cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3471839.v9
title: Serial Speakers: a TV Series Dataset

description: <b>Dataset of three TV Series</b> with <b>manual</b> annotations:<br><br>- <i>Breaking Bad</i>: S01--S05 (file 'bb.json')<br>- <i>Game of Thrones</i>: S01--07 (file 'got.json')<br>- <i>House of Cards</i>: S01--S02 (file 'hoc.json')<br><br>All three files are in .json format and contain TV Series annotated data.<br><br>Each TV Series is defined by its <b>name</b>,<br><br>A TV Series contains <b>seasons</b>, defined by their <b>id</b>s.<br><br>Every season is made of <b>episodes</b>, defined by their <b><b>id</b></b>s,<b> title</b>s, <b>duration </b>and<b> fps </b>.<br><br>Each episode contains two basic kinds of <b>data</b>: <b>scenes</b> and <b>speech segments</b>.<br><br>Scenes are defined by <b>start</b>ing points and are made of <b>shots </b>(Seasons 1 only)<b>.<br><br></b>A shot is defined by<b>:<br><br></b>- <b>Start</b>ing and <b>end</b>ing positions.-<b> </b>Recurring shot <b>id</b>s.<br>The speech segments are defined by their:<br>- <b>Start</b>ing and <b>end</b>ing points.<br>- <b>Text</b>ual content (here encrypted for copyright reasons).<br>- <b>Speaker</b>.<br>- Possible<b> interlocutors</b> (for the following episodes only: <b>bb</b>: S01E04, S01E06, S02E03, S02E04; <b>got</b>: S01E03, S01E07, S01E08; <b>hoc</b>: S01E01, S01E07, S01E11).<br><br>All timestamps are expressed in seconds and are valid for the video files extracted from the commercial DVDs (PAL 25 FPS), with recaps (unannotated) included at the beginning of the <i>House of Cards</i> episodes.<br>In you are interested in the textual content of the dataset, please consider using our text recovering tool on GitHub:<br>https://github.com/bostxavier/Serial-Speakers<br><b> </b><br>
DOI: 10.6084/m9.figshare.3471839.v10
title: Serial Speakers: a Dataset of TV Series

description: <b>Dataset of three TV Series</b> with <b>manual</b> annotations:<br><br>- <i>Breaking Bad</i>: S01--S05 (file 'bb.json')<br>- <i>Game of Thrones</i>: S01--07 (file 'got.json')<br>- <i>House of Cards</i>: S01--S02 (file 'hoc.json')<br><br>All three files are in .json format and contain TV Series annotated data.<br><br>Each TV Series is defined by its <b>name</b>,<br><br>A TV Series contains <b>seasons</b>, defined by their <b>id</b>s.<br><br>Every season is made of <b>episodes</b>, defined by their <b><b>id</b></b>s,<b> title</b>s, <b>duration </b>and<b> fps </b>.<br><br>Each episode contains two basic kinds of <b>data</b>: <b>scenes</b> and <b>speech segments</b>.<br><br>Scenes are defined by <b>start</b>ing points and are made of <b>shots </b>(Seasons 1 only)<b>.<br><br></b>A shot is defined by<b>:<br><br></b>- <b>Start</b>ing and <b>end</b>ing positions.-<b> </b>Recurring shot <b>id</b>s.<br>The speech segments are defined by their:<br>- <b>Start</b>ing and <b>end</b>ing points.<br>- <b>Text</b>ual content (here encrypted for copyright reasons).<br>- <b>Speaker</b>.<br>- Possible<b> interlocutors</b> (for the following episodes only: <b>bb</b>: S01E04, S01E06, S02E03, S02E04; <b>got</b>: S01E03, S01E07, S01E08; <b>hoc</b>: S01E01, S01E07, S01E11).<br><br>All timestamps are expressed in seconds and are valid for the video files extracted from the commercial DVDs (PAL 25 FPS), with recaps (unannotated) included at the beginning of the <i>House of Cards</i> episodes.<br>In you are interested in the textual content of the dataset, please consider using our text recovering tool on GitHub:<br>https://github.com/bostxavier/Serial-Speakers<br><b> </b><br>
DOI: 10.17028/rd.lboro.3471827
title: Miniaturization of circular patch microstrip antenna using an arc projection - dataset

