cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13643378.v1
title: Pedigrees

description: The file Pedigrees.zip includes pedigrees for all the scenarios we ran. Each file is named after the type of selection it ran (Gen for genomic and Class for conventional) followed by the availability of the initial training population (True / False), the number of phenotypic records per lactation ([1-11) and by the ratio of the cost of phenotyping and genotyping (2_1, 1_1, 1_2). The pedigree file contains Generation, individual's ID, father's ID, mother's ID, true genetic value (gvNormUnres1), phenotypic value (phenoNormUnres1), gender (sex) and herd number (herd).
DOI: 10.6084/m9.figshare.24550840.v1
title: Different Debt: An Addition to the Technical Debt Dataset and a Demonstration Using Developer Personality

description: This package contains the data and code for the article:Graf-Vlachy, L., & Wagner, S. 2024. Different Debt: An Addition to the Technical Debt Dataset and a Demonstration Using Developer Personality, Proceedings of the 7th ACM/IEEE International Conference on Technical Debt (Technical Track)
DOI: 10.6084/m9.figshare.25869385.v1
title: Supplementary_Data_Orthogroup_Tables

description: Supplementary_Data_Orthogroup_Tables
DOI: 10.6084/m9.figshare.28409219.v2
title: NEONATAL HYPERKALEMIA AND ITS ASSOCIATED FACTORS AMONG NEONATES ADMITTED WITH HYPERKALEMIA AT AMHARA REGION COMPREHENSIVE SPECIALIZED HOSPITALS, ETHIOPIA, 2023.ORDINAL REGRESSION

description: Neonatal care practices, and traditions can influence maternal and newborn care-seeking behaviors and may Limit awareness and understanding of prenatal and neonatal care practices because low literacy rates can impact health-seeking behaviors and delay appropriate interventions. Shortages of skilled health professionals, including neonatologists, as well as essential medical supplies and equipment, can limit the capacity to provide timely and quality care. Limited healthcare budgets and low spending in the region can lead to inadequate infrastructure, understaffing, and insufficient resources for maternal and neonatal healthcare. Inadequate coverage of skilled birth attendants, disparities in access to healthcare services, and variations in the quality of care can further contribute to the burden of neonatal hyperkalemia. Even among neonates with hyperkalemia, no study has been conducted to determine the prevalence, levels, and associated variables of hyperkalemia among neonates hospitalized in Neonatal Intensive Care Units (NICUs) in Ethiopia. To reduce this gap, this study aimed to assess neonatal hyperkalemia and its associated factors with neonatal hyperkalemia among neonates admitted to Amhara Region Comprehensive Specialized Hospitals
DOI: 10.6084/m9.figshare.14759510.v1
title: Additional file 4 of Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation

description: Additional file 4: Table S3. All of the predicted lncRNAs for 9 hub miRNAs.
DOI: 10.6084/m9.figshare.20425836.v1
title: CI and NH data.xlsx

description: Data contains demographics and results of online testing of cochlear implant users and normal hearing controls.
DOI: 10.6084/m9.figshare.12212570.v1
title: Supplementary Material for: Glomerular Transcriptome Profiles in Focal Glomerulosclerosis: New Genes and Pathways for Steroid Resistance

description: <b><i>Background:</i></b> Patients with focal segmental glomerulosclerosis (FSGS) characterized by steroid-resistant nephrotic syndrome (SRNS) are prone to progress to ESRD. Mechanism for the FSGS patients’ response to steroid treatment is still unknown and currently, it is impossible to predict the steroid resistance before treatment of patients with FSGS. <b><i>Methods:</i></b> To identify biomarkers and potential therapeutic targets of FSGS patients with SRNS, patients diagnosed as kidney biopsy-proven FSGS and nephrotic syndrome (NS) were prospectively enrolled. They were divided into 2 groups, steroid-sensitive NS and SRNS based on their treatment response. Cortical regions were selected from biopsied renal tissues, and glomeruli were isolated under an inverted microscope. RNA was prepared from the isolated glomeruli and further used for microarray analysis. Followed by multiple analyses, the top 6 highest and lowest, and a selected panel of differentially expressed genes obtained and their related pathways were validated via real-time PCR, western blot, and measurement of reactive oxygen species (ROS). <b><i>Results:</i></b> In SRNS group, we discovered that the most significant up-regulated pathway was primarily related to cellular amino acid and derivative metabolic process. Meanwhile, the most significant down-regulated pathway was primarily involved in anatomical structure morphogenesis. Moreover, we found <i>NADPH</i> <i>oxidase 4</i> (<i>NOX4</i>), one of the key regulators of renal ROS, at a much higher level in SRNS both at transcriptomic and proteomic levels. We also found the levels of ROS, p-p38 MAPK and matrix metalloproteinase (MMP)-2, which were all regulated by NOX4, were also higher in glomeruli isolated from SRNS patients. At last, we detected stimulated by retinoic acid gene 6 homolog (STRA6), a cell surface receptor formerly known as a gene preventing podocytes from over-proliferative lesion induced by HIV infection and was up-regulated by retinoic acid, expressed at a much higher level in SRNS kidneys. <b><i>Conclusion:</i></b> We found 2 potential mechanisms underline the SRNS, NOX4/ROS/P38 MAPK/MMP-2 pathway and STRA6. Our findings provided new insights into the steroid resistance.
DOI: 10.6084/m9.figshare.12237314.v4
title: FGF9 variant in 46,XY DSD patient suggests a role for dimerization in sex determination

