cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8288807.v1
title: Global spatio-temporally harmonised datasets for producing high-resolution gridded population distribution datasets

description: Multi-temporal, globally consistent, high-resolution human population datasets provide consistent and comparable population distributions in support of mapping sub-national heterogeneities in health, wealth, and resource access, and monitoring change in these over time. The production of more reliable and spatially detailed population datasets is increasingly necessary due to the importance of improving metrics at sub-national and multi-temporal scales. This is in support of measurement and monitoring of UN Sustainable Development Goals and related agendas. In response to these agendas, a method has been developed to assemble and harmonise a unique, open access, archive of geospatial datasets. Datasets are provided as global, annual time series, where pertinent at the timescale of population analyses and where data is available, for use in the construction of population distribution layers. The archive includes sub-national census-based population estimates, matched to a geospatial layer denoting administrative unit boundaries, and a number of co-registered gridded geospatial factors that correlate strongly with population presence and density. Here, we describe these harmonised datasets and their limitations, along with the production workflow. Further, we demonstrate applications of the archive by producing multi-temporal gridded population outputs for Africa and using these to derive health and development metrics. The geospatial archive is available at https://doi.org/10.5258/SOTON/WP00650.
DOI: 10.6084/m9.figshare.8288795
title: Isolation and molecular characterization of spermatogonia from male Sprague-Dawley rats exposed <i>in utero</i> and postnatally to dibutyl phthalate or acrylamide

description: The increased incidence of testicular disorders in young men and the possible influence of environmental chemicals, such as dibutyl phthalate (DBP) and acrylamide (AA), requires experimental models for identifying modes of action. Most published reproductive toxicologic studies use RNA samples from the total testis to evaluate testicular gene expression; however, analyses of isolated cell types could provide a more specific tool. Among testicular germ cells, spermatogonia are critical since they represent the onset of spermatogenesis. This study aimed, (1) to establish a technique for spermatogonia isolation; (2) to apply this isolation technique to verify possible gene expression alterations (Pou5f1, Kitlg, Mki-67, Bak1 and Spry4) in prepubertal post-natal day, (PND24) and pubertal (PND45) testes after <i>in utero</i> and postnatal exposure to DBP or AA. The technique was efficient for isolation of a majority of spermatogonia. <i>In utero</i> DBP exposure led to reduced litter body weight at birth, reduced anogenital distance of male pups on PND4, and increased frequency of male nipple retention on PND14 compared to controls. DBP-exposed relative testes weights were reduced only at PND24 compared to control but they did not differ at PND45. DBP-exposed animals showed reduced expression levels of Pou5f1 and Mki67 on PND24, and reduced expression of Pou5f1 and Spry4 on PND45. AA exposure reduced expression of Pou5f1, Mki67, and Spry4 at PND45 although not significantly. Our results suggest that DBP acts by reducing cell proliferation and impairing differentiation in prepubertal and pubertal testes.
DOI: 10.6084/m9.figshare.8288795.v1
title: Isolation and molecular characterization of spermatogonia from male Sprague-Dawley rats exposed <i>in utero</i> and postnatally to dibutyl phthalate or acrylamide

description: The increased incidence of testicular disorders in young men and the possible influence of environmental chemicals, such as dibutyl phthalate (DBP) and acrylamide (AA), requires experimental models for identifying modes of action. Most published reproductive toxicologic studies use RNA samples from the total testis to evaluate testicular gene expression; however, analyses of isolated cell types could provide a more specific tool. Among testicular germ cells, spermatogonia are critical since they represent the onset of spermatogenesis. This study aimed, (1) to establish a technique for spermatogonia isolation; (2) to apply this isolation technique to verify possible gene expression alterations (Pou5f1, Kitlg, Mki-67, Bak1 and Spry4) in prepubertal post-natal day, (PND24) and pubertal (PND45) testes after <i>in utero</i> and postnatal exposure to DBP or AA. The technique was efficient for isolation of a majority of spermatogonia. <i>In utero</i> DBP exposure led to reduced litter body weight at birth, reduced anogenital distance of male pups on PND4, and increased frequency of male nipple retention on PND14 compared to controls. DBP-exposed relative testes weights were reduced only at PND24 compared to control but they did not differ at PND45. DBP-exposed animals showed reduced expression levels of Pou5f1 and Mki67 on PND24, and reduced expression of Pou5f1 and Spry4 on PND45. AA exposure reduced expression of Pou5f1, Mki67, and Spry4 at PND45 although not significantly. Our results suggest that DBP acts by reducing cell proliferation and impairing differentiation in prepubertal and pubertal testes.
DOI: 10.6084/m9.figshare.8288789
title: New and old pole daughters differ in their glucose uptake patterns

