cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3443165.v2
title: Supplement 2 - Sex-related factor loadings

description: Supplement 2 - Sex-related factor loadings<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")
DOI: 10.6084/m9.figshare.3443165.v1
title: Supplement 2 - Sex-related factor loadings

description: Supplement 2 - Sex-related factor loadings<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")
DOI: 10.6084/m9.figshare.3443159
title: Supplement 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015).pdf

description: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015)<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")<br>
DOI: 10.6084/m9.figshare.3443159.v1
title: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015).pdf

description: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015)<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")<br>
DOI: 10.6084/m9.figshare.3443159.v3
title: Supplement 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015).pdf

description: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015)<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")<br>
DOI: 10.6084/m9.figshare.3443159.v2
title: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015).pdf

description: Supplements 1 - Sexual Preferences and Behaviors Inventory (SPBI-2015)<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")<br>
DOI: 10.6084/m9.figshare.3443132.v1
title: Texture Classification and Retrieval

description: Matlab package of tools for texture image classification and retrieval based on a local spatial frequency analysis method. This method can be catalogued among other statistical methods for texture classification and retrieval and supply tools for feature extraction (FE) and learning through a similarity measure (SM). The FE step consists in finding the<br>discrete spatial frequency histograms of multi-scale texture images, by means of a discrete 1-D pseudo-Wigner<br>distribution (PWD), directed upon the maximum angular activity of the von Mises distribution of image entropy. The learning process (LP) step compare the space-frequency histograms by a measure based on the Sørensen–Dice index. The LP refines the spatial-frequency histograms of texture models over a massive (several hundred) set of texture images. The philosophy of the retrieval operation consists in searching the best figure for the similarity measure, among a set of model-histograms vs. a given query histogram.
DOI: 10.6084/m9.figshare.3443129
title: Genotypes file.txt

description: Scomberomorus concolor Microsatellite genotypes for populations in genepop format<br>mtDNA-Cyt b haplotypes for S. concolor
DOI: 10.6084/m9.figshare.3443093
title: SART script

description: Script for SART (calls on Trialstructure_SART)
DOI: 10.6084/m9.figshare.3443093.v1
title: SART script

description: Script for SART (calls on Trialstructure_SART)
DOI: 10.6084/m9.figshare.3443090
title: A Central Asian Language Survey

description: TablesWe have documented language varieties (either Turkic or Indo-European) spoken in 23 test sites by 88 informants belonging to the major ethnic groups of Kyrgyzstan, Tajikistan and Uzbekistan (Karakalpaks, Kazakhs, Kyrgyz, Tajiks, Uzbeks, Yaghnobis). The recorded linguistic material concerns 176 words of the extended Swadesh list and will be made publically available with the publication of this paper. Phonological diversity is measured by the Levenshtein distance and displayed as a consensus bootstrap tree and as multidimensional scaling plots. Linguistic contact is measured as the number of borrowings, from one linguistic family into the other, according to a precision/recall analysis further validated by expert judgment. Concerning Turkic languages, the results of our sample do not support Kazakh and Karakalpak as distinct languages and indicate the existence of several separate Karakalpak varieties. Kyrgyz and Uzbek, on the other hand, appear quite homogeneous. Among the Indo-Iranian languages, the distinction between Tajik and Yaghnobi varieties is very clear-cut. More generally, the degree of borrowing is higher than average where language families are in contact in one of the many sorts of situations characterizing Central Asia: frequent bilingualism, shifting political boundaries, ethnic groups living outside the “mother” country.
DOI: 10.6084/m9.figshare.3443090.v1
title: A Central Asian Language Survey

description: TablesWe have documented language varieties (either Turkic or Indo-European) spoken in 23 test sites by 88 informants belonging to the major ethnic groups of Kyrgyzstan, Tajikistan and Uzbekistan (Karakalpaks, Kazakhs, Kyrgyz, Tajiks, Uzbeks, Yaghnobis). The recorded linguistic material concerns 176 words of the extended Swadesh list and will be made publically available with the publication of this paper. Phonological diversity is measured by the Levenshtein distance and displayed as a consensus bootstrap tree and as multidimensional scaling plots. Linguistic contact is measured as the number of borrowings, from one linguistic family into the other, according to a precision/recall analysis further validated by expert judgment. Concerning Turkic languages, the results of our sample do not support Kazakh and Karakalpak as distinct languages and indicate the existence of several separate Karakalpak varieties. Kyrgyz and Uzbek, on the other hand, appear quite homogeneous. Among the Indo-Iranian languages, the distinction between Tajik and Yaghnobi varieties is very clear-cut. More generally, the degree of borrowing is higher than average where language families are in contact in one of the many sorts of situations characterizing Central Asia: frequent bilingualism, shifting political boundaries, ethnic groups living outside the “mother” country.
DOI: 10.6084/m9.figshare.3442985
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v1
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemüller in MEE (201X)

