cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22714669.v1
title: Comparison of microbial profiles and viral status along the vagina-cervix-endometrium continuum of infertile patients

description: For decades, the endometrium was considered to be a sterile environment. However, now this concept is disputed, and there is growing evidence that microbiota composition might affect endometrial receptivity. Routine clinical management of infertility is still limited to a microbiological assessment of the lower reproductive tract. The purpose of this study was to compare the abundance of various bacterial, fungal, and viral species, qualitatively and quantitatively, in vaginal, cervical, and endometrial biomaterial of infertile patients. A total of 300 samples from 100 infertile patients of a private assisted reproduction clinic were analyzed. A broad real-time polymerase chain reaction panel was used to identify 28 relevant microbial taxa as well as three members of the Herpesviridae family. All patients underwent endometrial biopsy for further histopathological evaluation. Analysis of the microbial diversity (within the boundaries of the detection panel) revealed that Shannon indexes in the cervix and vagina were similar (1.4 × 10<sup>−2</sup> (1.6 × 10<sup>−3</sup> – 6.5 × 10<sup>−1</sup>) vs 1.9 × 10<sup>−2</sup> (2.3 × 10<sup>−3</sup> – 5.3 × 10<sup>−1</sup>), respectively, <i>p</i> = 0.502), whereas endometrial indexes differed significantly from both regions (0 (0 – 1.4 × 10<sup>−1</sup>), <i>p</i> &lt; 0.0001). Surprisingly, 17 microbial and viral taxa were detected in at least one sample. Endometrium exhibited a quite distinct microbiological profile, being different at the detection rates of 14 taxa (<i>p</i> &lt; 0.05). Remarkably, 4% and 2% of endometrial samples were positive for Cytomegalovirus and <i>Candida spp.</i>, respectively, while these were undetectable in corresponding cervical and vaginal samples. Prevalence of the <i>Gardnerella vaginalis</i> + <i>Prevotella bivia</i> + <i>Porphyromonas spp.</i> group in endometrium was associated with a low abundance of <i>Lactobacillus spp</i>. (<i>p</i> = 0.039). No noteworthy associations were identified between various microbiota characteristics and clinical parameters, such as chronic endometritis, uterine polyps and adhesions, endometriosis, and a history of sexually transmitted infections. These findings indicate that the microbiological profile of the endometrium is unique, and the analysis of the lower reproductive tract should supplement, rather than be a substitute for it.
DOI: 10.6084/m9.figshare.22572596
title: The use of <i>in silico</i> extreme pathway (ExPa) analysis to identify conserved reproductive transcriptional-regulatory networks in humans, mice, and zebrafish

description: Vertebrate sex determination and differentiation are coordinated by the activations and maintenance of reproductive transcriptional-regulatory networks (TRNs). There is considerable interest in studying the conserved design principles and functions of reproductive TRNs given that their intricate regulation is susceptible to disruption by gene mutations or exposures to exogenous endocrine disrupting chemicals (or EDCs). In this manuscript, the Boolean rules describing reproductive TRNs in humans, mice, and zebrafish, were represented as a pseudo-stoichiometric matrix model. This model mathematically described the interactions of 35 transcription factors with 21 sex determination and differentiation genes across the three species. The <i>in silico</i> approach of Extreme Pathway (ExPa) analysis was used to predict the extent of TRN gene activations subject to the species-specific transcriptomics data, from across various developmental life-stages. A goal of this work was to identify conserved and functional reproductive TRNs across the three species. ExPa analyses predicted the sex differentiation genes, DHH, DMRT1, and AR, to be highly active in male humans, mice, and zebrafish. Whereas FOXL2 was the most active gene in female humans and mice; and CYP19A1A in female zebrafish. These results agree with the expectation that regardless of a lack of sex determination genes in zebrafish, the TRNs responsible for canalizing male <i>vs.</i> female sexual differentiation are conserved with mammalian taxa. ExPa analysis therefore provides a framework with which to study the TRNs that influence the development of sexual phenotypes. And the <i>in silico</i> predicted conservation of sex differentiation TRNs between mammals and zebrafish identifies the piscine species as an effective <i>in vivo</i> model to study mammalian reproductive systems under normal or perturbed pathologies.
DOI: 10.6084/m9.figshare.22572596.v1
title: The use of <i>in silico</i> extreme pathway (ExPa) analysis to identify conserved reproductive transcriptional-regulatory networks in humans, mice, and zebrafish

