cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6809270.v1
title: Kiatmetha_Raw Data

description: <b>Figure 1A:</b> Agarose gel electrophoresis showing the expression of IHHNV capsid ORF at 990 bp upon transforming vectors into various transformed <i>E. coli</i>, S1-S4.<br><b> Figure 1B:</b> SDS-PAGE protein profiling of a highly purified IHHNV capsid protein at 37.5 kDa (arrowhead) through a Nikel affinity chromatography.<br><b>Figure 2A:</b> Physical stability tests of IHHNV-VLPs against long term storage at 4ºC, from 1 day storsge up to 30 days. <br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><br>
DOI: 10.6084/m9.figshare.6809255
title: ExperimentalDataM1M31.pdf

description: Data contains full PhD study experimental data of XRF analysis
DOI: 10.6084/m9.figshare.6809237
title: Changes In The Expression of Eight Clock Genes In Five Tissues From Fasting and Fed Sows

description: The goal of the current work was to investigate if such changes also take place in tissues containing peripheral (duodenum, dorsal fat, muscle, and liver) and central (hypothalamus) clocks. As animal material, we used 12 sows that fasted 12 h before slaughtering (T0) and 12 sows that were fed ad libitum 7 h. prior slaughtering (T2). Tissue samples were collected immediately after slaughter and total RNA was subsequently extracted. The expression of the ARNTL, BHLHE40, CRY2, NPAS2, NR1D1, PER1, PER2 and SIK1 genes was measured by quantitative reverse transcription PCR. <br>
DOI: 10.6084/m9.figshare.6809237.v2
title: Changes In The Expression of Eight Clock Genes In Five Tissues From Fasting and Fed Sows

description: The goal of the current work was to investigate if such changes also take place in tissues containing peripheral (duodenum, dorsal fat, muscle, and liver) and central (hypothalamus) clocks. As animal material, we used 12 sows that fasted 12 h before slaughtering (T0) and 12 sows that were fed ad libitum 7 h. prior slaughtering (T2). Tissue samples were collected immediately after slaughter and total RNA was subsequently extracted. The expression of the ARNTL, BHLHE40, CRY2, NPAS2, NR1D1, PER1, PER2 and SIK1 genes was measured by quantitative reverse transcription PCR. <br>
DOI: 10.6084/m9.figshare.6809237.v1
title: Nutrition Induced Expression Changes In Eight Clock Genes In Porcine Tissues

description: The goal of the current work was to investigate if such changes also take place in tissues containing peripheral (duodenum, dorsal fat, muscle, and liver) and central (hypothalamus) clocks. As animal material, we used 12 sows that fasted 12 h before slaughtering (T0) and 12 sows that were fed ad libitum 7 h. prior slaughtering (T2). Tissue samples were collected immediately after slaughter and total RNA was subsequently extracted. The expression of the ARNTL, BHLHE40, CRY2, NPAS2, NR1D1, PER1, PER2 and SIK1 genes was measured by quantitative reverse transcription PCR. <br>
DOI: 10.6084/m9.figshare.6809213
title: Supplementary Material for: Right Ventricular Index for Risk Stratification of Patients with Pulmonary Arterial Hypertension

description: <b><i>Background:</i></b> Right ventricular (RV) dysfunction is a major prognostic predictor in pulmonary arterial hypertension (PAH). <b><i>Objectives:</i></b> The objective of this study was to assess the prognostic impact of a newly developed index merging haemodynamic parameters into 1 variable. <b><i>Methods:</i></b> We retrospectively assessed 2 cohorts of 248 patients (164 from Hamburg and 84 from Heidelberg) with invasively diagnosed PAH. During a median follow-up time of 3.6 years (3.1 and 4.0 years for Hamburg and Heidelberg, respectively), the composite endpoint of all-cause mortality and lung transplantation occurred in 57 patients (53 and 4 patients for Hamburg and Heidelberg, respectively). The RV index was developed in the Hamburg cohort and validated in the Heidelberg cohort: (right atrial pressure × pulmonary vascular resistance)/mixed venous oxygen saturation. <b><i>Results:</i></b> Patients with a high RV index had a higher incidence of the combined endpoint in Kaplan-Meier analyses in the Hamburg and Heidelberg cohort (<i>p</i> = 0.017 and <i>p</i> = 0.034, respectively). The calculated RV index cut-off value was 91 and identified patients with a worse outcome in the Hamburg cohort and showed a trend in the Heidelberg cohort (<i>p</i> &lt; 0.001 and <i>p</i> = 0.089, respectively). The RV index in Cox regression hazard models was an independent predictor of outcomes after adjustment for sex and age in both cohorts (Hamburg: hazard ratio [HR] 1.26 [95% CI 1.08, 1.47], <i>p</i> = 0.0027; Heidelberg: HR 2.27 [95% CI 1.46, 3.51], <i>p</i> &lt; 0.001). A nomogram based on these results allowed risk stratification. <b><i>Conclusion:</i></b> Merging 3 haemodynamic variables into 1 variable, the RV index increased the prognostic power up to an independent risk factor. The RV index is easy to calculate and allows the construction of a nomogram for an individualized risk assessment.
DOI: 10.6084/m9.figshare.6809213.v1
title: Supplementary Material for: Right Ventricular Index for Risk Stratification of Patients with Pulmonary Arterial Hypertension