description: Supplemetary Material
DOI: 10.6084/m9.figshare.5121643.v1
title: Supplementary Material for: A Single D<sub>H</sub> Gene Segment Is Sufficient for the Establishment of an Asthma Phenotype in a Murine Model of Allergic Airway Inflammation

description: <i>Background:</i> We have previously shown that the allergic sensitization to ovalbumin does not represent a superantigen-like immune response. In gene-targeted mice (ΔD-iD) with a single modified <i>Diversity</i> gene segment (D<sub>H</sub>) of the immunoglobulin heavy chain, enriched for charged amino acids, the asthma phenotype in a murine model was markedly alleviated compared to wild-type animals. <i>Objective:</i> We now sought to determine whether the confinement to a single D<sub>H</sub> gene segment alone leads to a reduced allergic phenotype. <i>Methods:</i> We examined another gene-targeted mouse strain (ΔD-DFL) with a single D<sub>H</sub> gene segment which encodes for neutral amino acids, thus reflecting the preferential repertoire in wild-type mice. Mice were sensitized intraperitoneally to ovalbumin. <i>Results:</i> Despite the constraint to a single D<sub>H</sub> gene segment, ΔD-DFL mice mounted high total and allergen-specific IgG<sub>1</sub> and IgE serum levels after sensitization to ovalbumin. The affinity constants of allergen-specific IgG<sub>1</sub> antibodies did not differ between ΔD-DFL and wild type. Following challenge with aerosolized allergen, a marked local T<sub>H</sub>2 cytokine response and an eosinophilic airway inflammation developed. Quantitative histology revealed increased mucus production and intense goblet cell metaplasia which were identical to those in wild type. Moreover, ΔD-DFL mice developed an airway hyperreactivity to methacholine and to the specific allergen, which both did not differ from those in wild-type animals. <i>Conclusion:</i> A single D<sub>H</sub> gene segment is sufficient for the establishment of the asthma phenotype in a murine model of allergic airway inflammation. Thus, the allergic phenotype depends on the amino acid composition and not on the diversity of the classical antigen-binding site.
DOI: 10.6084/m9.figshare.9963065.v1
title: Capreolus_PNSG

description: We aim to determine whether livestock affect roe deer (<i>Capreolus capreolus</i> Linnaeus, 1758) by reducing habitat quality and increasing the probability of infection by shared parasites. We measured non-invasive fecal cortisol metabolites as an indicator of habitat quality and also lung nematode larvae burden of the Dictyocaulus genus. For this, a total of 120 fresh fecal samples of roe deer were collected from a total number of eight plots with an area ranging 100 to 168 ha (139±8.4 ha), 30 in pine with livestock 30 in pine without livestock and the same for oak forest, from October 2009 to March 2010.
DOI: 10.4121/uuid:ae55266d-777d-463a-a823-4af3c241d784
title: General graph datasets

description: The dataset contains graph instances used to test various optimization techniques for Roman domination problems. All instances are artificially generated. There are six subsets of graph instances provided: bipartite, grid, net, planar, random and recursive graphs.
DOI: 10.6084/m9.figshare.14980386.v4
title: SubInfo.mat: The list of all file names for participants

