cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26148253.v1
title: Dataset: The Combined Effectiveness of Acoustic Indices in Measuring Bird Species Richness in Biodiverse Sites in Cyprus, China, and Australia

description: Mammides, Christos and Wuyuan, Pan and Huang, Guohualing and Sreekar, Rachakonda and Ieronymidou, Christina and Jiang, Aiwu and Goodale, Eben, and Papadopoulos, Harris, The Combined Effectiveness of Acoustic Indices in Measuring Bird Species Richness in Biodiverse Sites in Cyprus, China, and Australia. Available at SSRN: https://ssrn.com/abstract=4823337 or http://dx.doi.org/10.2139/ssrn.4823337<br>"BIOMON: Using passive acoustic monitoring methods to survey bird communities in biodiverse agricultural farmlands in the EU"https://cordis.europa.eu/project/id/1010902731/6/2022 - 31/5/2024<br>
DOI: 10.3535/1mw-t1z-cpn
title: †Bucania J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zdq-yvl-kfe
title: Skarn

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bvp-dsq-tbm
title: †Rhynchotrema Hall, 1860

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rtc-lz9-4yf
title: Diabase

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.c.3831283_d17.v1
title: Additional file 6: of Hybrid assembly with long and short reads improves discovery of gene family expansions

description: Medicago assembly size statistics. (XLSX 37Â kb)
DOI: 10.17632/czjjdzc935
title: COVID-19 pandemic, and tourism customers behavior

description: COVID-19 pandemic, and tourism customers behavior
DOI: 10.17632/tcjfpgpdmn
title: Data of a lacustrine deposition in the Lushi Basin, China during the middle Eocene

description: We report the discovery of a remarkable 158-meter-thick Mg-carbonate precipitation during the middle Eocene in the Lushi Basin, central China. Six data tables are included in this dataset, including S1: Mineralogical compositions of the studied samples, S2: Relative compositions of clay minerals, S3: Evaluation of accuracy for Rietveld method, S4: Magnesium isotopes of standard and the studied samples, S5: Δ47 values and calculated T(Δ47) results of the studied samples, and S6: Eocene lacustrine magnesium carbonates in the central East Asia.
DOI: 10.3535/n1w-nn9-4ql
title: †Cymbularia Koken, 1896

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xk8-3gz-shq
title: †Liospira Ulrich & Scofield, 1897

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1476805.v1
title: Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels

description: Nav1.4 model
DOI: 10.6084/m9.figshare.26995963.v1
title: covid data 1-1.xlsx

description: The COVID-19 Pandemic in the recent past was one of the major worldwide diseases, causing huge mortality until the vaccine for the same disease was introduced. Numerous alternative medicinal approaches were used with varying outcomes but no scientific sustainability. During the pandemic times we used a novel innovative approach of using BioVolt Frequency Modulator device named E-Medica, which gave a promising result and had a sustainable scientific background.
DOI: 10.25376/hra.5965438.v1
title: Data for Applied Physiology Nutrition and Metabolism article (PMID: 29394491)

description: Data used in the study published in Applied Physiology Nutrition and Metabolism.DOI: 10.1139/apnm-2017-0696<br>
DOI: 10.3535/fzr-bfe-0j9
title: Granite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q70-kb2-fsh
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/w733gsdcsc
title: FeS2viv_Ma_etal_2023

description: Data for "Mechanism and kinetics of vivianite formation from mackinawite"
DOI: 10.3535/721-4at-evr
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.11920629.v1
title: Epidemiological data on the novel coronavirus 2019-nCoV infection cases in China

