cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6279857.v1
title: Additional file 4: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S4. Comparison of T. pallidum primary and tertiary structure-based functional annotations using only the top-ranked Phyre2 model template for each protein comparison. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.6279848
title: MOESM2 of Predictors of back disorder among Almeda textile factory workers, North Ethiopia

description: Additional file 2. Predictors of back disorder SPSS data.
DOI: 10.6084/m9.figshare.6279848.v1
title: MOESM2 of Predictors of back disorder among Almeda textile factory workers, North Ethiopia

description: Additional file 2. Predictors of back disorder SPSS data.
DOI: 10.6084/m9.figshare.6279836
title: Additional file 3: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S3. T. pallidum proteins (NÂ =â 46) modeled by Phyre2 with confidence scores below 90% with functional annotations in the published proteome. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6279836.v1
title: Additional file 3: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S3. T. pallidum proteins (NÂ =â 46) modeled by Phyre2 with confidence scores below 90% with functional annotations in the published proteome. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6279818
title: Additional file 2: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S2. T. pallidum proteins (NÂ =â 150) modeled by Phyre2 with confidence scores below 90% and annotated in the published T. pallidum proteome as hypothetical/putative membrane proteins. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6279818.v1
title: Additional file 2: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S2. T. pallidum proteins (NÂ =â 150) modeled by Phyre2 with confidence scores below 90% and annotated in the published T. pallidum proteome as hypothetical/putative membrane proteins. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6279809
title: Additional file 1: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S1 (Part 1). Raw unedited Phyre2 data corresponding to 19,560 templates used for T. pallidum whole proteome modeling. (XLSX) Part 2. Raw unedited Phyre2 data corresponding to 780Â T. pallidum proteins modeled with high confidence (â Ľ90% confidence; â Ľ10 alignment coverage). (XLSX 3537 kb)
DOI: 10.6084/m9.figshare.6279809.v1
title: Additional file 1: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S1 (Part 1). Raw unedited Phyre2 data corresponding to 19,560 templates used for T. pallidum whole proteome modeling. (XLSX) Part 2. Raw unedited Phyre2 data corresponding to 780Â T. pallidum proteins modeled with high confidence (â Ľ90% confidence; â Ľ10 alignment coverage). (XLSX 3537 kb)
DOI: 10.6084/m9.figshare.6279794
title: Additional file 13: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S13. Proteins of unknown function with potential roles in T. pallidum virulence. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6279794.v1
title: Additional file 13: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S13. Proteins of unknown function with potential roles in T. pallidum virulence. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6279782
title: Additional file 12: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S12. Genome-annotated T. pallidum proteins with potential novel virulence-related functions identified by Phyre2 modeling. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6279782.v1
title: Additional file 12: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S12. Genome-annotated T. pallidum proteins with potential novel virulence-related functions identified by Phyre2 modeling. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6279743
title: Additional file 10: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S10. Phyre2 Modeling of T. pallidum proteins previously annotated as putative virulence factors. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6279743.v1
title: Additional file 10: of Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis

description: Table S10. Phyre2 Modeling of T. pallidum proteins previously annotated as putative virulence factors. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6279476
title: Bioerosion traces on titanosaurian sauropod bones from the Upper Cretaceous Marília Formation of Brazil

