cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3409630.v1
title: SupplDataFile2.zip

description: Supplementary Data File 2. Concatenated alignments of mt- and nuc-encoded genes used to estimate <i>d</i><sub>N</sub>, <i>d</i><sub>S</sub>, and <i>ω</i> values for each of the 15 examined taxonomic groups. In the zipped file there are three directories for each of the three gene sets analyzed for <i>d</i><sub>N</sub>, <i>d</i><sub>S</sub>, and <i>ω</i> values: mitochondrial-encoded OXPHOS genes, nuclear-encoded OXPHOS genes, and nuclear-encoded glycolysis genes. In each directory there are 15 alignment files in fasta format, one for each of the 15 taxonomic groups investigated. Each of these alignment files contains at least 2 species and concatenated alignments from several genes. See Havird and Sloan for further details.
DOI: 10.6084/m9.figshare.3409513
title: Dynamic facial expressions are processed holistically, but not more holistically than static facial expressions

description: There is evidence that facial expressions are perceived holistically and featurally. The composite task is a direct measure of holistic processing (although the absence of a composite effect implies the use of other types of processing). Most composite task studies have used static images, despite the fact that movement is an important aspect of facial expressions and there is some evidence that movement may facilitate recognition. We created static and dynamic composites, in which emotions were reliably identified from each half of the face. The magnitude of the composite effect was similar for static and dynamic expressions identified from the top half (anger, sadness and surprise) but was reduced in dynamic as compared to static expressions identified from the bottom half (fear, disgust and joy). Thus, any advantage in recognising dynamic over static expressions is not likely to stem from enhanced holistic processing, rather motion may emphasise or disambiguate diagnostic featural information.
DOI: 10.6084/m9.figshare.3409501
title: CeTrAn data

description: here is uploaded the metadata of experiments analysed with CeTrAN.
DOI: 10.6084/m9.figshare.3409501.v1
title: CeTrAn data

description: here is uploaded the metadata of experiments analysed with CeTrAN.
DOI: 10.6084/m9.figshare.3409495
title: Fish allergy in patients with parvalbumin-specific immunoglobulin E depends on parvalbumin content rather than molecular differences in the protein among fish species

description: Allergenic characteristics of purified parvalbumins from different fish species have not been thoroughly investigated. We revealed that purified parvalbumins from nine different fish species have identical IgE-reactivities and high cross-reactivities. We also showed that fish allergenicity is associated with the parvalbumin content of the fish species, rather than species-specific differences in the molecular characteristics of the individual parvalbumin proteins.
DOI: 10.6084/m9.figshare.3409495.v1
title: Fish allergy in patients with parvalbumin-specific immunoglobulin E depends on parvalbumin content rather than molecular differences in the protein among fish species

description: Allergenic characteristics of purified parvalbumins from different fish species have not been thoroughly investigated. We revealed that purified parvalbumins from nine different fish species have identical IgE-reactivities and high cross-reactivities. We also showed that fish allergenicity is associated with the parvalbumin content of the fish species, rather than species-specific differences in the molecular characteristics of the individual parvalbumin proteins.
DOI: 10.6084/m9.figshare.3409471
title: LC-articles

description: Sample data for library carpentry training lessons<br>
DOI: 10.6084/m9.figshare.3409471.v1
title: LC-articles

description: Sample data for library carpentry training lessons<br>
DOI: 10.6084/m9.figshare.3409471.v2
title: LC-articles

description: Sample data for library carpentry training lessons<br>
DOI: 10.6084/m9.figshare.3409429
title: The S-canon and the multi-S-canon: an introduction