description: Vertebrate sex determination and differentiation are coordinated by the activations and maintenance of reproductive transcriptional-regulatory networks (TRNs). There is considerable interest in studying the conserved design principles and functions of reproductive TRNs given that their intricate regulation is susceptible to disruption by gene mutations or exposures to exogenous endocrine disrupting chemicals (or EDCs). In this manuscript, the Boolean rules describing reproductive TRNs in humans, mice, and zebrafish, were represented as a pseudo-stoichiometric matrix model. This model mathematically described the interactions of 35 transcription factors with 21 sex determination and differentiation genes across the three species. The <i>in silico</i> approach of Extreme Pathway (ExPa) analysis was used to predict the extent of TRN gene activations subject to the species-specific transcriptomics data, from across various developmental life-stages. A goal of this work was to identify conserved and functional reproductive TRNs across the three species. ExPa analyses predicted the sex differentiation genes, DHH, DMRT1, and AR, to be highly active in male humans, mice, and zebrafish. Whereas FOXL2 was the most active gene in female humans and mice; and CYP19A1A in female zebrafish. These results agree with the expectation that regardless of a lack of sex determination genes in zebrafish, the TRNs responsible for canalizing male <i>vs.</i> female sexual differentiation are conserved with mammalian taxa. ExPa analysis therefore provides a framework with which to study the TRNs that influence the development of sexual phenotypes. And the <i>in silico</i> predicted conservation of sex differentiation TRNs between mammals and zebrafish identifies the piscine species as an effective <i>in vivo</i> model to study mammalian reproductive systems under normal or perturbed pathologies.
DOI: 10.6084/m9.figshare.22714669
title: Comparison of microbial profiles and viral status along the vagina-cervix-endometrium continuum of infertile patients

description: For decades, the endometrium was considered to be a sterile environment. However, now this concept is disputed, and there is growing evidence that microbiota composition might affect endometrial receptivity. Routine clinical management of infertility is still limited to a microbiological assessment of the lower reproductive tract. The purpose of this study was to compare the abundance of various bacterial, fungal, and viral species, qualitatively and quantitatively, in vaginal, cervical, and endometrial biomaterial of infertile patients. A total of 300 samples from 100 infertile patients of a private assisted reproduction clinic were analyzed. A broad real-time polymerase chain reaction panel was used to identify 28 relevant microbial taxa as well as three members of the Herpesviridae family. All patients underwent endometrial biopsy for further histopathological evaluation. Analysis of the microbial diversity (within the boundaries of the detection panel) revealed that Shannon indexes in the cervix and vagina were similar (1.4 × 10<sup>−2</sup> (1.6 × 10<sup>−3</sup> – 6.5 × 10<sup>−1</sup>) vs 1.9 × 10<sup>−2</sup> (2.3 × 10<sup>−3</sup> – 5.3 × 10<sup>−1</sup>), respectively, <i>p</i> = 0.502), whereas endometrial indexes differed significantly from both regions (0 (0 – 1.4 × 10<sup>−1</sup>), <i>p</i> &lt; 0.0001). Surprisingly, 17 microbial and viral taxa were detected in at least one sample. Endometrium exhibited a quite distinct microbiological profile, being different at the detection rates of 14 taxa (<i>p</i> &lt; 0.05). Remarkably, 4% and 2% of endometrial samples were positive for Cytomegalovirus and <i>Candida spp.</i>, respectively, while these were undetectable in corresponding cervical and vaginal samples. Prevalence of the <i>Gardnerella vaginalis</i> + <i>Prevotella bivia</i> + <i>Porphyromonas spp.</i> group in endometrium was associated with a low abundance of <i>Lactobacillus spp</i>. (<i>p</i> = 0.039). No noteworthy associations were identified between various microbiota characteristics and clinical parameters, such as chronic endometritis, uterine polyps and adhesions, endometriosis, and a history of sexually transmitted infections. These findings indicate that the microbiological profile of the endometrium is unique, and the analysis of the lower reproductive tract should supplement, rather than be a substitute for it.
DOI: 10.6084/m9.figshare.22564087
title: Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players