description: This data record contains one dataset <b>deta of 2019-nCOV in China.xlsx</b>, in .<b>xlsx</b> file format.<br>The dataset includes the following information (in 8 separate columns) on the novel coronavirus (2019-nCoV) infection cases in China:<br>-total number of confirmed cases, -total number of suspected cases-total number of cured cases-total number of deaths-total number of new confirmed cases-total number of new suspected cases-total number of new cured cases-total number of new deaths<br>The number of cases are reported for each day from January 20<sup>th</sup> to February 21<sup>st </sup>2020.<br><b>Study background, aims and methodology</b>: The 2019–20 coronavirus outbreak is an ongoing public health emergency of international concern involving coronavirus disease 2019 (COVID-19). At the end of December 2019, the epidemic of the novel coronavirus 2019-nCOV infection has spread from the initial place of Wuhan, Huibei province in China, resulting in an epidemic throughout China, with sporadic cases reported globally.The elderly, as well as people with primary diseases, are more likely to die from the infection. Children with chronic kidney disease (CKD), and children on dialysis, are vulnerable, due to their primary diseases and low immunity, especially those who suffer from long-term hormone, immunosuppressive therapy, and maintenance hemodialysis.The aim of this study was to analyse the epidemiological and clinical characteristics of the novel coronavirus, and to explore the infection prevention and control strategies of 2019-nCoV in children with chronic kidney disease (CKD) and children on dialysis.Data were collected from the 2019-nCoV management plan of the National Health Commission of the People’s Republic of China and relevant guidelines. Data on the COVID-19 cases in China, including the number of people, clinical characteristics, effective prevention and control measures from January 20<sup>th</sup> to February 21<sup>st</sup>, 2020, and statistical data on CKD in children were collected.<br>
DOI: 10.6084/m9.figshare.5799000.v1
title: Wright-Fisher Simulation Model

description: C# Code that was used to implement Wright-Fisher simulation model for publication "Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium"<br>
DOI: 10.3535/n1j-bq3-m04
title: Animalia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sra-l77-qfc
title: †Cymbularia Koken, 1896

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28675790.v1
title: Supplementary Material for: Management of Metastatic Colorectal Cancer in Pregnancy - A Systematic Review of a Multidisciplinary Challenge

description: The global incidence of early-onset colorectal cancer (EO-CRC) has increased significantly, with CRC projected to be the leading cause of cancer-related deaths among individuals aged 20-49 by 2030. Concurrently, a trend towards later age at first childbirth has been observed in industrialized countries, indicating a potential rise in CRC diagnoses during pregnancy. However, reports on managing metastatic CRC during pregnancy are limited. Bioethical concerns and the rarity of this condition contribute to the lack of clinical studies and evidence-based guidelines. This literature review, complemented by an illustrative case from our institution, aims to summarize existing knowledge and discuss optimal therapeutic approaches for this complex clinical scenario.

Methods
A comprehensive literature review was conducted using PubMed, MEDLINE, and Embase to identify studies and case reports on metastatic CRC during pregnancy, focusing on therapeutic interventions and clinical outcomes. Articles published between 1990 and 2024 were screened, excluding studies where treatment was initiated postpartum. Data on patient characteristics, treatment, and outcomes were extracted and synthesized narratively due to heterogeneity in study designs. An anonymized illustrative case was constructed through a retrospective analysis of patient records.

Results
We identified 26 cases of metastatic CRC during pregnancy in the literature. Primary symptoms at diagnosis included abdominal pain, constipation, and rectal bleeding. Most cases involved hepatic metastases, with additional pulmonary, peritoneal, or ovarian spread noted in some. Chemotherapy regimens like FOLFOX and FOLFIRI were administered in many cases during pregnancy, with varying outcomes. Some reports documented normal child development and maternal survival, while others noted adverse outcomes such as stillbirth, small-for-gestational-age infants, and maternal mortality. Surgical interventions were performed selectively, with maternal and fetal outcomes differing based on the clinical context.