description: Paes Neto, V.D., Francischini, H., Martinelli, A.G., Marinho, T.S., Ribeiro, L.C.B., Soares, M.B. & Schultz, C.L. May.2018. Bioerosion traces on titanosaurian sauropod bones from the Upper Cretaceous Marília Formation of Brazil. <i>Alcheringa XXX</i>, X–X. ISSN 0311-5518. Bone bioerosions provide an important taphonomic record on fossils from continental deposits dating back to the late Paleozoic. The morphological diversity of bone bioerosions is especially high in vertebrate remains from the Late Cretaceous. Here we describe four morphotypes of bioeroson preserved on titanosaur dinosaur bones collected from the Maastrichtian Marília Formation of Brazil. These traces differ from previously described ichnotaxa, and include branching furrows and surface removal resembling insect bioerosions, channels with semicircular cross-sections consistent with either root etchings or insects, and bite traces left by vertebrates. Taphonomic sequencing shows that time-averaging was an important aspect in the genesis of the Marília Formation taphocoenosis and demonstrates that traces left on bones are significant tools for reconstructing Late Cretaceous ecosystems. <i>Voltaire Dutra Paes Neto [</i><i>voltairearts@gmail.com</i><i>] and Heitor Francischini [</i><i>heitorfrancischini@hotmail.com</i><i>] Programa de Pós-Graduação em Geociências (PPGGEO), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Agronomia, 91540-000, Porto Alegre, RS, Brazil; Agustín Guillermo Martinelli* [</i><i>agustin_martinelli@yahoo.com.ar</i><i>], Marina Bento Soares [</i><i>marina-soares@ufrgs.br</i><i>] and Cesar Leandro Schultz [</i><i>cesar.schultz@ufrgs.br</i><i>] Instituto de Geociências (IGeo), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Agronomia, 91540-000, Porto Alegre, RS, Brazil; Thiago da Silva Marinho† [</i><i>thiago.marinho@uftm.edu.br</i><i>] Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil; Luiz Carlos Borges Ribeiro [</i><i>lcbrmg@gmail.com</i><i>] Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil. *Also affiliated with: Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil. †Also affiliated with: Instituto de Ciências Exatas, Naturais e Educação (ICENE), Universidade Federal do Triângulo Mineiro (UFTM), Av. Randolfo Borges Jr. 1400, Univerdecidade, 38064-200, Uberaba, MG, Brazil.</i>
DOI: 10.6084/m9.figshare.6279476.v1
title: Bioerosion traces on titanosaurian sauropod bones from the Upper Cretaceous Marília Formation of Brazil

description: Paes Neto, V.D., Francischini, H., Martinelli, A.G., Marinho, T.S., Ribeiro, L.C.B., Soares, M.B. & Schultz, C.L. May.2018. Bioerosion traces on titanosaurian sauropod bones from the Upper Cretaceous Marília Formation of Brazil. <i>Alcheringa XXX</i>, X–X. ISSN 0311-5518. Bone bioerosions provide an important taphonomic record on fossils from continental deposits dating back to the late Paleozoic. The morphological diversity of bone bioerosions is especially high in vertebrate remains from the Late Cretaceous. Here we describe four morphotypes of bioeroson preserved on titanosaur dinosaur bones collected from the Maastrichtian Marília Formation of Brazil. These traces differ from previously described ichnotaxa, and include branching furrows and surface removal resembling insect bioerosions, channels with semicircular cross-sections consistent with either root etchings or insects, and bite traces left by vertebrates. Taphonomic sequencing shows that time-averaging was an important aspect in the genesis of the Marília Formation taphocoenosis and demonstrates that traces left on bones are significant tools for reconstructing Late Cretaceous ecosystems. <i>Voltaire Dutra Paes Neto [</i><i>voltairearts@gmail.com</i><i>] and Heitor Francischini [</i><i>heitorfrancischini@hotmail.com</i><i>] Programa de Pós-Graduação em Geociências (PPGGEO), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Agronomia, 91540-000, Porto Alegre, RS, Brazil; Agustín Guillermo Martinelli* [</i><i>agustin_martinelli@yahoo.com.ar</i><i>], Marina Bento Soares [</i><i>marina-soares@ufrgs.br</i><i>] and Cesar Leandro Schultz [</i><i>cesar.schultz@ufrgs.br</i><i>] Instituto de Geociências (IGeo), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Agronomia, 91540-000, Porto Alegre, RS, Brazil; Thiago da Silva Marinho† [</i><i>thiago.marinho@uftm.edu.br</i><i>] Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil; Luiz Carlos Borges Ribeiro [</i><i>lcbrmg@gmail.com</i><i>] Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil. *Also affiliated with: Centro de Pesquisas Paleontológicas ‘Llewelyn Ivor Price’ (CPPLIP), Complexo Cultural e Científico Peirópolis (CCCP), Universidade Federal do Triângulo Mineiro (UFTM), R. Estanislau Collenghi 194, 38039-755, Peirópolis, Uberaba, MG, Brazil. †Also affiliated with: Instituto de Ciências Exatas, Naturais e Educação (ICENE), Universidade Federal do Triângulo Mineiro (UFTM), Av. Randolfo Borges Jr. 1400, Univerdecidade, 38064-200, Uberaba, MG, Brazil.</i>
DOI: 10.6084/m9.figshare.6279455
title: Vaccine-related video network on YouTube