description: The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.
DOI: 10.6084/m9.figshare.22564087.v1
title: Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players

description: The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.
DOI: 10.25345/c5319sd1k
title: MassIVE MSV000093010 - 32Mix_Postcolumn_Reduction_ECell
title: LC-MS analysis of a mixture of standard compounds with postcolumn reduction at different potentials between 0-2500 mV, with and without post-cell injection of Cysteine 0.1 mM at 10uL flow rate.
DOI: 10.6084/m9.figshare.23995056
title: Flies for data analysis and R code for Perkins et al publication on establishing native wildflower habitat for pollinators

description: Data files and code used for Perkins et al. (in review) which is a study of establishing pollinator plantings and bee responses to different management approaches.
DOI: 10.6084/m9.figshare.23995056.v1
title: Flies for data analysis and R code for Perkins et al publication on establishing native wildflower habitat for pollinators

description: Data files and code used for Perkins et al. (in review) which is a study of establishing pollinator plantings and bee responses to different management approaches.
DOI: 10.25345/c5z892r6z
title: MassIVE MSV000093011 - Tuebingen Compounds Library_Postcolumn_Reduction_ECell
title: LC-MS analysis of a mixture of standard compounds coming from University of Tuebingen Compounds Library, with postcolumn reduction through Ecell with 2500 mV potential.
DOI: 10.6084/m9.figshare.23899770
title: Filtered SNPs data (Norway spruce 50K SNPs array)

description: The filtered dataset from 50K Norway spruce SNPchip (filtration parameters: only PolyHighResolution, NoMi-norHom, MonoHighResolution categories of markers were kept, DQC: ≥ 0.82, QC call rate: ≥ 90). Genomic data of resistant individuals, referred to as the "Last Trees Standing" (LTS) and randomly selected individuals from natural regeneration within concerned sites (seedlings, young trees) and in adjacent unaffected stands (mature trees).
DOI: 10.6084/m9.figshare.23899770.v1
title: Filtered SNPs data (Norway spruce 50K SNPs array)

description: The filtered dataset from 50K Norway spruce SNPchip (filtration parameters: only PolyHighResolution, NoMi-norHom, MonoHighResolution categories of markers were kept, DQC: ≥ 0.82, QC call rate: ≥ 90). Genomic data of resistant individuals, referred to as the "Last Trees Standing" (LTS) and randomly selected individuals from natural regeneration within concerned sites (seedlings, young trees) and in adjacent unaffected stands (mature trees).
DOI: 10.5517/ccdc.csd.cc2b8d23
title: CCDC 2153014: Experimental Crystal Structure Determination

description: Related Article: Xinxin Hang, Xiaoju Wang, Meilin Wang, Mengwei Chen, Yanfeng Bi|2022|Inorg.Chem.Front.|10|926|doi:10.1039/D2QI01885C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bwhrh
title: CCDC 2171387: Experimental Crystal Structure Determination

description: Related Article: Jianbo Xiong, Jie Chen, Yu Han, Yingchong Ge, Suijun Liu, Jianguo Ma, Shujuan Liu, Jianqiang Luo, Zhenzhen Xu, Xiaolan Tong|2023|J.Solid State Chem.|317|123678|doi:10.1016/j.jssc.2022.123678
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24230488
title: scattered_data