description: <b><i>Background:</i></b> Right ventricular (RV) dysfunction is a major prognostic predictor in pulmonary arterial hypertension (PAH). <b><i>Objectives:</i></b> The objective of this study was to assess the prognostic impact of a newly developed index merging haemodynamic parameters into 1 variable. <b><i>Methods:</i></b> We retrospectively assessed 2 cohorts of 248 patients (164 from Hamburg and 84 from Heidelberg) with invasively diagnosed PAH. During a median follow-up time of 3.6 years (3.1 and 4.0 years for Hamburg and Heidelberg, respectively), the composite endpoint of all-cause mortality and lung transplantation occurred in 57 patients (53 and 4 patients for Hamburg and Heidelberg, respectively). The RV index was developed in the Hamburg cohort and validated in the Heidelberg cohort: (right atrial pressure × pulmonary vascular resistance)/mixed venous oxygen saturation. <b><i>Results:</i></b> Patients with a high RV index had a higher incidence of the combined endpoint in Kaplan-Meier analyses in the Hamburg and Heidelberg cohort (<i>p</i> = 0.017 and <i>p</i> = 0.034, respectively). The calculated RV index cut-off value was 91 and identified patients with a worse outcome in the Hamburg cohort and showed a trend in the Heidelberg cohort (<i>p</i> &lt; 0.001 and <i>p</i> = 0.089, respectively). The RV index in Cox regression hazard models was an independent predictor of outcomes after adjustment for sex and age in both cohorts (Hamburg: hazard ratio [HR] 1.26 [95% CI 1.08, 1.47], <i>p</i> = 0.0027; Heidelberg: HR 2.27 [95% CI 1.46, 3.51], <i>p</i> &lt; 0.001). A nomogram based on these results allowed risk stratification. <b><i>Conclusion:</i></b> Merging 3 haemodynamic variables into 1 variable, the RV index increased the prognostic power up to an independent risk factor. The RV index is easy to calculate and allows the construction of a nomogram for an individualized risk assessment.
DOI: 10.6084/m9.figshare.6809135
title: Code for "Diversity-Driven Selection of Exploration Strategies in Multi-Armed Bandits"

description: Code for the article: F. C. Y. Benureau and P. Oudeyer, "Diversity-Driven Selection of Exploration Strategies in Multi-Armed Bandits," <i>ICDL-EpiRob</i>, 2015. 10.1109/devlrn.2015.7346130 <br>The code is also hosted at github: github.com/benureau/icdl2015 (clickable link below).<br>The code is in <b>code.tar.xz</b>, the results in <b>runs.tar.xz</b>. Read the readme file in the code archive, and unpack the results in the `runs/` folder inside the code folder, if you don't want to re-run the computations.<br>The code archive contains references figures, produced with the results from <b>runs.tar.xz</b>, in the <b>figures_ref/</b> folder.<br>Although the license mentioned is the GPL 3.0+ here, the license for the code is actually the <b>Open Science License</b>, which is the LGPL, with the additional requirement to distribute modification to the code, if you make any scientific claim deriving from the use of the code.<br>Do not hesitate to contact me about this code, my contact is available on my website, referenced below.
DOI: 10.6084/m9.figshare.6809132
title: Functional characterization of novel GLI2 mutations identified in patients with Combined Pituitary Hormone Deficiency