Conclusion
Despite limited data on metastatic CRC treatment during pregnancy, a multidisciplinary approach that includes chemotherapy, radiotherapy, and surgical interventions, when appropriate, appears feasible. Guideline-based therapy adapted to individual clinical scenarios is crucial. Treatment in such complex cases should be managed in specialized centers equipped to address the unique challenges, ensuring optimal outcomes for both the mother and the child, even in advanced disease stages.
DOI: 10.3535/6q1-8l5-rg7
title: Bivalvia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jys-3hw-n5m
title: Metagreywacke

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.3145828.v1
title: Registros de espécies vasculares em unidades de conservação e implicações para a lista da flora ameaçada de extinção no estado de São Paulo – Material suplementar

description: Esses dados compõem o Material suplementar do artigo “Registros de espécies vasculares em unidades de conservação e implicações para a lista da flora ameaçada de extinção no estado de São Paulo” publicado na <i>Rodriguésia</i>. O arquivo contém uma matriz de ocorrência de espécies de plantas vasculares nas unidades de conservação de proteção integral e RPPNs do estado de São Paulo, cujos registros foram obtidos no Herbário Virtual da Flora e dos Fungos (http://inct.splink.org.br) entre fevereiro de 2014 e maio de 2015. Esses dados estão disponíveis em formato xls, csv e ods. Os arquivos em formato xls e ods trazem também o nome completo das unidades de conservação.
DOI: 10.3535/5gh-yvd-xe5
title: Animalia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/p52-b0l-vp7
title: †Liospira Ulrich & Scofield, 1897

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.5729190.v1
title: CpAr_PECs from Interactions of C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

description: Potential energy curves for C+/Ar
DOI: 10.3535/0h8-kf7-9y7
title: Gneiss

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m7a-mbx-kvr
title: †Modiolopsis J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.25814047.v1
title: GFP_CoIP_unfiltered.xlsx

description:  In this study, we identified novel interaction partners of wt and truncated MAGEL2.
DOI: 10.3535/kz3-jnx-p87
title: Bursachitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zcp-h6c-216
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/enz-nd8-xlh
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vtw-9fb-gcq
title: Dictyonema

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.22688152.v1
title: shell scripts, R scripts, and data required to reproduce the main analyses in Sokolowski et al., 2023

description: These directories contain the scripts (shell and R) and data required for the primary analysis of Sokolowski et al., 2023. Title: Transcriptomic effects of the foraging gene shed light on pathways of pleiotropy and plasticity. Athors: Authors: Dustin J. Sokolowski1,2*, Oscar E. Vasquez3*, Michael D. Wilson1,2, Marla B. Sokolowski3,4, Ina Anreiter5 <br> Author Affiliations *Authors contributed equally 1Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada 2Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada 3Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada 4Program in Child and Brain Development, Canadian Institute for Advanced Research, ON, Canada. 5Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada Corresponding Author For Manuscript: ina-dot-anreiter-at-utoronto-dot-ca Data analysis and figshare generator: dustin-dot-sokolowski-at-sickkids-dot-ca - alternative email (for when moved on from PhD) - djsokolowski95-at-gmail-dot-com <br> Each folder has it's own readme explaining the contents within. Directories have not been changed. Therefore to re-generate any output, they would need to be switched for the indivudal The raw and processed data (outside of the fastq, bw, and bam files) to regenerate the major analyses of each paper are the in /data subdirectory already. This includes all of the DEGs, pathways, varimax genes, scMappR outputs, SNP vcf files etc. <br> The sequencing information associated with these data can be found on arrayexpress https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-12688?query=foraging <br> R packages used: - scMappR - DESeq2 - gplots - edgeR - reshape2 - ggplot2 - TxDb.Dmelanogaster.UCSC.dm6.ensGene - org.Dm.eg.db - ChIPseeker - ggfortify - scales - xlsx - ActivePathways - DEET - Seurat - WGCNA - pheatmap - gProfileR - dplyr - reshape <br> Genomics command-line modules used: - fastqc - STAR - trimmomatic - bwa - samtools - bedtools - bcftools - gatk (picard) - featurecounts - qualimap - DeepTools <br> <br>
DOI: 10.6084/m9.figshare.23739411.v1
title: U.S. Men's Shed interviews

