cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14935436.v1
title: Thaxterogaster revisited: A phylogenetic and taxonomic overview of sequestrate Cortinarius from Patagonia

description: In the Patagonian region, <i>Cortinarius</i> is the most diverse and abundant genus of ectomycorrhizal fungi with at least 250 species. Sequestrate forms were until recently documented within the genus <i>Thaxterogaster</i>, a genus now known to be polyphyletic, and many were consequently transferred to <i>Cortinarius</i>. Original descriptions were mostly available in German and Spanish and interpretations of morphological structures outdated. Despite recent advances in <i>Cortinarius</i> systematics, the current classification, diversity, and ecology of sequestrate “cortinarioid” fungi in Patagonia remain unclear. The objective of this study was to provide an update on sequestrate <i>Cortinarius</i> of southern South America. We documented each species with morphological descriptions, photographs, basidiospore scanning electron microscopy (SEM) images, and molecular characterization using nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S) sequence data. Original descriptions of taxa were also translated to English and revised based on fresh collections. We documented 24 species from Patagonia based on molecular data and conducted morphological and phylogenetic analysis for 18 previously described species based on type and reference specimens. In addition, we formally described two new species. Four additional taxa were provisionally determined as new but require further study. New ITS sequence data were produced from eight type specimens. We also provide a new name, <i>Cortinarius gloiodes</i>, nom. nov., for the taxon previously described as <i>Thaxterogaster gliocyclus</i>. In addition to the species treated in detail, we provided additional reference information and discussion on six described species that remained incompletely known or for which no recent collections were found. Of the 24 taxa documented from Patagonia, 15 species were assigned to 12 current sections in the genus <i>Cortinarius</i>. Analysis of spore ultrastructure showed that sequestrate forms of Patagonian <i>Cortinarius</i> lack a true perisporium.
DOI: 10.6084/m9.figshare.27637251.v3
title: Request Removal

description: Request Removal
DOI: 10.15468/dl.6ysj35
title: Occurrence Download

description: A dataset containing 21699 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Lasioglossum morio (Fabricius, 1793)"
 ]
}

 The dataset includes 21699 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009625-250426092105405/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.23611875.v1
title: Bioinspired flatfish detection using electrical impedance measurements - dataset

description: Dataset used to create figures demonstrating operation of the developed flatfish detection system based on electrical impedance measurements.
DOI: 10.6084/m9.figshare.24975591.v3
title: Additional data for the manuscript "Genetic barriers more than environmental associations explain Serratia marcescens population structure"

description: Here the source data produced in the main analyses performed in the study associated to the manuscript "Genetic barriers more than environmental associations explain Serratia marcescens population structure". Files are separated in subfolders corresponding to the main analyses performed in the study. Among the data, there are:The coreSNP alignment, phylogenetic tree and Mash distances used for the clustering analysis.The table with stratified Chi-squared residuals (see Methods in the manuscript) used to determine associations between isolation sources and phylogenetic clusters.Table with frequency of genes associated to clusters and gene presence absence.Cluster-specific orthologs and table with Youden scores and <i>S. marcescens</i> specificity for each ortholog, along with the output table of the marker genes found in MGnify metagenomic samples containing <i>S. marcescens.</i>Alingments and phylogenetic trees of 1062 core genes used for the HGT analysis; SNP alignment and phylogenetic tree for the strain subset used in these analyses; HGT-detection tool output; output of R-M systems identified, R-M compatibility and strain cluster table produced in the R-M analysis.A collection of custom in-house scripts used in the analyses.
DOI: 10.6084/m9.figshare.23935635.v1
title: Raw data for UHPLC-HRMS

description: This dataset contains the raw data of UHPLC-HRMS for intestine-absorbing chemical compounds in TCM CHQY granules at both positive and negative models.
DOI: 10.6084/m9.figshare.19550392.v1
title: Supplementary Material for: Development of a Checklist of Potentially Traumatic Events in Children and Adolescents (CEPT-CA)

