cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5319430
title: Supplementary Table S8 from Ancient whales did not filter feed with their teeth

description: The origin of baleen whales (Mysticeti), the largest animals on Earth, is closely tied to their signature filter-feeding strategy. Unlike their modern relatives, archaic whales possessed a well-developed, heterodont adult dentition. How these teeth were used, and what role their function and subsequent loss played in the emergence of filter feeding, is an enduring mystery. In particular, it has been suggested that elaborate tooth crowns may have enabled stem mysticetes to filter with their postcanine teeth in a manner analogous to living crabeater and leopard seals, thereby facilitating the transition to baleen-assisted filtering. Here we show that the teeth of archaic mysticetes are as sharp as those of terrestrial carnivorans, raptorial pinnipeds and archaeocetes, and thus were capable of capturing and processing prey. By contrast, the postcanine teeth of leopard and crabeater seals are markedly blunter, and clearly unsuited to raptorial feeding. Our results suggest that mysticetes never passed through a tooth-based filtration phase, and that the use of teeth and baleen in early whales was not functionally connected. Continued selection for tooth sharpness in archaic mysticetes is best explained by a feeding strategy that included both biting and suction, similar to that of most living pinnipeds and, probably, early toothed whales (Odontoceti).
DOI: 10.6084/m9.figshare.5319364
title: Dataset for: Novel landscape of HLA-G isoforms in clear cell renal cell carcinoma patients

description: Immune-checkpoints are powerful inhibitory molecules that promote tumor survival. Their blockade is now recognized as providing effective therapeutic benefit against cancer. HLA-G, a recently identified immune checkpoint, has been detected in many types of primary tumors and metastases, in malignant effusions as well as on tumor-infiltrating cells, particularly in patients with clear cell renal cell carcinoma (ccRCC). Here, in order to define a possible anti-cancer therapy, we used a molecular approach based on an unbiased strategy that combines transcriptome determination and immunohistochemical labeling, to analyze in-depth, the HLA-G isoforms expressed in these tumors. We found that the expression of HLA-G is highly variable among tumors and distinct areas of the same tumor, testifying a marked inter- and intra-tumor heterogeneity. Moreover, our results generate an inventory of novel HLA-G isoforms which includes spliced forms that have an extended 5’-region and lack the transmembrane and alpha-1 domains. So far, these isoforms could not be detected by any method available and their assessment may improve the procedure by which tumors are analyzed. Collectively, our approach provides the first extensive portrait of HLA-G in ccRCC and reveals data that should prove suitable for the tailoring of future clinical applications.
DOI: 10.6084/m9.figshare.5319430.v1
title: Supplementary Table S8 from Ancient whales did not filter feed with their teeth

description: The origin of baleen whales (Mysticeti), the largest animals on Earth, is closely tied to their signature filter-feeding strategy. Unlike their modern relatives, archaic whales possessed a well-developed, heterodont adult dentition. How these teeth were used, and what role their function and subsequent loss played in the emergence of filter feeding, is an enduring mystery. In particular, it has been suggested that elaborate tooth crowns may have enabled stem mysticetes to filter with their postcanine teeth in a manner analogous to living crabeater and leopard seals, thereby facilitating the transition to baleen-assisted filtering. Here we show that the teeth of archaic mysticetes are as sharp as those of terrestrial carnivorans, raptorial pinnipeds and archaeocetes, and thus were capable of capturing and processing prey. By contrast, the postcanine teeth of leopard and crabeater seals are markedly blunter, and clearly unsuited to raptorial feeding. Our results suggest that mysticetes never passed through a tooth-based filtration phase, and that the use of teeth and baleen in early whales was not functionally connected. Continued selection for tooth sharpness in archaic mysticetes is best explained by a feeding strategy that included both biting and suction, similar to that of most living pinnipeds and, probably, early toothed whales (Odontoceti).
DOI: 10.6084/m9.figshare.5319364.v1
title: Dataset for: Novel landscape of HLA-G isoforms in clear cell renal cell carcinoma patients

