cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19606063.v1
title: Janiak et al. 2022 Molecular Ecology - mtDNA of Amazonian primates

description: Files and data associated with the following publication: Janiak et al. (2022). 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. <em>Molecular Ecology</em>. We assembled new mitochondrial genomes (with https://github.com/RemiAllio/MitoFinder) for platyrrhine primates, most from the Amazon and with known sampling locations and used the data to assess support for the long-standing Riverine Barrier Hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Mitochondrial genomes are available on GenBank (accession numbers OM328861-OM329065), underlying Illumina short reads are available at ENA project ID PRJEB49549, and scripts to run analyses are available on GitHub (https://github.com/MareikeJaniak/Platyrrhine-mtDNA) and archived at 10.6084/m9.figshare.19610187. Files included: <strong>mitoFinder_results_final_length_cov_MolEcol.txt</strong> - lengths and coverages of all final mitochondrial contigs assembled with MitoFinder <strong>mitoFinder_results_multiple_contigs_all.txt</strong> - lengths and coverage of all contigs for samples for which multiple mitochondrial contigs were assembled by MitoFinder <strong>mtDNA_plat.untrimmed.aln.fasta</strong> - full alignment of mitochondrial genomes newly assembled by us, published platyrrhine mitogenomes, and six non-platyrrhine outgroups <strong>mtDNA_plat.July2021.trimmed.noND6.aln.nex</strong> - trimmed alignment of mitochondrial genomes newly assembled by us, published platyrrhine mitogenomes, and six non-platyrrhine outgroups with partitions, used as input to BEAUti to generate xml file for BEAST2 analysis <strong>mtDNA_plat_bModelTest_relaxedClock.xml</strong> - input file for BEAST2 analysis generated with BEAUti <strong>mtDNA_plat.trimmed.noND6.noProsim.aln.fasta </strong>- trimmed alignment used to build ML tree with RAxML and used as input for mPTP lineage delimitation <strong>partitions.txt</strong> - used as input for RAxML <strong>mtDNA_plat.trimmed.noND6.noProsim.tree</strong> - ML tree generated with RAxML, uesd as input for mPTP lineage delimitation <strong>mtDNA.chain1chain2.combo.posterior.trees.tree </strong>- posterior trees from BEAST2 analysis, used to retrieve node age estimate distributions and to generate MCC tree <strong>mtDNA.chain1chain2.combo.MCC.tree</strong> - maximum clade credibility tree from BEAST2 analysis, generated with TreeAnnotator <strong>SupplementalData_metadata_mtDNA_full.xlsx </strong>- Complete metadata for all samples, including sequencing, sample, and voucher specimen IDs where available; GenBank accession numbers; geographic coordinates of sample locations <br>
DOI: 10.6084/m9.figshare.27115516.v1
title: Data and code associtated with, "Experimental coral reef communities transform yet persist under mitigated future ocean warming and acidification"

description: This study examined the development of mesocosm coral reef communities over the course of about 2 years under warming (+2 C), acidification (-0.2 pH units) and the combination of both factors.
DOI: 10.6084/m9.figshare.29126396.v1
title: STRING Network Analysis

description: Significantly upregulated mRNAs (2,777 genes; p &lt; 0.05) identified by bulk RNA-seq were analyzed using the STRING module in Cytoscape v.2.2.0 (Institute for System Biology; WA; USA). A cluster network was constructed using the MCL algorithm with a granularity parameter of 4, followed by filtering nodes with mcl.cluster &gt; 10. The resulting 1,848 nodes were processed through STRING v12.0 (Swiss Institute of Bioinformatics; Lausanne; Switzerland) to generate a protein–protein interaction (PPI) network, incorporating evidence from text mining, genomic neighborhood, experimental data, curated databases, co-expression, gene fusion, and co-occurrence, with a minimum confidence score threshold of 0.40. Network modules were defined using the DBSCAN clustering algorithm with an ε parameter of 2. Cluster 1, representing the largest gene set (101 genes), was further analyzed by sorting the top 20 nodes with the highest node degree, resulting in a network comprising 101 nodes and 756 edges. Global network metrics indicated an average node degree of 15, a local clustering coefficient of 0.600, and a PPI enrichment p-value of &lt; 1 × 10⁻¹⁶. The average values of coexpression, experimentally determined interactions, automated text mining, and combined scores were calculated.
DOI: 10.17632/2r2jcxv88b
title: Urogenital gonorrhea in Mexico (2003-2020): impact of the COVID-19 pandemic on its epidemiological behavior  Gonorrea urogenital en México (2003-2020): impacto de la pandemia de COVID-19 en su comportamiento epidemiológico