description: <b><i>Introduction:</i></b> Since exposure to potentially traumatic events during childhood and adolescence has been shown to be very common, its screening is very important. Our aim was to develop a self-assessment checklist to perform screening of potentially traumatic events in childhood and adolescence. <b><i>Methods:</i></b> The development of the Checklist of Potentially Traumatic Events in Children and Adolescents (CEPT-CA) was based on: (a) the structure of Life Events Checklist that has been translated, back-translated, and adapted; (b) recommendations of renowned entities about trauma in childhood; (c) particularities of potentially traumatic events in childhood; (d) adapting the language to the target population’s age group; (e) Portugal’s sociocultural context. The preliminary version of the CEPT-CA was again discussed with the Review Committee. Subsequently, a pre-test was carried out with 30 children/adolescents between the ages of 7 and 18 years. <b><i>Results:</i></b> The CEPT-CA includes the assessment of 16 potentially traumatic events. It also includes a 17th item, in which “any other very difficult/stressful event” may be added. Each event can be selected according to “It happened to me,” “I saw it happen to someone else,” “They told me,” “I’m not sure,” and “Not applicable.” The mean time to complete the questionnaire was 9 min. <b><i>Conclusion:</i></b> This pioneering study presents a checklist of potentially traumatic events in childhood/adolescence. This tool is useful for tracking these traumatic events, thereby allowing an early and specific assessment and intervention.
DOI: 10.6084/m9.figshare.26103115.v5
title: Coss-sectional Study on Awareness and Atitudes towards Posthumous Organ Donation among residents of Al Riyadh, Khartoum, 2020

description: This study explores the awareness and attitudes towards posthumous organ donation among citizens in Al Riyadh, Khartoum, Sudan. A total of 200 participants were surveyed through structured interviews and self-administered questionnaires. The results indicate that 84% of respondents were willing to donate their organs after death, with the main reasons for acceptance being beneficence and charity. Religious beliefs and concerns about the body's integrity were the primary reasons for refusal. The study concludes that gender, higher educational levels, and increased knowledge are crucial factors influencing the decision to donate. The findings suggest the need for public campaigns, further research, and the establishment of organ donation registration centers in Sudan.
DOI: 10.6084/m9.figshare.3573888.v4
title: Driving with Intuition raw data

description: 1) Raw EEG data in TRC format of the 40 included participants (the file EEG_70 must be changed with the EEG_68 one) and the 7 excluded ones. Channels n= 30. <br>The TRC format can be read by using the plugin available in the EEGLab software.<br>Triggers for the passive condition: 58 no crash; 60 crash end.<br>The active condition is contaminated by the motor artifacts of the actions on the keyboard.<br><br>2) Random sequences of the trials of each of the 40 participants<br>
DOI: 10.6084/m9.figshare.14607876.v1
title: Divergent metabolomic profiles of cold-exposed mature and immature females of tropical versus temperate Drosophila species

description: Two datasets corresponding to the article "<i>Divergent metabolomic profiles of cold-exposed mature and immature females of tropical versus temperate </i>Drosophila<i> species</i>"
DOI: 10.6084/m9.figshare.12666185.v1
title: Annotation of Syngnathus typhle

description: GeneMark-ES v2.3e was run on the genome assembly and SNAP v20131129 on the genes found by CEGMA. MAKER v2.31 used the trained gene predictors, a Trinity transcriptome assembly, all repeats in RepBase as called by MAKER and proteins from UniProtKB/SwissProt r2014_9 for a first pass annotation of the genome assembly. The result of the first pass was used to retrain SNAP and train AUGUSTUS v3.0.2 and a second iteration was performed using the same set-up. The protein sequences from final output of MAKER were BLASTed against the UniProtKB/SwissProt proteins and InterProScan v5.4-47 was used to classify protein domains in the protein sequences. This information was transferred to all output of MAKER. This annotated 19,668 gene models. InterProScan was run on the predicted proteins of these and gene names were allocated based on match with proteins in UniProt/SwissProt.<br>The files starting with Syngnathus_typhle is a more recent annotation done with Funannotate. The files starting with syty is the MAKER annotation
DOI: 10.6084/m9.figshare.1018700.v1
title: Garden data set

description: Temperature data from a WSN node located in a garden. 5000 data points, 1 per minute.
DOI: 10.6084/m9.figshare.19128149.v1
title: results of a Dynamic Game Approach for VRP with Returns