description: This is the Gephi file of the video network that we have constructed to understand the centralities of anti- and pro-vaccine network on YouTube in September of 2016.
DOI: 10.6084/m9.figshare.6279455.v1
title: Vaccine-related video network on YouTube

description: This is the Gephi file of the video network that we have constructed to understand the centralities of anti- and pro-vaccine network on YouTube in September of 2016.
DOI: 10.6084/m9.figshare.6279431
title: Sources and downstream variation of surface water chemistry in the dammed Waitaki catchment, South Island, New Zealand

description: This article presents the results of a pilot study exploring downstream changes in water chemistry in the Waitaki catchment, which drains the eastern slopes of the Southern Alps. The headwaters of this catchment are glaciated, and both natural glacial lakes and hydroelectric reservoirs occur in the catchment. The dominant lithology is calcite-poor quartzo-feldspathic metasedimentary rock. We sampled surface waters from streams and the inflow and outflow of lakes in the catchment on four occasions over the course of 1year, at c. 3-monthly intervals between summer 2013 and spring 2014. We also sampled ice released from the terminus of the Tasman Glacier. Small but measurable variations were observed in the major element (Ca, Mg, K, Na, Si), trace element (Al, Fe, Rb, Sr) and Sr isotopic composition of the surface waters in the catchment. The composition of the waters is interpreted to reflect the change from calcite-dominated weathering near the top of the catchment toward more silicate weathering down the catchment that has been observed in other studies. The composition of samples collected from the uppermost part of the catchment displays more temporal variability than those samples collected from dammed lakes, suggesting that seasonality is dampened by anthropogenic modification of the catchment.
DOI: 10.6084/m9.figshare.6279431.v1
title: Sources and downstream variation of surface water chemistry in the dammed Waitaki catchment, South Island, New Zealand

description: This article presents the results of a pilot study exploring downstream changes in water chemistry in the Waitaki catchment, which drains the eastern slopes of the Southern Alps. The headwaters of this catchment are glaciated, and both natural glacial lakes and hydroelectric reservoirs occur in the catchment. The dominant lithology is calcite-poor quartzo-feldspathic metasedimentary rock. We sampled surface waters from streams and the inflow and outflow of lakes in the catchment on four occasions over the course of 1year, at c. 3-monthly intervals between summer 2013 and spring 2014. We also sampled ice released from the terminus of the Tasman Glacier. Small but measurable variations were observed in the major element (Ca, Mg, K, Na, Si), trace element (Al, Fe, Rb, Sr) and Sr isotopic composition of the surface waters in the catchment. The composition of the waters is interpreted to reflect the change from calcite-dominated weathering near the top of the catchment toward more silicate weathering down the catchment that has been observed in other studies. The composition of samples collected from the uppermost part of the catchment displays more temporal variability than those samples collected from dammed lakes, suggesting that seasonality is dampened by anthropogenic modification of the catchment.
DOI: 10.6084/m9.figshare.6279386
title: Mimosa_TimePar_Baoetal.txt

description: Data from manuscript titled: "Photosynthetic opportunity cost and energetic cost of a rapid leaf closure behavior in<em> Mimosa pudica</em>". Data is in tab-delimited .txt format. Metadata is in the .txt file.<br>
DOI: 10.6084/m9.figshare.6279359
title: Mission CO<sub>2</sub>ntrol: A Statistical Scientist's Role in Remote Sensing of Atmospheric Carbon Dioxide