description: The induced current and scatted field of the conducting cylinder in an anisotropic magnetoplasma
DOI: 10.6084/m9.figshare.24230488.v3
title: scattered_data

description: The induced current and scatted field of the conducting cylinder in an anisotropic magnetoplasma
DOI: 10.6084/m9.figshare.24230488.v2
title: scattered_data

description: The induced current and scatted field of the conducting cylinder in an anisotropic magnetoplasma
DOI: 10.5281/zenodo.8399386
title: UFES - Data Science - 1st assignment - 2023/2

description: Dataset for the 2023/2 Data Science class at Universidade Federal do Espírito Santo (UFES). A subset of https://www.kaggle.com/datasets/nikhilnayak123/5-million-song-lyrics-dataset tailored for the class assignment.
DOI: 10.5281/zenodo.8399387
title: UFES - Data Science - 1st assignment - 2023/2

description: Dataset for the 2023/2 Data Science class at Universidade Federal do Espírito Santo (UFES). A subset of https://www.kaggle.com/datasets/nikhilnayak123/5-million-song-lyrics-dataset tailored for the class assignment.
DOI: 10.5281/zenodo.8399410
title: UFES - Data Science - 1st assignment - 2023/2

description: Dataset for the 2023/2 Data Science class at Universidade Federal do Espírito Santo (UFES). A subset of https://www.kaggle.com/datasets/nikhilnayak123/5-million-song-lyrics-dataset tailored for the class assignment.
DOI: 10.21223/s0kwfu/5ox0pi
title: TMIN200412_AYMARA.xls

description: :unav
DOI: 10.21223/s0kwfu/ztkjrm
title: TPHEN200412_AYMARA.xls

description: :unav
DOI: 10.21223/s0kwfu/wjztog
title: TVIT200412_AYMARA.xls

description: :unav
DOI: 10.21223/s0kwfu/m5hvoc
title: 03_Fieldbook_TPHEN200412_AYMARA.txt

description: :unav
DOI: 10.21223/s0kwfu/d4gn86
title: 04_Material_list.txt

description: :unav
DOI: 10.21223/s0kwfu/wa38zw
title: 01_Fieldbook_TMIN200412_AYMARA.txt

description: :unav
DOI: 10.21223/s0kwfu/dbtgiw
title: 05_Datadictionary.txt

description: :unav
DOI: 10.21223/s0kwfu/fwdbiv
title: 02_Fieldbook_TVIT200412_AYMARA.txt

description: :unav
DOI: 10.20375/0000-0011-0dbd-b
title: data documentation ILO DDR_rev_200923.pdf
DOI: 10.20375/0000-0011-0dbe-a
title: indexex_summary.pdf
DOI: 10.20375/0000-0011-0dbf-9
title: LS_legislation_DDR.csv
DOI: 10.20375/0000-0011-0dc0-6
title: LS_legislation_DDR.xlsx
DOI: 10.48320/cf7655df-8db1-4865-b2a1-82eaf58f739d
title: ILO Legislative Series - index: GDR
DOI: 10.20375/0000-0011-0dc2-4
title: data documentation ILO Soviet Union_rev_200923.pdf
DOI: 10.20375/0000-0011-0dc3-3
title: Discuss Data abbreviations USSR-1.pdf
DOI: 10.20375/0000-0011-0dc4-2
title: indexex_summary.pdf
DOI: 10.20375/0000-0011-0dc5-1
title: LS_legislation_Russia.csv
DOI: 10.20375/0000-0011-0dc6-0
title: LS_legislation_Russia.xlsx
DOI: 10.48320/b2b7938a-296e-4b9f-a2f5-b57369aa71a3
title: ILO Legislative Series - index - USSR
DOI: 10.5281/zenodo.8399468
title: Spatially averaged test results comparing SP and DP COSMO simulations

