cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11557302
title: MOESM4 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 4. Comprehensive mapping of PTMs within moderately high-scoring human PrLDs. Human PTMs derived from the ActiveDriverDB were mapped to all human PrLDs with PAPA score &gt; 0.0. For each protein the maximum PAPA score, moderately high-scoring PrLD sequence (corresponding to all overlapping regions with PAPA score &gt; 0.0), amino acid positions bounding the PrLD sequence, and all PTMs mapping to the PrLD region are indicated. PLAAC predictions are also included, as indicated for Additional file 2.
DOI: 10.6084/m9.figshare.11557302.v1
title: MOESM4 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 4. Comprehensive mapping of PTMs within moderately high-scoring human PrLDs. Human PTMs derived from the ActiveDriverDB were mapped to all human PrLDs with PAPA score &gt; 0.0. For each protein the maximum PAPA score, moderately high-scoring PrLD sequence (corresponding to all overlapping regions with PAPA score &gt; 0.0), amino acid positions bounding the PrLD sequence, and all PTMs mapping to the PrLD region are indicated. PLAAC predictions are also included, as indicated for Additional file 2.
DOI: 10.6084/m9.figshare.11557296
title: MOESM3 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 3. Comparison of wild-type and disease-associated mutant PAPA scores. For all disease associated mutants in the ClinVar database, mutant sequences were generated by incorporating the indicated amino acid substitution at the appropriate position and re-scored using the modified PAPA algorithm. For each variant, both wild-type and mutant aggregation propensity scores are indicated, as well as the difference between mutant and wild-type scores. For each variant, the associated disease phenotype annotation is also included. PLAAC predictions are also included, as indicated for Additional file 2
DOI: 10.6084/m9.figshare.11557296.v1
title: MOESM3 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 3. Comparison of wild-type and disease-associated mutant PAPA scores. For all disease associated mutants in the ClinVar database, mutant sequences were generated by incorporating the indicated amino acid substitution at the appropriate position and re-scored using the modified PAPA algorithm. For each variant, both wild-type and mutant aggregation propensity scores are indicated, as well as the difference between mutant and wild-type scores. For each variant, the associated disease phenotype annotation is also included. PLAAC predictions are also included, as indicated for Additional file 2
DOI: 10.6084/m9.figshare.11557290
title: MOESM2 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 2. Aggregation propensity scores and inter-isoform score comparison for all human protein isoforms. Predicted aggregation propensity for all “high-confidence” human protein isoforms (derived from ActiveDriverDB) was calculated using the modified PAPA algorithm (see Methods section for details). Scores and corresponding full protein sequences are indicated for all isoforms, along with the maximum PAPA score among all isoforms mapping to the same gene, the difference between the PAPA score for the indicated isoform and the maximum PAPA score among related isoforms, and the protein sequence corresponding to the highest-scoring related isoform. Additionally, the PLAAC algorithm was used to analyze the same sequences. A binary variable indicates if the protein contains a PLAAC-predicted PrLD that overlaps with the PAPA-predicted PrLD for high-scoring proteins only and, if so, the position of the PLAAC-predicted PrLD
DOI: 10.6084/m9.figshare.11557290.v1
title: MOESM2 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 2. Aggregation propensity scores and inter-isoform score comparison for all human protein isoforms. Predicted aggregation propensity for all “high-confidence” human protein isoforms (derived from ActiveDriverDB) was calculated using the modified PAPA algorithm (see Methods section for details). Scores and corresponding full protein sequences are indicated for all isoforms, along with the maximum PAPA score among all isoforms mapping to the same gene, the difference between the PAPA score for the indicated isoform and the maximum PAPA score among related isoforms, and the protein sequence corresponding to the highest-scoring related isoform. Additionally, the PLAAC algorithm was used to analyze the same sequences. A binary variable indicates if the protein contains a PLAAC-predicted PrLD that overlaps with the PAPA-predicted PrLD for high-scoring proteins only and, if so, the position of the PLAAC-predicted PrLD
DOI: 10.6084/m9.figshare.11557281
title: MOESM1 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 1. PAPA scores derived from random sampling of sequence variant combinations for proteins with high-scoring PrLDs. For all proteins with a moderately high-scoring PrLD (PAPA&gt;â€‰0.0) and at least one single-amino acid variant, the minimum and maximum aggregation propensity scores obtained from randomly sampling PrLD sequence variants, along with the corresponding reference sequence score, are indicated (see Methods for a complete description of sequence variant calculations).
DOI: 10.6084/m9.figshare.11557281.v1
title: MOESM1 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 1. PAPA scores derived from random sampling of sequence variant combinations for proteins with high-scoring PrLDs. For all proteins with a moderately high-scoring PrLD (PAPA&gt;â€‰0.0) and at least one single-amino acid variant, the minimum and maximum aggregation propensity scores obtained from randomly sampling PrLD sequence variants, along with the corresponding reference sequence score, are indicated (see Methods for a complete description of sequence variant calculations).
DOI: 10.6084/m9.figshare.11557224
title: MOESM4 of On-site clinical mentoring as a maternal and new-born care quality improvement method: evidence from a nurse cohort study in Nepal

