cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3608060_d3.v1
title: Additional file 3 of Gene-specific patterns of expression variation across organs and species

description: Table S2–S7. Spreadsheet with multiple tables, from S2 to S7. Table S2. List of genome assemblies and annotation files used in the Barbosa-Morais et al. study. Table S3. List of 6283 protein-coding orthologs in the seven species studied here. Table S4. Several attributes for the 6283 orthologs. This table includes for each of the 6283 orthologs (rows), the following attributes (as columns): col 1: human gene ID (Ensembl), col 2: absolute sum of squares across organs, col 3: absolute sum of squares across species, col 4: absolute residual variation, col 5: proportion of variation across organs, col 6: proportion of variation across species, col 7: category assigned based on the proportions of variation across organs and species (see “Methods” for details), col 8: dynamic range, col 9: constrained class based on dynamic range. The final gene sets can be obtained by requiring the value in col 9 to be “unconstrained”. Table S5. List of genes identified by projection score. Table S6. List of the mouse ENCODE ChIP-seq datasets used here. Table S7. List of GTEx sample IDs used in the variance decomposition. (XLSX 777 kb)
DOI: 10.6084/m9.figshare.c.3608162_d2.v1
title: Additional file 1: of Association between maternal depression and child stunting in Northern Ghana: a cross-sectional study

description: Study dataset. (DTA 53Â kb)
DOI: 10.6084/m9.figshare.c.3608180_d6.v1
title: Additional file 5: Table S4. of Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq

description: Data for P. chrysosporium transcripts. (XLSX 2407Â kb)
DOI: 10.6084/m9.figshare.c.3608210_d1.v1
title: Additional file 3: of Serum tenascin-C discriminates patients with active SLE from inactive patients and healthy controls and predicts the need to escalate immunosuppressive therapy: a cohort study

description: a Cross-sectional associations between serum tenascin-C levels and positivity of anti-ds-DNA antibodies at the inception visit (univariate analysis). b Cross-sectional associations between serum tenascin-C levels and positivity of anti-nucleosome antibodies at the inception visit (univariate analysis). (ZIP 46 kb)
DOI: 10.6084/m9.figshare.c.3608216_d1.v1
title: Additional file 1: of Evaluation of the diagnostic potential of urinary N-Acetyltyramine-O,Î˛-glucuronide (NATOG) as diagnostic biomarker for Onchocerca volvulus infection

description: Overview of data obtained for all samples (urinary NATOG, urinary creatinine and Ov16 status). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3608180_d8.v1
title: Additional file 9: Table S7. of Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq

description: Orthologous analysis of Phlebia sp. MG-60 and P. chrysosporium. (XLSX 6512Â kb)
DOI: 10.6084/m9.figshare.c.3608261_d1.v1
title: Additional file 1: Table S1. of A novel cutoff for the waist-to-height ratio predicting metabolic syndrome in young American adults

description: Add Health Source Variables Used for Analysis (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3608261_d2.v1
title: Additional file 6: Table S5. of A novel cutoff for the waist-to-height ratio predicting metabolic syndrome in young American adults

description: Weighted Logistic Regression Predicting Presence of Metabolic Syndrome from WHtR Cutoff: National Health and Nutrition Examination Survey, 2005-2008, n = 1 236 (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3608264_d1.v1
title: Additional file 1: of Tuberculosis patientsâ   pre-hospital delay and non-compliance with a longstanding DOT programme: a mixed methods study in urban Zambia

description: Dataset quantitative part TBAC study. (XLS 230Â kb)
DOI: 10.6084/m9.figshare.c.3608261_d4.v1
title: Additional file 5: Table S4. of A novel cutoff for the waist-to-height ratio predicting metabolic syndrome in young American adults

description: Unweighted Logistic Regression Predicting Presence of Metabolic Syndrome from WHtR Cutoff: National Health and Nutrition Examination Survey, 2005-2008, n = 1 236 (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3608261_d5.v1
title: Additional file 3: Table S2. of A novel cutoff for the waist-to-height ratio predicting metabolic syndrome in young American adults

description: NHANES Source Variables Used for Validation Analysis (XLSX 46 kb)
DOI: 10.15468/dl.j6brz6
title: Occurrence Download

description: A dataset containing 224419 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Ocean Salmon Program - Barkley Sound Juvenile Salmon Study from 1987 to 1994"
 ]
}

