cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4892690.v1
title: Supplementary Material for: Diagnostic Accuracy of Combinations of Tumor Markers for Malignant Pleural Effusion: An Updated Meta-Analysis

description: <b><i>Background:</i></b> The role of combinations of tumor markers such as carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 125, 15-3, and 19-9, and CYFRA 21-1 (a fragment of cytokeratin 19) in diagnosing malignant pleural effusion (MPE) has not been clearly established. <b><i>Objectives:</i></b> This meta-analysis was performed to establish the overall diagnostic accuracies of combinations of these pleural fluid tumor markers for MPE. <b><i>Methods:</i></b> The PubMed, Ovid, Embase, Web of Science, and Cochrane bibliographic databases were searched. Sensitivity, specificity, and other measures of the accuracy of combinations of pleural CEA, CA 125, CA 15-3, CA 19-9, and CYFRA 21-1 in the diagnosis of MPE were pooled after a systematic review of English-language studies. <b><i>Results:</i></b> Twenty studies met the inclusion criteria. For pleural fluid tumor marker combinations including more than 3 studies, the summary estimates of the sensitivity/specificity for diagnosing MPE were as follows: CEA + CA 125, 0.65/0.98; CEA + CA 15-3, 0.64/0.98; CEA + CA 19-9, 0.58/0.98; CEA + CYFRA 21-1, 0.82/0.92; and CA 15-3 + CYFRA 21-1, 0.88/0.94. <b><i>Conclusions:</i></b> In patients with undiagnosed pleural effusion, the combinations of positive pleural CEA + CA 15-3 and CEA + CA 19-9 are highly suspicious for pleural malignancy, but the sensitivity of these tests is poor. Therefore, their routine role in the diagnostic algorithm of these patients is questionable, and management decisions should depend on positive cytological or biopsy results from the pleura.
DOI: 10.6084/m9.figshare.7370438.v3
title: DNA Methylome Profiling of Granulosa Cells Reveals Altered Methylation in Genes Vital to Ovarian Functions in PCOS

description: These are the supplemental file-sets for the DNA methylome profiling data of ovarian granulosa cells between controls and women with PCOS. The data was generated using a high throughput methyl-capture sequencing (MC-seq) approach and few of the identified differentially methylated genes (DMGs), which are vital for normal functioning of the ovary were validated using pyrosequencing and real-time PCR. Validation of genes such as <i>AKR1C3</i>, <i>CASR</i>, <i>GHRHR</i>, <i>RETN</i>, <i>MAMLD1</i>, <i>TNF</i> and <i>TF</i> provided novel insights on the involvement of epigenetic modifications in regulation of processes such as folliculogenesis, angiogenesis, steroidogenesis, luteal maintenance, ovulation, oocyte maturation, oocyte developmental competence and many more, which are compromised in women with PCOS. This data also generated valuable information on pathways and biological processes playing crucial roles in the pathophysiology of PCOS.<br>
DOI: 10.17632/5v6rngxh55.1
title: Dataset Environmental fatigue debonding of electrical steel laminates based on waterborne epoxy varnishes

description: Origin files: Environmental fatigue debonding curves & FTIR peak ratios
Python: Evaluation file for the simultaneous test bench
DOI: 10.6084/m9.figshare.12465254.v1
title: GO enrichment analysis

description: We present enrichment analysis for a set of comparison done for genome and transcriptome analysis of Thalictrum
DOI: 10.6084/m9.figshare.1197210.v1
title: Bird Distance Transect

description: 5 different transects were laid out in the grasslands and 5 different transects for the woodlot in York univeristy. Each transect was 25m long. The windspeed was estimated for each transect using the Beaufort wind scale. Birds were searched for in each transect using binoculars. Species that were found and the number of birds for each species in the transects were recorded. The distance of the birds from each transect was estimated in m. A total of 10 transects were made. If the birds could not be identified they were marked as unknown. If no birds were found in a transect it was marked as none.
DOI: 10.6084/m9.figshare.24514165.v1
title: Supplement.xlsx Genetic Data on Three Families with Daughter with Gigatomastia