description: Additional file 4: Table S2. Changes in assessment scores from baseline to end line by mentees' function status, Nepal, 2016-2018.
DOI: 10.6084/m9.figshare.11557221
title: MOESM3 of On-site clinical mentoring as a maternal and new-born care quality improvement method: evidence from a nurse cohort study in Nepal

description: Additional file 3: Table S1. Changes in assessment scores from baseline to end line by SBA status, Nepal, 2016-2018.
DOI: 10.6084/m9.figshare.11557224.v1
title: MOESM4 of On-site clinical mentoring as a maternal and new-born care quality improvement method: evidence from a nurse cohort study in Nepal

description: Additional file 4: Table S2. Changes in assessment scores from baseline to end line by mentees' function status, Nepal, 2016-2018.
DOI: 10.6084/m9.figshare.11557221.v1
title: MOESM3 of On-site clinical mentoring as a maternal and new-born care quality improvement method: evidence from a nurse cohort study in Nepal

description: Additional file 3: Table S1. Changes in assessment scores from baseline to end line by SBA status, Nepal, 2016-2018.
DOI: 10.6084/m9.figshare.11557200
title: MOESM1 of Influence of extension stem length and diameter on clinical and radiographic outcomes of revision total knee arthroplasty

description: Additional file 1:. raw data. The excel file incorporates the raw data of the patients included in the present study.
DOI: 10.6084/m9.figshare.11557200.v1
title: MOESM1 of Influence of extension stem length and diameter on clinical and radiographic outcomes of revision total knee arthroplasty

description: Additional file 1:. raw data. The excel file incorporates the raw data of the patients included in the present study.
DOI: 10.6084/m9.figshare.11557179
title: MOESM1 of Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes

description: Additional file 1: Table S1. Sample information for the data used in this study. Table S2. Results from our ADMIXTURE analysis showing the proportion of genetic diversity derived from each cluster for the ‘four-fold degenerate segregating sites’ dataset. Table S3. Results from our ADMIXTURE analysis showing the proportion of genetic diversity derived from each cluster for the ‘all segregating sites’ dataset. Table S4. The raw cross-validation (CV) error values from our ADMIXTURE analyses for both the ‘four-fold degenerate sites’ and ‘all segregating sites’ dataset analyses. Table S5. The results from the Structure Harvester analysis of our STRUCTURE results. Table S6. The posterior probability of each of five replicates for each K value in our structure analyses. Table S7. Pairwise unweighted and weighted Fst values for each of five taxonomic clusters.
DOI: 10.6084/m9.figshare.11557179.v1
title: MOESM1 of Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes

description: Additional file 1: Table S1. Sample information for the data used in this study. Table S2. Results from our ADMIXTURE analysis showing the proportion of genetic diversity derived from each cluster for the ‘four-fold degenerate segregating sites’ dataset. Table S3. Results from our ADMIXTURE analysis showing the proportion of genetic diversity derived from each cluster for the ‘all segregating sites’ dataset. Table S4. The raw cross-validation (CV) error values from our ADMIXTURE analyses for both the ‘four-fold degenerate sites’ and ‘all segregating sites’ dataset analyses. Table S5. The results from the Structure Harvester analysis of our STRUCTURE results. Table S6. The posterior probability of each of five replicates for each K value in our structure analyses. Table S7. Pairwise unweighted and weighted Fst values for each of five taxonomic clusters.
DOI: 10.6084/m9.figshare.11557131
title: MOESM1 of What does soil-transmitted helminth elimination look like? Results from a targeted molecular detection survey in Japan