description: Files related to paper published in IEEE APWL 2016. Simulations files were created using CST software. Also measured data is attached.
DOI: 10.17028/rd.lboro.3471827.v1
title: Miniaturization of circular patch microstrip antenna using an arc projection - dataset

description: Files related to paper published in IEEE APWL 2016. Simulations files were created using CST software. Also measured data is attached.
DOI: 10.6084/m9.figshare.3471824
title: The fish that cried wolf: the role of parental care in novel predator recognition in juvenile convict cichlids (Amatitlania siquia)

description: Video files showing cichlid parents and fry.This study tested if convict cichlids (<i>Amatitlania siquia</i>) with prior predator experience could socially transfer their predator knowledge to their offspring. Prior to reproduction, pairs were assigned to either an experimental or control associative learning treatment, and given novel predator odour from a wolf cichlid (<i>Parachromis dovii</i>) paired with either alarm cue or water respectively. We hypothesized that upon re-exposure to the odour, experimental pairs would socially transfer their acquired predator knowledge to their naïve offspring, which in turn would exhibit antipredator behaviour. While fry from both treatment groups did not show a difference in shoal formation, there is some evidence to suggest a trend in the experimental group regarding parental ability to transfer information to offspring and influence shoal behaviour. When tested individually, experimental fry decreased their activity more than control fry in the presence of the predator odour. This study provides evidence of a unique form of predator learning between parents and offspring, suggesting that biparental care may also serve to provide offspring with information about the habitat into which they are born.
DOI: 10.6084/m9.figshare.3471824.v1
title: The fish that cried wolf: the role of parental care in novel predator recognition in juvenile convict cichlids (Amatitlania siquia)

description: Video files showing cichlid parents and fry.This study tested if convict cichlids (<i>Amatitlania siquia</i>) with prior predator experience could socially transfer their predator knowledge to their offspring. Prior to reproduction, pairs were assigned to either an experimental or control associative learning treatment, and given novel predator odour from a wolf cichlid (<i>Parachromis dovii</i>) paired with either alarm cue or water respectively. We hypothesized that upon re-exposure to the odour, experimental pairs would socially transfer their acquired predator knowledge to their naïve offspring, which in turn would exhibit antipredator behaviour. While fry from both treatment groups did not show a difference in shoal formation, there is some evidence to suggest a trend in the experimental group regarding parental ability to transfer information to offspring and influence shoal behaviour. When tested individually, experimental fry decreased their activity more than control fry in the presence of the predator odour. This study provides evidence of a unique form of predator learning between parents and offspring, suggesting that biparental care may also serve to provide offspring with information about the habitat into which they are born.
DOI: 10.6084/m9.figshare.3471821
title: Analysis of TET Expression:Activity and 5mC Oxidation during Normal and Malignant Germ Cell Development

description: PLoS ONE
DOI: 10.6084/m9.figshare.3471821.v2
title: Analysis of TET Expression:Activity and 5mC Oxidation during Normal and Malignant Germ Cell Development

description: PLoS ONE
DOI: 10.6084/m9.figshare.3471821.v1
title: Analysis of TET Expression:Activity and 5mC Oxidation during Normal and Malignant Germ Cell Development.pdf

description: PLoS ONE
DOI: 10.6084/m9.figshare.3471815
title: BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma

description: PLoS Genetics
DOI: 10.6084/m9.figshare.3471815.v3
title: BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma

description: PLoS Genetics
DOI: 10.6084/m9.figshare.3471815.v2
title: BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma.pdf

description: PLoS Genetics
DOI: 10.6084/m9.figshare.3471782
title: Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

description: Nexus files from the phylogenetic analyses of the Colletotrichum acutatum species complex reported by Baroncelli et al 2016
DOI: 10.6084/m9.figshare.3471782.v1
title: Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

description: Nexus files from the phylogenetic analyses of the Colletotrichum acutatum species complex reported by Baroncelli et al 2016
DOI: 10.6084/m9.figshare.3471767
title: Crumple RNA

description: Crumple software for RNA folding
DOI: 10.6084/m9.figshare.3471743
title: Tracking the emergence of meaning in the brain during natural story comprehension

description: Poster presented at the International Conference on Cognitive Neuroscience (ICON) 2014
DOI: 10.6084/m9.figshare.3471740
title: Neural signatures of incremental text processing correlate with word entropy in a natural story context