description: Immune-checkpoints are powerful inhibitory molecules that promote tumor survival. Their blockade is now recognized as providing effective therapeutic benefit against cancer. HLA-G, a recently identified immune checkpoint, has been detected in many types of primary tumors and metastases, in malignant effusions as well as on tumor-infiltrating cells, particularly in patients with clear cell renal cell carcinoma (ccRCC). Here, in order to define a possible anti-cancer therapy, we used a molecular approach based on an unbiased strategy that combines transcriptome determination and immunohistochemical labeling, to analyze in-depth, the HLA-G isoforms expressed in these tumors. We found that the expression of HLA-G is highly variable among tumors and distinct areas of the same tumor, testifying a marked inter- and intra-tumor heterogeneity. Moreover, our results generate an inventory of novel HLA-G isoforms which includes spliced forms that have an extended 5’-region and lack the transmembrane and alpha-1 domains. So far, these isoforms could not be detected by any method available and their assessment may improve the procedure by which tumors are analyzed. Collectively, our approach provides the first extensive portrait of HLA-G in ccRCC and reveals data that should prove suitable for the tailoring of future clinical applications.
DOI: 10.6084/m9.figshare.5319250
title: First detection of N1575Y mutation in pyrethroid resistant Anopheles gambiae in Southern Côte d’Ivoire

description: <b>Dataset 1: </b>Raw data for mortality rates from WHO bioassays in Tiassalé.<b></b> <b>Dataset 2: </b>Raw data for mortality rates from WHO bioassays in Elibou.<b></b> <b>Dataset 3: </b>Raw data for N1575Y genotypes.<b></b>
DOI: 10.6084/m9.figshare.5319250.v1
title: First detection of N1575Y mutation in pyrethroid resistant Anopheles gambiae in Southern Côte d’Ivoire

description: <b>Dataset 1: </b>Raw data for mortality rates from WHO bioassays in Tiassalé.<b></b> <b>Dataset 2: </b>Raw data for mortality rates from WHO bioassays in Elibou.<b></b> <b>Dataset 3: </b>Raw data for N1575Y genotypes.<b></b>
DOI: 10.6084/m9.figshare.5319247
title: Tutorial for MWAS and regional plots

description: Step-by-step tutorial to calculate Effective Number of Tests via permutations, and regional plots as presented in Castagne et. al, 2017 (Submitted).
DOI: 10.6084/m9.figshare.5319388.v1
title: CERES - Meyers, Bryan, et al. Nature Genetics. 2017.

description: Datasets used in CERES publication.Meyers, Bryan, et al. Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics. 2017.<br><br>External data:<br>CCLE_RNAseq_081117.rpkm.gctCCLE gene expression data downloaded from https://data.broadinstitute.org/ccle/CCLE_RNAseq_081117.rpkm.gct<br><br>ccle2maf_081117.txtCCLE mutation data downloaded from https://data.broadinstitute.org/ccle/ccle2maf_081117.txt<br><br>Achilles_v2.20.2_GeneSolutions.gct<br>RNAi DEMETER gene dependencies downloaded from https://portals.broadinstitute.org/achilles/datasets/12/download/Achilles_v2.20.2_GeneSolutions.gct<br>CCDS.current.txtCCDS gene annotations downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/archive/15/CCDS.current.txt<br>c2.all.v6.0.symbols.gmt MSigDB genesets downloaded from http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/6.0/c2.all.v6.0.symbols.gmt<br><br>avana_rs2.txt and gecko_rs2.txtDoench-Root scores for sgRNAs provided by authors of Doench, et al. Nat. Biotechnol. 2016. <br> wang_pool_normalized.counts.txtDownloaded from supplement of Wang, et al. Cell. 2017. <br>
DOI: 10.6084/m9.figshare.5319247.v1
title: Tutorial for MWAS and regional plots

description: Step-by-step tutorial to calculate Effective Number of Tests via permutations, and regional plots as presented in Castagne et. al, 2017 (Submitted).
DOI: 10.15131/shef.data.5319118.v1
title: microarray data for "MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus" Published in PLoS Genetics 2017.

description: Organism: Human Embryonic (HEK) line samples: 3 x CRISPR Knockout HEK line cultures and 3x isogenic wild type HEK cell culturesArray: Clarion S array (Thermofisher)Experiment: whole genome gene expression profiling in MYT1L null HEK cell lines (generated by CRISPR) and 3 x isogenic wild type HEK cell lines. <br>Protocol provided in "MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus" Published in PLoS Genetics, 13 (8). e1006957. ISSN 1553-7390 DOI: 10.1371/journal.pgen.1006957<br><br>"C" files are from isogenic controls."21481" files are from MYT1L null cells <br>
DOI: 10.6084/m9.figshare.5319055
title: Fairness in the climate negotiations: what explains variation in parties’ expressed conceptions?

