cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16922764.v1
title: Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

description: Ribosomal DNA (rDNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large scale exploration of environmental microbial diversity through metabarcoding approaches have been focused mainly on the hypervariable regions V4 and V9 of the 18S rDNA gene. Yet, the accurate interpretation of such environmental surveys is hampered by technical (e.g., PCR and sequencing errors) and biological biases (e.g., intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with two different high-throughput sequencing platforms: Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet in some Spumellaria specimens we found two different copies of the V4 with a similarity lower than 97%. From the different sequencing methods, Illumina showed the highest number of contaminations (i.e., environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and Minion showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results, highlight the requirement for a careful interpretation of Illumina based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full environmental rDNA metabarcoding surveys.<br><br>Here you can find 7 files gathering raw data obtained in this study and its associated metadata:<br>Data obtained by <b>Sanger</b> sequencing:<br>sanger_raw.fasta.gz: A fasta file containing the sequences with the following sequence names: "Cell-identifier_primer_barcode_well"; please note the underscore delimiting fields.<br>Data obtained by <b>MinION (ONT)</b> sequencing:minion_raw.fastq.gz: Fastq file.minion_raw.fast5.tar.gz: Fast5 native MinION raw data for future implementations or re-analysis.info_minion_demultiplex.txt: The information file for demultiplexing MinION data.<br>Data obtained by <b>Illumina</b> sequencing: R1.fastq.gz: R1 fastq file.R2.fastq.gz: R2 fastq file.info_illumina_tags_cutadapt.txt: The information file for demultiplexing Illumina data.<br><br>For further details or if using these datasets, please see/cite the following study:<br>Sandin MM, Romac S, Not F (2021) <b>Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing</b>. <i>bioRxiv</i> 2021.10.05.463214; doi: doi.org/10.1101/2021.10.05.463214<br>
DOI: 10.6084/m9.figshare.25650960.v1
title: Supplementary Data from "Shell biomechanics suggests an aquatic palaeoecology at the dawn of turtle evolution"

description: In this Supplementary Dataset you will find:meshes_for_FEA.zip: the .stl files used as input to Hypermesh for the Finite Element AnalysesR-script_data.zip: a folder containing (<b>i:</b> Ferreira_et_al-SciRep.R) the R script used for the geometric morphometric analyses, calculation of average stress per element, and plotting figures; (<b>ii</b>) .stl and .pts files containing the landmark data for <i>Proganochelys </i>and <i>Proterochersis</i>; (<b>iii:</b> turtle_landm-1.csv) the original landmark dataset used in Stayton et al. (2018); (<b>iv:</b> species_data.csv) habitat and classification data for the species analysed (<b>v:</b> all-data.RData) the RData object.Stress-per-element-: four zip folders containing the stress values for each element in the four taxa analysed.<br>
DOI: 10.6084/m9.figshare.28311542.v1
title: Routine Performance Data 2017-2020.xlsx

description: This is a performance database showcasing routine performance data collected through the Adolescents 360 (A360) project's first investment phase from 2016-2020. The database presents key indicators tracked by the project over the course of 2.5 years of implementation. The definitions for these key indicators are provided below. Adopter numbers as reported in the database are also disaggregated by key variables, including (1) specific age of adopter; (2) method of uptake; and (3) region / state of adoption. <br><b>Key Performance Indicator</b><b>Definition</b><b>Ethiopia</b><b>Nigeria</b><b>Tanzania</b><b>Girls Reached / Attendees</b>The number of girls aged 15-19 years old who received counseling through <i>Smart Start</i> at active sites.The number of girls aged 15-19 who were registered as attending a <i>9ja Girls / MMA</i> clinic or event to receive services.The number of girls aged 15-19 who were issued a referral at <i>Kuwa Mjanja</i> events during outreach (in theory all girls attending events received a referral).<b>Adopters</b>The number of girls aged 15-19 who were not using a modern method of contraception at the time of receiving services and did not use emergency contraception (EC) or a condom at last sex who took up a modern method of contraception after attending <i>Smart Start</i> counseling.The number of girls aged 15-19 who were not using a modern method of contraception at the time of receiving services and did not use emergency contraception (EC) or a condom at last sex who took up a modern method of contraception at a <i>9ja Girls / MMA</i> clinic or event.The number of girls aged 15-19 who had never used a modern method of contraception previously who took up a modern method at a <i>Kuwa Mjanja </i>event.<b>Continuing Users</b>The number of girls aged 15-19 who attended a <i>Smart Start</i> counseling session and confirmed that they were using a modern method of contraception at the time of receiving services.The number of girls aged 15-19 that attended a <i>9ja Girls / MMA</i> clinic or event who received counseling and were using a modern method of contraception at the time of receiving services, inclusive of those who switched methods.The number of girls aged 15-19 who attended a <i>Kuwa Mjanja</i> event who received counseling and were using a modern method of contraception at the time of receiving services, inclusive of those who switched methods.<b>Conversion Rate</b>The proportion of girls counseled through Smart Start who were not pregnant or continuing users who adopted a modern method at the time of <i>Smart Start</i> counseling.The proportion of girls attending <i>9ja Girls / MMA</i> clinics or events who were not pregnant or continuing users who took up a modern method of contraception at the time of receiving counseling through <i>9ja Girls / MMA.</i>The proportion of girls receiving a referral who were not recorded as pregnant or continuing users who took up a modern method of contraception at a <i>Kuwa Mjanja</i> event.
DOI: 10.6084/m9.figshare.28738244.v29
title: Logic innovation