description: Three cases of gigantomastia are described and the whole genome analysis revealed several mutations which are listed here,
DOI: 10.6084/m9.figshare.14346059.v1
title: Supplementary Material for: The Prevalence of Allergic Rhinitis, its Triggers, and Associated Factors in Commonwealth of Independent States Countries (Ukraine, Kazakhstan, and Azerbaijan): Results of the CORE Study

description: <b><i>Background:</i></b> In the Commonwealth of Independent States (CIS) countries the epidemiology of allergic rhinitis (AR) is poorly characterized. The rationale and design of the CORE (Chronic Obstructive REspiratory diseases) study have been described elsewhere. <b><i>Methods:</i></b> A total of 2,842 adults (≥18 years) were recruited (964 in Kiev, Ukraine, 945 in Almaty, Kazakhstan, and 933 in Baku, Azerbaijan) between 2013 and 2015 and interviewed during household visits. Two-step cluster randomization was used for the sampling strategy. “Doctor-diagnosed AR” was considered when the respondent had previously been diagnosed with AR by a doctor, “self-reported AR symptoms” (was defined as watery runny nose during the last 12 months alone or in combination with any of the following: sneezing, nasal obstruction, nasal itching, or conjunctivitis). <b><i>Results:</i></b> The prevalence of doctor-diagnosed AR was 33.4, 92.1, and 82.7 per 1,000 persons, and the prevalence of self-reported AR symptoms was 44.7, 97.4, and 85.7 per 1,000 persons, in Ukraine, Kazakhstan, and Azerbaijan, respectively. In Ukraine, the peak of AR symptoms was in May, in Kazakhstan – in May–September, and in Azerbaijan in March–May. Sneezing and nasal congestion were the most frequent symptoms. Pollen as AR trigger was reported by 71.9% respondents in Ukraine, 70.1% in Kazakhstan, and 68.8% in Azerbaijan. Only 35–56% respondents with doctor diagnosed AR have had specific investigations (skin test, analysis for immunoglobulin etc.). The percent of subjects with chronic (nonrespiratory) health condition was higher in the respondents with self-reported AR symptoms compared to rest of the respondent: 100 versus 42% in Ukraine, 100 versus 21% in Kazakhstan, and 100 versus 50% in Azerbaijan, respectively. <b><i>Conclusion:</i></b> In CIS countries, the prevalence of self-reported AR symptoms was slightly higher than the prevalence of doctor-diagnosed AR. Compared to countries from other continents, the prevalence of doctor-diagnosed AR was similar; however, the prevalence of AR symptoms seems to be relatively lower.
DOI: 10.6084/m9.figshare.3544466.v1
title: Appendix B. Species richness for each successional stage before and after filtering of species lists.

description: Species richness for each successional stage before and after filtering of species lists.
DOI: 10.6084/m9.figshare.5755404.v3
title: PhyloSift markers database

description: Markers database for PhyloSift<br><br>PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.Using a reference database of protein sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and<br>amino acid sequence are generated.Software Download on GitHub: https://github.com/gjospin/PhyloSift<br>
DOI: 10.6084/m9.figshare.6694814.v1
title: MOESM1 of Quantifying spatial accessibility in public health practice and research: an application to on-premise alcohol outlets, United States, 2013

description: Additional file 1: Population-weighted spatial access to 7 nearest on-premise alcohol outlets by U.S. states, counties and census tracts, 2013.
DOI: 10.6084/m9.figshare.28801577.v1
title: Effect of acupuncture intervention on intestinal microorganisms in rats with experimental autoimmune thyroiditis

description: In order to investigate the therapeutic effect of acupuncture on experimental autoimmune thyroiditis in rats, and whether there is a common metabolite target with selenium yeast treatment, we examined the intestinal microorganisms of rats.
DOI: 10.17632/4jw4bpmj69.1
title: Dataset of DVI values of the La Maddalena Archipelago National Park (Northern Sardinia - Italy)

description: This database contains the values obtained from the D.V.I. (Dune Vulnerability Index) of 10 embayed beaches of the Maddalena Archipelago (Sardinia - Italy) for publication on Data in Brief Journal
DOI: 10.4225/49/595c4b61af669
title: Unicycler (v0.4.0) assemblies (hybrid Illumina and ONT)