 The dataset includes 224419 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037536-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3608333_d2.v1
title: Additional file 1: of New dominant spa type t2741 in livestock-associated MRSA (CC398-MRSA-V) in Finnish fattening pigs at slaughter

description: Overview on phenotypic and genotypic characteristics of each strain. (XLSX 31 kb)
DOI: 10.5281/zenodo.12723611
title: Supplements for "The Proteomic Code: Tracing Genetic and Biophysical Foundations for Protein Structure and Function"

description: Supplements for "The Proteomic Code: Tracing Genetic and Biophysical Foundations for Protein Structure and Function"

This supplement includes the following files:



Main_v01.R --- Script in R language to process protein structures and produce the datasets.

datasets.zip --- final filtered version of datasets produced in R language (by "Main_v01.R").   

Dataset key.txt --- key and descriptions to column names in ("datasets.zip").    


The article featuring these datasets is submitted to:

Journal:  Computers in Biology and Medicine  (manuscript number: CIBM-D-24-09857)Title: "The Proteomic Code: Tracing Genetic and Biophysical Foundations for Protein Structure and Function"Authors: Hameduh, Tareq; Miller, Andrew D. ; Heger, Zbynek; Haddad, Yazan

 

 
description: The financial support from the Czech Health Research Council (project no. NU21J-08-00043) is gratefully acknowledged. ADM was supported by OPVVV Project FIT (Pharmacology, Immunotherapy, nanoToxicology) awarded by the Czech Ministry of Education, Youth and Sports (MŠMT) (CZ.02.1.01/0.0/0.0/15_003/0000495) with financial support from the European Regional Development Fund.
DOI: 10.6084/m9.figshare.c.3608360_d1.v1
title: MOESM1 of Circulating microRNAs as biomarkers for diffuse myocardial fibrosis in patients with hypertrophic cardiomyopathy

description: Additional file 1. Human plasma/serum miRNA PCR arrayÂ data.
DOI: 10.6084/m9.figshare.c.3608345_d3.v1
title: Additional file 2: of Development and validation of a novel single nucleotide polymorphism (SNP) panel for genetic analysis of Blastomyces spp. and association analysis

description: SNP genotyping haplotypes. Raw SNP genotyping data obtained from all isolates, subsumed to 73 unique haplotypes. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3608366_d1.v1
title: MOESM7 of Transcriptome profiling of Camelina sativa to identify genes involved in triacylglycerol biosynthesis and accumulation in the developing seeds

description: Additional file 7: Table S7. GO information for the DEGs differentially regulated in Cs-21.
DOI: 10.6084/m9.figshare.c.3608366_d2.v1
title: MOESM3 of Transcriptome profiling of Camelina sativa to identify genes involved in triacylglycerol biosynthesis and accumulation in the developing seeds

description: Additional file 3: Table S3. List of the whole Camelina genes expressed in seed and leaf tissues.
DOI: 10.6084/m9.figshare.c.3608384_d1.v1
title: MOESM3 of Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

description: Additional file 3. SRM proteomics data. Contains Skyline output: raw and normalized data for transition, peptide and protein counts.
DOI: 10.6084/m9.figshare.c.3608366_d3.v1
title: MOESM6 of Transcriptome profiling of Camelina sativa to identify genes involved in triacylglycerol biosynthesis and accumulation in the developing seeds