description: Data set: Urogenital gonorrhea in Mexico (2003-2020): impact of the COVID-19 pandemic on its epidemiological behavior. Gonorrea urogenital en México (2003-2020): impacto de la pandemia de COVID-19 en su comportamiento epidemiológico
DOI: 10.6084/m9.figshare.14215850.v1
title: EmoMatchSpanishDB

description: These are the two datasets features used and described in the research paper entitled "EmoMatchSpanishDB: Study of Machine Learning Models in a New Spanish Elicited Dataset".<br>In this paper we address the task of real time emotion recognition for elicited emotions. For this purpose we have created a publicly accessible dataset composed by ﬁfty subjects expressing the emotions of anger, disgust, fear, happiness, sadness, and surprise in Spanish language. In addition, a neutral tone of each subject has been added. This article describes how this database have been created including the recording and the performed crowdsourcing perception test in order to statistically validate the emotionof each sample and remove noisy data samples. Moreover we present a baseline comparative study between different machine learning techniques in terms of accuracy, speciﬁcity, precision, and recall. Prosodic and spectral features are extracted and used for this classiﬁcation purpose. We expect that this database will be useful to get new insights within this area of study.<br>The first dataset is "EmoSpanishDB" that contains a set of 13 and 140 spectral and prosodic features for a total of 3550 audios of 50 individuals reproducing the 12 sentences for the six different emotions, ’anger, disgust, fear, happiness, sadness, surprise’ (Ekman’s basic emotions]) plus neutral.<br>The second dataset is "EmoMatchSpanishDB" and contains a set of 13 and 140 spectral and prosodic features for a total of 2050 audios of 50 individuals reproducing the 12 sentences for the six different emotions, ’anger, disgust, fear, happiness, sadness, surprise’ (Ekman’s basic emotions]) plus neutral. These 2050 audios' features are a subset of EmoSpanishDB resulting of the matched audios after application of a crowdsourcing process to validate that the elicited emotion corresponds with the expressed.<br><br>These datasets have been used in the paper "EmoMatchSpanishDB: Study of Machine Learning Models in a New Spanish Elicited Dataset" and their creation, its contents, and also a set of baseline machine learning experiments and results are fully described within it.<br>The features are available under MIT license and if you want to get access to the original raw audio files for creating your own features and research purposes you can get them under CC-BY-NC sending an email to esteban.garcia@upm.es or antonio.barba@universidadeuropea.es
DOI: 10.6084/m9.figshare.19753477.v1
title: Supplementary Material for: Fenretinide Reduces Intestinal Mucin-2-Positive Goblet Cells in Chronic Alcohol Abuse

description: <b><i>Introduction:</i></b> Alcohol-induced thickening of the gut mucosal layer and increased expression of goblet cell gel-forming mucins, such as mucin-2 (<i>MUC2</i>) are associated with disruptions to the gut barrier in alcoholic liver disease (ALD). Interest in drugs that can target gut mucins in ALD has grown; however to date, no studies have examined the properties of drugs on expression of gut mucins in models of ALD. We previously demonstrated that at 10 mg/kg/day, the drug fenretinide (N-[4-hydroxyphenyl] retinamide [Fen]), a synthetic retinoid, mitigates alcohol-associated damage to the gut barrier and liver injury in a murine model of ALD. <b><i>Methods:</i></b> In this study, we specifically sought to examine the effects of Fen on gut goblet cells, and expression of mucins, including <i>MUC2</i> using a 25-day Lieber-DeCarli model of chronic alcohol intake. <b><i>Results:</i></b> Our results show that chronic alcohol intake increased gut-mucosal thickening, goblet cell numbers, and mRNA and protein expression of <i>MUC2</i> in both the ileum and colon. Alcohol intake was associated with marked decreases in ileal and colonic Notch signaling, levels of Notch ligands <i>Dll1</i> and <i>Dll4</i>, and increases in the expression of Notch-associated genes indispensable for goblet cell specification, including Math1 and Spdef. Interestingly, ileal and colonic expression of <i>KLF4</i>, which is involved in terminal differentiation of goblet cells, was reduced in mice chronically fed alcohol. Coadministration of alcohol with Fen at 10 mg/kg/day significantly reduced alcohol-associated increases in ileal and colonic mucosal thickening, ileal <i>Muc2</i>, colonic <i>Muc2</i>, <i>Muc5ac</i> and <i>Muc6</i> mRNAs, and goblet cell numbers. We also found that Fen strongly prevented alcohol-mediated suppression of the Notch ligand <i>Dll1</i>, Notch signaling, and alcohol-induced increases in expression of Notch-associated goblet cell specification genes in both the ileum and colon. In the absence of alcohol, Fen treatments alone at 10 mg/kg/day had no effects on any of the goblet cell-related endpoints. <b><i>Conclusion:</i></b> These data show for the first time that the drug Fen possesses mucosal layer-modulating properties in response to chronic alcohol abuse. These data warrant further preclinical examination of Fen given the need for anti-ALD drugs and emerging evidence of a role for intestinal goblet cell mucins in the progression of ALD.
DOI: 10.6084/m9.figshare.22913123.v1
title: Social support and education, siblings.sav