description: Unicycler assemblies of 12 isolates of <i>Klebsiella pneumoniae</i>, generated with both Illumina and ONT reads.
DOI: 10.6084/m9.figshare.14923017.v1
title: EP2019_Electoral_Dataset.xlsx

description: Dataset on electoral system elements and effects for the 2019 EP Election
DOI: 10.6084/m9.figshare.28829981.v1
title: Search Terms, data extraction, PRISMA

description: Purpose: While electronic health records (EHRs) are a critical tool for clinical care in academic medical centers, there is a gap in the literature regarding utilization of EHRs for teaching and learning, outside of descriptions on EHR training or use for quality improvement projects. The research question for this scoping review is: How is the EHR purposefully used in educational interventions for teaching and learning in graduate medical education?Methods: We searched all publications in PubMed, SCOPUS, CINAHL, ERIC, Cochrane and MedEdPORTAL databases from 2010 to 2022 that met our search criteria. Using Arksey and O'Malley's framework, the abstracts were reviewed by three team members, and the full text was reviewed by all authors using a standardized data extraction sheet.Results: Of the 2431 records, 19 met inclusion criteria and were reviewed in full. All studies were set in North America, 79% at teaching hospitals, and 42% in Internal Medicine programs. The EHR was used purposefully to improve learning in sepsis, diabetes, asthma, critical care, post- and peri-operative care, and it was used to provide feedback about clinical performance, test utilization, costs of care, and errors. The educational interventions included simulation, direct feedback using EHR data, and workshops with pre-post knowledge and skills testing.Conclusions: This scoping review identifies how the EHR is being used as a teaching and learning tool for trainees. There is a need for more purposeful use of the EHR in designing educational interventions for residents.
DOI: 10.6084/m9.figshare.3566544.v1
title: Appendix G. A color version of Fig. 2.

description: A color version of Fig. 2.
DOI: 10.6084/m9.figshare.5117458.v3
title: Ulmus minor chorology

description: Distribution map of field elm (<i>Ulmus minor</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.21769886.v2
title: cancerhd.csv

description: Here, six anesthetized Sprague-Dawley rats were treated with a single 180-min experimental hemodialysis (HD) session after being fed a ketogenic diet for five days.
DOI: 10.17632/4jw4bpmj69.2
title: Dataset of DVI values of the La Maddalena Archipelago National Park (Northern Sardinia - Italy)

description: This database contains the values obtained from the D.V.I. (Dune Vulnerability Index) of 10 embayed beaches of the La Maddalena Archipelago (Sardinia - Italy)
DOI: 10.6084/m9.figshare.28726535.v1
title: <i>Genome Assembly of Orestias ascotanensis (genome_mod.fa)</i>

description: This file contains the genome assembly of the Andean killifish (Orestias ascotanensis) originally published in Di Genova et al. (2022) (Genomics 114:305-315). This assembly served as the reference genome for the unpublished manuscript titled 'Seasonal Transcriptome Profile Across Three Different Tissues of the Andean Killifish Orestias ascotanensis' (Manuscript ID: SDATA-24-04380) by Maldonado et al., currently under revision. The genome was used for RNA-seq read alignment, lncRNA prediction, and differential gene expression analysis across seasons and tissues.
DOI: 10.6084/m9.figshare.22713415.v1
title: M<strong>icrohabitat selection and underground movements of amphisbaenians under summer drought conditions</strong>

description: We examined the patterns of microhabitat selection and underground movements (using PIT-tag telemetry) of a strictly fossorial reptile, the North African checkboard amphisbaenian <em>Trogonophis wiegmanni</em>, during the summer drought period.
DOI: 10.6084/m9.figshare.5545057.v1
title: Initial Parametric Study Data

description: Spreadsheet of data used to obtain the initial parametric study data. This involves the analysis of material configurations and physical face sheet dimensions of the sandwich panel.
DOI: 10.6084/m9.figshare.5987197.v1
title: 3D data of bituminous coal heaps