description: Poster presented at 2014 meeting of the Society for the Neurobiology of Language<br>
DOI: 10.6084/m9.figshare.3471719
title: methylAnalysisData.tar.gz

description: The Illumina 450k methylation data and related files required to run the workflow presented in the paper by Maksimovic et al. (2016). All of the data and additional resources are otherwise publicly available from the original sources cited in the paper but have been packaged up and made available here to facilitate execution of the R workflow. <br><br>Maksimovic J, Phipson B and Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data [version 2; referees: 4 approved]. F1000Research 2016, <b>5</b>:1281 <br>(doi: doi.org/10.12688/f1000research.8839.2)
DOI: 10.6084/m9.figshare.3471665
title: Construction of genetic linkage map in winter faba bean using SNP and RAPD markers

description: A set of 101 biparental population of winter faba bean was genotyped using 111 SNP and 112 RAPD markers. The results revealed 29 linkage groups
DOI: 10.6084/m9.figshare.3471665.v1
title: Construction of genetic linkage map in winter faba bean using SNP and RAPD markers

description: A set of 101 biparental population of winter faba bean was genotyped using 111 SNP and 112 RAPD markers. The results revealed 29 linkage groups
DOI: 10.6084/m9.figshare.3471632
title: Gender specialty -LIRHUS

description: Gender association with the intention to choose a medical specialty in medical students: a cross-sectional study in 11 countries in Latin America
DOI: 10.6084/m9.figshare.3471632.v1
title: Gender specialty -LIRHUS

description: Gender association with the intention to choose a medical specialty in medical students: a cross-sectional study in 11 countries in Latin America
DOI: 10.6084/m9.figshare.3471626
title: Understanding the molecular consequences of inherited muscular dystrophies: advancements through proteomic experimentation

description: <b>Introduction</b>: Proteomic techniques offer insights into the molecular perturbations occurring in muscular-dystrophies (MD). Revisiting published datasets can highlight conserved downstream molecular alterations, which may be worth re-assessing to determine whether their experimental manipulation is capable of modulating disease severity. <b>Areas covered</b>: Here, we review the MD literature, highlighting conserved molecular insights warranting mechanistic investigation for therapeutic potential. We also describe a workflow currently proving effective for efficient identification of biomarkers & therapeutic targets in other neurodegenerative conditions, upon which future MD proteomic investigations could be modelled. <b>Expert commentary</b>: Studying disease models can be useful for identifying biomarkers and model specific degenerative cascades, but rarely offer translatable mechanistic insights into disease pathology. Conversely, direct analysis of human samples undergoing degeneration presents challenges derived from complex chronic degenerative molecular processes. This requires a carefully planed & reproducible experimental paradigm accounting for patient selection through to grouping by disease severity and ending with proteomic data filtering and processing.
DOI: 10.6084/m9.figshare.3471626.v1
title: Understanding the molecular consequences of inherited muscular dystrophies: advancements through proteomic experimentation

description: <b>Introduction</b>: Proteomic techniques offer insights into the molecular perturbations occurring in muscular-dystrophies (MD). Revisiting published datasets can highlight conserved downstream molecular alterations, which may be worth re-assessing to determine whether their experimental manipulation is capable of modulating disease severity. <b>Areas covered</b>: Here, we review the MD literature, highlighting conserved molecular insights warranting mechanistic investigation for therapeutic potential. We also describe a workflow currently proving effective for efficient identification of biomarkers & therapeutic targets in other neurodegenerative conditions, upon which future MD proteomic investigations could be modelled. <b>Expert commentary</b>: Studying disease models can be useful for identifying biomarkers and model specific degenerative cascades, but rarely offer translatable mechanistic insights into disease pathology. Conversely, direct analysis of human samples undergoing degeneration presents challenges derived from complex chronic degenerative molecular processes. This requires a carefully planed & reproducible experimental paradigm accounting for patient selection through to grouping by disease severity and ending with proteomic data filtering and processing.
DOI: 10.6084/m9.figshare.3471605
title: Avian Predation on Juvenile Salmonids: Spatial and Temporal Analysis Based on Acoustic and Passive Integrated Transponder Tags

