cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1245109.v1
title: OGrady Material Deposited in the Ambrose Monell Cryo Collection

description: I deposited a number of specimens at the AMCC based on the Hawaiian collections I made as a postdoctoral fellow in Rob DeSalle's lab. This fileset is composed of two files, one containing 54 accessions from 1998-2000 and another containing 180 accessions from 2002. These excel files contain more information than is available from the AMCC database search. Cross references to pinned vouchers present at AMNH, EMEC and BPBM will be added soon.
DOI: 10.6084/m9.figshare.1245105.v1
title: Phylogenetic Tree of Burkholderia gladioli str. UCD-UG_CHAPALOTE

description: Phylogenetic tree created by using a full length 16S of <em>Burkholderia gladioli</em> str. UCD-UG_CHAPALOTE from our assembly and aligning it to 59 <em>Burkholderia</em> isolates and an Archaea outgroup from the Ribosomal Database Project (RDP). The phylogenetic tree was constructed using FastTree 2.
DOI: 10.6084/m9.figshare.1245106.v1
title: Phylogenetic Tree of Enterobacter sp. str. UCD-UG_FMILLET

description: Phylogenetic tree created by using a full length 16S of <em>Enterobacter</em> sp. str. UCD-UG_FMILLET from our assembly and aligning it to 46 <em>Enterobacter</em> isolates and an Archaea outgroup from the Ribosomal Database Project (RDP). The phylogenetic tree was constructed using FastTree 2.
DOI: 10.6084/m9.figshare.1245649.v1
title: Additional files: Study of antecendents and an intervension impact of proactive behavior

description: Here you can find additional files to article Is newcomer proactive behavior matter? Study of antecendents and an intervension impact
DOI: 10.6084/m9.figshare.1245099
title: Viewing Time Measures of Sexual Orientation in Samoan Men

description: Viewing Time Measures of Sexual Orientation in Samoan Cisgender Men Who Engage in Sexual Interactions with Fa’afafine
DOI: 10.6084/m9.figshare.1245086
title: Morphological measurements of male anuran reproductive organ

description: These are the raw morphological data reported in the manuscript and with which we applied the statistical analysis.
DOI: 10.6084/m9.figshare.1245649.v3
title: Additional files: Study of antecendents and an intervension impact of proactive behavior

description: Here you can find additional files to article Is newcomer proactive behavior matter? Study of antecendents and an intervension impact
DOI: 10.6084/m9.figshare.1245099.v1
title: Viewing Time Measures of Sexual Orientation in Samoan Men

description: Viewing Time Measures of Sexual Orientation in Samoan Cisgender Men Who Engage in Sexual Interactions with Fa’afafine
DOI: 10.6084/m9.figshare.1245649.v2
title: Additional files: Study of antecendents and an intervension impact of proactive behavior

description: Here you can find additional files to article Is newcomer proactive behavior matter? Study of antecendents and an intervension impact
DOI: 10.6084/m9.figshare.1245086.v2
title: Morphological measurements of male anuran reproductive organ

description: These are the raw morphological data reported in the manuscript and with which we applied the statistical analysis.
DOI: 10.6084/m9.figshare.1245086.v1
title: Raw data

description: These are the raw morphological data reported in the manuscript and with which we applied the statistical analysis.
DOI: 10.6084/m9.figshare.1245103.v1
title: Oxford Digital Forestry Collection Repository Work

description: Slides and audio from a presentation at the Nov 12, 2014 E-Research Roundtable presented by CIRSS. The presentation covers a summary of work completed during my summer 2014 intership at Oxford Unviversity.
DOI: 10.6084/m9.figshare.1245072
title: Human impact on Ecosystem Interactions: The Influence of a Drainage Ditch on a population of Symphyotrichum ericoides In an Open Field

