2. Genomic variants targeted for deep sequencing.
DOI: 10.6084/m9.figshare.12307805
title: Additional file 1 of Prevalence of sexually transmitted infections among foreigners living in Guangzhou, China: a cross-sectional study (2010–2017)

description: Additional file 1: Table 1. The prevalence of HBV/HCV/HIV/TPPA detected in samples of 40,935 participants. (XLS 6437 kb)
DOI: 10.6084/m9.figshare.12307805.v1
title: Additional file 1 of Prevalence of sexually transmitted infections among foreigners living in Guangzhou, China: a cross-sectional study (2010–2017)

description: Additional file 1: Table 1. The prevalence of HBV/HCV/HIV/TPPA detected in samples of 40,935 participants. (XLS 6437 kb)
DOI: 10.6084/m9.figshare.19634863
title: Additional file 1 of Identifying causal genes for stroke via integrating the proteome and transcriptome from brain and blood

description: Additional file 1: Supplementary Tables 1–32.
DOI: 10.3886/icpsr06573.v2
title: Minimal Hearing Loss in Children, 1991-1994: [Davidson County, Tennessee]
title: Version 2

description: The purpose of this survey and follow-up case-control study was to estimate the prevalence of minimal hearing loss in school-age children and to determine whether children with minimal hearing loss experienced any psychoeducational or functional complications. Third-, sixth-, ninth-, and eleventh-grade children were evaluated for hearing threshold levels and type of hearing loss, as well as middle ear function and associated abnormalities. The data include results from acoustic otoscope, diagnostic immittance, and GSI-37 auto tymp tests. The case-control data contain scores from the Comprehensive Tests of Basic Skills, scores from the Revised Behavior Problem Checklist, and other variables.
description: The survey was planned as a probability-proportional-to-
size sample of schools.
description: Datasets: 
DS0: Study-Level Files
DS1: Audiology Results
DS2: GSI-37 Auto Tymp Results
DS3: History and COOP Results
DS4: Identification Information
DS5: Middle Ear Function Results
DS6: Otoscopic and Audioscopic Results
DS7: Consolidated Survey Data
DS8: Case-Control Data
description: School children attending public schools in Davidson
County, Tennessee.
description: The codebook refers to the original dataset numbers (part numbers) this study had before it was reorganized into eight datasets. In the original release, the study had separate datasets (parts) for the SAS versions of the data files which resulted in the following dataset numbers and titles: DS1: Audiology Results; DS2: SAS Transport File for Audiology Results; DS3: GSI-37 Auto Tymp Results; DS4: SAS Transport File for GSI-37 Auto Tymp Results; DS5: History and COOP Results; DS6: SAS Transport File for History and COOP Results; DS7: Identification Information; DS8: SAS Transport File for Identification Information; DS9: Middle Ear Function Results; DS10: SAS Transport File for Middle Ear Function Results; DS11: Otoscopic and Audioscopic Results; DS12: SAS Transport File for Otoscopic and Audioscopic Results; DS13: Consolidated Survey Data; DS14: SAS Transport File for Consolidated Survey Data; DS15: Case-Control Data; and DS16: SAS Transport File for Case-Control Data.The survey files (Parts 1-12) can be linked by the
ID variable at the beginning of each file.The SAS transport files
were generated by the SAS CPORT procedure.
DOI: 10.6084/m9.figshare.8113844.v1
title: Additional file 4: of Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae

description: Table S3. KEGG analysis of the response of Rhizoglomus intraradices-inoculated wild rice plants to infection by Magnaporthe oryzae in the ‘Wp+R vs. Wp’ (a) and ‘Cp+R vs. Cp’ (b) comparisons. Cp + R, AMF-inoculated cultivated rice infected with M. oryzae; Cp, AMF-uninoculated cultivated rice infected with M. oryzae; Wp + R, AMF-inoculated wild rice infected with M. oryzae; Wp, AMF-uninoculated wild rice infected with M. oryzae. (XLS 63 kb)
DOI: 10.6084/m9.figshare.24891068.v1
title: Estimating cell-type-specific gene co-expression networks from bulk gene expression data with an application to Alzheimer’s disease

description: Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregated view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing to reveal gene coordination that may be distinct across different cell types. In this paper, we introduce a flexible framework for estimating cell-type-specific gene co-expression networks from bulk sample data, without making specific assumptions on the distributions of gene expression profiles in different cell types. We develop a novel sparse least squares estimator, referred to as CSNet, that is efficient to implement and has good theoretical properties. Using CSNet, we analyzed the bulk gene expression data from a cohort study on Alzheimer’s disease and identified previously unknown cell-type-specific co-expressions among Alzheimer’s disease risk genes, suggesting cell-type-specific disease mechanisms.
DOI: 10.6084/m9.figshare.5492383.v1
title: Knockdown of REGγ inhibits the proliferation and migration and promotes the apoptosis of multiple myeloma cells by downregulating NF-κB signal pathway