description: How to differentiate efforts and obligations fairly between countries has been among the most central and controversial issues in climate negotiations. This article analyses countries’ fairness conceptions as expressed in position documents submitted during negotiations leading to the Paris Agreement. A regression analysis investigates which country characteristics predict relative support for three fundamental fairness principles – <i>Responsibility</i>, <i>Capability</i> and <i>Rights (needs)</i>. The most consistent and important explanatory variable turns out to be whether a country is included in Annex I to the United Nations Framework Convention on Climate Change (UNFCCC), which lists developed countries. This finding is compatible with the hypothesis that parties invoke fairness principles with the goal of advancing their own interests: non-Annex I parties wanted this particular scheme of differentiation to be upheld in the Paris Agreement, whereas Annex I parties advocated its removal. Notably, the outcome in Paris omits references to Annex I. However, the Agreement does contain multiple references to ‘developed’ versus ‘developing’ countries, hence introducing a more subtle and ambiguous differentiation than before. Post-Paris, seemingly technical discussions have encountered ‘roadblocks’ that partially derive from how the Agreement resolved the issue of differentiation between developed and developing countries. It therefore appears that negotiators will have to continue to deal with this issue, even though it may take on a new dynamic now that the Annex I division has less force. Looking for pragmatic solutions tailored to each substantive agenda point will be likely more fruitful than discussions at the level of fairness principles aiming for one overarching solution. <b>Policy relevance</b> Arguments supported by reference to fairness principles play an important role in the discourse on international climate cooperation. Understanding how fairness conceptions vary between countries – and what background variables explain this variation – is crucial for understanding the negotiation process and outcomes, and for identifying which institutional arrangements are universally acceptable. This understanding is particularly relevant for current negotiations on the modalities for the ‘global stocktake’ – a process set up to assess collective progress every five years ‘in the light of equity and best available science’.
DOI: 10.6084/m9.figshare.5319055.v1
title: Fairness in the climate negotiations: what explains variation in parties’ expressed conceptions?

description: How to differentiate efforts and obligations fairly between countries has been among the most central and controversial issues in climate negotiations. This article analyses countries’ fairness conceptions as expressed in position documents submitted during negotiations leading to the Paris Agreement. A regression analysis investigates which country characteristics predict relative support for three fundamental fairness principles – <i>Responsibility</i>, <i>Capability</i> and <i>Rights (needs)</i>. The most consistent and important explanatory variable turns out to be whether a country is included in Annex I to the United Nations Framework Convention on Climate Change (UNFCCC), which lists developed countries. This finding is compatible with the hypothesis that parties invoke fairness principles with the goal of advancing their own interests: non-Annex I parties wanted this particular scheme of differentiation to be upheld in the Paris Agreement, whereas Annex I parties advocated its removal. Notably, the outcome in Paris omits references to Annex I. However, the Agreement does contain multiple references to ‘developed’ versus ‘developing’ countries, hence introducing a more subtle and ambiguous differentiation than before. Post-Paris, seemingly technical discussions have encountered ‘roadblocks’ that partially derive from how the Agreement resolved the issue of differentiation between developed and developing countries. It therefore appears that negotiators will have to continue to deal with this issue, even though it may take on a new dynamic now that the Annex I division has less force. Looking for pragmatic solutions tailored to each substantive agenda point will be likely more fruitful than discussions at the level of fairness principles aiming for one overarching solution. <b>Policy relevance</b> Arguments supported by reference to fairness principles play an important role in the discourse on international climate cooperation. Understanding how fairness conceptions vary between countries – and what background variables explain this variation – is crucial for understanding the negotiation process and outcomes, and for identifying which institutional arrangements are universally acceptable. This understanding is particularly relevant for current negotiations on the modalities for the ‘global stocktake’ – a process set up to assess collective progress every five years ‘in the light of equity and best available science’.
DOI: 10.6084/m9.figshare.5319037
title: EEMs.zip

description: Contains excitation-emission matrices for all samples and a MQ blank.
DOI: 10.6084/m9.figshare.5319040
title: environmental data.txt