description: 1 meter by 1 meter quadrats were used. Aster height was measured in meters with a transect, from the base of the plan (at soil level), to its highest point. Density was measured by estimating what percentage of area in the quadrat was covered by white aster. The flower number values were determined by counting total number of open white aster flowers in each quadrat. Species richness was measured by counting the total number of plant species in each quadrat. Soil temperature was taken with a soil thermometer. Distance form drainage ditch was measured in meters with a transect
DOI: 10.6084/m9.figshare.1245073
title: Exóticas, exóticas, exóticas: reflexões sobre a monótona arborização de uma cidade brasileira - Dados suplementares ao artigo

description: Anexo digital ao artigo "<b>Exóticas, exóticas, exóticas: reflexões sobre a monótona arborização de uma cidade brasileira</b>", publicado na revista Rodriguésia. <br><br>As planilhas correspondem aos dados detalhados do levantamento das árvores e arbustos presentes na arborização da cidade de Forquilha, estado do Ceará, Nordeste Brasileiro, no ano de 2014. O mesmo conjunto de dados está disponível em formato 'xlsx', para o programa Excel; 'ods', para Open Office; e 'csv', para acesso em qualquer programa de planilha ou de texto. As planilhas informam quais árvores e arbustos foram amostrados em cada rua e praça ao longo do levantamento.<br>Também fornecemos um arquivo "kml" mostrando a localização geográfica das ruas e praças que foram amostradas pelo estudo para visualização dos dados com o software Google Earth ou outro SIG, permitindo ao leitor uma avaliação mais detalhada dos dados geográficos apresentados no mapa do artigo.<br>
DOI: 10.6084/m9.figshare.1245072.v1
title: Human impact on Ecosystem Interactions: The Influence of a Drainage Ditch on a population of Symphyotrichum ericoides In an Open Field

description: 1 meter by 1 meter quadrats were used. Aster height was measured in meters with a transect, from the base of the plan (at soil level), to its highest point. Density was measured by estimating what percentage of area in the quadrat was covered by white aster. The flower number values were determined by counting total number of open white aster flowers in each quadrat. Species richness was measured by counting the total number of plant species in each quadrat. Soil temperature was taken with a soil thermometer. Distance form drainage ditch was measured in meters with a transect
DOI: 10.6084/m9.figshare.1245073.v1
title: Exóticas, exóticas, exóticas: reflexões sobre a monótona arborização de uma cidade brasileira - Dados suplementares ao artigo

description: Anexo digital ao artigo "<b>Exóticas, exóticas, exóticas: reflexões sobre a monótona arborização de uma cidade brasileira</b>", publicado na revista Rodriguésia. <br><br>As planilhas correspondem aos dados detalhados do levantamento das árvores e arbustos presentes na arborização da cidade de Forquilha, estado do Ceará, Nordeste Brasileiro, no ano de 2014. O mesmo conjunto de dados está disponível em formato 'xlsx', para o programa Excel; 'ods', para Open Office; e 'csv', para acesso em qualquer programa de planilha ou de texto. As planilhas informam quais árvores e arbustos foram amostrados em cada rua e praça ao longo do levantamento.<br>Também fornecemos um arquivo "kml" mostrando a localização geográfica das ruas e praças que foram amostradas pelo estudo para visualização dos dados com o software Google Earth ou outro SIG, permitindo ao leitor uma avaliação mais detalhada dos dados geográficos apresentados no mapa do artigo.<br>
DOI: 10.6084/m9.figshare.1245062
title: The effects of crowdedness and shadiness on plant height of Solidago canadensis, Cirsium vulgare, and Aster prenanthoides

description: Methods: Two transects were laid down in the grasslands east of Stong Pond on two separate days. On Tuesday, October 14, 2014 samples were taken from the inner region of the grassland (I) and on Tuesday, October 21, 2014 samples were taken from the outer region of that same grassland (O). Every 5 metres along the transect, the heights of the nearest Solidago canadensis, Cirsium vulgare, and Aster prenanthoides found within 1m from the transect were measured from where the stem touched the ground to the highest point on the plant. Each plant’s level of shadiness and crowdedness around the plant was recorded. This was repeated for a total of 60 replicates (30 for each transect). This data was then used in ANOVA tests and Tukey post-hoc tests to analyze shadiness versus the average plant height of each different species. Next, correlation tests were used to analyze crowdedness versus plant height of each species. This experiment was done to test whether the amount of sunlight affects plant height and whether the amount of crowdedness affects plant height.
DOI: 10.6084/m9.figshare.1245063
title: The effect of sunlight exposure and crowdedness on plant height in Solidago canadensis, Cirsium vulgare and Aster prenanthoides.