description: This parent’s social support includes emotional/informational, tangible, affectionate, positive social, and additional. Emotional/informational support consists of 8 questionnaire items. Tangible support consists of 4 questionnaire items. Affectionate support consists of 3 questionnaire items. Positive social support consists of 3 questionnaire items. Additional support consists of 1 questionnaire item. The questions assess parental behaviors towards the child and are answered using a closed-ended format with Likert scale response options ranging from "never" to "always." This questionnaire consists of four separate social support subscales and an overall functional social support index. Test the validity and reliability with a score of 0.91.
DOI: 10.6084/m9.figshare.28751114.v1
title: Supplementary Dataset – Grey Literature Review (GLR) on Code and Community Smells in Code Samples.xlsx

description: This supplementary dataset contains the list of 17 grey literature sources selected for the Grey Literature Review (GLR) conducted in the study on the co-occurrence and evolution of Code Smells and Community Smells in open-source code samples. <br>Each entry in the dataset includes:- A document label (D1 to D17),- The document title,- A persistent or accessible URL source.<br>These documents were selected based on their relevance to the research questions, quality of information, and alignment with the socio-technical context of code samples in software development. The dataset supports the transparency, reproducibility, and open science principles adopted in this research.
DOI: 10.17632/rmn843c3bk
title: Ohio municipal solid waste landfill leachate volumes and surface areas

description: This dataset includes monthly leachate volumes (in gallons) and surface areas (in square feet) for municipal solid waste (MSW) landfills in Ohio, USA. The leachate data are categorized in a delimited text file (Ohio_Leachate_Volumes.csv) organized under header columns: (A) Year, (B) Month, (C) Landfill name, (D) Identification Number, (E) Date, (F) Leachate Volume (gallons), (G) Management Type, (H) Management Description, (I) Location, and (J) Notes. Management Types are Disposed, Generated, Recycled, Treated On-Site, or Stored. Management Descriptions are Discharged, Hauled, Recirculated, Solidified, Sprayback, Evaporated, or Stored. Data are from 1988-2020. Data are complete based on available documentation but not all annual reports were available for all landfills in all years. The surface area data are categorized in a delimited text file (Ohio_Landfill_Surface_Areas.csv) organized under header columns: (A) Year, (B) Landfill Name, (C) Identification Number, (D) Surface Area Containing Waste (square feet), (E) Notes, and (F) Data Source. The Dataset_Readme.csv provides additional information for potential users.

The Dataset_Readme.csv summarizes the datasets.

The SurfaceArea_Comparison.xlsx workbook compares the surface area dataset developed here with an existing surface area dataset within the US Environmental Protection Agency's Greenhouse Gas Reporting Program (GHGRP). The comparison is meant to evaluate the accuracy of this dataset.

