cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1407381.v2
title: Differential use of autophagy by primary dendritic cells specialized in cross-presentation

description: Antigen-presenting cells survey their environment and present captured antigens bound to major histocompatibility complex (MHC) molecules. Formation of MHC-antigen complexes occurs in specialized compartments where multiple protein trafficking routes, still incompletely understood, converge. Autophagy is a route that enables the presentation of cytosolic antigen by MHC class II molecules. Some reports also implicate autophagy in the presentation of extracellular, endocytosed antigen by MHC class I molecules, a pathway termed “cross-presentation.” The role of autophagy in cross-presentation is controversial. This may be due to studies using different types of antigen presenting cells for which the use of autophagy is not well defined. Here we report that active use of autophagy is evident only in DC subtypes specialized in cross-presentation. However, the contribution of autophagy to cross-presentation varied depending on the form of antigen: it was negligible in the case of cell-associated antigen or antigen delivered via receptor-mediated endocytosis, but more prominent when the antigen was a soluble protein. These findings highlight the differential use of autophagy and its machinery by primary cells equipped with specific immune function, and prompt careful reassessment of the participation of this endocytic pathway in antigen cross-presentation.
DOI: 10.6084/m9.figshare.1407381.v1
title: Differential use of autophagy by primary dendritic cells specialised in cross-presentation

description: ABSTRACTAntigen presenting cells survey their environment and present captured antigens bound to major histocompatibility complex (MHC) molecules. Formation of MHC-antigen complexes occurs in specialized compartments where multiple protein trafficking routes, still incompletely understood, converge. Autophagy is a route that enables the presentation of cytosolic antigen by MHC class II molecules. Some reports also implicate autophagy in the presentation of extracellular, endocytosed antigen by MHC class I molecules, a pathway termed “cross-presentation”. The role of autophagy in cross-presentation is controversial. This may be due to studies using different types of antigen presenting cells for which the use of autophagy is not well defined. Here we report that active use of autophagy is evident only in DC subtypes specialized in cross-presentation. However, the contribution of autophagy to cross-presentation varied depending on the form of antigen: it was negligible in the case of cell-associated antigen or antigen delivered via receptor-mediated endocytosis, but more prominent when the antigen was a soluble protein. These findings highlight the differential use of autophagy and its machinery by primary cells equipped with specific immune function, and prompt careful reassessment of the participation of this endocytic pathway in antigen cross-presentation.
DOI: 10.6084/m9.figshare.1407020
title: Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats

description: Data set corresponding to results reported in PLOS ONE mansucript: "Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats"
DOI: 10.6084/m9.figshare.1407020.v1
title: Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats

description: Data set corresponding to results reported in PLOS ONE mansucript: "Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats"
DOI: 10.6084/m9.figshare.1407004
title: Datasets

description: Contains all the datasets available in the TISSUES database with all the data, including the non-confident gene-tissue associations. The non-confident associations are not available at the TISSUES database but were used them in the fold enrichment analyses. The files format is: Taxon_id ENSP tissues_code BTO source evidences confidence_score(stars) linkout
DOI: 10.6084/m9.figshare.1407024.v2
title: figshare for institutions brochure

description: figshare for institutions is a research data management platform that helps institutions store, share and manage their research. This document gives an overview of the 4 modules of functionality, data management, data dissemination, user group administration, reporting and statistics.
DOI: 10.6084/m9.figshare.1406988
title: Associations between Variables of Interest and Perceived Neighborhood Quality

description: Associations between Variables of Interest and Telomere Length
DOI: 10.6084/m9.figshare.1406987
title: Associations between Variables of Interest and Telomere Length

description: Associations between Variables of Interest and Telomere Length
DOI: 10.6084/m9.figshare.1406988.v2
title: Associations between Variables of Interest and Perceived Neighborhood Quality

description: Associations between Variables of Interest and Telomere Length
DOI: 10.6084/m9.figshare.1406988.v1
title: Associations between Variables of Interest and Perceived Neighborhood Quality

description: Associations between Variables of Interest and Telomere Length
DOI: 10.6084/m9.figshare.1406986
title: Associations between Telomere Length and Perceived Neighborhood Quality

description: Associations between Telomere Length and Perceived Neighborhood Quality
DOI: 10.6084/m9.figshare.1406985
title: Sample Distribution

description: Sample Distribution
DOI: 10.6084/m9.figshare.1406987.v1
title: Associations between Variables of Interest and Telomere Length

description: Associations between Variables of Interest and Telomere Length
DOI: 10.6084/m9.figshare.1406984
title: Hemispheric asymmetries in repetition enhancement and suppression effects in the newborn brain