description: We evaluated the impact of predation on juvenile steelhead <i>Oncorhynchus mykiss</i> and yearling and subyearling Chinook Salmon <i>O. tshawytscha</i> by piscivorous waterbirds from 11 different breeding colonies in the Columbia River basin during 2012 and 2014. Fish were tagged with both acoustic tags and PIT tags and were tracked via a network of hydrophone arrays to estimate total smolt mortality (1 – survival) at various spatial and temporal scales during out-migration. Recoveries of PIT tags on bird colonies, coupled with the last known detections of live fish passing hydrophone arrays, were used to estimate the impact of avian predation relative to total smolt mortality. Results indicated that avian predation was a substantial source of steelhead mortality, with predation probability (proportion of available fish consumed by birds) ranging from 0.06 to 0.28 for fish traveling through the lower Snake River and the lower and middle Columbia River. Predation probability estimates ranged from 0.03 to 0.09 for available tagged yearling Chinook Salmon and from 0.01 to 0.05 for subyearlings. Smolt predation by gulls <i>Larus</i> spp. was concentrated near hydroelectric dams, while predation by Caspian terns <i>Hydroprogne caspia</i> was concentrated within reservoirs. No concentrated areas of predation were identified for double-crested cormorants <i>Phalacrocorax auritus</i> or American white pelicans <i>Pelecanus erythrorhynchos</i>. Comparisons of total smolt mortality relative to mortality from colonial waterbirds indicated that avian predation was one of the greatest sources of mortality for steelhead and yearling Chinook Salmon during out-migration. In contrast, avian predation on subyearling Chinook Salmon was generally low and constituted a minor component of total mortality. Our results demonstrate that acoustic and PIT tag technologies can be combined to quantify where and when smolt mortality occurs and the fraction of mortality that is due to colonial waterbird predation relative to non-avian mortality sources. Received November 4, 2015; accepted February 1, 2016 Published online June 27, 2016
DOI: 10.6084/m9.figshare.3471605.v1
title: Avian Predation on Juvenile Salmonids: Spatial and Temporal Analysis Based on Acoustic and Passive Integrated Transponder Tags

description: We evaluated the impact of predation on juvenile steelhead <i>Oncorhynchus mykiss</i> and yearling and subyearling Chinook Salmon <i>O. tshawytscha</i> by piscivorous waterbirds from 11 different breeding colonies in the Columbia River basin during 2012 and 2014. Fish were tagged with both acoustic tags and PIT tags and were tracked via a network of hydrophone arrays to estimate total smolt mortality (1 – survival) at various spatial and temporal scales during out-migration. Recoveries of PIT tags on bird colonies, coupled with the last known detections of live fish passing hydrophone arrays, were used to estimate the impact of avian predation relative to total smolt mortality. Results indicated that avian predation was a substantial source of steelhead mortality, with predation probability (proportion of available fish consumed by birds) ranging from 0.06 to 0.28 for fish traveling through the lower Snake River and the lower and middle Columbia River. Predation probability estimates ranged from 0.03 to 0.09 for available tagged yearling Chinook Salmon and from 0.01 to 0.05 for subyearlings. Smolt predation by gulls <i>Larus</i> spp. was concentrated near hydroelectric dams, while predation by Caspian terns <i>Hydroprogne caspia</i> was concentrated within reservoirs. No concentrated areas of predation were identified for double-crested cormorants <i>Phalacrocorax auritus</i> or American white pelicans <i>Pelecanus erythrorhynchos</i>. Comparisons of total smolt mortality relative to mortality from colonial waterbirds indicated that avian predation was one of the greatest sources of mortality for steelhead and yearling Chinook Salmon during out-migration. In contrast, avian predation on subyearling Chinook Salmon was generally low and constituted a minor component of total mortality. Our results demonstrate that acoustic and PIT tag technologies can be combined to quantify where and when smolt mortality occurs and the fraction of mortality that is due to colonial waterbird predation relative to non-avian mortality sources. Received November 4, 2015; accepted February 1, 2016 Published online June 27, 2016
DOI: 10.6084/m9.figshare.3471599
title: Gudowska et al. 2016_P.tricolor_data.xlsx

