cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21740544
title: Composition of Prokaryotic Communities in Anaerobic Enrichment Cultures of Crude Oil from Romashkino Oilfield (Russia)

description: Despite the many papers published on oilfield ecosystems, there is a lack of data about microbial community structure and functioning in many crude oils or oilfields and wells. One of such poorly studied oilfields is supergiant Romashkino situated in Tatarstan (Russia). In the present study, prokaryotic community composition and abundance of functional genes encoding sulfate reduction and rhamnolipid production, was investigated in enrichment cultures of four samples from Romashkino oilfield production wells with different oil/water ratios. The enrichment was conducted under anaerobic conditions, sulfate and nitrate were used as electron acceptors, and acetate – as an electron donor. In enrichment culture A and enrichment culture B, bacteria of the <i>Pseudomonadaceae</i> family predominated with 99% and 93% relative abundance, respectively. In enrichment culture C (obtained on the basis of initial sample contained oil with medium water content) and D (obtained on the basis of initial sample contained oil with very high water content), <i>Pseudomonadaceae</i> were one of the two predominating families, along with <i>Micrococcaceae</i> (enrichment culture C) and <i>Dietziaceae</i> (enrichment culture D). The proportion of <i>dsrA</i> and <i>apsA</i> genes encoding sulfate reduction to 16S rRNA gene copy numbers was quite low and ranged between 0.003% (enrichment cultures A, B) and 0.027% (enrichment culture D). The proportion of <i>rhlB</i> gene encoding rhamnolipid production from the total 16S rRNA gene copy number was 1.10% in sample A and 0.06% in sample B. In enrichment cultures C and D the <i>rhlB</i> gene was not found.
DOI: 10.6084/m9.figshare.21740544.v1
title: Composition of Prokaryotic Communities in Anaerobic Enrichment Cultures of Crude Oil from Romashkino Oilfield (Russia)

description: Despite the many papers published on oilfield ecosystems, there is a lack of data about microbial community structure and functioning in many crude oils or oilfields and wells. One of such poorly studied oilfields is supergiant Romashkino situated in Tatarstan (Russia). In the present study, prokaryotic community composition and abundance of functional genes encoding sulfate reduction and rhamnolipid production, was investigated in enrichment cultures of four samples from Romashkino oilfield production wells with different oil/water ratios. The enrichment was conducted under anaerobic conditions, sulfate and nitrate were used as electron acceptors, and acetate – as an electron donor. In enrichment culture A and enrichment culture B, bacteria of the <i>Pseudomonadaceae</i> family predominated with 99% and 93% relative abundance, respectively. In enrichment culture C (obtained on the basis of initial sample contained oil with medium water content) and D (obtained on the basis of initial sample contained oil with very high water content), <i>Pseudomonadaceae</i> were one of the two predominating families, along with <i>Micrococcaceae</i> (enrichment culture C) and <i>Dietziaceae</i> (enrichment culture D). The proportion of <i>dsrA</i> and <i>apsA</i> genes encoding sulfate reduction to 16S rRNA gene copy numbers was quite low and ranged between 0.003% (enrichment cultures A, B) and 0.027% (enrichment culture D). The proportion of <i>rhlB</i> gene encoding rhamnolipid production from the total 16S rRNA gene copy number was 1.10% in sample A and 0.06% in sample B. In enrichment cultures C and D the <i>rhlB</i> gene was not found.
DOI: 10.6084/m9.figshare.21803596
title: Heavy Crude Oil Biodegradation: Catechol Dioxygenase Gene Copy Number Variation Determination by Droplet Digital Polymerase Chain Reaction

description: The crude oil reserves in Oman mainly consist of heavy oil. Microbial enhanced heavy oil recovery (MEOR) has been proved to be an efficient technique in the tertiary heavy oil recovery. Five <i>Bacillus</i> species potential for enhanced heavy oil recovery (EHOR) were isolated and the biodegradation ability of these isolates was studied. As heavy crude oil comprises of aromatic hydrocarbons rather than aliphatic ones, the aromatic catabolism gene, catechol 2,3-dioxygenase (<i>C23O</i>) and catechol 1,2-dioxygenase (<i>C12O</i>) were the genes of interest in this study along with the reference gene, <i>16S</i> rDNA. The copy number variation of these genes was determined using droplet digital PCR (ddPCR). The primers and probes for ddPCR assay were designed targeting these genes. It was observed that the heavy crude oil biodegradation potential of the isolates correlated with the copy number of <i>C23O</i> gene in the microbial genomes. The isolate, <i>Paenibacillus ehimensis</i> BS1 had the highest <i>C23O</i> gene copy number (1.057) followed by <i>Bacillus firmus</i> BG4 (0.895) and <i>Bacillus halodurans</i> BG5 (0.031) as demonstrated by their biodegradation potential. This is one of the few studies deploying ddPCR in the field of heavy crude oil biodegradation by spore forming bacteria.
DOI: 10.6084/m9.figshare.21803596.v1
title: Heavy Crude Oil Biodegradation: Catechol Dioxygenase Gene Copy Number Variation Determination by Droplet Digital Polymerase Chain Reaction