description: <b>Objectives:</b> This study aimed to evaluate the effects of REGγ knockdown on the proliferation, apoptosis and migration of multiple myeloma (MM) cells, and reveal the potential regulatory mechanisms. <b>Methods:</b> The expression of REGγ on myeloma cells of 28 MM patients was detected by Western blot. shRNA-REGγ-1 and shRNA-REGγ-2 were constructed to downregulate REGγ in RPMI-8226 cells. The proliferation, apoptosis and migration of transfected cells were analyzed by Cell Counting Kit 8 (CCK8), flow cytometry and transwell chamber, respectively. The expression of phosphorylated p65 (p-p65), p65, NF-kappa-B inhibitor ε (IkBε), matrix metalloproteinase 2 (MMP2), B-cell lymphoma xL (Bcl-xL) and X-linked inhibitor of apoptosis protein (XIAP) in transfected cells was detected by Western blot. Using cycloheximide (CHX), the half-life period of IkBε was detected by Western blot. <b>Results:</b> The expression of REGγ was positive in myeloma cells. The proliferation and migration of RPMI-8226 cells were significantly inhibited by shRNA-REGγ-1/shRNA-REGγ-2, while the apoptosis rates were significantly increased (<i>p</i> &lt; 0.05). The expression of p-p65 and IkBε was significantly reduced in RPMI-8226 cells transfected with shRNA-REGγ-1/shRNA-REGγ-2. The degradation of IkBε was significantly lower in RPMI-8226 cells transfected with shRNA-REGγ-1 than the control (longer half-life period). Besides, the expression of MMP2, Bcl-xL and XIAP in RPMI-8226 cells was significantly inhibited by shRNA-REGγ-1/shRNA-REGγ-2. <b>Discussion:</b> Knockdown of REGγ may inhibit the proliferation and migration, and promote the apoptosis of RPMI-8226 cells possibly by downregulating NF-κB signal pathway.
DOI: 10.5066/p9qatarq
title: NASA GIFT Iceland Highlands: 2019 and 2021 Askja Ground Penetrating Radar (GPR) and Observations

description: This data collection includes ground-penetrating radar (GPR) data and related observations collected from the NASA Goddard Instrument Field Team (GIFT) Expedition to the Icelandic Highlands in July-August 2019 and August 2021. This dataset includes observations at the Askja Volcano and caldera and Vikrahraun lava flow. GPR data were collected using Geophysical Survey Systems, Inc (GSSI) shielded bistatic antennas at center frequencies of 200 MHz, 400 MHz, and 900 MHz. Common offset surveys were conducted to investigate the subsurface interfaces. The GPR data includes raw data obtained from the instrument (as GSSI .dzt files), line shapefiles of survey locations, and interpreted ice thickness GeoPackage files with radar picks of subsurface interfaces. Also included is a context orthoimage generated from uncrewed aerial system (UAS) images over the GPR site in 2021. A high-level readme file is provided that further describes the datasets.
DOI: 10.6084/m9.figshare.12308279
title: Additional file 3 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 3. A total of 1111 patients undergoing partial and radical nephrectomy in development cohort.
DOI: 10.6084/m9.figshare.12308285
title: Additional file 4 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 4. Characteristics of 751 patients after radical nephrectomy.
DOI: 10.6084/m9.figshare.12308291
title: Additional file 5 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 5. Multivariable logistic regression analysis for predictors of postoperative AKI following radical nephrectomy.
DOI: 10.6084/m9.figshare.12308291.v1
title: Additional file 5 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 5. Multivariable logistic regression analysis for predictors of postoperative AKI following radical nephrectomy.
DOI: 10.6084/m9.figshare.8113859
title: Additional file 6 of Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae

description: Table S5. MapMan 3.6.0 analysis of secondary metabolic pathway response for shikimate pathway (a), MVA (b), simple phenols (c) and terpenoids (d) in AMF-inoculated wild and cultivated rice in response to infection by Magnaporthe oryzae in the ‘Wp+R vs. Wp’ and ‘Cp+R vs. Cp’ comparisons. Cp + R, AMF-inoculated cultivated rice infected with M. oryzae; Cp, AMF-uninoculated cultivated rice infected with M. oryzae; Wp + R, AMF-inoculated wild rice infected with M. oryzae; Wp, AMF-uninoculated wild rice infected with M. oryzae. MVA, mevalonate. (XLS 46 kb)
DOI: 10.6084/m9.figshare.12308594
title: Additional file 2 of Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants

description: Additional file 2: Table S2. List and classification of ARF genes analyzed in angiosperms.
DOI: 10.6084/m9.figshare.12308279.v1
title: Additional file 3 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 3. A total of 1111 patients undergoing partial and radical nephrectomy in development cohort.
DOI: 10.6084/m9.figshare.19634924
title: Additional file 3 of Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L.