description: This is results of the paper: A dynamic game approach for VRP with Returns by Do Thi Thanh Tuyen and Nguyen Van Hop
DOI: 10.6084/m9.figshare.5129224.v1
title: Supplementary Material for: Alterations in Monocyte Phenotypes and Functions after a Hip Fracture in Elderly Individuals: A 6-Month Longitudinal Study

description: <b><i>Background:</i></b> Healthy elderly individuals are particularly prone to catastrophic events at any moment of their lives. One stressful event for individuals aged 65 and older is a fall that results in a fracture of the hip (HF). HF causes a state of inflammation that may affect immune responses. In this connection, we have reported that HF induced alterations in neutrophil functions. <b><i>Objective:</i></b> To assess the impact of HF on classical (cM), intermediate (iM) and non-classical (ncM) monocyte subsets. <b><i>Methods:</i></b> Distribution, functions (chemotaxis, phagocytosis, superoxide production and cytokine production), phenotype and activation (NF-κB and PI3K) were evaluated in monocyte subsets before surgery and 6 weeks and 6 months after the event. <b><i>Results:</i></b> The distribution of cM and ncM was unchanged, but iM transiently increased before surgery. Sustained increases (iM response to CCL2 and CX3CL1) and decreases (cM and ncM response to CCL2) in chemotaxis were observed. Phagocytosis and superoxide production were impaired in cM but not in iM or ncM. Sustained expression of HLA-DR occurred in cM but not in iM and ncM. Sustained decreased expression of CD11b occurred only in ncM. Sustained decreases (cM and ncM) and increases (iM) in CCR2 expression were observed. An elevated expression of CX3CR1 was found only in iM. cM produced elevated quantities of TNFα. There was a transient oxidative burst of production before surgery in iM and a sustained decrease in ncM. IL-10 production was severely impaired in cM and decreased in iM prior to surgery. Sustained activation (cM), inhibition (ncM) and transient activation (iM) of NF-κB were observed. Activation of PI3K was severely impaired in cM and ncM but was sustained in iM. <b><i>Conclusion:</i></b> HF had more impact on cM and ncM functions than on iM. HF triggered a switch in cM functions from phagocytic to inflammatory elevated TNFα-producing cells. These changes may impact clinical outcomes of HF with respect to inflammation, opportunistic infections and physical recovery.
DOI: 10.6084/m9.figshare.19164386.v1
title: S1 Data File

description: Meteorological data
DOI: 10.6084/m9.figshare.871544.v1
title: Workflow Results

description: The header row is the list of test species. Each column is a list of the results returned by the workflow described in this paper.
DOI: 10.6084/m9.figshare.24164388.v1
title: CosMx 6000-plex colon cancer dataset

description: A RData file containing the portions of a CosMx dataset used by analyses in the InSituCor manuscript.
DOI: 10.6084/m9.figshare.28060139.v2
title: <b><i>Streptococcus suis</i></b><b> </b><b>s</b><b>erotype</b><b> 5</b><b>: emerging </b><b>zoonotic </b><b>threat</b><b> with </b><b>distinct</b><b> genomic heterogeneity</b>

description: <i>Streptococcus suis</i> is a significant pig pathogen and an emerging zoonotic agent. Serotype 5 is becoming an increasing concern among pigs and humans with <i>S. suis</i> infection worldwide. This study investigated the population structure, phylogenetic relationship, genomic characteristics, and virulence of serotype 5 population, analyzing 89 isolates, including eight from human cases. The results revealed significant genomic heterogeneity and diverse virulence levels within serotype 5 population. Phylogenetic analysis identified two distinct lineages with notable differences in evolution and genomic traits. Thirty-two representative serotype 5 strains clustered into four groups: epidemic (E)(n=1), highly virulent plus (HV+)(n=4), HV(n=11), and virulent (V)(n=16). Virulence levels progressively decreased from the E group to HV+, HV, and V groups. The E, HV+, and HV strains induced significantly lethal infectionin mice during the early phase of infection. The lethal infection induced by E and HV+ strains was time-dependent but dose-independent. Ultra-high bacterial loads, excessive pro-inflammatory cytokines, and severe organ damage were responsible for the sudden death of mice infected with E strain at the early phase of infection. The capacity to establish infection, induce excessive pro-inflammatory cytokine production, and elevate biomarkers associated with organ damage varied significantly among HV+ strains. The V strains demonstrated the capacity to induce delayed lethal infection. These findings emphasized the serious public health risk posed by serotype 5 strains. The valuable information for developing effective prevention and control strategiesfor <i>S. suis</i> serotype 5 infections was provided.
DOI: 10.6084/m9.figshare.5120788.v1
title: Supplementary Material for: Phenotypic Analyses and Mutation Screening of the <i>SLC26A4</i> and <i>FOXI1</i> Genes in 101 Taiwanese Families with Bilateral Nonsyndromic Enlarged Vestibular Aqueduct (DFNB4) or Pendred Syndrome