description: environmental data measured for all lakes
DOI: 10.6084/m9.figshare.5319046
title: Schimmel et al. 2017 Plant Signaling & Behavior raw data

description: Raw data for the manuscript entitled "Spatiotemporal heterogeneity of tomato induced defense responses affects spider mite performance and behavior" by Schimmel et al.
DOI: 10.6084/m9.figshare.5319034
title: abs.txt

description: Contains absorbance spectra for all samples.
DOI: 10.6084/m9.figshare.5319046.v1
title: Schimmel et al. 2017 Plant Signaling & Behavior raw data

description: Raw data for the manuscript entitled "Spatiotemporal heterogeneity of tomato induced defense responses affects spider mite performance and behavior" by Schimmel et al.
DOI: 10.6084/m9.figshare.5319031
title: chewBBACA tutorial dataset

description: Set of genomes used on the chewBBACA tutorial. All genomes are already assembled genomes downloaded from NCBI on August 2016 marked as <i>Streptococcus agalactiae .</i><br>
DOI: 10.6084/m9.figshare.5319031.v1
title: chewBBACA tutorial gbs other NCBI genomes

description: Set of genomes used on the chewBBACA tutorial. All genomes are already assembled genomes downloaded from NCBI on August 2016 marked as <i>Streptococcus agalactiae .</i><br>
DOI: 10.6084/m9.figshare.5318992
title: experimental data

description: experimental data from the MFA algorithm
DOI: 10.6084/m9.figshare.5318992.v1
title: experimental data

description: experimental data from the MFA algorithm
DOI: 10.6084/m9.figshare.5318962
title: This Film is Restricted: Training Films of The British Security Service

description: In 1962, following a series of spy scandals, the Security Service and the Central Office of Information (COI) created a security education campaign to raise awareness of the Soviet espionage threat to state and industrial secrets, and to provide security training for military and civilian personnel handling classified material. Several instructional films were commissioned, using fictional scenarios to dramatise the cold war threat to security personnel. This paper will examine four of these declassified and highly inventive films – <i>It Can’t Happen to Me</i> (1962), <i>Persona Non Grata</i> (1964) and <i>The Lecture</i> (1968), produced by James Carr’s World Wide Pictures; and <i>Any One of Us</i> (1970), directed by Seafield Head for Verity Films. Drawing on COI production files at the National Archives and the films themselves, I explore the making and underlying message of these long-neglected and highly stylised pieces of cold war propaganda; how they anticipate key texts of the 1960s spy genre like <i>The Spy Who Came in from the Cold</i> (1965); and how they compare to American security education films from the same period.
DOI: 10.6084/m9.figshare.5318962.v1
title: This Film is Restricted: Training Films of The British Security Service

description: In 1962, following a series of spy scandals, the Security Service and the Central Office of Information (COI) created a security education campaign to raise awareness of the Soviet espionage threat to state and industrial secrets, and to provide security training for military and civilian personnel handling classified material. Several instructional films were commissioned, using fictional scenarios to dramatise the cold war threat to security personnel. This paper will examine four of these declassified and highly inventive films – <i>It Can’t Happen to Me</i> (1962), <i>Persona Non Grata</i> (1964) and <i>The Lecture</i> (1968), produced by James Carr’s World Wide Pictures; and <i>Any One of Us</i> (1970), directed by Seafield Head for Verity Films. Drawing on COI production files at the National Archives and the films themselves, I explore the making and underlying message of these long-neglected and highly stylised pieces of cold war propaganda; how they anticipate key texts of the 1960s spy genre like <i>The Spy Who Came in from the Cold</i> (1965); and how they compare to American security education films from the same period.
DOI: 10.17608/k6.auckland.5318959
title: Incipits Nokki 1

description: Incipits for Wanhal's mass Nokki 1<br>
DOI: 10.17608/k6.auckland.5318959.v1
title: Incipits Nokki 1

description: Incipits for Wanhal's mass Nokki 1<br>
DOI: 10.6084/m9.figshare.5318932
title: Research data supporting "Microbial mineralization of cellulose in frozen soils"