description: The technique of rhythmic tiling can be used to embed canons within a monophonic texture by ensuring that no two parts play on the same beat. This paper introduces the S-canon, a type of canon based on Sidon sets, in which the parts do overlap rhythmically but always do so in unison. We also introduce the multi-S-canon, which involves sets of S-canons that tile with each other in terms of rhythm and pitch. Multi-S-canons are defined and constructed in terms of Sidon Zn-tilings. We demonstrate that Sidon Zn-tilings have redundant representations and define a standard form that addresses these redundancies. Finally, we give an algorithm for finding the Sidon Zn-tilings that cover Zn using as few Sidon sets as possible, and we look at some of the results. There is an Online Supplement to this paper, which can be accessed at http://dx.doi.org/10.1080/17459737.2016.1168492). It includes audio files to accompany a few of the musical examples, as well as a spreadsheet listing minimal Sidon Zn-tilings for 12≤n≤30.
DOI: 10.6084/m9.figshare.3409429.v1
title: The S-canon and the multi-S-canon: an introduction

description: The technique of rhythmic tiling can be used to embed canons within a monophonic texture by ensuring that no two parts play on the same beat. This paper introduces the S-canon, a type of canon based on Sidon sets, in which the parts do overlap rhythmically but always do so in unison. We also introduce the multi-S-canon, which involves sets of S-canons that tile with each other in terms of rhythm and pitch. Multi-S-canons are defined and constructed in terms of Sidon Zn-tilings. We demonstrate that Sidon Zn-tilings have redundant representations and define a standard form that addresses these redundancies. Finally, we give an algorithm for finding the Sidon Zn-tilings that cover Zn using as few Sidon sets as possible, and we look at some of the results. There is an Online Supplement to this paper, which can be accessed at http://dx.doi.org/10.1080/17459737.2016.1168492). It includes audio files to accompany a few of the musical examples, as well as a spreadsheet listing minimal Sidon Zn-tilings for 12≤n≤30.
DOI: 10.6084/m9.figshare.3409423
title: data paper_Linking photosynthetic responses to drought with the changes in shrub species abundances under climate manipulation .xlsx

description: The dataset include plant physiology data (photosynthesis, stomatal conductance), plant morphology data (leaf mass index) species abundance data (relative plant cover) relative to the shrub species <i>Cistus monspeliensis</i>, <i>Dorycnium pentaphyllum </i>and <i>Helichrysum microphyllum</i>;furthermore, it include soil relative content data. All data are recorded at italian experimental site of the project INCREASE (an Integrated Network on Climate Research Activities on Shrubland Ecosystems) located in regional parc of Porto Conte - Capo Caccia, Sardinia, Italy.
DOI: 10.6084/m9.figshare.3409423.v1
title: data paper_Linking photosynthetic responses to drought with the changes in shrub species abundances under climate manipulation .xlsx

description: The dataset include plant physiology data (photosynthesis, stomatal conductance), plant morphology data (leaf mass index) species abundance data (relative plant cover) relative to the shrub species <i>Cistus monspeliensis</i>, <i>Dorycnium pentaphyllum </i>and <i>Helichrysum microphyllum</i>;furthermore, it include soil relative content data. All data are recorded at italian experimental site of the project INCREASE (an Integrated Network on Climate Research Activities on Shrubland Ecosystems) located in regional parc of Porto Conte - Capo Caccia, Sardinia, Italy.
DOI: 10.6084/m9.figshare.3409420
title: Sigma virus sequence alignments for Ceratitis capitata sigma virus (CCapSV), Drosophila immigrans sigma virus (DImmSV) and Pararge aegeria rhabdovirus (PAegRV) from: Longdon et al. Vertical transmission and rapid population dynamics of three insect rhabdoviruses

description: Ceratitis capitata sigma virus (CCapSV) concatenated N and L gene alignment (N 1:606, L 607:1278)<br>Drosophila immigrans sigma virus (DImmSV) concatenated N and L gene alignment (N 1:679, L 680:1279), plus alignment with ADAR preferred sites removed. <br>Pararge aegeria rhabdovirus (PAegRV) concatenated N and L gene alignment (N 1:609, L 610:1281)
DOI: 10.6084/m9.figshare.3409420.v1
title: Sigma virus alignments for Ceratitis capitata sigma virus (CCapSV), Drosophila immigrans sigma virus (DImmSV) and Pararge aegeria rhabdovirus (PAegRV) from: Longdon et al. Vertical transmission and rapid population dynamics of three insect rhabdoviruses