description: Too much carbon dioxide (CO<sub>2</sub>) in the atmosphere is a threat to long-term sustainability of Earth's ecosystem. Atmospheric CO<sub>2</sub> is a leading greenhouse gas that has increased to levels not seen since the middle Pliocene (approximately 3.6 million years ago). One of the US National Aeronautics Space Administration's (NASA) remote sensing missions is the Orbiting Carbon Observatory-2, whose principal science objective is to estimate the global geographic distribution of CO<sub>2</sub> sources and sinks at Earth's surface, through time. This starts with raw radiances (Level 1), moves on to retrievals of the atmospheric state (Level 2), from which maps of gap-filled and de-noised geophysical variables and their uncertainties are made (Level 3). With the aid of a model of transport in the atmosphere, CO<sub>2</sub> fluxes (Level 4) can be obtained from Level 2 data directly or possibly through Level 3. Decisions about how to mitigate or manage CO<sub>2</sub> could be thought of as Level 5. Hierarchical statistical modeling is used to qualify and quantify the uncertainties at each level. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6279359.v1
title: Mission CO<sub>2</sub>ntrol: A Statistical Scientist's Role in Remote Sensing of Atmospheric Carbon Dioxide

description: Too much carbon dioxide (CO<sub>2</sub>) in the atmosphere is a threat to long-term sustainability of Earth's ecosystem. Atmospheric CO<sub>2</sub> is a leading greenhouse gas that has increased to levels not seen since the middle Pliocene (approximately 3.6 million years ago). One of the US National Aeronautics Space Administration's (NASA) remote sensing missions is the Orbiting Carbon Observatory-2, whose principal science objective is to estimate the global geographic distribution of CO<sub>2</sub> sources and sinks at Earth's surface, through time. This starts with raw radiances (Level 1), moves on to retrievals of the atmospheric state (Level 2), from which maps of gap-filled and de-noised geophysical variables and their uncertainties are made (Level 3). With the aid of a model of transport in the atmosphere, CO<sub>2</sub> fluxes (Level 4) can be obtained from Level 2 data directly or possibly through Level 3. Decisions about how to mitigate or manage CO<sub>2</sub> could be thought of as Level 5. Hierarchical statistical modeling is used to qualify and quantify the uncertainties at each level. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6279149
title: Dataset for: Resolving the Optimal Selection of a Natural Reserve using the Particle Swarm Optimisation by Applying Transfer Functions

description: Provide the data set to be able to reproduce the experiment.
DOI: 10.6084/m9.figshare.6279149.v2
title: Dataset for: Resolving the Optimal Selection of a Natural Reserve using the Particle Swarm Optimisation by Applying Transfer Functions

description: Provide the data set to be able to reproduce the experiment.
DOI: 10.6084/m9.figshare.6279149.v1
title: Dataset

description: Provide the data set to be able to reproduce the experiment.
DOI: 10.6084/m9.figshare.6279137
title: Results for: Resolving the Optimal Selection of a Natural Reserve using the Particle Swarm Optimisation by Applying Transfer Functions

description: It provides the results as raw data of the experiment.
DOI: 10.6084/m9.figshare.6279137.v2
title: Results for: Resolving the Optimal Selection of a Natural Reserve using the Particle Swarm Optimisation by Applying Transfer Functions

description: It provides the results as raw data of the experiment.
DOI: 10.6084/m9.figshare.6279137.v1
title: Results

description: It provides the results as raw data of the experiment.
DOI: 10.6084/m9.figshare.6279134
title: Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort

description: Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium HumanMethylation450 BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds [hexachlorobenzene (HCB), <i>p,p’</i>-dichlorodiphenyldichloroethylene (<i>p,p’</i>-DDE) and <i>p,p’</i>-dichlorodiphenyltrichloroethane], and perfluoroalkyl substances. In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and <i>p,p’-</i>DDE in 10,598, 1,238, and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X-chromosome associated with neurological disorders. In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potential sex-specific epigenome responses to prenatal chemical exposures.
DOI: 10.6084/m9.figshare.6279134.v2
title: Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort

description: Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium HumanMethylation450 BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds [hexachlorobenzene (HCB), <i>p,p’</i>-dichlorodiphenyldichloroethylene (<i>p,p’</i>-DDE) and <i>p,p’</i>-dichlorodiphenyltrichloroethane], and perfluoroalkyl substances. In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and <i>p,p’-</i>DDE in 10,598, 1,238, and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X-chromosome associated with neurological disorders. In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potential sex-specific epigenome responses to prenatal chemical exposures.