description: Uptake of the fluorescent glucose analogue 2-(<i>N</i>-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose (2-NBDG) in 40 pairs of old pole and b) generation-matched new pole daughter cells collated from three independent mother machine experiments. Each pair was hosted in a different dead-end channel of the mother machine and constituted the 4<sup>th</sup> generation grown in the mother machine from an <i>E. coli</i> overnight culture. 2-NBDG was introduced in the mother machine at t = 0s.<br>
DOI: 10.6084/m9.figshare.8288789.v2
title: New and old pole daughters differ in their glucose uptake patterns

description: Uptake of the fluorescent glucose analogue 2-(<i>N</i>-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose (2-NBDG) in 40 pairs of old pole and b) generation-matched new pole daughter cells collated from three independent mother machine experiments. Each pair was hosted in a different dead-end channel of the mother machine and constituted the 4<sup>th</sup> generation grown in the mother machine from an <i>E. coli</i> overnight culture. 2-NBDG was introduced in the mother machine at t = 0s.<br>
DOI: 10.6084/m9.figshare.8288789.v1
title: New and old pole daughters differ in their glucose uptake patterns

description: Uptake of the fluorescent glucose analogue 2-(<i>N</i>-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose (2-NBDG) in 40 pairs of old pole and b) generation-matched new pole daughter cells collated from three independent mother machine experiments. Each pair was hosted in a different dead-end channel of the mother machine and constituted the 4<sup>th</sup> generation grown in the mother machine from an <i>E. coli</i> overnight culture. 2-NBDG was introduced in the mother machine at t = 0s. (c) At the end of each experiment (t = 840s) new pole daughters had accumulated intracellular glucose to a significantly higher level than old pole daughters (paired t-test, n = 40 pairs, p &lt; 0.0001).<br>
DOI: 10.6084/m9.figshare.8288714
title: Syntax.zip

description: syntax file for data generation and JAGS models
DOI: 10.6084/m9.figshare.8288714.v1
title: Syntax.zip

description: syntax file for data generation and JAGS models
DOI: 10.6084/m9.figshare.8288600
title: Body fat distribution influences ART outcomes

description: Body mass index (BMI) is the widely used method to evaluate obesity, but it cannot differentiate lean from fat mass neither mass distribution. Other methods have been proposed for this evaluation, as waist and hip circumferences (WC, HC) and ratio (WHR) and body fat analysis by bioimpedance (BF%), but they have not been applied to evaluate assisted reproduction (ART) outcomes. The present study aims at determining whether body composition and adipose tissue distribution are better than BMI on ART outcomes. Analysis was performed through five anthropometric measurements of 788 women submitted to controlled ovarian hyperstimulation and in vitro fertilization techniques. The increase of body fat, independently of the measurement method, was associated to worse reproductive results. However, a surprising finding was that eutrophic women with WC lower than 80 cm showed gestation rates two times superior (38.9% versus 14.3%) when compared to eutrophic women with WC larger than 80 cm (<i>p</i> = .002). Furthermore, obese women with WHR higher than 0.85 showed worse ART results, considering oocytes retrieved, mature oocytes and fertilization when compared to those with WHR lower than 0.85. As a conclusion, it was observed that the body fat distribution, especially WC, was more relevant than BMI to predict ART outcomes.
DOI: 10.6084/m9.figshare.8288600.v1
title: Body fat distribution influences ART outcomes