description: In a preliminary experiment, the GLI2ΔN-WT induced up to 10-fold reporter activity 306 (p&lt;0.0001) compared with GLI2FL-WT (Supplementary figure 1) due to the absence of the 307 repressor domain, in line with the previous reports.<br><br>Primers used for the amplification of the complete coding region of GLI2.<br>
DOI: 10.6084/m9.figshare.6809135.v1
title: Code for "Diversity-Driven Selection of Exploration Strategies in Multi-Armed Bandits"

description: Code for the article: F. C. Y. Benureau and P. Oudeyer, "Diversity-Driven Selection of Exploration Strategies in Multi-Armed Bandits," <i>ICDL-EpiRob</i>, 2015. 10.1109/devlrn.2015.7346130 <br>The code is also hosted at github: github.com/benureau/icdl2015 (clickable link below).<br>The code is in <b>code.tar.xz</b>, the results in <b>runs.tar.xz</b>. Read the readme file in the code archive, and unpack the results in the `runs/` folder inside the code folder, if you don't want to re-run the computations.<br>The code archive contains references figures, produced with the results from <b>runs.tar.xz</b>, in the <b>figures_ref/</b> folder.<br>Although the license mentioned is the GPL 3.0+ here, the license for the code is actually the <b>Open Science License</b>, which is the LGPL, with the additional requirement to distribute modification to the code, if you make any scientific claim deriving from the use of the code.<br>Do not hesitate to contact me about this code, my contact is available on my website, referenced below.
DOI: 10.6084/m9.figshare.6809105
title: Dataset for: Regulation of synaptic release-site-Ca2+-channel coupling as a mechanism to control release probability and short-term plasticity

description: Synaptic transmission relies on the rapid fusion of neurotransmitter-containing synaptic vesicles (SVs) which happens in response to action-potential (AP) induced Ca<sup>2+</sup> influx at active zones (AZs). A highly conserved molecular machinery cooperates at SV release sites to mediate SV-plasma membrane attachment & maturation, Ca<sup>2+</sup> sensing, and membrane fusion. Despite this high degree of conservation, synapses –even within the same organism, organ or neuron– are highly diverse regarding the probability of APs to trigger SV fusion. Additionally, repetitive activation can lead to either strengthening or weakening of transmission. In this review, we discuss mechanisms controlling release probability and this short-term plasticity. We argue that an important layer of control is exerted by evolutionarily conserved AZ scaffolding proteins which determine the coupling distance between SV fusion sites and voltage-gated Ca<sup>2+</sup> channels (VGCC), and thereby shape synapse-specific input/output behaviors. We propose that AZ-scaffold modifications may occur to adapt the coupling distance during synapse maturation and plastic regulation of synapse strength.
DOI: 10.6084/m9.figshare.6809042
title: Results Speed and duration.xlsx

description: Speed and duration of the illusion
DOI: 10.6084/m9.figshare.6808988
title: rami_as

description: This ontology describes the RAMI4.0 model, the Administration Shell and related concepts
DOI: 10.6084/m9.figshare.6808988.v1
title: rami_as

description: This ontology describes the RAMI4.0 model, the Administration Shell and related concepts
DOI: 10.6084/m9.figshare.6808892
title: Automated speech analysis tools for children’s speech production: A systematic literature review

description: <i>Purpose</i>: A systematic search and review of published studies was conducted on the use of automated speech analysis (ASA) tools for analysing and modifying speech of typically-developing children learning a foreign language and children with speech sound disorders to determine (i) types, attributes, and purposes of ASA tools being used; (ii) accuracy against human judgment; and (iii) performance as therapeutic tools. <i>Method</i>: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were applied. Across nine databases, 32 articles published between January 2007 and December 2016 met inclusion criteria: (i) focussed on children’s speech; (ii) tools used for speech analysis or modification; and (iii) reporting quantitative data on accuracy. <i>Result</i>: Eighteen ASA tools were identified. These met the clinical threshold of 80% agreement with human judgment when used as predictors of intelligibility, impairment severity, or error category. Tool accuracy was typically &lt;80% accuracy for words containing mispronunciations. ASA tools have been used effectively to improve to children’s foreign language pronunciation. <i>Conclusion</i>: ASA tools show promise for automated analysis and modification of children’s speech production within assessment and therapeutic applications. Further work is needed to train automated systems with larger samples of speech to increase accuracy for assessment and therapeutic feedback.
DOI: 10.6084/m9.figshare.6808892.v1
title: Automated speech analysis tools for children’s speech production: A systematic literature review