The dataset has been summarized in the article "Dataset of leachate volumes and surface areas for municipal solid waste (MSW) landfills in Ohio, USA from 1988-2020" within the Data in Brief journal. Data_for_DIB_Figures.xlsx contains the raw data for Figures 1-6 within that text. Figure 7 contains no data.
DOI: 10.6084/m9.figshare.13412246.v1
title: [IDT2] Integrated DNA Technologies xGen Non-small Cell Lung Cancer ctDNA assay

description: Variant calling with the Integrated DNA Technologies xGen Non-small Cell Lung Cancer ctDNA assay
DOI: 10.6084/m9.figshare.14073692.v1
title: Dataset Political Personalism in Social Media

description: This dataset covers
aspects of online politics in 25 democracies: 15 relatively old established
European democracies (Austria, Belgium, Denmark, Finland, France, Germany,
Iceland, Ireland, Italy, Luxembourg, Netherlands, Norway, Sweden, Switzerland,
United Kingdom); five non-European veteran democracies (Australia, Canada,
Israel, Japan, New Zealand); two early (Portugal, Spain) and three late (Czech
Republic, Hungary, Poland) third-wave (young) European democracies. The
research population includes, in each country, parties that won 4% or more of
the votes in two consecutive elections before April 2019 (a total of 141
parties<sup> </sup>and 145 leaders). The dataset includes external party level
information such as performance in the last national elections, governmental
status, party age, populism affiliation and leadership selection method. It
also includes information related to the party leaders such as their term in
leadership office and other formal positions. In addition it includes
information about online activity mainly on the consumption (user related
activities) of the parties and their leaders in Facebook and Twitter two of the
most used social media platforms for political purposes.
DOI: 10.6084/m9.figshare.14618403.v1
title: Contamination Fileset 3.1 (40-fold Coverage) 210511

description: These data are the 40-fold versions of data provided and analyzed in https://doi.org/10.1186/s13059-019-1914-x.
DOI: 10.6084/m9.figshare.25908040.v1
title: Surveys_Perceptions of Generative AI.xlsx

description: Survey of people's perceptions towards generative AI constructed multimedia content.
DOI: 10.17632/4xntsrdjv8
title: CAD model of an aesthetic wooden chair

description: Presented here is a CAD model of an aesthetic wooden chair. This can be used in 3D printing, or in manufacturing the chair. Also attached is the drawing of the CAD.
DOI: 10.17632/833pdbrhdr
title: Anthropometric Data Compilation for Children in Jordan: A Comprehensive Dataset

description: 354 children (6 months – 9 years age range) were considered for the analysis and the anthropometric measurements are 23 measures namely: stature, sitting height, back of the head height, ear height sitting, eye height sitting, height of prominent neck vertebra, shoulder height sitting, chest depth, lower abdominal depth, waist height sitting, hip breadth sitting, underside of elbow height to floor (sitting), underside of elbow height to seat (sitting), back of elbow to wrist crease, shoulder breadth, back of elbow to fingertip, shoulder finger tips depth, palm breadth, hand breadth, wrist breadth, index finger height, middle finger height, seat height, popliteal height (sitting), top of knee height (sitting), lumbar popliteal depth.
DOI: 10.17632/df45bjhby3
title: Immunoblots for Taylor et al. version 2

description: uncropped western blots associated with Taylor et al. October, Cell Host Microbe, 2023
DOI: 10.17632/kn3jz5m4gt
title: Supplementary Tables - Tumoral Melanosis

description: Summary of currently published de novo tumoral melanosis cases illustrated in two tables as follows: table 1 describing de novo tumoral melanosis cases and table 2 describing a subset of cases with lymph node involvement.
DOI: 10.34740/kaggle/dsv/12022301
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.6084/m9.figshare.21757703.v1
title: ELISA AngII.xlsx

description: raw data-ELISA
DOI: 10.6084/m9.figshare.28578947.v2
title: <b>A global dataset mapping the AI innovation from academic research to industrial patents</b>

description: The DeepInnovationAI dataset consists of three primary CSV files: DeepPatentAI.csv (patent data), DeepDiveAI.csv (academic paper data), and DeepCosineAI.csv (containing most relevant paper-patent pairs).
DOI: 10.6084/m9.figshare.9644990.v1
title: Hervías-Parejo et al. 2019_Functional Ecology_Drivers of bird linkage level in coupled pollination and seed-dispersal networks.