description: Raw data for PONE-D-14-28355R1 This figshare file contains the raw data underlying the study in the manuscript entitled "Hemispheric asymmetries in repetition enhancement and suppression effects in the newborn brain" sumitted to PlosOne by Bouchon, Nazzi and Gervain. Please find enclosed NIRS*.csv files corresponding to the individual NIRS data obtained for each participant in the study. The analysis of this dataset is described in the Data Analysis paragraph of our manuscript. In this study newborn participants were exposed to blocks of 6 CVCVCV words or stimuli: 12 adjacent blocks corresponded to the ABC condition, and 12 adjacent blocks to the ABB condition. Importantly the stimulus type, ABB or ABC, is indicated in the column entitled "Mark", with a mark for the onset and the offset of each word, using the following code: For ABC blocks: 4: onset of the 1st stimulus=block onset 4: offset of the 1st stimulus 1: onset of 2nd stimulus 1: offset of 2nd stimulus 1: onset of 3rd stimulus 1: offset of 3rd stimulus 1: onset of 4th stimulus 1: offset of 4th stimulus 1: onset of 5th stimulus 1: offset of 5th stimulus 5 onset of 6th and last stimulus 5 offset of 6th and last stimulus=end of block. For ABB blocks: 6: onset of 1st stimulus=block onset, 6: offset of 1st stimulus, 2: onset of 2nd stimulus, 2: offset of 2nd stimulus, 2: onset of 3rd stimulus, 2: offset of 3rd stimulus, 2: onset of 4th stimulus, 2: offset of 4th stimulus, 2: onset of 5th stimulus, 2: offset of 5th stimulus, 7: onset of 6th and last stimulus, 7: offset of 6th and last stimulus=end of block.
DOI: 10.6084/m9.figshare.1406985.v2
title: Sample Distribution

description: Sample Distribution
DOI: 10.6084/m9.figshare.1406986.v2
title: Associations between Telomere Length and Perceived Neighborhood Quality

description: Associations between Telomere Length and Perceived Neighborhood Quality
DOI: 10.6084/m9.figshare.1406985.v1
title: Sample Distribution

description: Sample Distribution
DOI: 10.6084/m9.figshare.1406986.v1
title: Associations between Telomere Length and Perceived Neighborhood Quality

description: Associations between Telomere Length and Perceived Neighborhood Quality
DOI: 10.6084/m9.figshare.1406982
title: The Recorder's Paradox: high fidelity from natural environments

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?
DOI: 10.6084/m9.figshare.1406984.v1
title: Raw data for PONE-D-14-28355R1

description: Raw data for PONE-D-14-28355R1 This figshare file contains the raw data underlying the study in the manuscript entitled "Hemispheric asymmetries in repetition enhancement and suppression effects in the newborn brain" sumitted to PlosOne by Bouchon, Nazzi and Gervain. Please find enclosed NIRS*.csv files corresponding to the individual NIRS data obtained for each participant in the study. The analysis of this dataset is described in the Data Analysis paragraph of our manuscript. In this study newborn participants were exposed to blocks of 6 CVCVCV words or stimuli: 12 adjacent blocks corresponded to the ABC condition, and 12 adjacent blocks to the ABB condition. Importantly the stimulus type, ABB or ABC, is indicated in the column entitled "Mark", with a mark for the onset and the offset of each word, using the following code: For ABC blocks: 4: onset of the 1st stimulus=block onset 4: offset of the 1st stimulus 1: onset of 2nd stimulus 1: offset of 2nd stimulus 1: onset of 3rd stimulus 1: offset of 3rd stimulus 1: onset of 4th stimulus 1: offset of 4th stimulus 1: onset of 5th stimulus 1: offset of 5th stimulus 5 onset of 6th and last stimulus 5 offset of 6th and last stimulus=end of block. For ABB blocks: 6: onset of 1st stimulus=block onset, 6: offset of 1st stimulus, 2: onset of 2nd stimulus, 2: offset of 2nd stimulus, 2: onset of 3rd stimulus, 2: offset of 3rd stimulus, 2: onset of 4th stimulus, 2: offset of 4th stimulus, 2: onset of 5th stimulus, 2: offset of 5th stimulus, 7: onset of 6th and last stimulus, 7: offset of 6th and last stimulus=end of block.
DOI: 10.6084/m9.figshare.1406903
title: Microbiota data level 6 ~ species

description: Level 6 data (species) microbiota data of jejunum content from two divergent chicken broiler lines at day 0, 4, and 16. Sequenced by Illumina MiSeq technology.
DOI: 10.6084/m9.figshare.1406932
title: Aerobic growth of Bacillus subtilis NRS-762 in LB Lennox (unbuffered) medium at 25 deg C