description: Additional file 6: Table S6. GO information for the DEGs differentially regulated in Cs-14.
DOI: 10.6084/m9.figshare.c.3608429_d2.v1
title: Additional file 5: Table S3. of NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

description: Spearmanâ  s Rho for pairwise comparisons of peak RPMs.
DOI: 10.6084/m9.figshare.c.3608429_d3.v1
title: Additional file 4: Table S2. of NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

description: Summary of Peak Locations when applying Gâ   Filtering at a 50Â % Cutoff.
DOI: 10.6084/m9.figshare.c.3608429_d5.v1
title: Additional file 3: Table S1. of NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

description: Percent of reads with mismatch at the 1st base (% X1) and 2nd base (% X2).
DOI: 10.5281/zenodo.14505668
title: LLM-Generated Microservice Implementations from RESTful API Definitions

description: This project presents a novel system that utilized Large Language Models (LLMs) to automate API-first development of RESTful microservices, generating server-side code from OpenAPI specifications and refining it through log analysis.

To validate the system's effectiveness, we conducted surveys with six industry practitioners, collecting feedback on its impact, usability, and limitations. The dataset includes responses highlighting key advantages, such as improved development speed, task automation, and prototyping efficiency, as well as concerns about handling advanced customizations and large-scale projects.

This dataset serves as a valuable resource for researchers and developers aiming to assess and further enhance LLM-driven microservice development systems.
DOI: 10.5281/zenodo.14505669
title: LLM-Generated Microservice Implementations from RESTful API Definitions

description: This project presents a novel system that utilized Large Language Models (LLMs) to automate API-first development of RESTful microservices, generating server-side code from OpenAPI specifications and refining it through log analysis.

To validate the system's effectiveness, we conducted surveys with six industry practitioners, collecting feedback on its impact, usability, and limitations. The dataset includes responses highlighting key advantages, such as improved development speed, task automation, and prototyping efficiency, as well as concerns about handling advanced customizations and large-scale projects.

This dataset serves as a valuable resource for researchers and developers aiming to assess and further enhance LLM-driven microservice development systems.
DOI: 10.6084/m9.figshare.c.3608492_d1.v1
title: Additional file 1: Table S1. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: a Primers used for gap filling in the H602 mitochondrial genome, b Primers used for gap filling in the Haruna Nijo mitochondrial genome. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6122141
title: Celebration as a source of power in archaic states: archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands

description: Large celebrations in ancient societies, when viewed through the lens of political economy theory, were opportunities for economic redistribution, elite rivalry and social integration. Metrics to evaluate celebratory behaviour – such as festive gatherings, offerings at temples and shrines, games and memorials – remain underdeveloped. Here the author examines the archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands. He takes a direct historical approach combining independent datasets to classify settings of celebrations and evaluate claims that the Makahiki festival originated, and was most elaborate, on Hawai’i Island, as well as that the festival was practised differently across the archipelago. The author finds that the relevant data collected over more than a century of archaeology are not sufficient to support these claims and that the distribution of tracks for the sledding sport (<i>hōlua</i>) might be a fruitful avenue for future research, especially when investigating elite rivalry. More speculatively, the author argues that it is possible to decipher choices in architectural design and location at royal centres that speak to attempts by the elite to artificially increase the density of crowds at low turn-out events while at the same time leaving enough room to accommodate high turn-out events.
DOI: 10.6084/m9.figshare.6122141.v2
title: Celebration as a source of power in archaic states: archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands

description: Large celebrations in ancient societies, when viewed through the lens of political economy theory, were opportunities for economic redistribution, elite rivalry and social integration. Metrics to evaluate celebratory behaviour – such as festive gatherings, offerings at temples and shrines, games and memorials – remain underdeveloped. Here the author examines the archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands. He takes a direct historical approach combining independent datasets to classify settings of celebrations and evaluate claims that the Makahiki festival originated, and was most elaborate, on Hawai’i Island, as well as that the festival was practised differently across the archipelago. The author finds that the relevant data collected over more than a century of archaeology are not sufficient to support these claims and that the distribution of tracks for the sledding sport (<i>hōlua</i>) might be a fruitful avenue for future research, especially when investigating elite rivalry. More speculatively, the author argues that it is possible to decipher choices in architectural design and location at royal centres that speak to attempts by the elite to artificially increase the density of crowds at low turn-out events while at the same time leaving enough room to accommodate high turn-out events.
DOI: 10.6084/m9.figshare.c.3608465_d7.v1
title: Additional file 2: of Importins promote high-frequency NF-κB oscillations increasing information channel capacity

description: Computational model in BNGL. (BNGL 14 kb)
DOI: 10.6084/m9.figshare.c.3608495_d1.v1
title: MOESM1 of Adrenal suppression in children treated with swallowed fluticasone and oral viscous budesonide for eosinophilic esophagitis

description: Additional file 1. Eosinophilic esophagitis adrenal suppression dataset.
DOI: 10.6084/m9.figshare.6122141.v1
title: Celebration as a source of power in archaic states: archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands

description: Large celebrations in ancient societies, when viewed through the lens of political economy theory, were opportunities for economic redistribution, elite rivalry and social integration. Metrics to evaluate celebratory behaviour – such as festive gatherings, offerings at temples and shrines, games and memorials – remain underdeveloped. Here the author examines the archaeological and historical evidence for the Makahiki festival in the Hawaiian Islands. He takes a direct historical approach combining independent datasets to classify settings of celebrations and evaluate claims that the Makahiki festival originated, and was most elaborate, on Hawai’i Island, as well as that the festival was practised differently across the archipelago. The author finds that the relevant data collected over more than a century of archaeology are not sufficient to support these claims and that the distribution of tracks for the sledding sport (<i>hōlua</i>) might be a fruitful avenue for future research, especially when investigating elite rivalry. More speculatively, the author argues that it is possible to decipher choices in architectural design and location at royal centres that speak to attempts by the elite to artificially increase the density of crowds at low turn-out events while at the same time leaving enough room to accommodate high turn-out events.
DOI: 10.6084/m9.figshare.c.3608492_d2.v1
title: Additional file 8: Table S8. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: BLASTN analysis between the mitochondrial sequences of H602 and pseudomolecules of seven chromosomes and un-anchored scaffolds and contigs published in Ensembl Plants Hordeum vulgare (Hordeum_vulgare.ASM32608v1.31.dna_sm.genome.fa.gz). (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3608492_d3.v1
title: Additional file 2: Table S2. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: Primer pairs used for SNP analysis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3608501_d1.v1
title: Additional file 2: Table S2. of Quality of life effects of androgen deprivation therapy in a prostate cancer cohort in New Zealand: can we minimize effects using a stratification based on the aldo-keto reductase family 1, member C3 rs12529 gene polymorphism?

description: Data used in the analysis -Karunasinghe et al. BMC Urology 2016. All parameters used in the analysis except for age data (that has been removed for patient anonymity). (XLSX 52 kb)
DOI: 10.6084/m9.figshare.c.3608504_d1.v1
title: Additional file 3: of Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment

description: Supplementary File 2. Significant and total proteins identified by SILAC in HeLa Gal-7+ and SiHa Gal-7+ CxCa cells. (XLSX 9105 kb)
DOI: 10.6084/m9.figshare.c.3608492_d4.v1
title: Additional file 3: Table S3. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: a Contigs of the mitochondrial genome of H602 generated by 454 sequencing, b Contigs of the mitochondrial genome of Haruna Nijo generated by 454 sequencing. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3608492_d5.v1
title: Additional file 9: Table S9. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: SNP genotypes of 5 wild and 247 cultivated barleys. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3608513_d1.v1
title: Additional file 12: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: Characteristics of the 54 neogenes derived from DNA transposons in the human and RJF genomes. A table summarize the features of 54 genes derived from DNA transposons in the human and RJF genomes. (ODT 32 kb)
DOI: 10.6084/m9.figshare.c.3608492_d6.v1
title: Additional file 4: Table S4. of Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)