description: Recessive mutations in the <i>SLC26A4</i> gene are responsible for nonsyndromic enlarged vestibular aqueduct (EVA) and Pendred syndrome. However, in some affected families, only 1 or 0 mutated allele can be identified, as well as no clear correlation between <i>SLC26A4</i> genotypes and clinical phenotypes, hampering the accuracy of genetic counseling. To elucidate the genetic composition of nonsyndromic EVA and Pendred syndrome, we screened related genomic fragments, including the <i>SLC26A4</i> coding regions, the <i>SLC26A4</i> promoter and the <i>FOXI1 </i>transcription factor gene, in 101 Taiwanese families, and analyzed their phenotypic and genotypic results. Mutation screening in the <i>SLC26A4</i> coding regions by direct sequencing and quantitative polymerase chain reaction detected 2 mutations in 63 (62%) families, 1 mutation in 24 (24%) families and no mutation in 14 (14%) families. The radiological findings, the presence of goiters and the audiological results were not different among probands (i.e. index cases of the families) with different <i>SLC26A4</i> genotypes. Specifically, probands heterozygous for <i>SLC26A4</i> mutations demonstrated clinical features indistinguishable from those of probands with 2 mutated alleles, implicating that there might be undetected mutations. However, except for a variant (c.–2554G&gt;A of <i>SLC26A4</i>) with possible pathological consequences, no definite mutation was detected after extensive screening in the <i>SLC26A4</i> promoter and <i>FOXI1</i>. In other words, in most Taiwanese families nonsyndromic EVA or Pendred syndrome might not result from aberrance in the transcriptional control of <i>SLC26A4</i> by <i>FOXI1</i>. Meanwhile, exploration of undetected mutations in the <i>SLC26A4</i> noncoding regions revealed 9 divergent haplotypes among the 21 no-mutation-detected <i>SLC26A4</i> alleles of the c.919-2A&gt;G heterozygotes, indicating that there might be no common and predominant mutations in the <i>SLC26A4</i> introns.
DOI: 10.6084/m9.figshare.3457751.v2
title: Is voice a marker of ASD? Dataset and analysis script

description: Dataset reporting the statistical estimates of acoustic patterns in ASD retrieved from a systematic review of the literature. <br>The data is used in a soon to be published article in Autism Research:Fusaroli, R., Lambrechts, A., Bang, D., Bowler, D., Gaigg, S. (in press) Is voice a marker of ASD? A systematic review and meta-analysis. Autism Research.<br>The data and statistical script are available also on:https://github.com/fusaroli/AcousticPatternsInASD
DOI: 10.6084/m9.figshare.25879375.v2
title: MS# 2025JC022801 Model outputs

description: Arabian Gulf regional hydrodynamic simulation outputs
DOI: 10.25387/g3.14732073.v1
title: Supplemental Material for Petrasch et al., 2021