description: The SubInfo.mat contains information about the file names for MEG data, eye movement data and Psychtoolbox dataIn total, we have 39 participants for both datasets. The field names for the first dataset is 'Targ60', for the second one is 'JEP60' (adapted from Degno et al. 2019, Journal of Experimental Psychology).The SubInfo.mat also contains the MRI codes. For participants who do not have MRI (T1) images, nan is the code and a template T1 images will be used in the source modeling. We have T1 images for 36 participants.<br>
DOI: 10.6084/m9.figshare.24919629.v1
title: GrassSyn dataset - Soil organic carbon stocks in Brazilian grassy ecosystems

description: The GrassSyn dataset offers comprehensive soil organic carbon (SOC) stock data from diverse Brazilian grassy ecosystems. It includes spatially explicit SOC stocks, physical soil properties, and ancillary information compiled from 182 studies (1996–2021) across 803 sites, covering 35° latitude and 28° longitude. Organized in relational tables, the dataset reports soil carbon stocks and associated parameters at depths up to 100 cm. SOC stocks vary by grassy ecosystem type and sampling depth. Detailed descriptions and summary statistics are available in the following reference:Andrade, B. O., Gamboa, C. H., Ferreira, G. W. D., Wiesmeier, M., Assad, E. D., Cerri, C. E. P., Mello, J. M., Morais, V. A., Overbeck, G. E., Pinto‐Junior, H. V., Scolforo, J. R. S., & Tornquist, C. G. (2024). The GrassSyn dataset: Soil organic carbon stocks in Brazilian grassy ecosystems. Journal of Environmental Quality, 1–13. https://doi.org/10.1002/jeq2.20665
DOI: 10.6084/m9.figshare.27100411.v1
title: <b>Exploring AI literacy and perceptions among library and information science students in Asia and the Middle East</b>

description: With the proliferation of AI tools, it is crucial to understand the level of AI literacy among university students. This study investigates the AI literacy of Library and Information Science (LIS) students in South Asia e.g., Bangladesh, India and Pakistan, and the Middle East namely Jordan, Lebanon and Saudi Arabia. A quantitative design was employed in this study, which targets 816 LIS students at various academic institutions.
DOI: 10.6084/m9.figshare.7492226.v1
title: Picture Naming Times, Cuetos et al. (1999)

description: Naming times for the Snodgrass and Vanderwart pictures in Spanish<br>reference_to_cite: "Cuetos, F., Ellis, A.W., Alvarez, B. (1999). Naming times for the Snodgrass and Vanderwart pictures in Spanish. Behavior Research Methods, Instruments, & Computers, 31(4), 650-658."<br>url_information: "http://psychonomic.org/archive/"
DOI: 10.6084/m9.figshare.20059655.v1
title: Gonioscopy-Assisted Transluminal Trabeculotomy: A Review

description: To review the recent evidence in the literature regarding the efficacy and safety of gonioscopy-assisted transluminal trabeculotomy (GATT) in the management of pediatric and adult glaucoma. A literature search was performed in the electronic databases of PubMed, Google Scholar, Embase the Register of Controlled Trials, and Ovid Medline for studies evaluating the safety and outcomes of GATT in glaucoma. GATT is a novel minimally invasive glaucoma surgery that allows the incision of the inner wall of Schlemm’s canal increasing aqueous drainage through the physiologic outflow pathway with subsequent intraocular pressure reduction in different types if of glaucoma. GATT demonstrated favorable results in a wide range of both primary and secondary open-angle and angle-closure glaucoma.
DOI: 10.6084/m9.figshare.27978480.v2
title: In this table, we excluded metabolites that exhibit horizontal pleiotropy and are not associated with both BMI and NAFLD. We attempted to merge Tables 2-4, but we encountered an unresolved issue: the mediation analysis identifies metabolites that are associated with both BMI and NAFLD simultaneously, whereas many metabolites are only associated with one of these (either BMI or NAFLD). Although we tried to integrate the tables, we found that forced integration would paradoxically increase the complexity of the table. As shown in this table, there are a total of 157 metabolites, but only 86 of them are potential mediators. Therefore, merging the three tables would actually increase the complexity of the presentation.