description: Research data supporting "Microbial mineralization of cellulose in frozen soils". The files uploaded contain solid state and liquid state NMR data in TOPSPIN, Bruker format. A word document contains the NMR_data_key information.<br>An Excel file summarizes the data from NMR and GC experiments and is the base of the figures generated for the manuscript.
DOI: 10.6084/m9.figshare.5318932.v1
title: Research data supporting "Microbial mineralization of cellulose in frozen soils"

description: Research data supporting "Microbial mineralization of cellulose in frozen soils". The files uploaded contain solid state and liquid state NMR data in TOPSPIN, Bruker format. A word document contains the NMR_data_key information.<br>An Excel file summarizes the data from NMR and GC experiments and is the base of the figures generated for the manuscript.
DOI: 10.6084/m9.figshare.5318449
title: The biomechanical origin of extreme wing allometry in hummingbirds

description: These are data and JAGS model files for Skandalis et al. 2017, The biomechanical origin of extreme wing allometry in hummingbirds<br>For descriptions of the data, see README analysis_data_power.txt, and for an overview of the JAGS models, see README JAGS_models.txt.MCC_analysis_data.nex is the Maximum Clade Credibility hummingbird species tree found by McGuire et al. 2014<br>posttrees_analysis_data.nex is the posterior distribution of trees generated as described in the text.<br><br>JAGS model codes are published under MIT license.<br>
DOI: 10.6084/m9.figshare.5318305
title: Oakland County, Michigan Civil Defense, Registration and Information Training Certificate for Marjorie Winona Lyon, 1958

description: Oakland County, Michigan Civil Defense, Registration and Information Training Certificate for Marjorie Winona Lyon, 1958
DOI: 10.6084/m9.figshare.5318449.v1
title: The biomechanical origin of extreme wing allometry in hummingbirds

description: These are data and JAGS model files for Skandalis et al., The biomechanical origin of extreme wing allometry in hummingbirds<br>For descriptions of the data, see README analysis_data_power.txt, and for an overview of the JAGS models, see README JAGS_models.txt.MCC_analysis_data.nex is the Maximum Clade Credibility hummingbird species tree found by McGuire et al. 2014<br>posttrees_analysis_data.nex is the posterior distribution of trees generated as described in the text.<br><br>JAGS model codes are published under MIT license.
DOI: 10.6084/m9.figshare.5318302
title: Oakland County, Michigan Civil Defense, Medical Training Certificate for Marjorie Winona Lyon, 1959

description: Oakland County, Michigan Civil Defense, Medical Training Certificate for Marjorie Winona Lyon, 1959
DOI: 10.6084/m9.figshare.5318305.v1
title: Oakland County, Michigan Civil Defense, Registration and Information Training Certificate for Marjorie Winona Lyon, 1958

description: Oakland County, Michigan Civil Defense, Registration and Information Training Certificate for Marjorie Winona Lyon, 1958
DOI: 10.6084/m9.figshare.5318281
title: Role of interoceptive accuracy in topographical changes in emotion-induced bodily sensations

description: This dataset is from a study "Role of interoceptive accuracy in topographical changes in emotion-induced bodily sensations". This dataset does not include individual sensation map because participants did not consent to have their sensation map made publicly available. The present study investigated whether or not interoceptive accuracy was associated with topographical changes in this map following emotion-induced bodily sensations. This study included 31 participants who observed short video clips containing emotional stimuli and then reported their sensations on the body map. Interoceptive accuracy was evaluated with a heartbeat detection task and the spatial patterns of bodily sensations to specific emotions, including anger, fear, disgust, happiness, sadness, and neutral, were visualized using Statistical Parametric Mapping (SPM) analyses. Distinct patterns of bodily sensations were identified for different emotional states. In addition, positive correlations were found between the magnitude of sensation in emotion-specific regions and interoceptive accuracy across individuals. A greater degree of interoceptive accuracy was associated with more specific topographical changes after emotional stimuli.
DOI: 10.6084/m9.figshare.5318302.v1
title: Oakland County, Michigan Civil Defense, Medical Training Certificate for Marjorie Winona Lyon, 1959

description: Oakland County, Michigan Civil Defense, Medical Training Certificate for Marjorie Winona Lyon, 1959
DOI: 10.6084/m9.figshare.5318245
title: Data formatted as within participants

description: The data formatted as within participants setup using first and second drink.
DOI: 10.6084/m9.figshare.5318245.v1
title: Data formatted as within participants

description: The data formatted as within participants setup using first and second drink.