description: This Dataset is related to the manuscript "Reduced floating-point precision in regional climate simulations: An<br> ensemble-based statistical verification" (Banderier et al., submitted). It contains spatially averaged test results for all five tests described in the manuscript : Identical, Single Precision, and all three Modified Diffusion experiments, for all ten years and 100 random selections. This Dataset also contains the final decisions, step d of the methodology, based on thresholding at the 95th percentile of the control rejections vs. the mean of the test rejections (see article for details).
DOI: 10.5281/zenodo.8399467
title: Spatially averaged test results comparing SP and DP COSMO simulations

description: This Dataset is related to the manuscript "Reduced floating-point precision in regional climate simulations: An<br> ensemble-based statistical verification" (Banderier et al., submitted). It contains spatially averaged test results for all five tests described in the manuscript : Identical, Single Precision, and all three Modified Diffusion experiments, for all ten years and 100 random selections. This Dataset also contains the final decisions, step d of the methodology, based on thresholding at the 95th percentile of the control rejections vs. the mean of the test rejections (see article for details).
DOI: 10.5281/zenodo.7599124
title: Daily meteorological data extracted from ERA5 based on DHS-GIS (2000-2020)

description: Daily meteorological dataset extracted from ERA5 based on DHS-GIS (2000-2020). It has three meteorological variables: relative humidity (1000hpa), daily 2m temperature, daily maximumu 2m temperature, daily minimum 2m temperature, and total precipitation.
description: Adding daily maximumu 2m temperature, daily minimum 2m temperature
DOI: 10.5281/zenodo.7599125
title: Daily meteorological data extracted from ERA5 based on DHS-GIS (2000-2020)

description: Daily meteorological dataset extracted from ERA5 based on DHS-GIS (2000-2020). It has three meteorological variables: relative humidity (1000hpa), 2m temperature, and total precipitation.
DOI: 10.5281/zenodo.7634009
title: Daily meteorological data extracted from ERA5 based on DHS-GIS (2000-2020)

description: Daily meteorological dataset extracted from ERA5 based on DHS-GIS (2000-2020). It has three meteorological variables: relative humidity (1000hpa), 2m temperature, and total precipitation.
description: Modifying Coordinate Index Error
DOI: 10.5281/zenodo.8399273
title: Daily meteorological data extracted from ERA5 based on DHS-GIS (2000-2020)

description: Daily meteorological dataset extracted from ERA5 based on DHS-GIS (2000-2020). It has three meteorological variables: relative humidity (1000hpa), daily 2m temperature, daily maximumu 2m temperature, daily minimum 2m temperature, and total precipitation.
description: Adding daily maximumu 2m temperature, daily minimum 2m temperature
DOI: 10.25420/britishmuseum.20059529
title: Koropkwen glade

description: Approximate area of the current extent of Koropkwen glade in the Embobut forest. habitation was historically confined to this area, but over the latter half of the twentieth century has changed in size and expanse.
DOI: 10.25420/britishmuseum.20059529.v1
title: Koropkwen glade

description: Approximate area of the current extent of Koropkwen glade in the Embobut forest. habitation was historically confined to this area, but over the latter half of the twentieth century has changed in size and expanse.
DOI: 10.25420/britishmuseum.20059529.v2
title: Koropkwen glade

description: Approximate area of the current extent of Koropkwen glade in the Embobut forest. habitation was historically confined to this area, but over the latter half of the twentieth century has changed in size and expanse.
DOI: 10.26275/z5vh-t0fb
title: Pseudouridine Quantification Data

description: Synthetic and native direct RNA sequencing data
DOI: 10.25420/britishmuseum.20059685
title: Geolocation of project activities

description: Shapefile depicting the points of activity across the landscape assoicated with the making of the beehive for the EMKP project.
DOI: 10.25420/britishmuseum.20059685.v2
title: Geolocation of project activities

description: Shapefile depicting the points of activity across the landscape assoicated with the making of the beehive for the EMKP project.