description: The crude oil reserves in Oman mainly consist of heavy oil. Microbial enhanced heavy oil recovery (MEOR) has been proved to be an efficient technique in the tertiary heavy oil recovery. Five <i>Bacillus</i> species potential for enhanced heavy oil recovery (EHOR) were isolated and the biodegradation ability of these isolates was studied. As heavy crude oil comprises of aromatic hydrocarbons rather than aliphatic ones, the aromatic catabolism gene, catechol 2,3-dioxygenase (<i>C23O</i>) and catechol 1,2-dioxygenase (<i>C12O</i>) were the genes of interest in this study along with the reference gene, <i>16S</i> rDNA. The copy number variation of these genes was determined using droplet digital PCR (ddPCR). The primers and probes for ddPCR assay were designed targeting these genes. It was observed that the heavy crude oil biodegradation potential of the isolates correlated with the copy number of <i>C23O</i> gene in the microbial genomes. The isolate, <i>Paenibacillus ehimensis</i> BS1 had the highest <i>C23O</i> gene copy number (1.057) followed by <i>Bacillus firmus</i> BG4 (0.895) and <i>Bacillus halodurans</i> BG5 (0.031) as demonstrated by their biodegradation potential. This is one of the few studies deploying ddPCR in the field of heavy crude oil biodegradation by spore forming bacteria.
DOI: 10.6084/m9.figshare.21916218
title: Diagnostic accuracy of circulating-free DNA for the determination of hepatocellular carcinoma: a systematic review and meta-analysis

description: Circulating cell-free DNA (cfDNA) is a good diagnostic tool for hepatocellular carcinoma as it can comprehensively reflect the heterogeneity of tumors and aid in their early detection. This study aimed to assess the diagnostic value of circulating cfDNA for hepatocellular carcinoma. PubMed, EMBASE, Web of Science, Cochrane Library, and Scopus databases were searched to identify all relevant literature from their dates of establishment to 6 April 2022, and a total of 2,467 articles were found. Methodological quality assessment was performed using QUADAS-2. Fifteen articles with 3,686 patients were included in this study after screening. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve were 0.83 (95% confidence interval [CI]: 0.78, 0.87), 0.90 (95% CI: 0.86, 0.93), 8.4 (95% CI: 5.9, 12.0), 0.19 (95% CI: 0.15, 0.24), 44 (95% CI: 30, 66), and 0.93 (95% CI: 0.90, 0.95), respectively. Deek’s funnel plot test did not show significant publication bias (P = 0.28). Results of this meta-analysis suggest that circulating cfDNA has moderate sensitivity and excellent specificity for the detection of hepatocellular carcinoma as a noninvasive test (0.83 and 0.90, respectively).
DOI: 10.6084/m9.figshare.21916218.v1
title: Diagnostic accuracy of circulating-free DNA for the determination of hepatocellular carcinoma: a systematic review and meta-analysis

description: Circulating cell-free DNA (cfDNA) is a good diagnostic tool for hepatocellular carcinoma as it can comprehensively reflect the heterogeneity of tumors and aid in their early detection. This study aimed to assess the diagnostic value of circulating cfDNA for hepatocellular carcinoma. PubMed, EMBASE, Web of Science, Cochrane Library, and Scopus databases were searched to identify all relevant literature from their dates of establishment to 6 April 2022, and a total of 2,467 articles were found. Methodological quality assessment was performed using QUADAS-2. Fifteen articles with 3,686 patients were included in this study after screening. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve were 0.83 (95% confidence interval [CI]: 0.78, 0.87), 0.90 (95% CI: 0.86, 0.93), 8.4 (95% CI: 5.9, 12.0), 0.19 (95% CI: 0.15, 0.24), 44 (95% CI: 30, 66), and 0.93 (95% CI: 0.90, 0.95), respectively. Deek’s funnel plot test did not show significant publication bias (P = 0.28). Results of this meta-analysis suggest that circulating cfDNA has moderate sensitivity and excellent specificity for the detection of hepatocellular carcinoma as a noninvasive test (0.83 and 0.90, respectively).
DOI: 10.18112/openneuro.ds004520.v1.0.1
title: EsterPytel2023
DOI: 10.18112/openneuro.ds004521.v1.0.0
title: Changes in behavioral priority influence the accessibility of working memory content - Experiment 2
DOI: 10.6084/m9.figshare.22121477
title: Lending Club