description: Genes identified in the mitochondrial genome of barley. (XLSX 18 kb)
DOI: 10.23708/j64o03
title: Cartographie des réseaux sociaux et des stratégies communautaires dans le sud de Madagascar (étude MAPNET) : outils méthodologiques, données d'enquête et documentation

description: Létude MAPNET Mapping social networks and community strategies in Southern Madagascar est une expertise collective conduite en 2019 pour la Banque mondiale. A quelle protection sociale les habitants du Sud de Madagascar ont-ils effectivement accès ? Alors que la politique nationale de protection sociale est en pleine reconfiguration à Madagascar, le taux de couverture de la population reste très faible et les dispositifs diffèrent largement d’une région à l’autre. Afin d’étudier les mécanismes de protection sociale effectivement accessibles localement, nous proposons la notion de système local de protection sociale, ou SLPS. Composante du système socio-écologique local, le SLPS produit et régule les pratiques de protection sociales accessibles au niveau local. Il est le produit d’interactions sociales multiples, régulées par les rapports sociaux encadrant les règles de réciprocité et de pouvoir. A partir de données empiriques originales, cette étude vise à caractériser les formes prises par le système local de protection sociale en pays Tandroy, région particulièrement vulnérable du Sud de Madagascar, et à étudier les inégalités d’accès à ce système, en fonction de caractéristiques socio-économiques-clé. La compréhension des dynamiques locales à différentes échelles (fokontany, ménage, personne) oblige à privilégier une approche mixte de production de donnée, articulant des éléments de diagnostic systémique, des enquêtes par questionnaires, des récits de vie, et d’entretiens collectifs auprès des organisations locales. Lenquête sest déroulée dans 6 sites : Beheloka et Maniry (zone Mahafaly), Ambahitra et Ambazoa (zone Androy), Mahatalaky et Ifotaka (zone Anosy) Nous présentons ici les outils méthodologiques, les données denquête et la documentation des 3 enquêtes de létude MAPNET : lenquête systémique, lenquête organisations locales (OL) et lenquête ménages-individus-réseaux (enquête MIR).
DOI: 10.6084/m9.figshare.c.3608513_d8.v1
title: Additional file 4: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: Diagram showing programs in both REPET TEdenovo and TEannot components. The programs below were run either successively or in parallel from top to bottom as indicated by the red triangles. The three programs in TEannot with blue or pink backgrounds were removed from our analyses and the outputs of the program in yellow were verified by hand. Note: RepeatMasker is part of the TEannot component. (ODT 73 kb)
DOI: 10.6084/m9.figshare.c.3608537_d1.v1
title: Additional file 1: Figure S1. of Relationships between mitochondrial content and bioenergetics with obesity, body composition and fat distribution in healthy older adults

description: Regression analysis comparing Vastus lateralis mitochondrial content, measured as citrate synthase enzyme activity with percent fat and subcutaneous thigh fat mass. (ODP 37 kb)
DOI: 10.15468/dl.qtk5q2
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Burmannia tenella Benth."
 ]
}

 The dataset includes 167 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016513-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3608522_d5.v1
title: Additional file 6: of Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine

description: Multiple regression analysis between phenotypic traits and population structure (genetic groups membership coefficients). R2 indicates the proportion of explained variance. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3608537_d2.v1
title: Additional file 2: Table S1. of Relationships between mitochondrial content and bioenergetics with obesity, body composition and fat distribution in healthy older adults

description: Respiratory Control Ratio Correlation Coefficients with Obesity and Total and Thigh Body Composition and Body Fat Distribution for All Participants and Split by Gender (ODP 32 kb)