cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2ddnq6
title: CCDC 2216708: Experimental Crystal Structure Determination

description: Related Article: Jing Sun, Fang Sun, Jiaqi Tang, Xiongkai Tang, Qingyuan Wu, Rong Huo, Ayisha He, Sachurilatu, Xueli Sun, Chaolumen, Qing Tang, Hui Shen|2023|Inorg.Chem.Front.|10|2618|doi:10.1039/D3QI00409K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7376059
title: Data for the publication "Addressing complexity in global aerosol climate model cloud microphysics"

description: This repository contains the data for the paper: Authors: Ulrike Proske, Sylvaine Ferrachat, and Ulrike Lohmann<br> Titel: Addressing complexity in global climate model cloud microphysics<br> Date: 2022 Note that the scripts can be found in the accompanying package (https://doi.org/10.5281/zenodo.7375978).
description: {"references": ["Proske et al. (2023). \"Addressing Complexity in Global Aerosol Climate Model Cloud Microphysics.\" Journal of Advances in Modeling Earth Systems 15, no. 5 (May 2023): e2022MS003571. https://doi.org/10.1029/2022MS003571."]}
DOI: 10.6084/m9.figshare.22732925
title: SUPPLEMENTAL TABEL 01

description: Primer sequences for RT-qPCR and Figure 5 statistics results from Bonferroni corrections
DOI: 10.6084/m9.figshare.22732925.v1
title: SUPPLEMENTAL TABEL 01

description: Primer sequences for RT-qPCR and Figure 5 statistics results from Bonferroni corrections
DOI: 10.15139/s3/ayofeu
title: Sex Differences in the Presentation of Tuberculosis in Uganda

description: Tuberculosis is a global disease that threatens both individual and public health. Tuberculosis, however, is a disease of disparities. Worldwide, it is more common in countries with low socioeconomic status or in settings overwhelmed by the HIV epidemic. But there is another disparity with tuberculosis that is not fully appreciated nor well understood: that is the disparity of tuberculosis between men and women. The World Health Organization, among others, has highlighted the untoward effects of tuberculosis on women, largely attributed to access to care and treatment, effects of pregnancy, and gender roles which diminish their social capital. Yet men have a higher incidence and prevalence of disease and may have worse outcomes with treatment compared to women. Biologic mechanisms may underlie some of these differences between men and women with tuberculosis. A complex interplay of endocrine, metabolic, and immune interactions likely affect the expression of M. tuberculosis. We hypothesize that total body energy stores, and the balance of that energy, determine the outcomes of tuberculosis, whether treated or not. Since the balance of fat and lean tissue differ in men and women, we further hypothesize that there will be differences in total energy stores between men and women at the time of diagnosis of tuberculosis. Finally, we hypothesize that the immune activation cause by infection with M. tuberculosis is modified by the hormonal milieu to affect metabolism of fat and protein in patients. We proposed to compare metabolic, immune, and hormonal profiles between men and women at the time of tuberculosis diagnosis. This study will lay the groundwork for future studies that can assess the effect of these differences on tuberculosis mortality and other treatment outcomes. The Specific Aims of the supplement are: 1. Compare immune and metabolic measures between men and women and relate them to total body energy as measured by body composition. 2. Discover new biomarkers by comparing RNA expression profiles between men and women presenting with tuberculosis.
DOI: 10.6084/m9.figshare.21970808
title: BinSPreader binning refining protocol

description: Metagenome analysis based on high-throughput sequencing data often includes contig binning as an essential step to recover complete genomes from metagenomic data (MAGs). Binning is carried out by clustering contigs, presumably belonging to the same species. Interspecies repeats, uneven coverage, and varying numbers of related strains make the assembly process difficult and therefore affect binning, as shorter contigs are often discarded by binners. In the original paper in STAR protocols journal (2023) we introduce instructions on how to refine binning with BinSPreader – a tool that corrects binning errors and propagates binning to shorter contigs using the assembly graph topology and other connectivity information. This repo contains all files that are needed to reproduce the protocol.
DOI: 10.6084/m9.figshare.21970808.v2
title: BinSPreader binning refining protocol

description: Metagenome analysis based on high-throughput sequencing data often includes contig binning as an essential step to recover complete genomes from metagenomic data (MAGs). Binning is carried out by clustering contigs, presumably belonging to the same species. Interspecies repeats, uneven coverage, and varying numbers of related strains make the assembly process difficult and therefore affect binning, as shorter contigs are often discarded by binners. In the original paper in STAR protocols journal (2023) we introduce instructions on how to refine binning with BinSPreader – a tool that corrects binning errors and propagates binning to shorter contigs using the assembly graph topology and other connectivity information. This repo contains all files that are needed to reproduce the protocol.
DOI: 10.25824/redu/2vlpqg
title: Raw Fermentative Data.tab
DOI: 10.25824/redu/stpoux
title: Dataset associated to master research: “Polyols: a study of the simultaneous biological production of xylitol and arabitol from agroindustrial waste"