description: Bird-plant interaction data sampled on two Galápagos islands by collecting pollen and faecal samples from individual birds captured with mist-nets across an entire year.<br>
DOI: 10.17632/hdtv3vvhs2
title: Database_Anthropometric and Physical characteristics

description: Database of Anthropometric and Physical characteristics U16, U18, U20
DOI: 10.6084/m9.figshare.19287920.v1
title: Checklist of metrics used in studies on the assessment of biotic integrity in estuaries

description: Here is presenting a checklist of metrics used in studies on the assessment of biotic integrity in estuaries.
DOI: 10.6084/m9.figshare.22227490.v1
title: Preclinical CBCT scans

description: CBCT datasets to accompany "Feasibility and guidelines for the use of an injectable fiducial marker (BioXmark®) to improve target delineation in preclinical radiotherapy studies using mouse models."
DOI: 10.6084/m9.figshare.28294727.v1
title: Physiological response of <i>Neoseiulus bicaudus</i> to cold acclimation

description: Physiological response of <i>Neoseiulus bicaudus</i> to cold acclimation
DOI: 10.6084/m9.figshare.6446027.v1
title: Supplementary Material for: Advanced Mucinous Colorectal Cancer: Epidemiology, Prognosis and Efficacy of Chemotherapeutic Treatment

description: <b><i>Background:</i></b> The clinicopathological significance of the mucinous subtype of colorectal cancer (CRC) remains controversial. As of today, none of the current guidelines differentiate treatment with respect to mucinous or nonmucinous cancer. Due to the lack of substantiated data, best treatment remains unclear and the mucinous subtype of CRC is usually treated along the lines of recommendations for adenocarcinoma of the colon. <b><i>Methods:</i></b> We investigated an East-Bavarian cohort of 8,758 patients with CRC. These included 613 (7.0%) patients with a mucinous subtype, who were analyzed for assessing their characteristics in clinical course and for evaluating the efficacy of common chemotherapy protocols. <b><i>Results and Conclusion:</i></b> Mucinous CRC was predominantly located in the right hemicolon; it was diagnosed at more advanced stages and occurred with preponderance in women. A higher rate of G3/4 grading was observed at diagnosis (all <i>p</i> &lt; 0.001). An association of mucinous CRC with younger age at initial diagnosis, previously reported by other groups, could not be confirmed. Patients with mucinous stage IV colon cancer demonstrated poorer survival (<i>p</i> = 0.006). In contrast, no differences in survival were observed for specific stages I–III colon cancer. Stage-dependent analysis of rectal cancer stages I–IV also showed no differences in survival. However, univariable overall analysis resulted in significant poorer survival of mucinous compared to nonmucinous rectal cancer (<i>p</i> = 0.029). Also, combined analysis of all patients with mucinous CRC revealed poorer overall survival (OS) of these patients compared to nonmucinous CRC patients (median 48.4 vs. 60.2 months, <i>p</i> = 0.049) but not in multivariable analysis (<i>p</i> = 0.089). Chemotherapeutic treatment showed comparable efficacy regarding OS for mucinous and nonmucinous cancers in both an adjuvant and palliative setting for colon cancer patients (<i>p</i> values comparing mucinous and nonmucinous cancers &lt; 0.001–0.005).
DOI: 10.17632/yhgdzfpnym
title: Irish Building Energy Rating Database - (Cleaned 05/10/2023)

description: Found in the database of the Sustainable Energy Authority of Ireland, other than occasional erroneous entries, when a field is unknown the chosen default imputed values used are based on pessimistic estimates. Especially with the economic bounce back in Ireland, these values have become unrepresentative and skewed. It was determined that a more representative alternative be used. Research into this has provided a cleaning methodology that can be used to extract and process information the database.

This dataset contains a cleaned pull from the BER database that occurred on the 5th October 2023.
DOI: 10.6084/m9.figshare.24235444.v1
title: Extended Data Table 1.xlsx

description: This is CO2/SO2 time series from measurements of gas emissions during the 2021 eruption of Tajogaite, La Palma
DOI: 10.6084/m9.figshare.3115156.v1
title: Common Workflow Language, draft 3

description: <pre>The Common Workflow Language (CWL) is an informal, multi-vendor working group consisting of various organizations and individuals that have an interest in portability of data analysis workflows. Our goal is to create specifications that enable data scientists to describe analysis tools and workflows that are powerful, easy to use, portable, and support reproducibility.</pre><pre>CWL builds on technologies such as JSON-LD and Avro for data modeling and Docker for portable runtime environments. CWL is designed to express workflows for data-intensive science, such as Bioinformatics, Medical Imaging, Chemistry, Physics, and Astronomy.</pre><pre>This is draft 3 of the CWL tool and workflow specification, released on 2016-02-05.</pre><pre>The specification, in HTML format, is in the draft-3/docs folder.</pre>
DOI: 10.6084/m9.figshare.7938122.v1
title: gVCF_NA20511

description: 1000 Genomes gVCF mapped to hs37d5 for NA20511. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307