cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5378341
title: Synthesis and X−ray structures of thioxo− and selenoxo−phosphino species derived from monooxidation of new <i>N</i>-(4-acetylphenyl)-<i>P, P</i>-diphenylphosphinous amide ligand

description: The reaction of <i>p</i>-acetylaniline with chlorodiphenylphosphine afforded the new ligand (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)PPh<sub>2</sub> (<b>1</b>) in good yield. Monooxidized thioxo (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)P(S)Ph<sub>2</sub> (<b>2</b>) and selenoxo (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)P(Se)Ph<sub>2</sub> (<b>3</b>) were synthesized by the reaction of <b>1</b> with elemental sulfur or grey selenium. Compounds <b>1</b>–<b>3</b> were identified and characterized by multinuclear NMR spectroscopy (<sup>1</sup>H, <sup>13</sup>C, <sup>31</sup>P, <sup>77</sup>Se NMR) and elemental analysis. Compounds <b>2</b> and <b>3</b> were structurally characterized by single crystal X-ray diffraction which showed that the <i>p</i>-acetyl substituent on the aniline aromatic ring has a profound influence on the elongation of the P−N bond distance compared to several structurally characterized analogues found in literature. As such, subsequent reactions involving the P-N bond (i.e. insertion reactions) may be influenced in a favorable manner and proceed with ease.
DOI: 10.6084/m9.figshare.5378344
title: Mitochondrial mutations in human cancer: Curation of translation

description: As a genetic disease, cancer is caused by the activation of oncogenes and the inhibition of tumor suppressor genes via genetic and epigenetic mechanisms. Given the important role of energy metabolism in tumors, we analyzed the cancer-derived mutations occurring in the DNA of the mitochondrion. Mutations in the mitochondrial DNA (mtDNA) compared to nuclear DNA are 62% decreased relative to the coding length per chromosome. We find that the majority of these mutations affects highly conserved nucleotides – significantly exceeding the conservation of the mtDNA – and are devoid of single nucleotide polymorphisms (SNPs). Surprisingly, the leading resources for tumor genetics information universally use the standard genetic code for translation of nucleotide into amino acid sequences in their online resources. However, the nuclear and mitochondrial genetic codes differ for four codons and the usage of incomplete STOP codons. Hence, we analyze and curate the consequences for all mutations in the mtDNA and comprehensively reclassify missense, nonsense and synonymous mutations accordingly. In total, 10% of the mutations are incorrectly translated leading to significant changes in the distribution of mutation types with tripling of nonsense and 69% loss of nonstop extension mutations. Lastly, we provide a curated dataset of coding and non-coding mitochondrial mutations in cancer merged, standardized, duplicate-free and aggregated from two databases as a resource including orthogonal data on their high conservation and SNPs. This study generally highlights the need to universally regard the important differences between the standard and mitochondrial genetic code in life science research.
DOI: 10.6084/m9.figshare.5378317
title: Workshop

description: <b>Software Requirements</b><br>You will need to install R from http://cran.r-project.org/ onto your computer. We've tested the workflow on R version 3.4.1.<br>You will also need RStudio from http://www.rstudio.com/products/rstudio/download/.<br>After installing, open RStudio, which opens an R session, and paste in the following commands into the Console window. Hitting enter will execute the lines.<br><br>source("https://bioconductor.org/biocLite.R")biocLite("biomaRt")biocLite("DESeq2")biocLite("org.Dr.eg.db")biocLite("topGO")biocLite("tximport")install.packages("rbokeh")install.packages("readr")install.packages("rjson")<br><br>Once installed, scripts will be able to utilize the libraries via loading which occurs each time you execute a given workflow or script. In our case, that environment loads in the following section:<br><br>library("readr")library("rjson")library("tximport")library("DESeq2")library("biomaRt")library("rbokeh")library("topGO")library("org.Dr.eg.db")<br><br>These lines should execute without error. If you encounter an error like:<br>&gt; Error in library("topGO") : there is no package called ‘topGO’<br>Then that package failed to install and you can retry its from above:<br>biocLite("topGO")<br>And read the console for any prompts.<br><b>Other Downloads</b><b><br></b>Download the osu-workshop.zip file and extract. This contains the data, some intermediate data, our working examples for this workshop. The hands-on portion will be going through the DE.Rmd document in RStudio.
DOI: 10.6084/m9.figshare.5378344.v2
title: Mitochondrial mutations in human cancer: Curation of translation