description: Additional file 1: Table S1. Number of detected STH cases at each branch of BML, Inc. (courtesy of BML). Table S2. Number of detected STH cases at each branch of JAPC [37–45]. Table S3. Study sites and their historic levels of STH. Table S4. Participation percentage of each school, kindergarten and a nursery. Table S5. Potential risk factors and behaviors per location.
DOI: 10.6084/m9.figshare.11557131.v1
title: MOESM1 of What does soil-transmitted helminth elimination look like? Results from a targeted molecular detection survey in Japan

description: Additional file 1: Table S1. Number of detected STH cases at each branch of BML, Inc. (courtesy of BML). Table S2. Number of detected STH cases at each branch of JAPC [37–45]. Table S3. Study sites and their historic levels of STH. Table S4. Participation percentage of each school, kindergarten and a nursery. Table S5. Potential risk factors and behaviors per location.
DOI: 10.6084/m9.figshare.11556255
title: Data-Ecotoxicology.xlsx

description: data set for the body stoichiometry and macromolecues of different Daphnia magan clones from experimental evolution that exposured to nano zinc oxide and warming
DOI: 10.6084/m9.figshare.11556255.v1
title: Data-Ecotoxicology.xlsx

description: data set for the body stoichiometry and macromolecues of different Daphnia magan clones from experimental evolution that exposured to nano zinc oxide and warming
DOI: 10.6084/m9.figshare.11556117
title: SB restaurant turnover data.csv

description: Longitudinal data for restaurant openings and closing in Santa Barbara annually aggregated. Data derived from blog maintained by John Dickson. https://www.santabarbara.com/dining/news/2019/12/27/2019-year-in-review/<br><br>Specifically, data digitally extracted using DigitizeIt app Version 2.4.0
DOI: 10.6084/m9.figshare.11556117.v1
title: SB restaurant turnover data.csv

description: Longitudinal data for restaurant openings and closing in Santa Barbara annually aggregated. Data derived from blog maintained by John Dickson. https://www.santabarbara.com/dining/news/2019/12/27/2019-year-in-review/<br><br>Specifically, data digitally extracted using DigitizeIt app Version 2.4.0
DOI: 10.6084/m9.figshare.11556117.v2
title: SB restaurant turnover data.csv

description: Longitudinal data for restaurant openings and closing in Santa Barbara annually aggregated. Data derived from blog maintained by John Dickson. https://www.santabarbara.com/dining/news/2019/12/27/2019-year-in-review/<br><br>Specifically, data digitally extracted using DigitizeIt app Version 2.4.0
DOI: 10.6084/m9.figshare.11556060
title: Western North Atlantic Seabird Ecology

description: Seabird ecology and distribution in the Western North Atlantic. Only those are vulnerable to high-seas pelagic longline fishing operations are compiled here.See https://hvoltbb.github.io/data/ for more.
DOI: 10.6084/m9.figshare.11556060.v2
title: Western North Atlantic Seabird Ecology

description: Seabird ecology and distribution in the Western North Atlantic. Only those are vulnerable to high-seas pelagic longline fishing operations are compiled here.See https://hvoltbb.github.io/data/ for more.
DOI: 10.6084/m9.figshare.11556060.v1
title: Western North Atlantic Seabird Ecology

description: Seabird ecology and distribution in the Western North Atlantic. Only those are vulnerable to high-seas pelagic longline fishing operations are compiled here.
DOI: 10.6084/m9.figshare.11555844
title: Global Water Quality Database

description: These files represent the raw data used to generate a global model of median dissolved and total nitrogen and phosphorus concentrations. This was used in an assessment of the likelihood of periphyton growth.<br>Prospective users are to acknowledge and abide by the policies of the data providers (e.g. GEMStat.org; www.lawa.org.nz etc). Use of this processed database should acknowledge the authors.
DOI: 10.6084/m9.figshare.11555661
title: Misoprostol administration prior to intrauterine contraceptive device insertion: a systematic review and meta-analysis of randomised controlled trials