description: Ceratitis capitata sigma virus (CCapSV) concatenated N and L gene alignment (N 1:606, L 607:1278)<br>Drosophila immigrans sigma virus (DImmSV) concatenated N and L gene alignment (N 1:679, L 680:1279), plus alignment with ADAR preferred sites removed. <br>Pararge aegeria rhabdovirus (PAegRV) concatenated N and L gene alignment (N 1:609, L 610:1281)
DOI: 10.6084/m9.figshare.3409420.v3
title: Sigma virus sequence alignments for Ceratitis capitata sigma virus (CCapSV), Drosophila immigrans sigma virus (DImmSV) and Pararge aegeria rhabdovirus (PAegRV) from: Longdon et al. Vertical transmission and rapid population dynamics of three insect rhabdoviruses

description: Ceratitis capitata sigma virus (CCapSV) concatenated N and L gene alignment (N 1:606, L 607:1278)<br>Drosophila immigrans sigma virus (DImmSV) concatenated N and L gene alignment (N 1:679, L 680:1279), plus alignment with ADAR preferred sites removed. <br>Pararge aegeria rhabdovirus (PAegRV) concatenated N and L gene alignment (N 1:609, L 610:1281)
DOI: 10.6084/m9.figshare.3409420.v2
title: Sigma virus sequence alignments for Ceratitis capitata sigma virus (CCapSV), Drosophila immigrans sigma virus (DImmSV) and Pararge aegeria rhabdovirus (PAegRV) from: Longdon et al. Vertical transmission and rapid population dynamics of three insect rhabdoviruses

description: Ceratitis capitata sigma virus (CCapSV) concatenated N and L gene alignment (N 1:606, L 607:1278)<br>Drosophila immigrans sigma virus (DImmSV) concatenated N and L gene alignment (N 1:679, L 680:1279), plus alignment with ADAR preferred sites removed. <br>Pararge aegeria rhabdovirus (PAegRV) concatenated N and L gene alignment (N 1:609, L 610:1281)
DOI: 10.6084/m9.figshare.3409387
title: dolite_gene.txt

description: associations between disease terms of DOLite and genes
DOI: 10.6084/m9.figshare.3409387.v1
title: dolite_gene.txt

description: associations between disease terms of DOLite and genes
DOI: 10.6084/m9.figshare.3409375.v1
title: Encuesta de percepción y uso de Wikipedia

description: Encuesta de percepción y uso de Wikipedia.
DOI: 10.6084/m9.figshare.3409372
title: Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.

description: Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.
DOI: 10.6084/m9.figshare.3409372.v2
title: Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.

description: Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.
DOI: 10.6084/m9.figshare.3409372.v1
title: Tabla 2. Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.

description: Encuesta de percepción y uso de Wikipedia entre estudiantes y profesores.
DOI: 10.6084/m9.figshare.3409348
title: MSAViewer example files

description: VP24 Filoviridae example files
DOI: 10.6084/m9.figshare.3409321
title: Pesticides and Ozofractionation: An Investigation to Remove Organic and Inorganic Contaminants from Industrial Wastewater

description: <br> In the last 50 years a significant amount of research has been carried out on the treatment of pesticides and industrial wastewater using physicochemical methods. However, ozofractionation has not been investigated as a means to remove pesticides from wastewater, possibly because it is more typically associated with the treatment of water in aquariums. Therefore, the present study was undertaken to assess the impact of ozofractionation on pesticide-contaminated industrial wastewater. A sample was collected from a stormwater holding tank at a pesticide manufacturing site in Australia containing chlorpyrifos, dichlorodiphenyltrichloroethane (DDT), dichlorodiphenyldichloroethylene (DDE), arsenic and zinc. After preliminary analysis, the sample was subjected to ozofractionation and promising results were observed. Chlorpyrifos, DDT, DDE, arsenic and zinc concentrations were 7.2 µg/L, 108 µg/L, 9.5 µg/L, 0.14 mg/L and 0.44 mg/L before treatment and reduced to &lt;0.5µg/L, &lt;2.0 µg/L, &lt;0.5 µg/L, 0.01 mg/L and &lt;0.005 mg/L respectively after treatment. Before treatment, pesticides and metal concentrations were beyond discharge limits, however ozofractionation brought them within the permissible limits set by environmental agencies and processed wastewater could be discharged to an aquatic ecosystem. These findings indicate that ozofractionation may be a useful method for destroying intractable pesticides and removing heavy metals from industrial wastewater.
DOI: 10.6084/m9.figshare.3409321.v1
title: Pesticides and Ozofractionation: An Investigation to Remove Organic and Inorganic Contaminants from Industrial Wastewater