description: Logic innovation 9-pdf
DOI: 10.6084/m9.figshare.22220011.v1
title: Clothing8

description: clothing classfication
DOI: 10.6084/m9.figshare.23797077.v1
title: FT-IR raw data from plastic debris at Kung Wiman beach

description: FT-IR raw data from plastic debris at Kung Wiman beach
DOI: 10.6084/m9.figshare.7039436.v1
title: Supplementary Material for: <b><i>Staphylococcus epidermidis</i></b> Activates Aryl Hydrocarbon Receptor Signaling in Human Keratinocytes: Implications for Cutaneous Defense

description: Bacterial challenge of keratinocytes with the abundant skin commensal <i>Staphylococcus epidermidis</i> induces distinct innate immune responses, but the underlying molecular mechanisms are still emerging. We report that the aryl hydrocarbon receptor (AhR) was activated in human primary keratinocytes infected with <i>S. epidermidis</i>, leading to induction of the AhR-responsive gene cytochrome P450 1A1 (CYP1A1). In addition, functional AhR was required for <i>S. epidermidis</i>-mediated induction of IL-1β expression in keratinocytes. AhR-dependent gene induction of IL-1β and CYP1A1 was mediated by factor(s) &lt; 2 kDa secreted by <i>S. epidermidis</i>. Blockade of the AhR in a 3D organotypic skin equivalent infected with <i>S. epidermidis</i> attenuated the <i>S. epidermidis</i>-induced CYP1A1 and IL-1β expression. Moreover, <i>S. epidermidis</i> also induced expression of IL-1α and of the antimicrobial peptide human β-defensin-3 in an AhR-dependent manner in a 3D skin equivalent. An increased outgrowth of <i>S. epidermidis</i> on the surface of skin explants treated with a specific AhR inhibitor further indicate a pivotal role of the AhR in mediating an epidermal defense response. Taken together, our data expand the role of the AhR in innate immunity and support a previously unappreciated contribution for the AhR in cutaneous defense.
DOI: 10.6084/m9.figshare.28756745.v1
title: Responses of water use strategies to seasonal drought stress differed among <i>Eucalyptus urophylla × E. grandis</i> plantations along with stand ages

description: This study used stable isotope techniques (δD, δ18O and δ13C) combined with the MixSIAR model to quantify the seasonal changes in water use sources and water use efficiency (WUE) of <i>Eucalyptus urophylla × E. grandis</i> at four stand ages (2-, 4-, 9- and 14-year-old) and to identify their influencing factors.
DOI: 10.6084/m9.figshare.8310773.v1
title: Data validation files of six tailing samples metagenome

description: Quality control files of the metagenomic analysis of the six tailing samples
DOI: 10.6084/m9.figshare.13720471.v1
title: Supplementary Material for: Two Siblings with Kaufman Oculocerebrofacial Syndrome Resembling Oculoauriculovertebral Spectrum