description: This dataset is a modified version of the Kaggle Lending Club dataset found at https://www.kaggle.com/datasets/wordsforthewise/lending-club, including a model trained on the training set. <br> The data contains 2007 through 2018 Lending Club accepted and rejected loan data. <br> The dataset is licenced under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication https://creativecommons.org/publicdomain/zero/1.0/
DOI: 10.17909/5ry6-7r85
title: HST data for prompt emission of AT2018cow
DOI: 10.5281/zenodo.7702530
title: EVALUATION OF EDUCATIONAL POLICIES FOR EMERGENCY REMOTE EDUCATION AND THE POST-PANDEMIC: A STUDY BASED ON THE LEGAL FRAMEWORKS OF THE STATE SCHOOL SYSTEM OF RORAIMA, BRAZIL

description: This article provides an assessment of the legal framework built during the social isolation phase of the COVID-19 pandemic, by the Federal Government and the State Government of Roraima, regarding the provision of Emergency Remote Teaching (ERE). This is a research with a qualitative approach, developed through document analysis and bibliographical research, with the selection and categorization of all educational regulations issued by the Union and the state of Roraima in the years 2020 and 2021, as well as articles that deal with of the theme of ERE in the Scielo database and in the Capes Catalog of Theses and Dissertations. The normative instruments that sought to guarantee the right to education of children, young people and adults in basic education when school attendance was prohibited were highlighted. Among the main conclusions, it was found that the lack of infrastructure and technological knowledge of school communities were obstacles, as the bibliography shows, even though legally there was a significant effort from the Roraima Government, to guarantee autonomy to schools in offering ERE.
DOI: 10.5281/zenodo.7702529
title: EVALUATION OF EDUCATIONAL POLICIES FOR EMERGENCY REMOTE EDUCATION AND THE POST-PANDEMIC: A STUDY BASED ON THE LEGAL FRAMEWORKS OF THE STATE SCHOOL SYSTEM OF RORAIMA, BRAZIL

description: This article provides an assessment of the legal framework built during the social isolation phase of the COVID-19 pandemic, by the Federal Government and the State Government of Roraima, regarding the provision of Emergency Remote Teaching (ERE). This is a research with a qualitative approach, developed through document analysis and bibliographical research, with the selection and categorization of all educational regulations issued by the Union and the state of Roraima in the years 2020 and 2021, as well as articles that deal with of the theme of ERE in the Scielo database and in the Capes Catalog of Theses and Dissertations. The normative instruments that sought to guarantee the right to education of children, young people and adults in basic education when school attendance was prohibited were highlighted. Among the main conclusions, it was found that the lack of infrastructure and technological knowledge of school communities were obstacles, as the bibliography shows, even though legally there was a significant effort from the Roraima Government, to guarantee autonomy to schools in offering ERE.
DOI: 10.6084/m9.figshare.19590712
title: Analysis files from Douglas et al. (2023)

description: Analysis files from: Douglas, H.B, et al. 2023. <br> Douglas, H., Konstantinov, A., Brunke, A., Moseyko, A., Chapados, J., Eyres, J., Richter, R., Savard, K., Sears, E., Prathapan, K.D., Ruan, Y. and Dettman, J. 2023. Phylogeny of the flea beetles (Galerucinae: Alticini) and the position of <em>Aulacothorax</em> elucidated through anchored phylogenomics (Coleoptera: Chrysomelidae: Alticini). Systematic Entomology. Early View. https://doi.org/10.1111/syen.12582 <br> Alignments, partition files, trees with concordance factor values, and taxon name key.
DOI: 10.25345/c5k931g92
title: MassIVE MSV000091416 - Functional redundancy for the metabolic exchange of siderophores, vitamins, nitrogen, and phosphorus underpins the interactions in the Trichodesmium consortium
title: Proteomic measurements from cyanobacteria colonies picked from the Gulf of Aqaba (Red Sea); analyzed to reveal interaction of cyanobacteria Trichodesmium and its taxonomically diverse microbial community partners. Samples were digested with trypsin, fractionated, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against a metagenomics FASTA file sequenced at JGI.
DOI: 10.17909/fmz6-9b21
title: HST data for underlying source of AT2018cow
DOI: 10.6084/m9.figshare.15124843.v1
title: COVID-19 Unmasked Global Collaboration Protocol: longitudinal cohort study examining mental health of young children and caregivers during the pandemic