description: In this table, we excluded metabolites that exhibit horizontal pleiotropy and are not associated with both BMI and NAFLD. We attempted to merge Tables 2-4, but we encountered an unresolved issue: the mediation analysis identifies metabolites that are associated with both BMI and NAFLD simultaneously, whereas many metabolites are only associated with one of these (either BMI or NAFLD). Although we tried to integrate the tables, we found that forced integration would paradoxically increase the complexity of the table. As shown in this table, there are a total of 157 metabolites, but only 86 of them are potential mediators. Therefore, merging the three tables would actually increase the complexity of the presentation.
DOI: 10.25403/upresearchdata.26242694.v1
title: Narratives of belonging in/to South Africa from young, middle-class, South African women

description: Twenty individual interviews and a focus group discussion from the research component of the Masters (Sociology) dissertation entitled 'Safety and Belonging: Constructing a sense of belonging amongst young, middle-class, South African feminine bodies within and 'unsafe' place'. The participants of this study were between the ages of 21 and 30, born and raised in South Africa, all but one (Julia) held an undergraduate degree, and were mix of races (twelve white, seven black, and one Indian).
Using a semi-structured format, the participants were interviewed for approximately 60 minutes about how they had constructed their sense of belonging in/to South Africa despite the gender-based violence that is seemingly characteristic of this context. Thus, the participants’ lived experiences of (not) belonging, experiences of violence, and being a woman in South Africa were the focus of this data collection process. Therefore, these interviews primarily cover topics like: a persistent sense of unsafety, safe keeping strategies (safety precautions), personal experiences of (gendered) violence and their ramifications, emotive constructions of belonging, and an apparent constant gendered vulnerability. All of which were contextualised to South Africa. When viewed together these twenty interviews produce a possible feminine South African narrative of belonging which accounts for the violent (gendered) realties of this context. However, one interview (Mary) could not be transcribed as the audio file was corrupted.
The focus group was conducted after all the individual interviews had been done, transcribed, and analysed thematically. This discussion took place over an online chat platform (Zoom), and consisted of three white participants that were recruited from the existing participant pool. The small participant sample was due to scheduling conflicts and time constraints. The discussion points were developed from common themes that were identified through the thematic analysis of the induvial interviews. This was done to test the validity of these themes and to investigate them further. As all the participants were white, this discussion focused on lived experiences of belonging in/to South Africa from the perspectives of white South African women. And thus, primarily covered topics like: whiteness, racial conflicts, a sense of not-belonging, and a sense of feminine unsafety. Critically, while it was the intention to view this data as a possible ‘master’ narrative of the feminine South African sense of belonging, the sample was too small and only consisted of white women. Thus, this discussion ought to be viewed as a group narrative of white belonging in/to South Africa.
Note that all the transcripts were transcribed verbatim and research pseudonyms were used so to be in accordance with the POPIA Act.
DOI: 10.6084/m9.figshare.783077.v4
title: TreeOTU

description: Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms, especially the bacteria and archaea, is mostly based upon studies of sequences of the small- subunit rRNAs (ssu-rRNAs). To address the limitation of ssu-rRNA as a phylogenetic marker, such as copy number variation among organisms and complications introduced by horizontal gene transfer, convergent evolution, or evolution rate variations, we have identified protein- coding gene families as alternative Phylogenetic and Phylogenetic Ecology markers (PhyEco). Current nucleotide sequence similarity based Operational Taxonomic Unit (OTU) classification methods are not readily applicable to amino acid sequences of PhyEco markers. We report here the development of TreeOTU, a phylogenetic tree structure based OTU classification method that takes into account of differences in rates of evolution between taxa and between genes. OTU sets built by TreeOTU are more faithful to phylogenetic tree structures than sequence clustering (non phylogenetic) methods for ssu-rRNAs. OTUs built from phylogenetic trees of protein coding PhyEco markers are comparable to our current taxonomic classification at different levels. With the included OTU comparing tools, the TreeOTU is robust in phylogenetic referencing with different phylogenetic markers and trees. The TreeOTU package includes OTU classification, comparison and tree rooting scripts, as well as the alignments, trees and NCBI/IMG taxonomic classification information related to this research. The contents in he package are described in the file README.txt.
DOI: 10.6084/m9.figshare.11807577.v1
title: CTD data for water mass analysis

description: The CTD data used to calculate the potential spicity and potential density
DOI: 10.6084/m9.figshare.28756370.v1
title: Digital infrastructure and intra-provincial balanced development: Evidence from China's provincial panel data

description: The variables involved in this paper can be found in this DTA file.
DOI: 10.6084/m9.figshare.10048724.v2
title: Data Repository

description: Collection of experimentally measured data, FEM simulation scripts, and numerically derived data.<br>
DOI: 10.6084/m9.figshare.21505626.v2
title: Gridded India Meteorological Department (IMD) datasets