description: Kaufman oculocerebrofacial syndrome is a rare autosomal recessive disorder which represents a phenotype mainly involving craniofacial and neurodevelopmental manifestations due to <i>UBE3B</i> gene mutations. The vast majority of the affected individuals exhibit microcephaly, eye abnormalities, and typical facial gestalt including blepharophimosis, ptosis, telecanthus, upslanting palpebral fissures, dysplastic ears, and micrognathia. We encountered 2 siblings in whom severe psychomotor delay, distinctive facial features, hearing loss, and respiratory distress were observed. Some clinical manifestations of the patients, including epibulbar dermoid, microtia, and multiple preauricular tags, were reminiscent of the oculoauriculovertebral spectrum. However, 2 affected siblings exhibited a similar clinical picture consisting of microcephaly, severe developmental and cognitive disabilities, failure to thrive, and dysmorphic features, which were not fully consistent with oculoauriculovertebral spectrum. Also, hypoplastic nails, considered as a core manifestation of Coffin-Siris syndrome, were present in our patients. Therefore, whole-exome sequencing was carried out in order to identify the underlying genetic alterations, contributing to the complex phenotype shared by the 2 siblings. A homozygous pathogenic mutation was found in both affected siblings in the <i>UBE3B</i> gene which caused Kaufman oculocerebrofacial syndrome. Kaufman oculocerebrofacial syndrome should be considered among the autosomal recessive causes of blepharophimosis-mental retardation syndromes, particularly in populations with a high rate of consanguineous marriages, even if there are dysmorphic facial features that are not typically associated with the phenotype.
DOI: 10.6084/m9.figshare.20442783.v1
title: JFB_Skeeles et al. 2022_Chronic_hyperoxia...Raw_Data.xlsx

description: Raw data for the manuscript entitled " <strong>Chronic experimental hyperoxia elevates aerobic scope: a valid method to test for physiological oxygen limitations in fish" </strong>
DOI: 10.6084/m9.figshare.3208345.v1
title: OctylPyrimidopyrimidine

description: Chemdraw structure of dioctyl 2-oxopyrimido[4,5-<em>d</em>] pyrimidin-5(<em>6H</em>)-one and cyclic hexamer
DOI: 10.6084/m9.figshare.16809970.v1
title: Supplementary Material for: Transcriptome Analysis Identified 2 New lncRNAs Associated with the Metastasis of Papillary Thyroid Carcinoma

description: <b><i>Introduction:</i></b> Papillary thyroid microcarcinoma (PTMC) is a specific subgroup of papillary thyroid carcinoma and defined with the dimension ≤1 cm by the WHO. Although it shows a relatively high 10-year livability, the metastasis of PTMC into other tissues and organs seriously affects the daily life of patients with relatively high mortality. Therefore, the genetic basis for the metastasis of PTMC needs to be explored for effective therapeutic targets. Here, we conducted a series of comparative analysis of the transcriptional expression profile between PTMC patients with and without lymph node metastasis. <b><i>Methods:</i></b> Gene expression profile and gene function were analyzed using RNA extracted from pathological tissues of 12 patients with PTMC, and the core biomarkers closely related to its metastasis were identified. <b><i>Results:</i></b> Our results showed that 7,507 genes and 42 RNAs showed remarkably different expression patterns. More sophisticated analysis showed that the high expression of 2 lncRNAs (T077499 and T004533) resulted in the metastasis of PTMC, which suggests that the expression pattern of the 2 lncRNAs may act as a potential biomarker for pathogenesis and prognosis of PTMC metastasis. <b><i>Conclusion:</i></b> Our findings preliminarily reveal the molecular mechanisms for PTMC metastasis, which will provide vital reference for subsequent studies about the genetic basis and molecular targeted therapy for PTMC metastasis.
DOI: 10.6084/m9.figshare.5719336.v1
title: Antifungal activities of the essential oil and its fractions rich in sesquiterpenes from leaves of Casearia sylvestris Sw.

description: ABSTRACT Casearia genus (Salicaceae) is found in sub-tropical and tropical regions of the world and comprises about 160-200 species. It is a medicinal plant used in South America, also known as “guaçatonga”, “erva-de-tiú”, “cafezinho-do-mato”. In Brazil, there are about 48 species and 12 are registered in the State of Rio de Janeiro, including Casearia sylvestris Sw. There are many studies related to the chemical profile and cytotoxic activities of extracts from these plants, although few studies about the antifungal potential of the essential oil have been reported. In this work, we have studied the antifungal properties of the essential oil of C. sylvestris leaves, as well as of their fractions, against four yeasts (Saccharomyces cerevisae, Candida albicans, C. glabrata and C. krusei) for the first time. The chemical analysis of the essential oil revealed a very diversified (n = 21 compounds) volatile fraction composed mainly of non-oxygenated sesquiterpenes (72.1%). These sesquiterpenes included α-humulene (17.8%) and α-copaene (8.5%) and the oxygenated sesquiterpene spathulenol (11.8%) were also identified. Monoterpenes were not identified. The fractions are mainly composed of oxygenated sesquiterpenes, and the most active fraction is rich in the sesquiterpene 14-hydroxy -9-epi-β-caryophyllene. This fraction was the most effective in inhibiting the growth of three yeast strains.
DOI: 10.6084/m9.figshare.15074208.v1
title: Dataset