description: This is a dataset containing the time course evolution of optical density (at 600 nm) and pH variation that describes aerobic growth of <em>Bacillus subtilis</em> NRS-762 (ATCC 8473) in LB Lennox (unbuffered) medium at 25 oC (room temperature) on a non-temperature controlled orbital shaker. The shaking speed was 250 rpm, and the culture format was 250 mL glass shake-flasks containing 100 mL medium. Optical density was measured using a Shimadzu Biospec Mini UV-Visible Spectrophotometer, and pH of culture broth monitored via a Mettler Toledo AE-100 pH meter outfitted with an Orion pH electrode. While <em>B. subtilis</em> NRS-762 exhibited good growth till 22.5 hours post-inoculation, drastic decline in optical density occurred after attainment of maximal optical density. Significantly, cellular debris was also absent in the shake-flasks after autoclave decontamination at 121 oC for 20 minutes. Flies were also observed on and around the cotton plug of the shake-flasks after evolution of a pungent odour during stationary phase. The aforementioned observations suggested possible interkingdom signaling between<em> B. subtilis</em> and flies via a volatile compound secreted by the bacterium. Coincidence of flies attraction with stationary phase further point to possible long-range dispersal function of volatile compound-mediated interkingdom signaling upon nutritional stress. A coherent conceptual model has been put forward in describing the observations, and is available at <em>PeerJ Preprints</em>, “Possible odour-mediated attraction of flies to <em>Bacillus subtilis</em> NRS-762 stationary phase culture.” (https://peerj.com/preprints/541v2/) Release of the original dataset would hopefully help interested researchers determine the extent of reproducibility, and also serve as reference data for comparing the growth performance of the bacterium with other microbes under similar conditions.
DOI: 10.6084/m9.figshare.1406982.v2
title: The Recorder

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?
DOI: 10.6084/m9.figshare.1405701
title: Cuke Particle Positions - 1998-2007 - Grid sites

description: LTRANS V2 raw output: Longitude, Latitude, depth, boundary status, and release site. Directories are structured as G1998\152\1\ meaning treatmentyear\releaseday\bin\. Files are named para 1002.csv which contains all the positions (of that treatment, year, site, and release day) at the end of the first day. Text files labeled as rl_01.txt are the release locations. The grid shapefile is represents the cucumber habitat from which larvae were released
DOI: 10.6084/m9.figshare.1406982.v3
title: The Recorder's Paradox

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?
DOI: 10.6084/m9.figshare.1406982.v4
title: The Recorder

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?
DOI: 10.6084/m9.figshare.1405694.v1
title: Modulation of Insulin Degrading Enzyme activity and liver cell proliferation

description: Diabetes mellitus type 2 (T2DM), insulin therapy, and hyperinsulinemia are independent risk factors of liver cancer. Recently, the use of a novel inhibitor of insulin degrading enzyme (IDE) was proposed as a new therapeutic strategy in T2DM. However, IDE inhibition might stimulate liver cell proliferation via increased intracellular insulin concentration. The aim of this study was to characterize effects of inhibition of IDE activity in HepG2 hepatoma cells and to analyze liver specific expression of <i>IDE</i> in subjects with T2DM. HepG2 cells were treated with 10 nM insulin for 24 h with or without inhibition of IDE activity using <i>IDE</i> RNAi, and cell transcriptome and proliferation rate were analyzed. Human liver samples (n=22) were used for the gene expression profiling by microarrays. In HepG2 cells, <i>IDE</i> knockdown changed expression of genes involved in cell cycle and apoptosis pathways. Proliferation rate was lower in <i>IDE</i> knockdown cells than in controls. Microarray analysis revealed the decrease of hepatic <i>IDE</i> expression in subjects with T2DM accompanied by the downregulation of the p53-dependent genes <i>FAS</i> and <i>CCNG2,</i> but not by the upregulation of proliferation markers <i>MKI67, MCM2</i> and <i>PCNA</i>. Similar results were found in the liver microarray dataset from GEO Profiles database. In conclusion, <i>IDE</i> expression is decreased in liver of subjects with T2DM which is accompanied by the dysregulation of p53 pathway. Prolonged use of IDE inhibitors for T2DM treatment should be carefully tested in animal studies regarding its potential effect on hepatic tumorigenesis.
DOI: 10.6084/m9.figshare.1405701.v1
title: Cuke Particle Positions - 1998-2007 - Grid sites

description: LTRANS V2 raw output: Longitude, Latitude, depth, boundary status, and release site. Directories are structured as G1998\152\1\ meaning treatmentyear\releaseday\bin\. Files are named para 1002.csv which contains all the positions (of that treatment, year, site, and release day) at the end of the first day.
DOI: 10.6084/m9.figshare.1406982.v5
title: The Recorder's Paradox