description: The datasets are in a gridded filed format at 0.25-degree spatial resolution where the location of the grid is in the filename itself. Three columns in a file are daily observed precipitation (mm), maximum temperature (oC), and minimum temperature (oC) datasets. IMD datasets are available from 1951-2021.
DOI: 10.6084/m9.figshare.24160329.v1
title: Supplementary Material for: Clinicopathological Features and Outcomes of IgA Nephropathy with Serum Antineutrophil Cytoplasmic Autoantibody Positivity

description: Objective: IgA nephropathy (IgAN) with serum Antineutrophil Cytoplasmic Autoantibody (ANCA) positivity is uncommon. This study analyzed the clinicopathologic features and prognosis of IgAN patients with serum ANCA positivity. Methods: 2864 IgAN patients were tested for ANCA by the indirect immunofluorescence assay and chemiluminescence immunoassay. Patients with serum ANCA positivity (n=85) were identified and their clinical, pathological and prognostic characteristics were analyzed. They were compared with ANCA negative IgAN patients (n=170) and ANCA-associated systemic vasculitis (AAV) with renal involvement patients (n=85) selected randomly. Result：2.97% (85/2864) of IgAN were ANCA positive and 4 patients were diagnosed as crescentic IgAN with ANCA positivity. The clinicopathological characteristics of ANCA-positive IgAN patients were comparable to ANCA-negative IgAN patients, but they had higher antinuclear antibodies (ANA) positive rates and lower levels of renal interstitial inflammation and less immune depositions than ANCA-negative IgAN patients. Compared with AAV patients, ANCA-positive IgAN patients were younger, fewer extrarenal manifestations, milder renal damage and more immune complexes depositions. The renal outcomes were similar between IgAN patients with and without ANCA positivity. Multivariate Cox analysis revealed that in IgAN patients with ANCA positivity, male, ANA positivity, higher serum creatinine and proteinuria, and more severe renal tubular atrophy/interstitial fibrosis were risk factors for adverse renal outcomes. Conclusion: The clinical, pathological features and prognosis of ANCA-positive IgAN patients were similar with ANCA-negative IgAN patients except for higher ANA positive rate, milder renal inflammation and less immune depositions. ANA positivity was an independent risk factor for adverse renal outcomes in ANCA-positive IgAN patients.
DOI: 10.6084/m9.figshare.11522373.v1
title: Pre-existing atrial fibrillation is associated with high grade post-operative complications following colorectal cancer resection

description: Dataset for above research paper
DOI: 10.6084/m9.figshare.27273900.v1
title: Physiological species distribution model

description: A physiological species distribution model (pSDM) was used to to predict the species further distributions.
DOI: 10.6084/m9.figshare.6935867.v1
title: ELP_data.zip

description: This file contains the data recorded during the study "Age-related changes in spinal and lower limb kinematics and trunk muscle activity during gait"<br>Once opened, the .zip file reveals one individual folder per subject. Each folders contains .sig files (EMG data) and .qtm files (kinematic data). <br>
DOI: 10.6084/m9.figshare.28735508.v1
title: Data Set for Can Climate Change Save the Plastic World.xlsx

description: Raw Data for <b>Can Climate Change Perceptions Drive Plastic Policy Support? Effects of Climate Change Skepticism, Guilt, and Efficacy on the Acceptance of the Plastic Tax</b>
DOI: 10.6084/m9.figshare.7616264.v1
title: 16S reads (Illumina) from Small et al. 2019

description: Overlapped 16S Illumina reads from a study of microbial community variation among stickleback guts.<br>Small_etal_16S.fa.gz contains reads merged and cleaned using QIIME1.<br>Small_etal_16S_Qiime2_set1.tar.gz and Small_etal_16S_Qiime2_set2.tar.gz contain reads merged, cleaned, and demultiplexed using QIIME2.<br>This study has been accepted for publication in mSystems:Small CM, Currey M, Beck EA, Bassham S, Cresko WA. 2019. Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback gut microbiome. mSystems 4:e00331-19. https:// doi.org/10.1128/mSystems.00331-19.
DOI: 10.6084/m9.figshare.28701482.v1
title: UC diet study_metadata file

description: This pilot study investigated the effects of a reduced-sulfur (RS) diet on gut microbiome composition and fecal metabolome in individuals with remitted or active ulcerative colitis (UC).