description: <b>Objectives:</b> Misoprostol has been used before intrauterine contraceptive device (IUCD) insertion to prime the cervical os. As the literature about this topic is controversial, we aimed to evaluate IUCD insertion failure, women’s pain perception, use of cervical dilators and prevalence of side effects following the administration of misoprostol. <b>Methods:</b> Trials published in MEDLINE, Scopus, the Cochrane Library and ClinicalTrials.gov were searched (last search on 23 October 2019). The primary outcome was IUCD insertion failure; secondary outcomes were women’s pain perception, use of cervical dilators to facilitate insertion, and prevalence of side effects. <b>Results:</b> Fourteen studies were eligible for inclusion. Misoprostol premedication reduced IUCD insertion failure rates and the use of cervical dilators but significantly increased the prevalence of side effects. The risk of IUCD insertion failure with misoprostol premedication was reduced among women who had undergone previous caesarean section and among women who had experienced previous IUCD insertion failure. Nulliparas did not benefit from misoprostol premedication. Buccal misoprostol administration did not seem to be effective in reducing IUCD insertion failure. Visual analogue scale pain scores were increased with both sublingual and buccal misoprostol administration if IUCD insertion was performed ≤2.5 h after misoprostol premedication. <b>Conclusion:</b> Our data demonstrate reduced IUCD insertion failure among women with previous caesarean section and those with previous IUCD insertion failure, suggesting that misoprostol may be a reasonable choice in these groups of women. Although misoprostol premedication reduced insertion failures, it significantly increased side effects and had a heterogeneous pattern of efficacy; thus, its routine use is not supported by the evidence.
DOI: 10.6084/m9.figshare.11555637
title: Data independent acquisition mass spectrometry of irradiated mouse lung endothelial cells reveals a STAT-associated inflammatory response

description: <b>Purpose:</b> Pulmonary inflammation is an adverse consequence of radiation therapy in breast cancer. The aim of this study was to elucidate biological pathways leading to this pathology. <b>Materials and methods:</b> Lung endothelial cells were isolated 24 h after thorax-irradiation (sham or 10 Gy X-ray) from female C57Bl/6 mice and cultivated for 6 days. <b>Results:</b> Quantitative proteomic analysis of lung endothelial cells was done using data independent acquisition (DIA) mass spectrometry. The data were analyzed using Ingenuity Pathway Analysis and STRINGdb. In total, 4220 proteins were identified using DIA of which 60 were dysregulated in the irradiated samples (fold change ≥2.00 or ≤0.50; <i>q</i>-value &lt;0.05). Several (12/40) upregulated proteins formed a cluster of inflammatory proteins with STAT1 and IRF3 as predicted upstream regulators. The several-fold increased expression of STAT1 and STAT-associated ISG15 was confirmed by immunoblotting. The expression of antioxidant proteins SOD1 and PRXD5 was downregulated suggesting radiation-induced oxidative stress. Similarly, the phosphorylated (active) forms of STING and IRF3, both members of the cGAS/STING pathway, were downregulated. <b>Conclusions:</b> These data suggest the involvement of JAK/STAT and cGas/STING pathways in the genesis of radiation-induced lung inflammation. These pathways may be used as novel targets for the prevention of radiation-induced lung damage.
DOI: 10.6084/m9.figshare.11555631
title: The effects of DNA repair polymorphisms on chromosome aberrations in the population of Kazakhstan

description: <b>Purpose:</b> To analyze the effects of DNA repair polymorphism and other factors on the frequency chromosome aberrations in an irradiated cohort of subjects living around the Semipalatinsk nuclear test site and non-exposed group of subjects from ecologically favorable zones of Kazakhstan. <b>Materials and methods:</b> Blood samples were collected in the rural areas of the East Kazakhstan district around the Semipalatinsk nuclear test site and ecologically favorable zones of Almaty region of Kazakhstan. Chromosome aberrations in the fresh and cryopreserved peripheral blood lymphocyte cultures were analyzed by Giemsa staining. Single nucleotide polymorphisms at eight DNA repair genes (<i>XRCC1</i> rs1799782, <i>XRCC1</i> rs25487, <i>XRCC3</i> rs861539, <i>ATM</i> rs1801516, <i>XPD</i> rs1799793, <i>XPD</i> rs13181, <i>APEX1</i> rs1130409, and <i>hOGG1</i> rs1052133) were determined by PCR-RFLP method. <b>Results:</b> The age of donors and smoking significantly affected the frequency of chromosome aberrations among the irradiated and control subjects. In the irradiated and control cohorts, the frequency of chromosome aberrations was significantly increased in the heterozygous <i>ATM</i> rs1801516 (1853 Asp/Asn) individuals; for the rest of the loci no significant associations between polymorphism and the frequency of chromosome aberrations were detected. <b>Conclusions:</b> The age of donors, smoking, and the <i>ATM</i> rs1801516 polymorphism significantly affect the frequency of chromosome aberrations among individuals inhabiting contaminated area around the Semipalatinsk nuclear weapon test site, as well as among those inhabiting ecologically favorable zones of Kazakhstan.
DOI: 10.6084/m9.figshare.11555631.v1
title: The effects of DNA repair polymorphisms on chromosome aberrations in the population of Kazakhstan