description: Additional file 3: Table S3. The 16 pairs of segmental duplications in Nicotiana tabacum L. bZIPs.bZIP: basic leucine zipper.
DOI: 10.6084/m9.figshare.8113973.v1
title: Additional file 1: of Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits

description: Primers used for MAS during CSSLs development. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.12308285.v1
title: Additional file 4 of Acute kidney injury after nephrectomy: a new nomogram to predict postoperative renal function

description: Additional file 4. Characteristics of 751 patients after radical nephrectomy.
DOI: 10.6084/m9.figshare.12308393
title: Additional file 2 of Transcriptomic analysis reveals mechanism of light-sensitive albinism in tea plant Camellia sinensis ‘Huangjinju’

description: Additional file 2: Table S2. Summary of gene ontology (GO) analyses.
DOI: 10.6084/m9.figshare.12308396.v1
title: Additional file 3 of Transcriptomic analysis reveals mechanism of light-sensitive albinism in tea plant Camellia sinensis ‘Huangjinju’

description: Additional file 3: Table S3. Summary of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
DOI: 10.6084/m9.figshare.8114246.v1
title: Docker image for signature comparison workflows

description: Docker image for signature comparison workflows. This image is for archive purpose. Please download the latest Docker image at https://hub.docker.com/r/sfrs/sfsigdb.
DOI: 10.5281/zenodo.10610893
title: Data and code for "Resource gradients drive the distribution and photobiont characteristics of two lichen species in a subarctic lava field"

description: This project described how the distribution and morphology of two species of lichen varied along a transect perpendicular to Lake Myvatn in Iceland. All data were collected in a recent (1729) lava field and we focused on two species Flavocetraria cucullata and Peltigera leucophlebia. Lake Myvatn is famous for large midge (Diptera: Chironomidae) emergences of which many are deposited on land. Thus, the transect reflects variation in midge deposition. P. leucophlebia contains both green algae and cynaobacterial endosymbionts and thus is able to fix atmospheric nitrogen, while F. cucullata contains only green algae and is therefore dependent on environmental nutrients. We suspected that these species differed in their response to the midge-derived nutrient gradient.

We measured the distribution of each lichen along a 400 x 15 m transect perpendicular to the lake, characterized their surrounding vegetation, and took thin sections of thalli on which we characterized photobiont thickness and chlorophyll-a concentrations using images taken with a near infrared camera.

The data are housed in the Data folder. FLG_Transect_Points.csv contains the location and names of each lichen plot. FLG_Surrounding_Vegetation.csv contains the vegetation inside each plot. Lichen_IR.csv contains the ENDVI, our metric of chlorophyll-a concentration, and photobiont thickness, in units of pixels taken using a standardized zoom.

All scripts associated with the project are housed in the Analysis folder. IRProcessing.R contains the code used to calculate the chlorophyll-a concentration and thickness from each of the photographs of the lichen thin sections. Myv_analysis.R contains all the code used for the statistical analyses and to generate figures. GOLichenAnalysis2019.Rproj is the RStudio project, which sets the relative locations of files. See https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects for more information on .Rproj files.
DOI: 10.5281/zenodo.10610894
title: Data and code for "Resource gradients drive the distribution and photobiont characteristics of two lichen species in a subarctic lava field"

description: This project described how the distribution and morphology of two species of lichen varied along a transect perpendicular to Lake Myvatn in Iceland. All data were collected in a recent (1729) lava field and we focused on two species Flavocetraria cucullata and Peltigera leucophlebia. Lake Myvatn is famous for large midge (Diptera: Chironomidae) emergences of which many are deposited on land. Thus, the transect reflects variation in midge deposition. P. leucophlebia contains both green algae and cynaobacterial endosymbionts and thus is able to fix atmospheric nitrogen, while F. cucullata contains only green algae and is therefore dependent on environmental nutrients. We suspected that these species differed in their response to the midge-derived nutrient gradient.

We measured the distribution of each lichen along a 400 x 15 m transect perpendicular to the lake, characterized their surrounding vegetation, and took thin sections of thalli on which we characterized photobiont thickness and chlorophyll-a concentrations using images taken with a near infrared camera.

The data are housed in the Data folder. FLG_Transect_Points.csv contains the location and names of each lichen plot. FLG_Surrounding_Vegetation.csv contains the vegetation inside each plot. Lichen_IR.csv contains the ENDVI, our metric of chlorophyll-a concentration, and photobiont thickness, in units of pixels taken using a standardized zoom.