description: Early empirical data shows that school-aged children, adolescents and adults are experiencing elevated levels of anxiety and depression during the COVID-19 pandemic. Currently, there is very little research on mental health outcomes for young children. To describe the formation of a global collaboration entitled, ‘COVID-19 Unmasked<b>’</b>. The collaborating researchers aim to (1) describe and compare the COVID-19 related experiences within and across countries; (2) examine mental health outcomes for young children (1 to 5 years) and caregivers over a 12-month period during the COVID-19 pandemic; (3) explore the trajectories/time course of psychological outcomes of the children and parents over this period and (4) identify the risk and protective factors for different mental health trajectories. Data will be combined from all participating countries into one large open access cross-cultural dataset to facilitate further international collaborations and joint publications. COVID-19 Unmasked is an online prospective longitudinal cohort study. An international steering committee was formed with the aim of starting a global collaboration. Currently, partnerships have been formed with 9 countries (Australia, Cyprus, Greece, the Netherlands, Poland, Spain, Turkey, the UK, and the United States of America). Research partners have started to start data collection with caregivers of young children aged 1–5 years old at baseline, 3-months, 6-months, and 12-months. Caregivers are invited to complete an online survey about COVID-19 related exposure and experiences, child’s wellbeing, their own mental health, and parenting. Primary study outcomes will be child mental health as assessed by scales from the Patient-Reported Outcomes Measurement Information System – Early Childhood (PROMIS-EC) and caregiver mental health as assessed by the Depression Anxiety Stress Scale (DASS-21). The trajectories/time course of mental health difficulties and the impact of risk and protective factors will be analysed using hierarchical linear models, accounting for nested effects (e.g. country) and repeated measures. This article describes the formation of a global collaboration between 9 countries that are collecting data to examine mental health outcomes for young children (1 to 5 years) and caregivers over a 12-month period during the COVID-19 pandemic. This article describes the formation of a global collaboration between 9 countries that are collecting data to examine mental health outcomes for young children (1 to 5 years) and caregivers over a 12-month period during the COVID-19 pandemic.
DOI: 10.6084/m9.figshare.22221325
title: CWC DATA SET SPSS FINAL MERGED COMPLETED 22-11-22_1.sav

description: This data is on child welfare clinic attendance during the covid-19 pandemic era and the nutritional status of children as well as mother's nutritional knowledge
DOI: 10.6084/m9.figshare.22221325.v1
title: CWC DATA SET SPSS FINAL MERGED COMPLETED 22-11-22_1.sav

description: This data is on child welfare clinic attendance during the covid-19 pandemic era and the nutritional status of children as well as mother's nutritional knowledge
DOI: 10.6084/m9.figshare.16676673.v2
title: Psychometric properties and validity of the German version of the Post-Traumatic Diagnostic Scale for DSM-5 (PDS-5)