description: <b>Purpose:</b> To analyze the effects of DNA repair polymorphism and other factors on the frequency chromosome aberrations in an irradiated cohort of subjects living around the Semipalatinsk nuclear test site and non-exposed group of subjects from ecologically favorable zones of Kazakhstan. <b>Materials and methods:</b> Blood samples were collected in the rural areas of the East Kazakhstan district around the Semipalatinsk nuclear test site and ecologically favorable zones of Almaty region of Kazakhstan. Chromosome aberrations in the fresh and cryopreserved peripheral blood lymphocyte cultures were analyzed by Giemsa staining. Single nucleotide polymorphisms at eight DNA repair genes (<i>XRCC1</i> rs1799782, <i>XRCC1</i> rs25487, <i>XRCC3</i> rs861539, <i>ATM</i> rs1801516, <i>XPD</i> rs1799793, <i>XPD</i> rs13181, <i>APEX1</i> rs1130409, and <i>hOGG1</i> rs1052133) were determined by PCR-RFLP method. <b>Results:</b> The age of donors and smoking significantly affected the frequency of chromosome aberrations among the irradiated and control subjects. In the irradiated and control cohorts, the frequency of chromosome aberrations was significantly increased in the heterozygous <i>ATM</i> rs1801516 (1853 Asp/Asn) individuals; for the rest of the loci no significant associations between polymorphism and the frequency of chromosome aberrations were detected. <b>Conclusions:</b> The age of donors, smoking, and the <i>ATM</i> rs1801516 polymorphism significantly affect the frequency of chromosome aberrations among individuals inhabiting contaminated area around the Semipalatinsk nuclear weapon test site, as well as among those inhabiting ecologically favorable zones of Kazakhstan.
DOI: 10.6084/m9.figshare.11555619
title: SHR:SHR-GFP in scr4 mutant

description: CTCF, N&B, and quantification of QC division in SHR:SHR-GFP in scr4 mutant
DOI: 10.6084/m9.figshare.11555622
title: SHR:SHR-GFP N&B 6D 16H

description: N&B of SHR:SHR-GFP at 6D 16H
DOI: 10.6084/m9.figshare.11555622.v1
title: SHR:SHR-GFP N&B 6D 16H

description: N&B of SHR:SHR-GFP at 6D 16H
DOI: 10.6084/m9.figshare.11555613
title: SCR:SCR-GFP CTCF in QC and CEI

description: CTCF of SCR:SCR-GFP in QC and CEI cells
DOI: 10.6084/m9.figshare.11555607
title: seu3 and wox5 cell division quantification

description: QC and CEI division quantification in the wox5 and seu3 mutants.
DOI: 10.6084/m9.figshare.11555607.v1
title: seu3 and wox5 cell division quantification

description: QC and CEI division quantification in the wox5 and seu3 mutants.
DOI: 10.6084/m9.figshare.11555610
title: SHR:SHR-GFP CTCF in QC and CEI

description: CTCF quantification of SHR:SHR-GFP in QC and CEI over time.
DOI: 10.6084/m9.figshare.11555610.v1
title: SHR:SHR-GFP CTCF in QC and CEI

description: CTCF quantification of SHR:SHR-GFP in QC and CEI over time.
DOI: 10.6084/m9.figshare.11555514
title: WOX5 TPT line

description: Phenotyping and qPCR of the WOX5 TPT line
DOI: 10.6084/m9.figshare.11555514.v1
title: WOX5 TPT line

description: Phenotyping and qPCR of the WOX5 TPT line
DOI: 10.6084/m9.figshare.11555505
title: ODE Model Code

description: All code used for the ODE model.
DOI: 10.6084/m9.figshare.11555505.v1
title: ODE Model Code

description: All code used for the ODE model.
DOI: 10.6084/m9.figshare.11553534
title: Code to reproduce analyses from "The influence of stochasticity, landscape structure, and species traits on abundant-centre relationships"

description: Code to reproduce simulation analyses from <br>&gt; Dallas, TA, and L Santini. 2020. "The influence of stochasticity, landscape structure, and species traits on abundant-centre relationships" <br><br><br><br>