description: The dataset contains raw experimental data of Candida tropicalis fermentation for the production of xylitol and arabitol from agroindustrial residues.
DOI: 10.6073/pasta/9cdfc8d6407d0b45648e53fa727c042e
title: Sediment pigment concentrations from lagoon sites along the Alaska Beaufort Sea coast, 2018-ongoing

description: The Beaufort Lagoon Ecosystems Long Term Ecological Research (BLE LTER) project seasonally collects undisturbed surface sediments during full ice cover (April), ice break-up (mid-June to early July), and open water (late July and August) periods from lagoon sites along the Beaufort Sea (Elson, Simpson, Jago, and Kaktovik lagoons, plus Stefansson Sound) to quantify algal pigment concentrations. Pigments reported are chlorophyll a, pheophorbide, pheophytin, chlorophyllide, fucoxanthin, zeaxanthin, alloxanthin, and peridinin. Pigment concentrations are measured using high-precision liquid chromatography (HPLC). Concentrations are represented both as an areal basis (mg/m2 of surface sediment) and a mass basis (μg/g of dry sediment). In 2022 we found that a post-analysis mathematical error generated incorrect concentration values for pigments. This error was identified in subsequent QA/QC and immediately corrected since the raw data were not in error. The entire dataset to date (2018-2021) was revised in spring 2022 with the corrected data (revision knb-lter-ble.12.2).
DOI: 10.5281/zenodo.7885458
title: From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

description: With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus <em>Pocillopora</em>, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus <em>Pocillopora</em>. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em>, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species. This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific <em>Pocillopora </em>corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803 See 0_README.txt for more content details.
description: {"references": ["Oury N, No\u00ebl C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803"]}
DOI: 10.5281/zenodo.7885457
title: From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

description: With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus <em>Pocillopora</em>, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus <em>Pocillopora</em>. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em>, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species. This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific <em>Pocillopora </em>corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803 See 0_README.txt for more content details.
description: {"references": ["Oury N, No\u00ebl C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803"]}
DOI: 10.3886/e136741v1-137820
title: Data and Code for: Historical Lynching and the Contemporary Voting Behavior of Blacks

description: This file contains the data replication files for Historical Lynchings and the Contemporary Voting Behavior of Blacks. This paper analyzes the extent to which the political participation of blacks can be traced to historical lynchings that took place from1882 to 1930. Using county-level voter registration data, I show that blacks who reside in southern counties that experienced a relatively higher number of historical lynchings have lower voter registration rates today. This relationship holds after accounting for a variety of historical and contemporary characteristics of counties. There exists evidence of the persistence of cultural voting norms among blacks yet this relationship does not exist for whites.
DOI: 10.34943/c775dbf4-b65f-4765-b508-65726fec0085
title: Fraser River Delta Upper Slope Acoustic Doppler Current Profiler 300 kHz Deployed 2021-03-25

description: The RDI Workhorse Monitor ADCP 300 kHz (15551) was deployed on 2021-03-25 at Fraser River Delta Upper Slope. This site is located on the upper slope of the Fraser River delta, where depth is approximately 100 metres. This device is a Acoustic Doppler Current Profiler 300 kHz. Acoustic Doppler Current Profilers (ADCP) are hydroacoustic instruments, similar to sonars. ADCPs measure current speed and direction at multiple predetermined depths simultaneously. ADCPs use the Doppler effect of sound waves that are scattered by particles in seawater over a depth range. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/f3b0685f-e13a-4d24-ae38-16e3e586cd31
title: Fraser River Delta Upper Slope Acoustic Doppler Current Profiler 300 kHz Deployed 2021-03-25

description: The RDI Workhorse Monitor ADCP 300 kHz (15551) was deployed on 2021-03-25 at Fraser River Delta Upper Slope. This site is located on the upper slope of the Fraser River delta, where depth is approximately 100 metres. This device is a Acoustic Doppler Current Profiler 300 kHz. Acoustic Doppler Current Profilers (ADCP) are hydroacoustic instruments, similar to sonars. ADCPs measure current speed and direction at multiple predetermined depths simultaneously. ADCPs use the Doppler effect of sound waves that are scattered by particles in seawater over a depth range. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 2.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.3886/e136741v1-137821
title: Data and Code for: Historical Lynching and the Contemporary Voting Behavior of Blacks

description: This file contains the data replication files for Historical Lynchings and the Contemporary Voting Behavior of Blacks. This paper analyzes the extent to which the political participation of blacks can be traced to historical lynchings that took place from1882 to 1930. Using county-level voter registration data, I show that blacks who reside in southern counties that experienced a relatively higher number of historical lynchings have lower voter registration rates today. This relationship holds after accounting for a variety of historical and contemporary characteristics of counties. There exists evidence of the persistence of cultural voting norms among blacks yet this relationship does not exist for whites.
DOI: 10.3886/e136741v1-137822
title: Data and Code for: Historical Lynching and the Contemporary Voting Behavior of Blacks