description: Plant heights were gathered using transects in the grasslands south of Stong College at the York University Keele campus on October 14th and 21st 2014 at approximately 3:00 pm. The three plant species studies were Solidago canadensis (Golden Rod), Cirsium vulgare (Spear Thistle), and Aster prenanthoides (Purple Aster). Transects were set out twice; once deep into the grassland and the other time on the edge of the field. Every five meters, one of each plant species was randomly selected within 1ft and the height was measured using a second transect. 60 replicates were gathered in total and each time a measurement was taken for each of the three species. The shadiness was estimated on a nominal basis so that the plant being measured was in lots of shade (L), some shade (S) or no shade (S). In addition, the crowdedness of the area the plants were in was observed and recorded on a scale from 0 to 3, where 0 is not crowded at all and 3 is very crowded.
DOI: 10.6084/m9.figshare.1245061
title: The Precision-Recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets

description: T1 and T2 data for the re-analysis of the MiRFinder study. <strong>testdata.tar.bz2</strong>: it contains the test datasets for T1 and T2. Both T1 and T2 consist of positive and negative datasets separately. <strong>predictiondata.tar.bz2</strong>: It contains the prediction data of five different miRNA gene prediction algorithms.
DOI: 10.6084/m9.figshare.1245030
title: Progress towards structural understanding of infectious sheep PrP-amyloid

description: The still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP-amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N‑terminus, some residues with secondary chemical shifts typical of α‑helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β‑sheet core C‑terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterization of non-infectious and infectious PrP-amyloid in the near future.
DOI: 10.6084/m9.figshare.1245029
title: <b>TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells</b>

description: A key step in the process of metastasis is the epithelial-to-mesenchymal transition (EMT). We hypothesized that epigenetic mechanisms play a key role in EMT and to test this hypothesis we analyzed global and gene-specific changes in DNA methylation during TGF-β-induced EMT in ovarian cancer cells. Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive (<i>P</i> &lt; 0.01) methylation changes after TGF-β stimulation (468 and 390 CpG sites altered at 48 and 120 h post cytokine treatment, respectively). The majority of gene-specific TGF-β-induced methylation changes occurred in CpG islands located in or near promoters (193 and 494 genes hypermethylated at 48 and 120 h after TGF-β stimulation, respectively). Furthermore, methylation changes were sustained for the duration of TGF-β treatment and reversible after the cytokine removal. Pathway analysis of the hypermethylated loci identified functional networks strongly associated with EMT and cancer progression, including cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Altered methylation and corresponding expression of specific genes during TGF-β-induced EMT included <i>CDH1</i> (E-cadherin) and <i>COL1A1</i> (collagen 1A1). Furthermore, TGF-β induced both expression and activity of DNA methyltransferases (DNMT) -1, -3A, and -3B, and treatment with the DNMT inhibitor SGI-110 prevented TGF-β-induced EMT. These results demonstrate that dynamic changes in the DNA methylome are implicated in TGF-β-induced EMT and metastasis. We suggest that targeting DNMTs may inhibit this process by reversing the EMT genes silenced by DNA methylation in cancer.
DOI: 10.6084/m9.figshare.1245027
title: Fetal lung and placental methylation is associated with in utero nicotine exposure

description: In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the <i>PKP3</i> (<i>P</i> = 2.94 × 10<sup>−03</sup>), <i>ANKRD33B</i> (<i>P</i> = 3.12 × 10<sup>−03</sup>), <i>CNTD2</i> (<i>P</i> = 4.9 × 10<sup>−03</sup>) and <i>DPP10</i> (<i>P</i> = 5.43 × 10<sup>−03</sup>) genes. In the placental methylome, the most significant CpG sites mapped to the <i>GTF2H2C</i> and <i>GTF2H2D</i> genes (<i>P</i> = 2.87 × 10<sup>−06</sup> − 3.48 × 10<sup>−05</sup>). One hundred and one unique CpG sites with <i>P</i>-values &lt; 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
DOI: 10.6084/m9.figshare.1245030.v1
title: Progress towards structural understanding of infectious sheep PrP-amyloid