description: The availability of psychometrically sound instruments for the assessment of Post-Traumatic Stress Disorder (PTSD) is indispensable for clinical and scientific work with individuals suffering from trauma-related distress. The aim of the present study was to translate the Post-Traumatic Diagnostic Scale for DSM-5 (PDS-5) into German and to evaluate its psychometric properties as well as convergent, discriminant, and factorial validity. The authorized German translation of the PDS-5 was completed by 270 patients admitted to specialized outpatient trauma clinics. Of these, 57.8% completed the PDS for a second time (mean time between assessments was 12.0 days). In order to examine convergent and discriminant validity of the PDS-5, the Post-traumatic Stress Disorder Checklist for DSM-5 as well as Patient Health Questionnaire subscales assessing depression (PHQ-9), somatization (PHQ-15), and Generalized Anxiety Disorder (GAD-7) were applied. The PDS-5 total score showed excellent internal consistency (α = .91) and re-test reliability (rho = .84). Convergent validity was supported by a strong correlation with the total score of the Post-traumatic Stress Disorder Checklist for DSM-5 (PCL-5; rho = .91). Correlations with Patient Health Questionnaire subscales of depression (rho = .81), anxiety (rho = .72), and somatization (rho = .65) were significantly lower (all <i>p</i> &lt; .001) indicating discriminant validity of the PDS-5. Confirmative Factor Analysis did not result in a clear preference for one of the tested models. Defining a diagnostic cut-off value of ≥36 based on ROC analysis resulted in high sensitivity (.92) and specificity (.96) compared to a probable PTSD diagnosis according to the PCL-5. In summary, our results indicate that the German PDS-5 translation provides valid and reliable information concerning both PTSD severity and diagnosis. The Post-traumatic Diagnostic Scale for DSM-5 (PDS-5) is one of the most frequently applied self-rating scales for assessing PTSD severity.This study indicates that the German PDS-5 version provides valid and reliable information concerning both PTSD severity and diagnosis. The Post-traumatic Diagnostic Scale for DSM-5 (PDS-5) is one of the most frequently applied self-rating scales for assessing PTSD severity. This study indicates that the German PDS-5 version provides valid and reliable information concerning both PTSD severity and diagnosis.
DOI: 10.5281/zenodo.7702637
title: BLASTN results for CRISPR mini-array protospacers search

description: <strong>Supplementary file 1: BLASTN results for protospacers search</strong> This file contains the output of the BLASTN search of the spacers in the same genomic partition. See materials and methods for more details regarding the BLASTN search. All sequences between two adjacent repeats (less than 60bp apart) were retrieved and marked with the first repeat coordinates, spacer coordinates, and “Array” flag. For all single repeat-like sequences, 30bp up/downstream as potential spacers and marked with the repeat coordinates, spacer coordinates, and “SingleUpstream” or “SingleDownstream” flags.
DOI: 10.5281/zenodo.7702636
title: BLASTN results for CRISPR mini-array protospacers search

description: <strong>Supplementary file 1: BLASTN results for protospacers search</strong> This file contains the output of the BLASTN search of the spacers in the same genomic partition. See materials and methods for more details regarding the BLASTN search. All sequences between two adjacent repeats (less than 60bp apart) were retrieved and marked with the first repeat coordinates, spacer coordinates, and “Array” flag. For all single repeat-like sequences, 30bp up/downstream as potential spacers and marked with the repeat coordinates, spacer coordinates, and “SingleUpstream” or “SingleDownstream” flags.
DOI: 10.5281/zenodo.7699825
title: Data for the manuscript "Electronic excitations of the charged nitrogen-vacancy center in diamond obtained using time-independent variational density functional calculations"

description: This folder contains all the input, output, and geometry files used to produce the results for the manuscript. We included unprocessed data for LDA, PBE, TPSS, and r2SCAN functionals. We also provide a keynote file for figure 1 and a jupyter notebook which we used to make figures 2-4.
DOI: 10.5281/zenodo.7699824
title: Data for the manuscript "Electronic excitations of the charged nitrogen-vacancy center in diamond obtained using time-independent variational density functional calculations"

description: This folder contains all the input, output, and geometry files used to produce the results for the manuscript. We included unprocessed data for LDA, PBE, TPSS, and r2SCAN functionals. We also provide a keynote file for figure 1 and a jupyter notebook which we used to make figures 2-4.
DOI: 10.5281/zenodo.7702647
title: Dataset of the paper: "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"

description: All practical artifacts of the submitted PACIS2023 paper with the title "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"
DOI: 10.5281/zenodo.7702646
title: Dataset of the paper: "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"

description: All practical artifacts of the submitted PACIS2023 paper with the title "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"
DOI: 10.5281/zenodo.7702652
title: Dataset of the paper: "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"

description: All practical artifacts of the submitted PACIS2023 paper with the title "Creating Common Ground: Formalizing and Designing an Employee-driven Innovation Process with Decision Points"
DOI: 10.48331/scielo.h8pj2e/ljmj6g
title: Gender Equity for SciELO Feb 2023.pptm

description: :unav
DOI: 10.48331/scielo.h8pj2e
title: Gender equity initiatives at Lancet journals and EASE

description: Presentation by Dr Joan Marsh at the ABEC Brazil - SciELO 25 Years Seminar: Gender equity in scientific publishing. Event page: https://25.scielo.org/en/seminars/deia-abec/
DOI: 10.34740/kaggle/dsv/5117497
title: Nigerian Presidential Election 2023 Tweets