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>
DOI: 10.6084/m9.figshare.3442985.v2
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemüller in MEE (201X)

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v3
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v4
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v5
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v7
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442985.v6
title: R and WinBUGS code for Brewer, O'Hara, Anderson and Ohlemueller in MEE

description: Files in support of the paper "Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling" to appear in Methods in Ecology and Evolution.<br><br>The main RMarkDown file is "Plateau.rmd"; this contains the code for running the examples.<br><br>The files "AFE.List.Mapping.RData", "AFE17spp.csv" and "climate raw data.csv" need to be placed in a folder called "Data".<br><br>This set also contains both binary and source versions of the package "plateau" for R.<br><br><br>
DOI: 10.6084/m9.figshare.3442973
title: Make a Black Life, and Bid It Sing: Sacred Song in <i>The Life, History, and Unparalleled Sufferings of John Jea</i>

description: Scholarship on the American-born Afro-British author John Jea (<i>c.</i> 1773–after 1817) has focused on his <i>c.</i> 1816 autobiography. Scholars have examined Jea's life a sailor, his literacy, his opposition to slavery, and his indifference to dependent or marginalized people, whether free or enslaved. This essay argues that Jea's 1816 <i>Collection of Hymns</i> should be read as a companion to his memoir. When the two books are read together, scholars gain a clearer insight into his opposition to slavery and his empathy with seemingly lowly people, including black Christians in evangelical churches.
DOI: 10.6084/m9.figshare.3442973.v1
title: Make a Black Life, and Bid It Sing: Sacred Song in <i>The Life, History, and Unparalleled Sufferings of John Jea</i>

description: Scholarship on the American-born Afro-British author John Jea (<i>c.</i> 1773–after 1817) has focused on his <i>c.</i> 1816 autobiography. Scholars have examined Jea's life a sailor, his literacy, his opposition to slavery, and his indifference to dependent or marginalized people, whether free or enslaved. This essay argues that Jea's 1816 <i>Collection of Hymns</i> should be read as a companion to his memoir. When the two books are read together, scholars gain a clearer insight into his opposition to slavery and his empathy with seemingly lowly people, including black Christians in evangelical churches.
DOI: 10.6084/m9.figshare.3442901
title: Current management of Alström syndrome and recent advances in treatment

description: <b>Introduction</b>: Alström syndrome is a recessively inherited condition (OMIM 203800) characterised by dual sensory loss, type 2 diabetes, coronary artery disease, organ fibrosis, and smooth muscle dysfunction. <b>Areas covered</b>: This paper covers family support, educational needs, cardiomyopathy, blindness, deafness, metabolic syndrome, diabetes, smooth muscle dysfunction, hepatic and renal fibrosis. Sources of data include multidisciplinary clinic audits, a research database, Alström Syndrome International clinics, PubMed and Embase searches. <b>Expert opinion</b>: A single intervention to prevent or reverse all manifestations of Alström syndrome is not currently possible. Multidisciplinary annual review is essential to plan treatments and intervene early to treat complications. Braille, IT skills and digital hearing aids are crucial to support education and social integration. Lifestyle modification will prevent type 2 diabetes and mitigate metabolic syndrome and coronary artery disease. Renal transplantation is safe. Hepatic cirrhosis, oesophageal reflux and bladder dystonia are treated as in the general population. Multiple organ dysfunction confers a high risk of death from pneumonia and post-operative hypoxia. Therefore influenza and pneumococcus vaccinations are strongly recommended. Intensive care after all invasive procedures and for infant cardiomyopathy is crucial. Exploration of new therapies to slow retinal degeneration and organ fibrosis is at an early stage.
DOI: 10.6084/m9.figshare.3442901.v1
title: Current management of Alström syndrome and recent advances in treatment