description: <i>Purpose</i>: A systematic search and review of published studies was conducted on the use of automated speech analysis (ASA) tools for analysing and modifying speech of typically-developing children learning a foreign language and children with speech sound disorders to determine (i) types, attributes, and purposes of ASA tools being used; (ii) accuracy against human judgment; and (iii) performance as therapeutic tools. <i>Method</i>: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were applied. Across nine databases, 32 articles published between January 2007 and December 2016 met inclusion criteria: (i) focussed on children’s speech; (ii) tools used for speech analysis or modification; and (iii) reporting quantitative data on accuracy. <i>Result</i>: Eighteen ASA tools were identified. These met the clinical threshold of 80% agreement with human judgment when used as predictors of intelligibility, impairment severity, or error category. Tool accuracy was typically &lt;80% accuracy for words containing mispronunciations. ASA tools have been used effectively to improve to children’s foreign language pronunciation. <i>Conclusion</i>: ASA tools show promise for automated analysis and modification of children’s speech production within assessment and therapeutic applications. Further work is needed to train automated systems with larger samples of speech to increase accuracy for assessment and therapeutic feedback.
DOI: 10.6084/m9.figshare.6808682
title: Co-exposure to silver nanoparticles and cadmium induce metabolic adaptation in HepG2 cells

description: Although multiple studies have reported the toxicological effects and underlying mechanisms of toxicity of silver nanoparticles (AgNP) in a variety of organisms, the interactions of AgNP with environmental contaminants such as cadmium are poorly understood. We used biochemical assays and mass spectrometry-based proteomics to assess the cellular and molecular effects induced by a co-exposure of HepG2 cells to AgNP and cadmium. Cell viability and energy homeostasis were slightly affected after a 4-h exposure to AgNP, cadmium, or a combination of the two; these endpoints were substantially altered after a 24-h co-exposure to AgNP and cadmium, while exposure to one of the two contaminants led only to minor changes. Proteomics analysis followed the same trend: while a 4-h exposure induced minor protein deregulation, a 24-h exposure to a combination of AgNP and cadmium deregulated 43% of the proteome. The toxicity induced by a combined exposure to AgNP and cadmium involved (1) inactivation of Nrf2, resulting in downregulation of antioxidant defense and proteasome-related proteins, (2) metabolic adaptation and ADP/ATP imbalance, and (3) increased protein synthesis possibly to reestablish homeostasis. The adaptation strategy was not sufficient to restore ADP/ATP homeostasis and to avoid cell death.
DOI: 10.6084/m9.figshare.6808682.v1
title: Co-exposure to silver nanoparticles and cadmium induce metabolic adaptation in HepG2 cells

description: Although multiple studies have reported the toxicological effects and underlying mechanisms of toxicity of silver nanoparticles (AgNP) in a variety of organisms, the interactions of AgNP with environmental contaminants such as cadmium are poorly understood. We used biochemical assays and mass spectrometry-based proteomics to assess the cellular and molecular effects induced by a co-exposure of HepG2 cells to AgNP and cadmium. Cell viability and energy homeostasis were slightly affected after a 4-h exposure to AgNP, cadmium, or a combination of the two; these endpoints were substantially altered after a 24-h co-exposure to AgNP and cadmium, while exposure to one of the two contaminants led only to minor changes. Proteomics analysis followed the same trend: while a 4-h exposure induced minor protein deregulation, a 24-h exposure to a combination of AgNP and cadmium deregulated 43% of the proteome. The toxicity induced by a combined exposure to AgNP and cadmium involved (1) inactivation of Nrf2, resulting in downregulation of antioxidant defense and proteasome-related proteins, (2) metabolic adaptation and ADP/ATP imbalance, and (3) increased protein synthesis possibly to reestablish homeostasis. The adaptation strategy was not sufficient to restore ADP/ATP homeostasis and to avoid cell death.
DOI: 10.6084/m9.figshare.6808580
title: Gold nanoparticles ingested by oyster larvae are internalized by cells through an alimentary endocytic pathway