description: As a genetic disease, cancer is caused by the activation of oncogenes and the inhibition of tumor suppressor genes via genetic and epigenetic mechanisms. Given the important role of energy metabolism in tumors, we analyzed the cancer-derived mutations occurring in the DNA of the mitochondrion. Mutations in the mitochondrial DNA (mtDNA) compared to nuclear DNA are 62% decreased relative to the coding length per chromosome. We find that the majority of these mutations affects highly conserved nucleotides – significantly exceeding the conservation of the mtDNA – and are devoid of single nucleotide polymorphisms (SNPs). Surprisingly, the leading resources for tumor genetics information universally use the standard genetic code for translation of nucleotide into amino acid sequences in their online resources. However, the nuclear and mitochondrial genetic codes differ for four codons and the usage of incomplete STOP codons. Hence, we analyze and curate the consequences for all mutations in the mtDNA and comprehensively reclassify missense, nonsense and synonymous mutations accordingly. In total, 10% of the mutations are incorrectly translated leading to significant changes in the distribution of mutation types with tripling of nonsense and 69% loss of nonstop extension mutations. Lastly, we provide a curated dataset of coding and non-coding mitochondrial mutations in cancer merged, standardized, duplicate-free and aggregated from two databases as a resource including orthogonal data on their high conservation and SNPs. This study generally highlights the need to universally regard the important differences between the standard and mitochondrial genetic code in life science research.
DOI: 10.6084/m9.figshare.5378317.v1
title: Workshop

description: <b>Software Requirements</b><br>You will need to install R from http://cran.r-project.org/ onto your computer. We've tested the workflow on R version 3.4.1.<br>You will also need RStudio from http://www.rstudio.com/products/rstudio/download/.<br>After installing, open RStudio, which opens an R session, and paste in the following commands into the Console window. Hitting enter will execute the lines.<br><br>source("https://bioconductor.org/biocLite.R")biocLite("biomaRt")biocLite("DESeq2")biocLite("org.Dr.eg.db")biocLite("topGO")biocLite("tximport")install.packages("rbokeh")install.packages("readr")install.packages("rjson")<br><br>Once installed, scripts will be able to utilize the libraries via loading which occurs each time you execute a given workflow or script. In our case, that environment loads in the following section:<br><br>library("readr")library("rjson")library("tximport")library("DESeq2")library("biomaRt")library("rbokeh")library("topGO")library("org.Dr.eg.db")<br><br>These lines should execute without error. If you encounter an error like:<br>&gt; Error in library("topGO") : there is no package called ‘topGO’<br>Then that package failed to install and you can retry its from above:<br>biocLite("topGO")<br>And read the console for any prompts.<br><b>Other Downloads</b><b><br></b>Download the osu-workshop.zip file and extract. This contains the data, some intermediate data, our working examples for this workshop. The hands-on portion will be going through the DE.Rmd document in RStudio.
DOI: 10.6084/m9.figshare.5378344.v1
title: Mitochondrial mutations in human cancer: Curation of translation