description: This repository includes genotypic (File S2), phenotypic (File S3), and other supplemental data files, figures, and tables for Petrasch et al. (2021). File S1 is a text file with a custom macro developed to process photographic images of strawberry fruit using ImageJ, a "public domain Java image processing program" (https://imagej.nih.gov/ij/index.html). File S2 stores 50K Axiom SNP array genotypic data for the multifamily and the Royal Royce x Tangi population. File S3 stores the phenotypic data from our study. Custom R and PERL scripts developed for genetic mapping analyses are stored in File S4. File S5 stores information on candidate genes linked to gray mold resistance QTL with physical addresses and genome annotations from the <i>F</i>. x <i>ananassa</i> 'Camarosa' v1.0 reference genome (Edger et al., 2019). The latter is available at the Genome Database for Rosaceae (https://www.rosaceae.org/species/fragaria_x_ananassa/genome_v1.0.a1). File S6 stores the estimated marginal means (EMMs) and genomic-estimated breeding values (GEBVs) for gray mold resistance and fruit quality phenotypes among 380 individuals in a multi-family training population and 233 individuals in the Royal Royce x Tangi population. Fig. S1 displays time-series photographs of fruit of the long shelf life summer-plant cultivars 'Finn' and 'Mojo' at 0, 7, and 14 days of postharvest storage. Fig. S2 displays the phenotypic distributions and parent EMMs for gray mold resistance phenotypes within full-sib families. Fig. S3 displays kernel densities for genomic prediction accuracy estimated by cross-validation using support vector machine.
DOI: 10.6084/m9.figshare.4162161.v1
title: Supplementary Material for: Blood-Based Oxidative Stress Markers and Cognitive Performance in Early Old Age: The HAPIEE Study

description: <b><i>Background/Aims:</i></b> Oxidative stress is involved in Alzheimer disease pathology, but its impact on cognitive function in community-dwelling older adults remains unknown. We estimated associations between serum oxidative stress markers and cognitive function in early old age. <b><i>Methods:</i></b> Subjects aged 45-69 years recruited in urban centers in Central and Eastern Europe had memory, verbal fluency, and processing speed assessed at baseline (2002-2005) and 3 years later. Derivatives of reactive oxygen metabolites (d-ROMs), biological antioxidant potential (BAP), and total thiol levels (TTLs) were measured at baseline in a subsample. Linear regression was used to estimate associations of biomarkers with cognitive test scores cross-sectionally (<i>n</i> = 4,304) and prospectively (<i>n</i> = 2,882). <b><i>Results:</i></b> Increased d-ROM levels were inversely associated with global cognition and verbal fluency cross-sectionally and in prospective analysis; observed effects corresponded to 3-4 years' higher age. TTL was inconsistently associated with memory. BAP was not related to cognitive function. <b><i>Conclusion:</i></b> This study found modest evidence for a relationship between serum d-ROMs and cognitive function in a population sample of older adults.
DOI: 10.6084/m9.figshare.13153277.v1
title: Supplementary Material for: Intravenous Edaravone plus Therapeutic Hypothermia Offers Limited Neuroprotection in the Hypoxic-Ischaemic Newborn Piglet

description: <b><i>Background:</i></b> Therapeutic hypothermia (TH) is a standard therapy for neonatal hypoxic-ischaemic encephalopathy. One potential additional therapy is the free radical scavenger edaravone (EV; 3-methyl-1-phenyl-2-pyrazolin-5-one). <b><i>Objectives and Methods:</i></b> This study aimed to compare the neuroprotective effects of edaravone plus therapeutic hypothermia (TH + EV) with those of TH alone after a hypoxic-ischaemic insult in the newborn piglet. Anaesthetized piglets were subjected to 40 min of hypoxia (3–5% inspired oxygen), and cerebral ischaemia was assessed using cerebral blood volume. Body temperature was maintained at 39.0 ± 0.5°C in the normothermia group (NT, <i>n</i> = 8) and at 33.5 ± 0.5°C (24 h after the insult) in the TH (<i>n</i> = 7) and TH + EV (3 mg/kg intravenous every 12 h for 3 days after the insult; <i>n</i> = 6) groups under mechanical ventilation. <b><i>Results:</i></b> Five days after the insult, the mean (standard deviation) neurological scores were 10.9 (5.7) in the NT group, 17.0 (0.4) in the TH group (<i>p</i> = 0.025 vs. NT), and 15.0 (3.9) in the TH + EV group. The histopathological score of the TH + EV group showed no significant improvement compared with that of the other groups. <b><i>Conclusion:</i></b> TH + EV had no additive neuroprotective effects after hypoxia-ischaemia in neurological and histopathological assessments.
DOI: 10.6084/m9.figshare.14113076.v1
title: TABLE S1. Sample parameter settings for sensitivity test and simulation.

description: Sample parameter settings for sensitivity test and simulation.