description: <b>Introduction</b>: Alström syndrome is a recessively inherited condition (OMIM 203800) characterised by dual sensory loss, type 2 diabetes, coronary artery disease, organ fibrosis, and smooth muscle dysfunction. <b>Areas covered</b>: This paper covers family support, educational needs, cardiomyopathy, blindness, deafness, metabolic syndrome, diabetes, smooth muscle dysfunction, hepatic and renal fibrosis. Sources of data include multidisciplinary clinic audits, a research database, Alström Syndrome International clinics, PubMed and Embase searches. <b>Expert opinion</b>: A single intervention to prevent or reverse all manifestations of Alström syndrome is not currently possible. Multidisciplinary annual review is essential to plan treatments and intervene early to treat complications. Braille, IT skills and digital hearing aids are crucial to support education and social integration. Lifestyle modification will prevent type 2 diabetes and mitigate metabolic syndrome and coronary artery disease. Renal transplantation is safe. Hepatic cirrhosis, oesophageal reflux and bladder dystonia are treated as in the general population. Multiple organ dysfunction confers a high risk of death from pneumonia and post-operative hypoxia. Therefore influenza and pneumococcus vaccinations are strongly recommended. Intensive care after all invasive procedures and for infant cardiomyopathy is crucial. Exploration of new therapies to slow retinal degeneration and organ fibrosis is at an early stage.
DOI: 10.6084/m9.figshare.3442844
title: Cloning and identification of saprolmycin biosynthetic gene cluster from <i>Streptomyces</i> sp. TK08046

description: Saprolmycins A–E are anti-<i>Saprolegnia parasitica</i> antibiotics. To identify the gene cluster for saprolmycin biosynthesis in <i>Streptomyces</i> sp. TK08046, polymerase chain reaction using aromatase and cyclase gene-specific primers was performed; the <i>spr</i> gene cluster, which codes for angucycline biosynthesis, was obtained from the strain. The cluster consists of 36 open reading frames, including minimal polyketide synthase, ketoreductase, aromatase, cyclase, oxygenase, and deoxy sugar biosynthetic genes, as defined by homology to the corresponding genes of the urdamycin, Sch-47554, and grincamycin biosynthetic gene clusters in <i>Streptomyces fradiae</i>, <i>Streptomyces</i> sp. SCC-2136, and <i>Streptomyces lusitanus</i>, respectively. To establish the function of the gene cluster, an expression cosmid vector containing all 36 open reading frames was introduced into <i>Streptomyces lividans</i> TK23. The transformant was confirmed to express the biosynthetic genes and produce saprolmycins by liquid chromatography–mass spectrometry analysis of the extract. We identified and cloned a <i>spr</i> gene cluster, which is involved in the biosynthesis of saprolmycin, and succeeded in heterologous production of saprolmycin.
DOI: 10.6084/m9.figshare.3442844.v1
title: Cloning and identification of saprolmycin biosynthetic gene cluster from <i>Streptomyces</i> sp. TK08046

description: Saprolmycins A–E are anti-<i>Saprolegnia parasitica</i> antibiotics. To identify the gene cluster for saprolmycin biosynthesis in <i>Streptomyces</i> sp. TK08046, polymerase chain reaction using aromatase and cyclase gene-specific primers was performed; the <i>spr</i> gene cluster, which codes for angucycline biosynthesis, was obtained from the strain. The cluster consists of 36 open reading frames, including minimal polyketide synthase, ketoreductase, aromatase, cyclase, oxygenase, and deoxy sugar biosynthetic genes, as defined by homology to the corresponding genes of the urdamycin, Sch-47554, and grincamycin biosynthetic gene clusters in <i>Streptomyces fradiae</i>, <i>Streptomyces</i> sp. SCC-2136, and <i>Streptomyces lusitanus</i>, respectively. To establish the function of the gene cluster, an expression cosmid vector containing all 36 open reading frames was introduced into <i>Streptomyces lividans</i> TK23. The transformant was confirmed to express the biosynthetic genes and produce saprolmycins by liquid chromatography–mass spectrometry analysis of the extract. We identified and cloned a <i>spr</i> gene cluster, which is involved in the biosynthesis of saprolmycin, and succeeded in heterologous production of saprolmycin.
DOI: 10.6084/m9.figshare.3442796
title: Supplementary Material for: Expression of Antimicrobial Peptides in Human Monocytic Cells and Neutrophils in Response to Dengue Virus Type 2