description: As a genetic disease, cancer is caused by the activation of oncogenes and the inhibition of tumor suppressor genes via genetic and epigenetic mechanisms. Given the important role of energy metabolism in tumors, we analyzed the cancer-derived mutations occurring in the DNA of the mitochondrion. Mutations in the mitochondrial DNA (mtDNA) compared to nuclear DNA are 62% decreased relative to the coding length per chromosome. We find that the majority of these mutations affects highly conserved nucleotides – significantly exceeding the conservation of the mtDNA – and are devoid of single nucleotide polymorphisms (SNPs). Surprisingly, the leading resources for tumor genetics information universally use the standard genetic code for translation of nucleotide into amino acid sequences in their online resources. However, the nuclear and mitochondrial genetic codes differ for four codons and the usage of incomplete STOP codons. Hence, we analyze and curate the consequences for all mutations in the mtDNA and comprehensively reclassify missense, nonsense and synonymous mutations accordingly. In total, 10% of the mutations are incorrectly translated leading to significant changes in the distribution of mutation types with tripling of nonsense and 69% loss of nonstop extension mutations. Lastly, we provide a curated dataset of coding and non-coding mitochondrial mutations in cancer merged, standardized, duplicate-free and aggregated from two databases as a resource including orthogonal data on their high conservation and SNPs. This study generally highlights the need to universally regard the important differences between the standard and mitochondrial genetic code in life science research.
DOI: 10.6084/m9.figshare.5378308
title: Publication Report for EB_215046_DB052615.xls

description: Publication report exported from Scaffold containing the search parameters and settings.
DOI: 10.6084/m9.figshare.5378341.v2
title: Synthesis and X−ray structures of thioxo− and selenoxo−phosphino species derived from monooxidation of new <i>N</i>-(4-acetylphenyl)-<i>P, P</i>-diphenylphosphinous amide ligand

description: The reaction of <i>p</i>-acetylaniline with chlorodiphenylphosphine afforded the new ligand (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)PPh<sub>2</sub> (<b>1</b>) in good yield. Monooxidized thioxo (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)P(S)Ph<sub>2</sub> (<b>2</b>) and selenoxo (<i>p</i>-CH<sub>3</sub>CO)C<sub>6</sub>H<sub>4</sub>N(H)P(Se)Ph<sub>2</sub> (<b>3</b>) were synthesized by the reaction of <b>1</b> with elemental sulfur or grey selenium. Compounds <b>1</b>–<b>3</b> were identified and characterized by multinuclear NMR spectroscopy (<sup>1</sup>H, <sup>13</sup>C, <sup>31</sup>P, <sup>77</sup>Se NMR) and elemental analysis. Compounds <b>2</b> and <b>3</b> were structurally characterized by single crystal X-ray diffraction which showed that the <i>p</i>-acetyl substituent on the aniline aromatic ring has a profound influence on the elongation of the P−N bond distance compared to several structurally characterized analogues found in literature. As such, subsequent reactions involving the P-N bond (i.e. insertion reactions) may be influenced in a favorable manner and proceed with ease.
DOI: 10.6084/m9.figshare.5378347.v1
title: PeerJ - CA3 - Scripts and raw data

description: Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion
DOI: 10.6084/m9.figshare.5378308.v1
title: Publication Report for EB_215046_DB052615.xls

description: Publication report exported from Scaffold containing the search parameters and settings.
DOI: 10.6084/m9.figshare.5378299
title: Protein Report for EB_215046_DB052615.xls

description: Protein report exported from Scaffold containing search parameters, hits, and FDR corrected p-values.
DOI: 10.6084/m9.figshare.5378299.v1
title: Protein Report for EB_215046_DB052615.xls

description: Protein report exported from Scaffold containing search parameters, hits, and FDR corrected p-values.
DOI: 10.6084/m9.figshare.5378194
title: ஆத்மாவின் ராகங்கள்

description: இது ஒரு காந்தீய சகாப்த நாவல்; ஆனால் ஒன்றல்ல இரண்டு சகாப்தங்களை நீங்கள் இந்த நாவலில் சந்திக்கிறீர்கள். ஒரு தலைமுறையின் தேசபக்தர்கள் அனைவருமே இந்த நாவலின் கதாபாத்திரங்களாக வருகிறார்கள். உப்புச் சத்தியாக்கிரகத்திலிருந்து நேற்று வரை உள்ள நிலைமைகளினூடே இந்தக் கதை பாய்கிறது; வளர்கிறது, நிறைகிறது.<br><br>
DOI: 10.6084/m9.figshare.5378164
title: அறப்போர்