description: ABSTRACTThe still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP<sup>−</sup>amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N-terminus, some residues with secondary chemical shifts typical of α-helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β-sheet core C-terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterisation of non-infectious and infectious PrP-amyloid in the near future.
DOI: 10.6084/m9.figshare.1245027.v1
title: Fetal lung and placental methylation is associated with in utero nicotine exposure

description: :In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the <i>PKP3</i> (<i>P</i> = 2.94×10<sup>−03</sup>), <i>ANKRD33B</i> (<i>P</i> = 3.12×10<sup>−03</sup>), <i>CNTD2</i> (<i>P</i> = 4.9×10<sup>−03</sup>) and <i>DPP10</i> (<i>P</i> = 5.43×10<sup>−03</sup>) genes. In the placental methylome, the most significant CpG sites mapped to the <i>GTF2H2C</i> and <i>GTF2H2D</i> genes (<i>P</i> = 2.87×10<sup>−06</sup> - 3.48×10<sup>−05</sup>). One hundred and one unique CpG sites with <i>P</i>-values &lt; 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
DOI: 10.6084/m9.figshare.1245027.v3
title: Fetal lung and placental methylation is associated with in utero nicotine exposure

description: In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the <i>PKP3</i> (<i>P</i> = 2.94 × 10<sup>−03</sup>), <i>ANKRD33B</i> (<i>P</i> = 3.12 × 10<sup>−03</sup>), <i>CNTD2</i> (<i>P</i> = 4.9 × 10<sup>−03</sup>) and <i>DPP10</i> (<i>P</i> = 5.43 × 10<sup>−03</sup>) genes. In the placental methylome, the most significant CpG sites mapped to the <i>GTF2H2C</i> and <i>GTF2H2D</i> genes (<i>P</i> = 2.87 × 10<sup>−06</sup> − 3.48 × 10<sup>−05</sup>). One hundred and one unique CpG sites with <i>P</i>-values &lt; 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
DOI: 10.6084/m9.figshare.1245029.v1
title: TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells

description: A key step in the process of metastasis is the epithelial-to-mesenchymal transition (EMT). We hypothesized that epigenetic mechanisms play a key role in EMT and to test this hypothesis we analyzed global and gene-specific changes in DNA methylation during TGF-β-induced EMT in ovarian cancer cells. Epigenetic profiling using the Infinium HumanMethylation450 BeadChip (HM450) revealed extensive (<i>P</i> &lt; 0.01) methylation changes after TGF-β stimulation (468 and 390 CpG sites altered at 48 and 120 hour post cytokine treatment, respectively). The majority of gene-specific TGF-β-induced methylation changes occurred in CpG islands located in or near promoters (193 and 494 genes hypermethylated at 48 and 120 hours after TGF-β stimulation, respectively). Furthermore, methylation changes were sustained for the duration of TGF-β treatment and reversible after the cytokine removal. Pathway analysis of the hypermethylated loci identified functional networks strongly associated with EMT and cancer progression, including cellular movement, cell cycle, organ morphology, cellular development, and cell death and survival. Altered methylation and corresponding expression of specific genes during TGF-β-induced EMT included <i>CDH1</i> (E-cadherin) and <i>COL1A1</i> (collagen 1A1). Furthermore, TGF-β induced both expression and activity of DNA methyltransferases (DNMT) -1, -3A, and -3B, and treatment with the DNMT inhibitor SGI-110 prevented TGF-β-induced EMT. These results demonstrate that dynamic changes in the DNA methylome are implicated in TGF-β-induced EMT and metastasis. We suggest that targeting DNMTs may inhibit this process by reversing the EMT genes silenced by DNA methylation in cancer.