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?
DOI: 10.6084/m9.figshare.1405694.v2
title: Modulation of insulin degrading enzyme activity and liver cell proliferation

description: Diabetes mellitus type 2 (T2DM), insulin therapy, and hyperinsulinemia are independent risk factors of liver cancer. Recently, the use of a novel inhibitor of insulin degrading enzyme (IDE) was proposed as a new therapeutic strategy in T2DM. However, IDE inhibition might stimulate liver cell proliferation via increased intracellular insulin concentration. The aim of this study was to characterize effects of inhibition of IDE activity in HepG2 hepatoma cells and to analyze liver specific expression of <i>IDE</i> in subjects with T2DM. HepG2 cells were treated with 10 nM insulin for 24 h with or without inhibition of IDE activity using <i>IDE</i> RNAi, and cell transcriptome and proliferation rate were analyzed. Human liver samples (n = 22) were used for the gene expression profiling by microarrays. In HepG2 cells, <i>IDE</i> knockdown changed expression of genes involved in cell cycle and apoptosis pathways. Proliferation rate was lower in <i>IDE</i> knockdown cells than in controls. Microarray analysis revealed the decrease of hepatic <i>IDE</i> expression in subjects with T2DM accompanied by the downregulation of the p53-dependent genes <i>FAS</i> and <i>CCNG2</i>, but not by the upregulation of proliferation markers <i>MKI67, MCM2</i> and <i>PCNA</i>. Similar results were found in the liver microarray dataset from GEO Profiles database. In conclusion, <i>IDE</i> expression is decreased in liver of subjects with T2DM which is accompanied by the dysregulation of p53 pathway. Prolonged use of IDE inhibitors for T2DM treatment should be carefully tested in animal studies regarding its potential effect on hepatic tumorigenesis.
DOI: 10.6084/m9.figshare.1405694
title: Modulation of insulin degrading enzyme activity and liver cell proliferation

description: Diabetes mellitus type 2 (T2DM), insulin therapy, and hyperinsulinemia are independent risk factors of liver cancer. Recently, the use of a novel inhibitor of insulin degrading enzyme (IDE) was proposed as a new therapeutic strategy in T2DM. However, IDE inhibition might stimulate liver cell proliferation via increased intracellular insulin concentration. The aim of this study was to characterize effects of inhibition of IDE activity in HepG2 hepatoma cells and to analyze liver specific expression of <i>IDE</i> in subjects with T2DM. HepG2 cells were treated with 10 nM insulin for 24 h with or without inhibition of IDE activity using <i>IDE</i> RNAi, and cell transcriptome and proliferation rate were analyzed. Human liver samples (n = 22) were used for the gene expression profiling by microarrays. In HepG2 cells, <i>IDE</i> knockdown changed expression of genes involved in cell cycle and apoptosis pathways. Proliferation rate was lower in <i>IDE</i> knockdown cells than in controls. Microarray analysis revealed the decrease of hepatic <i>IDE</i> expression in subjects with T2DM accompanied by the downregulation of the p53-dependent genes <i>FAS</i> and <i>CCNG2</i>, but not by the upregulation of proliferation markers <i>MKI67, MCM2</i> and <i>PCNA</i>. Similar results were found in the liver microarray dataset from GEO Profiles database. In conclusion, <i>IDE</i> expression is decreased in liver of subjects with T2DM which is accompanied by the dysregulation of p53 pathway. Prolonged use of IDE inhibitors for T2DM treatment should be carefully tested in animal studies regarding its potential effect on hepatic tumorigenesis.
DOI: 10.6084/m9.figshare.1405701.v2
title: Cuke Particle Positions - 1998-2007 - Grid sites

description: LTRANS V2 raw output: Longitude, Latitude, depth, boundary status, and release site. Directories are structured as G1998\152\1\ meaning treatmentyear\releaseday\bin\. Files are named para 1002.csv which contains all the positions (of that treatment, year, site, and release day) at the end of the first day.
DOI: 10.6084/m9.figshare.1406982.v6
title: The Recorder

description: The need to access vernacular speech styles, which appear in informal, uncontrolled environments poses a problem for the recording of audio high enough in quality for acoustic analysis. As a result, sociolinguistic interviews are either relatively formal and controlled resulting in more formal speech and decent quality audio OR informal, uncontrolled contexts with a decent level of vernacular speech yet low quality audio. This poses a problem for the analysis of vernacular speech. Studies show the effects of noise on voice quality properties but are noisy environments actually detrimental to analysis of formant frequencies? Does noise affect all formants equally? What types of noise should be avoided?