description: <br> In the last 50 years a significant amount of research has been carried out on the treatment of pesticides and industrial wastewater using physicochemical methods. However, ozofractionation has not been investigated as a means to remove pesticides from wastewater, possibly because it is more typically associated with the treatment of water in aquariums. Therefore, the present study was undertaken to assess the impact of ozofractionation on pesticide-contaminated industrial wastewater. A sample was collected from a stormwater holding tank at a pesticide manufacturing site in Australia containing chlorpyrifos, dichlorodiphenyltrichloroethane (DDT), dichlorodiphenyldichloroethylene (DDE), arsenic and zinc. After preliminary analysis, the sample was subjected to ozofractionation and promising results were observed. Chlorpyrifos, DDT, DDE, arsenic and zinc concentrations were 7.2 µg/L, 108 µg/L, 9.5 µg/L, 0.14 mg/L and 0.44 mg/L before treatment and reduced to &lt;0.5µg/L, &lt;2.0 µg/L, &lt;0.5 µg/L, 0.01 mg/L and &lt;0.005 mg/L respectively after treatment. Before treatment, pesticides and metal concentrations were beyond discharge limits, however ozofractionation brought them within the permissible limits set by environmental agencies and processed wastewater could be discharged to an aquatic ecosystem. These findings indicate that ozofractionation may be a useful method for destroying intractable pesticides and removing heavy metals from industrial wastewater.
DOI: 10.6084/m9.figshare.3409243
title: Comparison of genome-scale DNA methylation profiles in hepatocellular carcinoma by viral status

description: Hepatocellular carcinoma (HCC) incidence has steadily increased in the US over the past 30 years. Our understanding of epigenetic regulation in HCC is still limited, especially the impact of hepatitis B virus (HBV) or hepatitis C virus (HCV) infection on aberrant DNA methylation. We performed genome-wide DNA methylation profiling in 33 fresh frozen tumor samples, including 10 HBV-HCC, 13 HCV-HCC, and 10 non-infected (NIV-HCC) using the Illumina HumanMethylation450 BeadChip. Gene expression profiling was also performed using the Illumina whole-genome DASL HT Assay. Biological influences and gene networks of the differentially-methylated (DM) CpG loci were predicted using the Ingenuity Pathway Analysis. Genome-wide methylation analysis identified 7, 26, and 98 DM loci between HBV-HCC vs. HCV-HCC, HBV-HCC vs. NIV-HCC, and HCV-HCC vs. NIV-HCC, respectively, at <i>P</i> &lt; 5 × 10<sup>−5</sup> for each. Overall, the DM loci were highly enriched for enhancers (48%), promoters (37%), or CpG islands and surrounding regions (37%). Most DM loci were hypermethylated in HCV-HCC compared to HBV-HCC or NIV-HCC. The DM loci were associated with a variety of biological functions including Cell Morphology (HBV-HCC vs. NIV-HCC), Cell Death/ Survival (HBV-HCC vs. NIV-HCC), or Cellular Growth and Proliferation (HCV-HCC vs. NIV-HCC). A subset of the DM loci were correlated (either positively or negatively) with their gene expression or associated with alcohol consumption, BMI, cirrhosis, diabetes, and cigarette smoking. Our findings of differential methylation by viral infection lend insights into the potential effects of viral infection on the epigenetic regulation and further the development and progression of HCC.
DOI: 10.6084/m9.figshare.3409243.v2
title: Comparison of genome-scale DNA methylation profiles in hepatocellular carcinoma by viral status