All scripts associated with the project are housed in the Analysis folder. IRProcessing.R contains the code used to calculate the chlorophyll-a concentration and thickness from each of the photographs of the lichen thin sections. Myv_analysis.R contains all the code used for the statistical analyses and to generate figures. GOLichenAnalysis2019.Rproj is the RStudio project, which sets the relative locations of files. See https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects for more information on .Rproj files.
DOI: 10.6084/m9.figshare.9162698
title: Additional file 1: of Lactobacillus plantarum C88 protects against aflatoxin B1-induced liver injury in mice via inhibition of NF-ÎşBâ mediated inflammatory responses and excessive apoptosis

description: The raw datas of biochemical parameters in serum, include ALT, AST, ALP, total cholesterol, triglycerides, total protein and albumin. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9162710.v1
title: Additional file 3: of Lactobacillus plantarum C88 protects against aflatoxin B1-induced liver injury in mice via inhibition of NF-ÎşBâ mediated inflammatory responses and excessive apoptosis

description: The raw datas of Bax, Bcl-2 and Caspase-3 in liver. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.17026931.v2
title: Role of Rho guanine nucleotide exchange factors in non-small cell lung cancer

description: Conventionally, Rho guanine nucleotide exchange factors (GEFs) are known activators of Rho guanosine triphosphatases (GTPases) that promote tumorigenesis. However, the role of Rho GEFs in non-small cell lung cancer (NSCLC) remains largely unknown. Through the screening of 81 Rho GEFs for their expression profiles and correlations with survival, four of them were identified with strong significance for predicting the prognosis of NSCLC patients. The four Rho GEFs, namely ABR, PREX1, DOCK2 and DOCK4, were downregulated in NSCLC tissues compared to normal tissues. The downregulation of ABR, PREX1, DOCK2 and DOCK4, which can be attributfed to promoter methylation, is correlated with poor prognosis. The underexpression of the four key Rho GEFs might be related to the upregulation of MYC signaling and DNA repair pathways, leading to carcinogenesis and poor prognosis. Moreover, overexpression of ABR was shown to have a tumor-suppressive effect in PC9 and H1703 cells. In conclusion, the data reveal the unprecedented role of ABR as tumor suppressor in NSCLC. The previously unnoticed functions of Rho GEFs in NSCLC will inspire researchers to investigate the distinct roles of Rho GEFs in cancers, in order to provide critical strategies in clinical practice.
DOI: 10.3886/icpsr32922.v1
title: National Profile of Local Health Departments, 2010
title: Version 1

description: Conducted by the National Association of County and City Health Officials (NACCHO), the purpose of this survey of local health departments (LHDs) was to advance and support the development of a database for LHDs to describe and understand their structure, function, and capacities. A core set of questions was submitted to every LHD. In addition, some LHDs received one of two randomly assigned modules of supplemental questions. The core questions covered governance, funding, workforce (staffing levels, occupations employed, top executive education and licensure, and percentages of staff by race and Hispanic origin), LHD activities, and community health assessment and health improvement planning. The surveyed LHD activities include immunization, screening for diseases and conditions, treatment for communicable diseases, maternal and child health, epidemiology and surveillance activities, population-based primary prevention activities, and regulation, inspection and/or licensing activities. Topics covered by Module 1 included quality improvement, familiarity with a voluntary national accreditation program for state and local health departments, sharing of resources with other LHDs, emergency preparedness, and information technology. Module 2 examined human resources, policy-making and advocacy, access to health care services, practice-based research, health impact assessments, public health and law, and use of public health reports.
description: ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major statistical software formats as well as standard codebooks to accompany the data. In addition to these procedures, ICPSR performed the following processing steps for this data collection: Checked for undocumented or out-of-range codes..
description: Response Rates: Overall, the study had a response rate of 82 percent: 2,107 of 2,565 LHDs.
description: Datasets: DS0: Study-Level Files DS1: Public-Use Version of the Data DS2: Restricted-Use Version of the Data
description: National Profile of Local Health Departments Series
description: web-based survey
description: All LHDs in the United States. LHDs were defined as administrative or service units of local or state government concerned with health and carrying some responsibility for the health of a jurisdiction smaller than the state. The study excluded Hawaii and Rhode Island because their state health departments operate on behalf of local public health and have no sub-state units.
description: The survey attempted to interview all of the LHDs in the United States. Stratified random sampling was used to select the LHDs that were assigned one of the two modules of supplementary questions. Altogether, 1,316 LHDs received the core questions only, 624 the core questions plus Module 1, and 625 the core questions plus Module 2.