description: Body mass index (BMI) is the widely used method to evaluate obesity, but it cannot differentiate lean from fat mass neither mass distribution. Other methods have been proposed for this evaluation, as waist and hip circumferences (WC, HC) and ratio (WHR) and body fat analysis by bioimpedance (BF%), but they have not been applied to evaluate assisted reproduction (ART) outcomes. The present study aims at determining whether body composition and adipose tissue distribution are better than BMI on ART outcomes. Analysis was performed through five anthropometric measurements of 788 women submitted to controlled ovarian hyperstimulation and in vitro fertilization techniques. The increase of body fat, independently of the measurement method, was associated to worse reproductive results. However, a surprising finding was that eutrophic women with WC lower than 80 cm showed gestation rates two times superior (38.9% versus 14.3%) when compared to eutrophic women with WC larger than 80 cm (<i>p</i> = .002). Furthermore, obese women with WHR higher than 0.85 showed worse ART results, considering oocytes retrieved, mature oocytes and fertilization when compared to those with WHR lower than 0.85. As a conclusion, it was observed that the body fat distribution, especially WC, was more relevant than BMI to predict ART outcomes.
DOI: 10.6084/m9.figshare.8288480
title: Additional file 2: of Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization

description: DESeq2 results using MG1655 as the reference librabry (divisor) and MG1655::Ď PA8 as the comparison library (numerator). (XLSX 697 kb)
DOI: 10.6084/m9.figshare.8288480.v1
title: Additional file 2: of Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization

description: DESeq2 results using MG1655 as the reference librabry (divisor) and MG1655::Ď PA8 as the comparison library (numerator). (XLSX 697 kb)
DOI: 10.6084/m9.figshare.8288471
title: Additional file 1: of Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization

description: DESeq2 results using MG1655 as the reference librabry (divisor) and MG1655::Ď O104 as the comparison library (numerator). (XLSX 633 kb)
DOI: 10.6084/m9.figshare.8288471.v1
title: Additional file 1: of Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization

description: DESeq2 results using MG1655 as the reference librabry (divisor) and MG1655::Ď O104 as the comparison library (numerator). (XLSX 633 kb)
DOI: 10.6084/m9.figshare.8288414
title: Additional file 35: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S21. EPS Model V3 Drug Screen Data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8288417
title: Additional file 36: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S22. PPTI Drug Screening Data â UPS. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8288411
title: Additional file 34: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S20. Druggable Exome Targets - PCB490. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8288408
title: Additional file 33: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S19. RNA Sequencing data - PCB490. (XLSX 3314 kb)
DOI: 10.6084/m9.figshare.8288414.v1
title: Additional file 35: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S21. EPS Model V3 Drug Screen Data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8288411.v1
title: Additional file 34: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S20. Druggable Exome Targets - PCB490. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8288417.v1
title: Additional file 36: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S22. PPTI Drug Screening Data â UPS. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8288405
title: Additional file 32: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S18. Exome Sequencing Data - PCB490. (XLSX 345 kb)
DOI: 10.6084/m9.figshare.8288399
title: Additional file 30: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S16.â V3 Drug Screen data - PCB490. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288402
title: Additional file 31: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S17. Roche Drug Screen data - PCB490. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8288408.v1
title: Additional file 33: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S19. RNA Sequencing data - PCB490. (XLSX 3314 kb)
DOI: 10.6084/m9.figshare.8288399.v1
title: Additional file 30: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S16.â V3 Drug Screen data - PCB490. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288405.v1
title: Additional file 32: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S18. Exome Sequencing Data - PCB490. (XLSX 345 kb)
DOI: 10.6084/m9.figshare.8288390
title: Additional file 28: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S14. Combination Index Values - U23674. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8288393
title: Additional file 29: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S15. Rewiring Screening Data - U23674. (XLSX 270 kb)
DOI: 10.6084/m9.figshare.8288402.v1
title: Additional file 31: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S17. Roche Drug Screen data - PCB490. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8288390.v1
title: Additional file 28: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S14. Combination Index Values - U23674. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8288393.v1
title: Additional file 29: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S15. Rewiring Screening Data - U23674. (XLSX 270 kb)
DOI: 10.6084/m9.figshare.8288381
title: Additional file 25: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S11. Rapid Screen vs Drug screen - U23674. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288384
title: Additional file 26: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S12. Phospho Screen data - U23674. (XLSX 657 kb)
DOI: 10.6084/m9.figshare.8288387
title: Additional file 27: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S13. PTIM Map Scores. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8288387.v1
title: Additional file 27: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S13. PTIM Map Scores. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8288384.v1
title: Additional file 26: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S12. Phospho Screen data - U23674. (XLSX 657 kb)
DOI: 10.6084/m9.figshare.8288381.v1
title: Additional file 25: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S11. Rapid Screen vs Drug screen - U23674. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288369
title: Additional file 22: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S8. Exome Sequencing Data - U23674. (XLSX 1792 kb)
DOI: 10.6084/m9.figshare.8288375
title: Additional file 24: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S10. RAPID siRNA Screen data - U23674. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8288366
title: Additional file 21: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S7. PPTI Screen Merged data - U23674. (XLSX 130 kb)
DOI: 10.6084/m9.figshare.8288372
title: Additional file 23: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S9. RNA Sequencing Data - U23674. (XLSX 2157 kb)
DOI: 10.6084/m9.figshare.8288366.v1
title: Additional file 21: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S7. PPTI Screen Merged data - U23674. (XLSX 130 kb)
DOI: 10.6084/m9.figshare.8288375.v1
title: Additional file 24: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S10. RAPID siRNA Screen data - U23674. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8288369.v1
title: Additional file 22: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S8. Exome Sequencing Data - U23674. (XLSX 1792 kb)
DOI: 10.6084/m9.figshare.8288363
title: Additional file 20: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S6. PPTI screen IC50 data - U23674. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288372.v1
title: Additional file 23: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S9. RNA Sequencing Data - U23674. (XLSX 2157 kb)
DOI: 10.6084/m9.figshare.8288357
title: Additional file 19: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S5. Roche screen IC50 data - U23674. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8288354
title: Additional file 18: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S4. Roche screen hit references. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8288363.v1
title: Additional file 20: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S6. PPTI screen IC50 data - U23674. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8288354.v1
title: Additional file 18: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S4. Roche screen hit references. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8288357.v1
title: Additional file 19: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S5. Roche screen IC50 data - U23674. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8288348
title: Additional file 16: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S2. GSK Screen Data IC50 Data - U23674. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8288351
title: Additional file 17: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S3. Roche Screen Merged Data - U23674. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8288345
title: Additional file 15: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S1. Merged GSK Screen Data - U23674. (XLSX 271 kb)
DOI: 10.6084/m9.figshare.8288348.v1
title: Additional file 16: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S2. GSK Screen Data IC50 Data - U23674. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8288351.v1
title: Additional file 17: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S3. Roche Screen Merged Data - U23674. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8288345.v1
title: Additional file 15: of Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

description: Table S1. Merged GSK Screen Data - U23674. (XLSX 271 kb)
DOI: 10.6084/m9.figshare.8288258
title: Additional file 16: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: SOM-CHIP for IGN-enriched expression (XLSX 838 kb)
DOI: 10.6084/m9.figshare.8288261
title: Additional file 17: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: IGN-CHIP for SOM-enriched expression (XLSX 737 kb)
DOI: 10.6084/m9.figshare.8288258.v1
title: Additional file 16: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: SOM-CHIP for IGN-enriched expression (XLSX 838 kb)
DOI: 10.6084/m9.figshare.8288261.v1
title: Additional file 17: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: IGN-CHIP for SOM-enriched expression (XLSX 737 kb)
DOI: 10.6084/m9.figshare.8288249
title: Additional file 15: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: SOM_H3K4me3_q0.001_peaks_ce10 (XLSX 4603 kb)
DOI: 10.6084/m9.figshare.8288243
title: Additional file 14: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

description: IGN_H3K4me3_q0.001_peaks_ce10 (XLSX 3928 kb)