description: Contains STL meshes, raw 3D scan data and images
DOI: 10.6084/m9.figshare.12122010.v1
title: Supplementary Material for: Neoadjuvant Radio(chemo)therapy for Breast Cancer: An Old Concept Revisited

description: <b><i>Background:</i></b> The international standard of care for the treatment of high-risk breast cancer (BC) consists of neoadjuvant chemotherapy (NACT) and surgery followed by adjuvant whole breast/chest wall irradiation. In this setting, the time interval from the start of NACT to the end of radiotherapy (RT) is usually postponed to 6 months or longer. In addition to this, a high percentage of capsular fibrosis may occur when breast implants are irradiated. Most of these disadvantages could be avoided by using preoperative RT (PRT). PRT is already the standard of care in several other tumor entities (rectal cancer, esophagus carcinoma, lung cancer, and soft tissue sarcoma). Nevertheless, PRT in BC has been tested in several trials, but randomized prospective trials using modern radiation technology and systemic therapies are lacking. The available evidence summarized in this review indicates that PRT may improve survival and reduce long-term toxicity in patients with a higher risk of recurrence and should be consequently tested in a randomized trial. <b><i>Summary:</i></b> Prospective, randomized trials concerning PRT in high-risk BC are needed. We plan to conduct a NeoRad trial (NACT followed by PRT in high-risk BC). <b><i>Key Messages:</i></b> Prospective, randomized studies concerning PRT in high-risk BC are needed.
DOI: 10.6084/m9.figshare.23550108.v4
title: Fig 2 Raw data

description: Antigen identification of Ab 009
DOI: 10.6084/m9.figshare.9699938.v1
title: ACPFLII-COA-STRUCTURE-1

description: ACPFLII-COA-STRUCTURE-1Optimized geometries of intermediates F, G and H and transition states TS5 and 6 starting from structure 1 taken from MD trajectory of acetylated (AcPFL II) topology with CoA in the active site.
DOI: 10.15468/dl.z836py
title: Occurrence Download

description: A dataset containing 397 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 Nephrotoma flavescens (Linnaeus, 1758)"
 ]
}

 The dataset includes 397 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009442-250426092105405/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.28030355.v1
title: Supplementary materials

description: Stunting still represents a major public health problem in Egypt, affecting around one-third of children under five and leading to a 2-3% drop in gross domestic product (GDP). Therefore, this study examined the trends in the prevalence of stunting and its associated factors among children aged 0-23 months, 24-59 months and 0-59 months in Egypt. The study used combined data from the 2005, 2008, and 2014 Egypt Demographic and Health Surveys (EDHS).
DOI: 10.6084/m9.figshare.4880009.v1
title: Evolution of mutualism from parasitism in experimental virus populations

description: The following files are in association with the manuscript "Evolution of mutualism from parasitism in experimental virus populations" by JW Shapiro and PE Turner.
DOI: 10.17632/rjdrgg9fgd
title: cost analysis

description: cost analysis of palliative care
DOI: 10.17632/rjdrgg9fgd.1
title: cost analysis

description: cost analysis of palliative care
DOI: 10.6084/m9.figshare.5127331.v1
title: Supplementary Material for: Microwave Ablation for Twin-Reversed Arterial Perfusion Sequence: A Novel Application of Technology

description: <b><i>Introduction:</i></b> Twin-reversed arterial perfusion sequence is a rare complication of monochorionic pregnancies that is characterized by the presence of an acardiac mass perfused by an apparently normal pump twin. The risk of death to the pump twin has led to a range of therapeutic interventions aimed at separating their vascular connection. We report a novel application of microwave ablation for vessel coagulation in the treatment of twin-reversed arterial perfusion sequence. <b><i>Material and Methods:</i></b> Microwave ablation has been adopted by surgical subspecialties as a superior energy source for vessel and tissue ablation as it creates heat without a circuit and has less thermal spread. We describe the use of a 2.45-GHz microwave system using a 1.8-mm antenna to coagulate the intra-abdominal portion of umbilical vessels of the acardiac mass. <b><i>Results:</i></b> We report 6 cases of twin-reversed arterial perfusion sequence treated by microwave ablation. All patients were treated with microwave ablation with successful coagulation of intra-abdominal umbilical cord vessels of the acardiac mass with cessation of flow. <b><i>Discussion:</i></b> Microwave ablation is an excellent energy source for vessel coagulation due to its thermal properties and can be used effectively in the treatment of twin-reversed arterial perfusion sequence.
DOI: 10.6084/m9.figshare.22155260.v1
title: The distribution and establishment of non-native earthworm populations and their impact on organic layer thickness in the Acadian Forest