description: சங்கநூற் காட்சிகள் என்ற வரிசையில் இது ஐந்தாவது புத்தகம். இதற்குமுன் வந்த நான்கும் அகப்பொருளைப் பற்றியவை. இது புறப்பொருளைப் பற்றியது. ஆகவே அந்தப் புத்தகங்களில் உள்ள கட்டுரைகளின் போக்குக்கும் இதில் உள்ள விளக்கங்களின் போக்குக்குமிடையே சில வேறுபாடுகள் இருக்கக் காணலாம். செய்யுட்களின் உரைகளில் பழைய உரையாசிரியர் உரைக்கு வேறுபட்ட பகுதிகள் சில இருக்கும். சில இடங்களில் அவர் இரண்டாவதாக ஓர் உரை எழுதுகிறார். அந்த உரை சிறப்பாகத் தோன்றியதால் அதையே தழுவி விளக்கம் எழுதிய சில இடங்களும் உண்டு. இதிலே வரும் மன்னர்கள், புலவர் களைப்பற்றிய செய்திகள் அனைத்தையும் தொகுத்துத் தருவ தானால் மிக விரியுமாதலால், பாட்டின் விளக்கத்துக்குப் போதிய அளவில் அவற்றைக் கொடுத்திருக்கிறேன்
DOI: 10.6084/m9.figshare.5378194.v1
title: ஆத்மாவின் ராகங்கள்

description: இது ஒரு காந்தீய சகாப்த நாவல்; ஆனால் ஒன்றல்ல இரண்டு சகாப்தங்களை நீங்கள் இந்த நாவலில் சந்திக்கிறீர்கள். ஒரு தலைமுறையின் தேசபக்தர்கள் அனைவருமே இந்த நாவலின் கதாபாத்திரங்களாக வருகிறார்கள். உப்புச் சத்தியாக்கிரகத்திலிருந்து நேற்று வரை உள்ள நிலைமைகளினூடே இந்தக் கதை பாய்கிறது; வளர்கிறது, நிறைகிறது.<br><br>
DOI: 10.6084/m9.figshare.5378098
title: Srimath Bhagavat Geetha

description: உலகமெல்லாம் கடவுள் மயம் என்ற உண்மையான வேதாந்தத்தைக் கீதை ஆதாரமாக உடையது. மாயை பொய்யில்லை. பொய் தோன்றாது. பின் மாறுகிறதேயெனில், மாறுதல் இயற்கை. மாயை பொய்யில்லை. அது கடவுளின் திருமேனி. இங்கு தீமைகள் வென்றொழித்தற்குரியன, நன்மைகள் செய்தற்கும் எய்தற்கும் உரியன. சரணாகதியால் - கடவுளிடம் தீராத மாறாத பக்தியால் யோகத்தை எய்துவீர்கள். எல்லா ஜீவர்களையும் சமமாகக் கருதக் கடவீர்கள்.<br>அதனால், விடுதலையடைவீர்கள். சத்திய விரதத்தால் ஆனந்தத்தை அடைவீர்கள். இல்லறத் தூய்மையால் ஈசத்தன்மை அடைவீர்கள்.<br><br>இந்த மகத்தான உண்மையையே கீதை உபதேசிக்கிறது.
DOI: 10.6084/m9.figshare.5378071
title: The Molecular Evolutionary Dynamics of Oxidative Phosphorylation (OXPHOS) Genes in Hymenoptera

description: Data and scripts for the OXPHOS gene evolution analysis. A README file is included in the .gz file. Details about how to run the analysis is included in additional file 3 of the manuscript
DOI: 10.6084/m9.figshare.5378098.v1
title: Srimath Bhagavat Geetha

description: உலகமெல்லாம் கடவுள் மயம் என்ற உண்மையான வேதாந்தத்தைக் கீதை ஆதாரமாக உடையது. மாயை பொய்யில்லை. பொய் தோன்றாது. பின் மாறுகிறதேயெனில், மாறுதல் இயற்கை. மாயை பொய்யில்லை. அது கடவுளின் திருமேனி. இங்கு தீமைகள் வென்றொழித்தற்குரியன, நன்மைகள் செய்தற்கும் எய்தற்கும் உரியன. சரணாகதியால் - கடவுளிடம் தீராத மாறாத பக்தியால் யோகத்தை எய்துவீர்கள். எல்லா ஜீவர்களையும் சமமாகக் கருதக் கடவீர்கள்.<br>அதனால், விடுதலையடைவீர்கள். சத்திய விரதத்தால் ஆனந்தத்தை அடைவீர்கள். இல்லறத் தூய்மையால் ஈசத்தன்மை அடைவீர்கள்.<br><br>இந்த மகத்தான உண்மையையே கீதை உபதேசிக்கிறது.
DOI: 10.6084/m9.figshare.5378164.v1
title: அறப்போர்