description: The discontinuous gas exchange (DGE) pattern of respiration shown by many arthropods includes periods of spiracle closure (C-phase) and is largely thought to serve as a physiological adaptation to restrict water loss in terrestrial environments. One major challenge to this hypothesis is to explain the presence of DGE in insects in moist environments. Here, we show a novel ecological correlate of the C-phase, namely, diving behaviour in mesic Paracinema tricolor grasshoppers. Notably, maximal dive duration is positively correlated with C-phase length, even after accounting for mass scaling and absolute metabolic rate. Here, we propose that an additional advantage of DGE may be conferred by allowing the tracheal. Spiracle closure may facilitate underwater submersion, which, in turn, may contribute to predator avoidance, the survival of accidental immersion or periodic flooding and the exploitation of underwater resources.
DOI: 10.6084/m9.figshare.3471599.v1
title: P.tricolor_data.xlsx

description: The discontinuous gas exchange (DGE) pattern of respiration shown by many arthropods includes periods of spiracle closure (C-phase) and is largely thought to serve as a physiological adaptation to restrict water loss in terrestrial environments. One major challenge to this hypothesis is to explain the presence of DGE in insects in moist environments. Here, we show a novel ecological correlate of the C-phase, namely, diving behaviour in mesic Paracinema tricolor grasshoppers. Notably, maximal dive duration is positively correlated with C-phase length, even after accounting for mass scaling and absolute metabolic rate. Here, we propose that an additional advantage of DGE may be conferred by allowing the tracheal. Spiracle closure may facilitate underwater submersion, which, in turn, may contribute to predator avoidance, the survival of accidental immersion or periodic flooding and the exploitation of underwater resources.
DOI: 10.6084/m9.figshare.3471596
title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

description: Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation biomarkers might improve lymph node metastases detection. To identify epigenetically regulated genes associated with lymph node metastases, genome-wide methylation analysis was performed on 6 OOSCC with (pN+) and 6 OOSCC without (pN0) lymph node metastases and combined with a gene expression signature predictive for pN+ status in OOSCC. Selected genes were validated using an independent OOSCC cohort by immunohistochemistry and pyrosequencing, and on data retrieved from The Cancer Genome Atlas. A two-step statistical selection of differentially methylated sequences revealed 14 genes with increased methylation status and mRNA downregulation in pN+ OOSCC. <i>RAB25</i>, a known tumor suppressor gene, was the highest-ranking gene in the discovery set. In the validation sets, both <i>RAB25</i> mRNA (<i>P</i> = 0.015) and protein levels (<i>P</i> = 0.012) were lower in pN+ OOSCC. <i>RAB25</i> mRNA levels were negatively correlated with <i>RAB25</i> methylation levels (<i>P</i> &lt; 0.001) but RAB25 protein expression was not. Our data revealed that promoter methylation is a mechanism resulting in downregulation of RAB25 expression in pN+ OOSCC and decreased expression is associated with lymph node metastasis. Detection of <i>RAB25</i> methylation might contribute to lymph node metastasis diagnosis and serve as a potential new therapeutic target in OOSCC.
DOI: 10.6084/m9.figshare.3471596.v1
title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

description: Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation biomarkers might improve lymph node metastases detection. To identify epigenetically regulated genes associated with lymph node metastases, genome-wide methylation analysis was performed on 6 OOSCC with (pN+) and 6 OOSCC without (pN0) lymph node metastases and combined with a gene expression signature predictive for pN+ status in OOSCC. Selected genes were validated using an independent OOSCC cohort by immunohistochemistry and pyrosequencing, and on data retrieved from The Cancer Genome Atlas. A two-step statistical selection of differentially methylated sequences revealed 14 genes with increased methylation status and mRNA downregulation in pN+ OOSCC. <i>RAB25</i>, a known tumor suppressor gene, was the highest-ranking gene in the discovery set. In the validation sets, both <i>RAB25</i> mRNA (<i>P</i> = 0.015) and protein levels (<i>P</i> = 0.012) were lower in pN+ OOSCC. <i>RAB25</i> mRNA levels were negatively correlated with <i>RAB25</i> methylation levels (<i>P</i> &lt; 0.001) but RAB25 protein expression was not. Our data revealed that promoter methylation is a mechanism resulting in downregulation of RAB25 expression in pN+ OOSCC and decreased expression is associated with lymph node metastasis. Detection of <i>RAB25</i> methylation might contribute to lymph node metastasis diagnosis and serve as a potential new therapeutic target in OOSCC.