description: <b><i>Background/Aims:</i></b> The innate immune response is remarkably important for controlling infections. Information about the participation of antimicrobial peptides (AMPs) in response to dengue virus (DENV) is scarce. The aim of this study was to examine the AMP response to DENV-2 in human THP-1 cells and neutrophils. <b><i>Methods:</i></b> Protein and mRNA levels of two AMPs - hBD-1 and cathelicidin LL-37 - were assessed in DENV-infected macrophage-like THP-1 cells using qRT-PCR and indirect immunofluorescence. Also, mRNA levels of α-defensins (hDEFAs) and LL-37 were examined by qRT-PCR in human neutrophils taken from peripheral blood and treated with DENV-2. <b><i>Results:</i></b> mRNA expression of hBD-1 rose in THP-1 cells at 24-72 h, while protein expression increased later, from 48 to 72 h after infection. Cathelicidin LL-37 mRNA expression of DENV-infected THP-1 cells was observed at 6-48 h after infection, while protein levels increased importantly up to 72 h after infection. Regarding neutrophils, the mRNA expression of hDEFAs and LL-37 increased slightly at 2 and 5 h after the contact with DENV-2. <b><i>Conclusion:</i></b> THP-1 cells and human neutrophils strongly respond to DENV by producing AMPs: hBD-1 and LL-37 for the THP-1 cells and hDEFAs and LL-37 for neutrophils. However, the direct effect of these molecules on DENV particles remains unclear.
DOI: 10.6084/m9.figshare.3442796.v1
title: Supplementary Material for: Expression of Antimicrobial Peptides in Human Monocytic Cells and Neutrophils in Response to Dengue Virus Type 2

description: <b><i>Background/Aims:</i></b> The innate immune response is remarkably important for controlling infections. Information about the participation of antimicrobial peptides (AMPs) in response to dengue virus (DENV) is scarce. The aim of this study was to examine the AMP response to DENV-2 in human THP-1 cells and neutrophils. <b><i>Methods:</i></b> Protein and mRNA levels of two AMPs - hBD-1 and cathelicidin LL-37 - were assessed in DENV-infected macrophage-like THP-1 cells using qRT-PCR and indirect immunofluorescence. Also, mRNA levels of α-defensins (hDEFAs) and LL-37 were examined by qRT-PCR in human neutrophils taken from peripheral blood and treated with DENV-2. <b><i>Results:</i></b> mRNA expression of hBD-1 rose in THP-1 cells at 24-72 h, while protein expression increased later, from 48 to 72 h after infection. Cathelicidin LL-37 mRNA expression of DENV-infected THP-1 cells was observed at 6-48 h after infection, while protein levels increased importantly up to 72 h after infection. Regarding neutrophils, the mRNA expression of hDEFAs and LL-37 increased slightly at 2 and 5 h after the contact with DENV-2. <b><i>Conclusion:</i></b> THP-1 cells and human neutrophils strongly respond to DENV by producing AMPs: hBD-1 and LL-37 for the THP-1 cells and hDEFAs and LL-37 for neutrophils. However, the direct effect of these molecules on DENV particles remains unclear.
DOI: 10.6084/m9.figshare.3442793
title: supl_Table_S1.xls

description: Supplementary table S1: Gene Ontology categories for unigenes with gene expression changes associated to the presence of B chromosomes<br>
DOI: 10.6084/m9.figshare.3442793.v1
title: supl_Table_S1.xls

description: Supplementary table S1: Gene Ontology categories for unigenes with gene expression changes associated to the presence of B chromosomes<br>
DOI: 10.6084/m9.figshare.3442787
title: Supplementary Material for: Bovine Mammary Nutrigenomics and Changes in the Milk Composition due to Rapeseed or Sunflower Oil Supplementation of High-Forage or High-Concentrate Diets

description: <b><i>Background:</i></b> Fatty acid (FA) composition plays a crucial role in milk nutritional quality. Despite the known nutritional regulation of ruminant milk composition, the overall mammary mechanisms underlying this regulation are far from being understood. The aim of our study was to determine nutritional regulation of mammary transcriptomes in relation to the cow milk composition. <b><i>Methods:</i></b> Twelve cows received diets differing in the forage-to-concentrate ratio [high forage (HF) and low forage (LF)] supplemented or not with lipids [HF with whole intact rapeseeds (RS) and LF sunflower oil (SO)] in a 4 × 4 Latin square design. Milk production and FA composition were determined. The gene expression profile was studied using RT-qPCR and a bovine microarray. <b><i>Results:</i></b> Our results showed a higher amplitude of milk composition and mammary transcriptome responses to lipid supplementation with the LF-SO compared with the LF diet than with the HF-RS compared with the HF diet. Forty-nine differentially expressed genes, including genes involved in lipid metabolism, were identified with LF-SO versus LF, whereas RS supplementation to the HF diet did not affect the mammary transcriptome. <b><i>Conclusions:</i></b> This study highlights different responses to lipid supplementation of milk production and composition and mammary transcriptomes depending on the nature of lipid supplementation and the percentage of dietary concentrate.