description: Full dataset used in the paper (long format)
DOI: 10.6084/m9.figshare.16622284.v1
title: Supplementary data: Phylogenomic analysis, reclassification, and evolution of South American nemesioid burrowing mygalomorph spiders.

description: *Total data set comprised 456 loci (of 85374 nucleotides) for 101 terminals*Partition File*RaxML tree* Exabayes tree* IQ tree* Astral tree* TableS1
DOI: 10.6084/m9.figshare.25997386.v1
title: Preprocessed EEG Data.rar

description: The dataset contains EEG ( processed data) from 20 participants in five conditions (Eyes open, white light 300 lux (rest 1), white light 800 lux (rest 2), blue light 300 lux (rest 3), blue light 800 lux (rest 4))
DOI: 10.6084/m9.figshare.26037664.v1
title: <b>Supplementary Data</b>

description: Datasets underlying the main Figures for "Predicting future hospital antimicrobial resistance prevalence using machine learning" https://doi.org/10.1101/2023.11.30.23299234 .
DOI: 10.6084/m9.figshare.28517219.v1
title: apical.stl

description: Isthmus model derived from Micro-CT parameters of maxillary first premolars, located in the apical third of the root.
DOI: 10.6084/m9.figshare.28693397.v2
title: <b>Fluorine-Doped Micropore-</b><b>Covered</b><b> Mesoporous Carbon Nanofibers for Long-Lasting </b><b>Initially Active Material-Free Negative Electrode</b><b> Sodium Metal Batteries</b>

description: <b>Original data of “</b><b>Fluorine-Doped Micropore-</b><b>Covered</b><b> Mesoporous Carbon Nanofibers for Long-Lasting </b><b>Initially Active Material-Free Negative Electrode</b><b> Sodium Metal Batteries</b><b>”</b>
DOI: 10.6084/m9.figshare.5122489.v1
title: Supplementary Material for: Blood Biomarkers for the Diagnosis of Acute Cerebrovascular Diseases: A Prospective Cohort Study

description: <i>Background:</i> The diagnosis of stroke or TIA in the emergency department is difficult, though important for early treatment. Circulating biomarkers might improve upon clinical assessment at admission. <i>Methods:</i> We recruited symptomatic patients with suspected stroke or TIA and drew blood soon after admission. Each patient was assessed with the Face Arm Speech Test (FAST). We measured a panel of 15 circulating inflammatory, thrombotic, cardiac, and cerebral tissue damage biomarkers. Improvement in diagnostic performance was assessed by adding biomarkers to the FAST in logistic regression models to predict a final diagnosis of stroke or TIA (verified by expert review and imaging). <i>Results:</i> 405 patients had suspected stroke: 285 with TIA or stroke (230 definite or probable ischemic stroke, 40 TIA, 15 hemorrhagic stroke) and 120 with other diagnoses. Only the markers t-PA and NT-proBNP were associated positively and significantly (p &lt; 0.01) with a diagnosis of TIA or stroke. The FAST had a sensitivity of 82% (95% CI 78–87) and specificity of 38% (95% CI 29–46) for the diagnosis of TIA or stroke. No biomarker individually improved the sensitivity or specificity of the FAST. A model containing the FAST, age, systolic blood pressure, NT-proBNP and t-PA had a better sensitivity (88%, p &lt; 0.006) and a better specificity (48%, p = 0.04) than the FAST test alone. <i>Conclusions:</i> No single blood marker improved the diagnostic performance of a validated clinical stroke scale. Panels of biomarkers may marginally improve diagnosis, but their practicability is uncertain, and requires further study.
DOI: 10.6084/m9.figshare.12366734.v3
title: DECM Machine Learning Training Corpus