description: The biological fate of nanoparticles (NPs) taken up by organisms from their environment is a crucial issue for assessing ecological hazard. Despite its importance, it has scarcely been addressed due to the technical difficulties of doing so in whole organism <i>in vivo</i> studies. Here, by using transmission electron microscopy and energy dispersive X-ray spectroscopy (TEM-EDS), we describe the key aspects that characterize the interaction between an aquatic organism of global ecological and economic importance, the early larval stage of the Japanese oyster (<i>Crassostrea gigas</i>), and model gold NPs dispersed in their environment. The small size of the model organism allowed for a high-throughput visualization of the subcellular distribution of NPs, providing a comprehensive and robust picture of the route of uptake, mechanism of cellular permeation, and the pathways of clearance counterbalancing bioaccumulation. We show that NPs are ingested by larvae and penetrate cells through alimentary pinocytic/phagocytic mechanisms. They undergo intracellular digestion and storage inside residual bodies, before excretion with feces or translocation to phagocytic coelomocytes of the visceral cavity for potential extrusion or further translocation. Our mechanistically-supported findings highlight the potential of oyster larvae and other organisms which feature intracellular digestion processes to be exposed to man-made NPs and thus any risks associated with their inherent toxicity.
DOI: 10.6084/m9.figshare.6808580.v1
title: Gold nanoparticles ingested by oyster larvae are internalized by cells through an alimentary endocytic pathway

description: The biological fate of nanoparticles (NPs) taken up by organisms from their environment is a crucial issue for assessing ecological hazard. Despite its importance, it has scarcely been addressed due to the technical difficulties of doing so in whole organism <i>in vivo</i> studies. Here, by using transmission electron microscopy and energy dispersive X-ray spectroscopy (TEM-EDS), we describe the key aspects that characterize the interaction between an aquatic organism of global ecological and economic importance, the early larval stage of the Japanese oyster (<i>Crassostrea gigas</i>), and model gold NPs dispersed in their environment. The small size of the model organism allowed for a high-throughput visualization of the subcellular distribution of NPs, providing a comprehensive and robust picture of the route of uptake, mechanism of cellular permeation, and the pathways of clearance counterbalancing bioaccumulation. We show that NPs are ingested by larvae and penetrate cells through alimentary pinocytic/phagocytic mechanisms. They undergo intracellular digestion and storage inside residual bodies, before excretion with feces or translocation to phagocytic coelomocytes of the visceral cavity for potential extrusion or further translocation. Our mechanistically-supported findings highlight the potential of oyster larvae and other organisms which feature intracellular digestion processes to be exposed to man-made NPs and thus any risks associated with their inherent toxicity.
DOI: 10.6084/m9.figshare.6808388
title: Additional file 1: of Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

description: Table S1. (A) Correlation between predicted activity and target site conservation. (B) Correlation between measured and predicted activity. (C) Correlation between measured activity and target site prevalence. Table S2. List of highly conserved, subtype-specific triplet/paired gRNAs. Table S3. Analysis of the number of guides needed to target all available LANL sequences for LTR, gag, and pol for group M and subtypes Aâ C. Table S4. GFP knockdown with candidate guides tested using fluorescent reporter. Table S5. Sequences used in intra-host analysis. Table S6. Guides from globally conserved list (using LANL sequences) that have matches in patient sequence. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.6808388.v1
title: Additional file 1: of Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

description: Table S1. (A) Correlation between predicted activity and target site conservation. (B) Correlation between measured and predicted activity. (C) Correlation between measured activity and target site prevalence. Table S2. List of highly conserved, subtype-specific triplet/paired gRNAs. Table S3. Analysis of the number of guides needed to target all available LANL sequences for LTR, gag, and pol for group M and subtypes Aâ C. Table S4. GFP knockdown with candidate guides tested using fluorescent reporter. Table S5. Sequences used in intra-host analysis. Table S6. Guides from globally conserved list (using LANL sequences) that have matches in patient sequence. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.6808352
title: Additional file 1: of Predictors of consent to cell line creation and immortalisation in a South African schizophrenia genomics study

description: Database. The original database used for analysis in this manuscript. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.6808352.v1
title: Additional file 1: of Predictors of consent to cell line creation and immortalisation in a South African schizophrenia genomics study

description: Database. The original database used for analysis in this manuscript. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.6808211
title: Additional file 2: of Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms

description: Table S2. Per sample total read counts and absolute read counts for each species and genus detected by QIIME analysis of raw fasta files. Tab 1 (otu_table_L6) is all taxonomic assignments down to genus level. Tab 2 (otu_table_L7) is all taxonomic assignments down to species level. Tab 3 (CompHOMINGS-qiime) has total, matched, and unmatched read counts for each biofilm for HOMINGS and QIIME analysis, as well as the total number of species detected by each method. (XLSX 135 kb)