description: Transcribed interviews with U.S. Men's Shed members.
DOI: 10.3535/dmf-51p-a1g
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ebx-5ar-lm8
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.21926499.v2
title: Robinson et al. 2023 Conifer Drought Data.xlsx

description: Data from Robinson et al. 2023 "Drought survival strategies differ between coastal and montane conifers in northern California" in Ecosphere. <br> Methods for collection included in aforementioned publication. Please contact wallisrobinson@gmail.com with any questions.
DOI: 10.17632/h75yyspxv6
title: Proteomic Profiling of Salmonella enterica Strains from Environmental and Laboratory Sources: Comparative Analysis of Wastewater Isolates and Lab Strain UK-1

description: This dataset represents a comprehensive proteomic analysis of three Salmonella enterica strains, specifically two wastewater isolates—Salmonella enterica serovar Diarizonae (61:c:1,5,7) and S. enterica serovar Enteritidis (9:g,m:-)—alongside the well-characterized S. Typhimurium UK-1 lab strain. The preparation and analysis methods were carefully optimized to provide high-quality protein identifications and quantifications across these distinct strains, allowing for comparative proteomic analysis.

To generate the dataset, stationary-phase cultures of each strain were processed meticulously. Cultures were centrifuged at high speed (13,000 x g) at 4ºC to obtain cell pellets, which were washed twice—initially with PBS containing 5 mM EDTA to eliminate metal ion contaminants and then with PBS alone to enhance sample purity. The cells were lysed using a Sonifier Cell Disruptor, a sonication-based technique that preserves protein integrity, and then centrifuged again to yield a protein-rich supernatant, which was subsequently filter-sterilized using a 0.22-µm PES filter.

For protein separation, 25 µg of protein from each sample was loaded onto SDS-PAGE gels, with three biological replicates for each strain, ensuring reproducibility and robustness in measurements. Each gel lane was sectioned, and in-gel digestion with trypsin was performed to produce peptides suitable for mass spectrometry. The resulting peptide samples were analyzed using a 250-mm Ultrahigh-Performance Liquid Chromatography (UHPLC) system coupled to an Orbitrap Fusion mass spectrometer. This setup enabled high-resolution detection and precise mass spectrometry data collection.

Mass spectrometry data were analyzed using Sequest and X! Tandem, which compared spectral data against a Salmonella Uniprot database, assuming trypsin digestion specificity. Scaffold software validated peptide and protein identifications using a stringent probability threshold (&gt;95.0%) through the Scaffold Local FDR algorithm. Additionally, protein probabilities were refined with the Protein Prophet algorithm, requiring at least two peptides for protein identification. Proteins with overlapping peptide sequences were grouped to streamline interpretation, with the top-scoring hit reported.

The dataset achieved a peptide-level false discovery rate (FDR) of 0.35%, well below the commonly accepted threshold of 1%, and a protein FDR of 3.3%, within the standard 1-5% range, ensuring high reliability in protein identifications. Quantification across strains was performed using normalized spectral counts, and statistical significance was evaluated using t-test.

This dataset provides a resource for understanding the proteomic landscape across two environmentally derived Salmonella wastewater isolates and compared to a lab strain.
DOI: 10.3535/09d-4fb-rfq
title: †Lophospira Whitfield, 1886

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v16-ly0-xw8
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.57745/mbnpqp
title: Historical-Pictures.zip

description: This dataset contains historical pictures about Meudon, Paris, Pic du Midi, Saint Véran Observatories
DOI: 10.3535/4vb-qrs-8dz
title: igneous- and metamorphic rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8wp-rfz-r9d
title: Ancyrochitina  aff. convexa