description: The DECM Corpus is a digital corpus of the texts of Relaciones Geográficas de Nueva España (the Geographic Reports of New Spain) with different versions, including a machine ready version, a gold standard annotated dataset, and an automatically annotated version ready for text mining and machine learning experiments.This version contains a sample of the RGs manually annotated by multiple researchers with the software of our industry partner, Tagtog. This corpus has been used to carry out the NLP and ML experiments and the files are available in JSON and TSV format. These files are composed by texts and annotations. This is also accompanied by the DECM ontology which provides an explanation of the entities and labels produced. This corpus can be used for further experimentation with Artificial Intelligence methods.<br>
DOI: 10.6084/m9.figshare.27908685.v1
title: Dataset for 'Hemispheric consistency of language production, comprehension and reading in typically and atypically lateralized left-handers: implications for reading performance'

description: Dataset supporting the findings described in the research article titled: 'Hemispheric consistency of language production, comprehension and reading in typically and atypically lateralized left-handers: implications for reading performance'
DOI: 10.6084/m9.figshare.21673889.v1
title: Supplementary Material for: Neurochemical Correlates of Cue Reactivity in Individuals with Excessive Smartphone Use

description: <b><i>Background:</i></b> Excessive smartphone use (ESU), that is, a pattern of smartphone use that shows specific features of addictive behavior, has increasingly attracted societal and scientific interest in the past years. On the neurobiological level, ESU has recently been related to structural and functional variation in reward and salience processing networks, as shown by, for example, aberrant patterns of neural activity elicited by specific smartphone cues. <b><i>Objectives:</i></b> Expanding on these findings, using cross-modal correlations of magnetic resonance imaging (MRI)-based measures with nuclear imaging-derived estimates, we aimed at identifying neurochemical pathways that are related to ESU. <b><i>Methods:</i></b> Cross-modal correlations between functional MRI data derived from a cue-reactivity task administered in persons with and without ESU and specific PET/SPECT receptor probability maps. <b><i>Results:</i></b> The endogenous mu-opioid receptor (MOR) system was found to be significantly (FDR-corrected) correlated with fMRI data, and z-transformed correlation coefficients showed an association (albeit nonsignificant after FDR-correction) between MOR and the Smartphone Addiction Inventory “withdrawal” dimension. <b><i>Conclusions:</i></b> We could identify the MOR system as a neurochemical pathway associated with ESU. The MOR system is closely linked to the reward system, which has been recognized as a key player in addictive disorders. Together with its potential link to withdrawal, the MOR system hints toward a biologically highly relevant marker, which should be taken into consideration in the ongoing scientific discussion on technology-related addictive behaviors.
DOI: 10.6084/m9.figshare.5127844.v1
title: Supplementary Material for: Clinical Relevance of Cluster Analysis in Phenotyping Allergic Rhinitis in a Real-Life Study

description: <b><i>Background:</i></b> Disease stratification, using phenotypic characterization performed either by hypothesis- or data-driven methods, was developed to improve clinical decisions. However, cluster analysis has not been used for allergic rhinitis. <b><i>Objective:</i></b> To define clusters in allergic rhinitis and to compare them with ARIA (Allergic Rhinitis and Its Impact on Asthma), a hypothesis-driven approach. <b><i>Methods:</i></b> A French observational prospective multicenter study (EVEIL: Echelle visuelle analogique dans la rhinite allergique) was carried out on 990 patients consulting general practitioners for allergic rhinitis and treated as per clinical practice. In this study, changes in symptom scores, visual analogue scales and quality of life were measured at baseline and after 14 days of treatment. A post hoc analysis was performed to identify clusters of patients with allergic rhinitis - using Ward's hierarchical method - and to define their clinical relevance at baseline and after 14 days of treatment. The cluster approach was compared to the ARIA approach. <b><i>Results:</i></b> Patients were clustered into 4 phenotypes which partly followed the ARIA classes. These phenotypes differed in their disease severity including symptoms and quality of life. Physicians in real-life practice prescribed medication regardless of the phenotype and severity, with the exception of patients with ocular symptoms. Prescribed treatments were comparable in hypothesis- and data-driven analyses. The prevalence of uncontrolled patients during treatment was similar in the 4 clusters, but was significantly different according to the ARIA classes. <b><i>Conclusion:</i></b> Cluster analysis using demographic and clinical parameters only does not appear to add relevant information for disease stratification in allergic rhinitis.