description: சங்கநூற் காட்சிகள் என்ற வரிசையில் இது ஐந்தாவது புத்தகம். இதற்குமுன் வந்த நான்கும் அகப்பொருளைப் பற்றியவை. இது புறப்பொருளைப் பற்றியது. ஆகவே அந்தப் புத்தகங்களில் உள்ள கட்டுரைகளின் போக்குக்கும் இதில் உள்ள விளக்கங்களின் போக்குக்குமிடையே சில வேறுபாடுகள் இருக்கக் காணலாம். செய்யுட்களின் உரைகளில் பழைய உரையாசிரியர் உரைக்கு வேறுபட்ட பகுதிகள் சில இருக்கும். சில இடங்களில் அவர் இரண்டாவதாக ஓர் உரை எழுதுகிறார். அந்த உரை சிறப்பாகத் தோன்றியதால் அதையே தழுவி விளக்கம் எழுதிய சில இடங்களும் உண்டு. இதிலே வரும் மன்னர்கள், புலவர் களைப்பற்றிய செய்திகள் அனைத்தையும் தொகுத்துத் தருவ தானால் மிக விரியுமாதலால், பாட்டின் விளக்கத்துக்குப் போதிய அளவில் அவற்றைக் கொடுத்திருக்கிறேன்
DOI: 10.6084/m9.figshare.5376091
title: Study Protocol

description: Materials describing the study protocol
DOI: 10.6084/m9.figshare.5376430
title: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper

description: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper<br>
DOI: 10.6084/m9.figshare.5376091.v1
title: Study Protocol

description: Materials describing the study protocol
DOI: 10.6084/m9.figshare.5378233.v1
title: Landscape connectivity among remnant populations of guanaco (Lama guanicoe, Müller, 1776) in an arid region of Chile impacted by global change.

description: In this study, we modelled landscape connectivity between the 11 remnant coastal and Andean populations of the guanaco <i>Lama guanicoe</i>, an emblematic herbivore indigenous to South America, in Chile's arid Norte Chico. We first produced a habitat surface model to derive a regional surface resistance map; and we then used circuit theory to map functional connectivity, investigate the degree of isolation of the populations, and identify those that most contribute to the network patch connectivity. Predicted suitable habitat for <i>L. guanicoe</i> represented about 25% of the study region (i.e. 29,173 km<sup>2</sup>), and was heterogeneously distributed along a continuous stretch along the Andes, and discontinuous patches along the coast. As a result, we found that high connectivity current flows in the mid and high Andes formed a wide continuous connectivity corridor enabling connectivity between all the high Andean populations. Coastal populations, in contrast, were predicted to be more isolated. They only connect to medium and high altitude populations, and for two of them, animal movement was linked to the effectiveness of wildlife crossings. Based on the degree of connectivity, population size, and local threats, the coastal and the northernmost populations were identified as being most vulnerable, while the Andean populations appeared to be least at risk, even when located near areas of mining activity. Collectively, our results suggest that functional connectivity is an issue of concern for <i>L. guanicoe</i> in Chile’s Norte Chico, and that future conservation and management plans should adopt a landscape strategy aiming at conserving the functional connectivity between the coastal and Andean populations, and at protecting the habitat patches likely to act as stepping stones within the connectivity network.<br> <br>The raw material it is composed of three folders:<br> <br>1. Maxent_products folder contains the main results and analysis of Maxent model results.<b><br></b>2. ResistanceSurf folder: this folder show the final landscape resistance used to build the connectivity model by using Circuitscape program. <br>3. Circuitscape matrix folder: contains the resistance matrix generated by circuitscape as from logistic output of maxent model.<br><br>This study has been sumitted to PeerJ journal.<br>
DOI: 10.6084/m9.figshare.5376430.v2
title: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper

description: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper<br>
DOI: 10.6084/m9.figshare.5376430.v1
title: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper

description: Supporting data for "Can atmospheric reanalysis datasets be used to reproduce flooding over large scales?" paper<br>
DOI: 10.6084/m9.figshare.5378071.v1
title: The Molecular Evolutionary Dynamics of Oxidative Phosphorylation (OXPHOS) Genes in HymenopteraUntitled Item

description: Sequences, scripts for the OXPHOS gene evolution analysis. A README file is included in the .gz file. Details about how to run the analysis is included in additional file 3 of the manuscript
DOI: 10.6084/m9.figshare.5378233.v2
title: Landscape connectivity among remnant populations of guanaco (Lama guanicoe, Müller, 1776) in an arid region of Chile impacted by global change.

description: In this study, we modelled landscape connectivity between the 11 remnant coastal and Andean populations of the guanaco <i>Lama guanicoe</i>, an emblematic herbivore indigenous to South America, in Chile's arid Norte Chico. We first produced a habitat surface model to derive a regional surface resistance map; and we then used circuit theory to map functional connectivity, investigate the degree of isolation of the populations, and identify those that most contribute to the network patch connectivity. Predicted suitable habitat for <i>L. guanicoe</i> represented about 25% of the study region (i.e. 29,173 km<sup>2</sup>), and was heterogeneously distributed along a continuous stretch along the Andes, and discontinuous patches along the coast. As a result, we found that high connectivity current flows in the mid and high Andes formed a wide continuous connectivity corridor enabling connectivity between all the high Andean populations. Coastal populations, in contrast, were predicted to be more isolated. They only connect to medium and high altitude populations, and for two of them, animal movement was linked to the effectiveness of wildlife crossings. Based on the degree of connectivity, population size, and local threats, the coastal and the northernmost populations were identified as being most vulnerable, while the Andean populations appeared to be least at risk, even when located near areas of mining activity. Collectively, our results suggest that functional connectivity is an issue of concern for <i>L. guanicoe</i> in Chile’s Norte Chico, and that future conservation and management plans should adopt a landscape strategy aiming at conserving the functional connectivity between the coastal and Andean populations, and at protecting the habitat patches likely to act as stepping stones within the connectivity network.<br> <br>The raw material it is composed of three folders:<br> <br>1. Maxent_products folder contains the main results and analysis of Maxent model results.<b><br></b>2. ResistanceSurf folder: this folder show the final landscape resistance used to build the connectivity model by using Circuitscape program. <br>3. Circuitscape matrix folder: contains the resistance matrix generated by circuitscape as from logistic output of maxent model.<br><br>This study has been sumitted to PeerJ journal.<br>
DOI: 10.6084/m9.figshare.5378071.v3
title: The Molecular Evolutionary Dynamics of Oxidative Phosphorylation (OXPHOS) Genes in Hymenoptera

description: Data and scripts for the OXPHOS gene evolution analysis. A README file is included in the .gz file. Details about how to run the analysis is included in additional file 3 of the manuscript
DOI: 10.6084/m9.figshare.5378071.v2
title: The Molecular Evolutionary Dynamics of Oxidative Phosphorylation (OXPHOS) Genes in HymenopteraUntitled Item

description: Sequences, scripts for the OXPHOS gene evolution analysis. A README file is included in the .gz file. Details about how to run the analysis is included in additional file 3 of the manuscript
DOI: 10.6084/m9.figshare.5375911
title: Fig 9 revised.tif

description: IL-10 treatment effects.
DOI: 10.6084/m9.figshare.5375470
title: The looks matter; Aggression escalation from changes in the phenotypic appearance in the domestic fowl

description: Dataset of aggression among groups of laying hens. Effects of group size and phenotypic appeareance alterations during adulthood.
DOI: 10.6084/m9.figshare.5375911.v1
title: Fig 9 revised.tif

description: IL-10 treatment effects.