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24511531.v1
title: all_vOTU_data.tsv

description: All vOTU data (includes read counts, tss values, completeness + quality info, and taxonomic info etc)
DOI: 10.6084/m9.figshare.28533506.v1
title: PDL1-68

description: <b>Project Description:</b>· Datasets:o PD-L1 Project &gt; PDL1-68· Animal Model: N/A· Animal Age: 8-12 Weeks· Animal Strain: Lyz2<sup>cre</sup> BALB/c mice· Number:o PDL1-68: 3 controls and 4 i.v. injection· Experimental Conditions: Mice were i.v. injected with AAV-TdTomato control vectors (2.1×10<sup>11</sup> GC/mouse) and immunized with cardiac myosin peptides. Control mice were injected with PBS, followed by immunization. Mice were sacrificed on day 21 after the AAV vector injection.<b>Code/Scripts: </b>None<b>Licenses: </b>N/A
DOI: 10.17632/xzx3y9b9j8
title: Programs for the dynamic simulation of liquids and solids II. MDIONS: Rigid ions using the ewald sum

description: Title of program: MDIONS Catalogue Id: AARM_v1_0 Nature of problem Study of the thermodynamic, structural and dynamic properties of ionic solids or liquids, or mixtures thereof. CORRECTION SUMMARY: Vol:Year:Page 28:1983:323 "000A CORRECTION 09/09/82" "Programs for the dynamic simulation of liquids and solids. II. MDIONS: rigid ions using the Ewald sum. (C.P.C. 25(1982)159)." N. Anastasiou; D. Fincham Note: correction instructions are contained in source code Versions of this program held in the CPC repository in Mendeley Data AARM_v1_0; MDIONS; 10.1016/0010-4655(82)90032-7 AARM_v2_0; MDIONS (VECTORISED); 10.1016/0010-4655(82)90033-9 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.3535/6z9-fzc-nn1
title: Volcanic bomb

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.3557769.v1
title: Appendix B. A detailed introduction to the Cox process model.

description: A detailed introduction to the Cox process model.
DOI: 10.6084/m9.figshare.6974417.v1
title: Sorghum version 3, maize versions 3 and 4 syntenic gene list

description: This pan-grass synteny list was generated using the methodology described in: <br>Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. (2017) “Differentially regulated orthologs in sorghum and the subgenomes of maize.” The Plant Cell doi: 10.1105/tpc.17.00354 bioRxiv preprint doi: 10.1101/120303<br>Here the species analyzed are sorghum (BTx623 version 3), maize (both B73_refgen3 and B73_refgen4, treated as separate species for the purpose of this analysis), Setaria viridis (v1), Setaria italica (Yugu1 v2.2), Oropetium (v1), Brachypodium distachyon, and rice (MSU v7). <br>Both maize v3 and maize v4 were split into subgenomes using the definitions first published in:<br>Schnable JC, Springer NM, Freeling M. (2011) “Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.” PNAS doi: 10.1073/pnas.1101368108<br>
DOI: 10.17632/pn7htgv4dv
title: Development of a species-level field diagnostic kit for Nipaecoccus viridis (Newstead) (Hemiptera: Pseudococcidae), an invasive and regulatory pest in the United States 

description: One of the main limitations in developing a species-level field diagnostic kit for Nipaecoccus viridis is the potential safety hazards associated with KOH. KOH is corrosive and causes damage to the skin, eyes, and mucous membranes. It remains unknow whether the potassium in the 10% KOH solution or the change in the pH that turned N. viridis hemolymph green. If the change in hemolymph color was caused by the pH and not associated with potassium, then finding a safe alternative to KOH that can change the pH could resolve the situation. Therefore, we tested different solutions, along with KOH, covering the whole pH spectrum to 1) figure out whether it is the potassium in 10% KOH or its pH that turns hemolymph green; 2) explore a relatively safe alternative to 10% KOH in laboratory and field experiments, and 3) develop a species-level field diagnostic kit for N. viridis.
DOI: 10.3535/nlf-zme-hnk
title: Cyathochitina cf. calix

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sv4-g7c-qfl
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14478162.v1
title: Calculate_PCbased_Genetic_Distance.R

description: R script to calculate individual-based genetic distance using principal components following:Shirk, A. J., E. L. Landguth, and S. A. Cushman. 2017. A comparison of individual-based genetic distance metrics for landscape genetics. Molecular Ecology Resources:1-10.<br>