description: The distribution and impacts of non-native earthworms are poorly documented in Atlantic Canada meaning that we have limited knowledge of the relationship between earthworms and forest properties. To address this knowledge gap, we surveyed earthworms and sampled the soil organic horizon in 41 forest stands located in New Brunswick to investigate their relationship with forest properties and impact on organic horizon thickness and carbon content. We found earthworms at 39% of the sites that we surveyed. Earthworms were more common in hardwood stands than softwood stands, at low elevations, and near current or historical human activity. Sites with earthworms had thinner organic horizons and less carbon. A simple two-pool Lotka-Volterra model described the relationship between earthworm abundance and organic horizon carbon well. The model predicted that earthworm invasions take about a decade to reach numbers typical of invaded sites and half a century to reach carrying capacity. Together these data suggest that, despite their long-term regional presence, much of the Acadian Forest that is not adjacent to human activity remains unimpacted and vulnerable to the effects of non-native earthworms.
DOI: 10.6084/m9.figshare.27993887.v1
title: <i>Diaphorina citri </i>Combined dataset SKA mtDNA haplotyping

description: Repository of scripts, file inputs, and unpublished mitogenomes curated in Dr. Michelle Heck's Laboratory within the USDA ARS at Cornell University in conjunction with Dr. Liliana Cano at UF IRREC in Fort Pierce, FL. This collection of code and data was used to analyze and produce figures from mtDNA datasets using split kmer analysis (SKA) and is associated with the manuscript "Rapid and reproducible haplotyping of complete mitochondria from related individuals using split kmers".
DOI: 10.6084/m9.figshare.22010846.v3
title: ECOPICS_MX Monolith soil chemical analysis

description: ECOPICS Project : Monolith Soil Data In the field, after the extraction of the monolith and root and fauna collection , a composite soil sample ( ±500 g) was collected. Beside the monolith a soil cylinder (98.17 cm3) was extracted at a depth of 0.10 m, dried at 105 ° C and weighed to determine the bulk density (g /cm3). There were in total 83 samples. From each of these samples 100g were frozen (for nitrate and ammonium analysis), the rest were air dried and sieved at 2 mm for the rest of physicochemical analysis (% carbon,% hydrogen,% nitrogen and real density) the texture and the other chemical analysis described below were analyzed with the fresh sample. Ca, Mg, K, Na and cation exchange capacity (CEC, cmol / kg1) were determined by 1N ammonium acetate, pH7. Nitrate and ammonium were measured by extraction with potassium chloride solution and then by steam distillation with magnesium oxide and Dervada alliance. (Bremner, J. M., 1965) Available P was measured by Bray-Kurtz 1. Total P (mg / Kg) by wet digestion with nitric acid: perchloric acid 1: 2 and then quantified with sodium metavanadate. % P retained was measured by the Blackmore technique. Soil texture was measured using the pipette (Pleijsier, 1986). Soil particles were classified into size fractions: clay (0.002 m), silt (0.02mm), silt (0.05 mm), sand (&lt;0.25 mm), sand (&gt; 0.25 &lt;0.05mm) and sand (&gt; 0.5mm). The electrical conductivity in distilled water, a 1:5 ratio, is mixed and after 24 h it is measured with a Corning brand conductivity meter. The pH in water was in a 1:2 ratio. Humidity was determined using the oven technique at 105 ° C. The field capacity was determined in a pressure cooker at 0.33 Bar and then dried at 105 ° C. Organic matter and % organic C was determined by the Walker-Black technique. % C,% H and% N were determined by combustion (Dumas method) by the Perkin Elmer CHN 2400 analyzer.