description: This file contains the data replication files for Historical Lynchings and the Contemporary Voting Behavior of Blacks. This paper analyzes the extent to which the political participation of blacks can be traced to historical lynchings that took place from1882 to 1930. Using county-level voter registration data, I show that blacks who reside in southern counties that experienced a relatively higher number of historical lynchings have lower voter registration rates today. This relationship holds after accounting for a variety of historical and contemporary characteristics of counties. There exists evidence of the persistence of cultural voting norms among blacks yet this relationship does not exist for whites.
DOI: 10.6084/m9.figshare.7732814.v1
title: Narceus_americanus_2009.csv

description: Narceus_americanus_2009.csv<br>Measurements from Narceus americanus corpses collected two different days in 2009 on Tuckernuck Island, Nantucket County. All the millipedes were missing their heads. All were collected along the dirt roads around the island.<br>Data dictionary:MillipedeID: A number that corresponds to the picture of 13 corpses.<br>Date: Date the corpse was recovered.<br>Intact Segments Left: Count of the number of undamaged segments on the body.<br>Condition: A subjective measure of how recently the head had been removed<br>Length: length of corpse in mm<br>Width @ middle: width of corpse halfway along length in mm<br>13JuneHeadlessLineup1 small.jpgPhoto of the first 13 millipedes measured.<br><br>
DOI: 10.3886/e136741v1-137823
title: Data and Code for: Historical Lynching and the Contemporary Voting Behavior of Blacks

description: This file contains the data replication files for Historical Lynchings and the Contemporary Voting Behavior of Blacks. This paper analyzes the extent to which the political participation of blacks can be traced to historical lynchings that took place from1882 to 1930. Using county-level voter registration data, I show that blacks who reside in southern counties that experienced a relatively higher number of historical lynchings have lower voter registration rates today. This relationship holds after accounting for a variety of historical and contemporary characteristics of counties. There exists evidence of the persistence of cultural voting norms among blacks yet this relationship does not exist for whites.
DOI: 10.6084/m9.figshare.22734056
title: Deus ex machina tool - Confusion matrix computation analyses

description: Deus ex machina tool - Confusion matrix computation analyses <br> The <em>Deus ex machina</em> code is available on GitHub via this link: https://github.com/code56/ontologiesreproducibility.git Briefly, the code performs semantic annotations on PDF articles and their associated ArrayExpress XML files and computes a Reproducibility Metric Score (RMS) based on various assessment parameters. The case studies are in the field of wheat crop transcriptomics. The accuracy of the Deus ex machina tool of correctly annotating the Plant Ontology terms within wheat transcriptomic articles, was assessed by comparing the manually annotated results and the automatically annotated results, produced by the Deus ex machina tool, with the help of a confusion matrix. The Excel file has 3 tabs that show in detail all the computation analyses (manual annotation of the papers) and the automatic annotation results by the Deus ex machina tool. Some terms were not possible to assign a specific ontology term with confidence (this is the issue where authors did not clarify the terms and describe their research using standardised ontology terms), and these terms are denoted clearly in the computation analysis file. Nonetheless, as the terms were only a few, they do not affect the results of the confusion matrix to any significant degree.
DOI: 10.6084/m9.figshare.22734062
title: Traffic and roadkill data 2023

description: Traffic, road attributes and roadkill data 2023
DOI: 10.6084/m9.figshare.22734062.v1
title: Traffic and roadkill data 2023

description: Traffic, road attributes and roadkill data 2023
DOI: 10.5281/zenodo.7515737
title: Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

description: This archive contains all the code and data to reproduce the results of the associated manuscript: Piovani <em>et al</em>, "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories". We provide filtered scRNA-seq matrices, protein fasta files for each specie used to run SAMap and GenERA as well as the R-code used to generate the datasets and the jupyter notebook to generate SAMap results. In addition we provide the final Seurat objects and all analysis results which can be consulted without re-running the code.
DOI: 10.5281/zenodo.7515738
title: Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

description: This archive contains all the code and data to reproduce the results of the associated manuscript: Piovani <em>et al</em>, "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories". We provide filtered scRNA-seq matrices, protein fasta files for each specie used to run SAMap and GenERA as well as the R-code used to generate the datasets. In addition we provide the final Seurat objects and all analysis results which can be consulted without re-running the code.
DOI: 10.5281/zenodo.7887050
title: Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

description: This archive contains all the code and data to reproduce the results of the associated manuscript: Piovani <em>et al</em>, "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories". We provide filtered scRNA-seq matrices, protein fasta files for each specie used to run SAMap and GenERA as well as the R-code used to generate the datasets and the jupyter notebook to generate SAMap results. In addition we provide the final Seurat objects and all analysis results which can be consulted without re-running the code.