description: Hepatocellular carcinoma (HCC) incidence has steadily increased in the US over the past 30 years. Our understanding of epigenetic regulation in HCC is still limited, especially the impact of hepatitis B virus (HBV) or hepatitis C virus (HCV) infection on aberrant DNA methylation. We performed genome-wide DNA methylation profiling in 33 fresh frozen tumor samples, including 10 HBV-HCC, 13 HCV-HCC, and 10 non-infected (NIV-HCC) using the Illumina HumanMethylation450 BeadChip. Gene expression profiling was also performed using the Illumina whole-genome DASL HT Assay. Biological influences and gene networks of the differentially-methylated (DM) CpG loci were predicted using the Ingenuity Pathway Analysis. Genome-wide methylation analysis identified 7, 26, and 98 DM loci between HBV-HCC vs. HCV-HCC, HBV-HCC vs. NIV-HCC, and HCV-HCC vs. NIV-HCC, respectively, at <i>P</i> &lt; 5 × 10<sup>−5</sup> for each. Overall, the DM loci were highly enriched for enhancers (48%), promoters (37%), or CpG islands and surrounding regions (37%). Most DM loci were hypermethylated in HCV-HCC compared to HBV-HCC or NIV-HCC. The DM loci were associated with a variety of biological functions including Cell Morphology (HBV-HCC vs. NIV-HCC), Cell Death/ Survival (HBV-HCC vs. NIV-HCC), or Cellular Growth and Proliferation (HCV-HCC vs. NIV-HCC). A subset of the DM loci were correlated (either positively or negatively) with their gene expression or associated with alcohol consumption, BMI, cirrhosis, diabetes, and cigarette smoking. Our findings of differential methylation by viral infection lend insights into the potential effects of viral infection on the epigenetic regulation and further the development and progression of HCC.
DOI: 10.6084/m9.figshare.3409243.v1
title: Comparison of genome-scale DNA methylation profiles in hepatocellular carcinoma by viral status

description: Hepatocellular carcinoma (HCC) incidence has steadily increased in the US over the past 30 years. Our understanding of epigenetic regulation in HCC is still limited, especially the impact of hepatitis B virus (HBV) or hepatitis C virus (HCV) infection on aberrant DNA methylation. We performed genome-wide DNA methylation profiling in 33 fresh frozen tumor samples, including 10 HBV-HCC, 13 HCV-HCC, and 10 non-infected (NIV-HCC) using the Illumina HumanMethylation450 BeadChip. Gene expression profiling was also performed using the Illumina whole-genome DASL HT Assay. Biological influences and gene networks of the differentially-methylated (DM) CpG loci were predicted using the Ingenuity Pathway Analysis. Genome-wide methylation analysis identified 7, 26, and 98 DM loci between HBV-HCC vs. HCV-HCC, HBV-HCC vs. NIV-HCC, and HCV-HCC vs. NIV-HCC, respectively, at <i>P</i> &lt; 5 × 10<sup>−5</sup> for each. Overall, the DM loci were highly enriched for enhancers (48%), promoters (37%), or CpG islands and surrounding regions (37%). Most DM loci were hypermethylated in HCV-HCC compared to HBV-HCC or NIV-HCC. The DM loci were associated with a variety of biological functions including Cell Morphology (HBV-HCC vs. NIV-HCC), Cell Death/ Survival (HBV-HCC vs. NIV-HCC), or Cellular Growth and Proliferation (HCV-HCC vs. NIV-HCC). A subset of the DM loci were correlated (either positively or negatively) with their gene expression or associated with alcohol consumption, BMI, cirrhosis, diabetes, and cigarette smoking. Our findings of differential methylation by viral infection lend insights into the potential effects of viral infection on the epigenetic regulation and further the development and progression of HCC.
DOI: 10.6084/m9.figshare.3409228
title: Conservation of Native Pacific Trout Diversity in Western North America

description: Pacific trout <i>Oncorhynchus</i> spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus <i>Oncorhynchus</i>. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.
DOI: 10.6084/m9.figshare.3409228.v1
title: Conservation of Native Pacific Trout Diversity in Western North America

description: Pacific trout <i>Oncorhynchus</i> spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus <i>Oncorhynchus</i>. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.