cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9891446
title: Metadata record for: A dataset of continuous affect annotations and physiological signals for emotion analysis

description: This dataset contains key characteristics about the data described in the Data Descriptor A dataset of continuous affect annotations and physiological signals for emotion analysis. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br> <br> <br> <br>
DOI: 10.6084/m9.figshare.9891449
title: Dataset from Transposable temperate phages promote the evolution of divergent social strategies in <i>Pseudomonas aeruginosa</i> populations

description: Results from pyoverdine assays and density over the course of the evolution experiment
DOI: 10.6084/m9.figshare.9891449.v1
title: Dataset from Transposable temperate phages promote the evolution of divergent social strategies in <i>Pseudomonas aeruginosa</i> populations

description: Results from pyoverdine assays and density over the course of the evolution experiment
DOI: 10.6084/m9.figshare.9891446.v2
title: Metadata record for: A dataset of continuous affect annotations and physiological signals for emotion analysis

description: This dataset contains key characteristics about the data described in the Data Descriptor A dataset of continuous affect annotations and physiological signals for emotion analysis. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br> <br> <br> <br>
DOI: 10.6084/m9.figshare.9891416
title: Allele assignments obtained by our Nanopore workflow and by Sanger sequencing

description: Allele assignments obtained by our Nanopore workflow and by Sanger sequencing
DOI: 10.6084/m9.figshare.9891431
title: NIAB Wheat pedigree. Helium categorical info format (updated 12.09.19).txt

description: Input files for use with Helium crop pedigree visualisation software (https://github.com/cardinalb/helium-docs/wiki/Download-Helium). This dataset is an updated and edited version of the original pedigree published in (https://doi.org/10.1371/journal.pbio.3000071).<br><br>
DOI: 10.6084/m9.figshare.9891446.v1
title: Metadata record for: A dataset of continuous affect annotations and physiological signals for emotion analysis

description: This dataset contains key characteristics about the data described in the Data Descriptor A dataset of continuous affect annotations and physiological signals for emotion analysis. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.9891398
title: PASS-based prediction of metabolites detection in biological systems

description: Metabolite identification is an essential part of the drug discovery and development process. Experimental methods allow identifying metabolites and estimating their relative amount, but they require cost-intensive and time-consuming techniques. Computational methods for metabolite prediction are devoid of these shortcomings and may be applied at the early stage of drug discovery. In this study, we investigated the possibility of creating SAR models for the prediction of the qualitative metabolite yield (‘major’, ‘minor’, ”trace” and ”negligible”) depending on species and biological experimental systems. In addition, we have created models for prediction of xenobiotic excretion depending on its administration route for different species. The prediction is based on an algorithm of naïve Bayes classifier implemented in PASS software. The average accuracy of prediction was 0.91 for qualitative metabolite yield prediction and 0.89 for prediction of xenobiotic excretion. The created models were included as a component of MetaTox web application, which allows predicting the xenobiotic metabolism pathways (http://www.way2drug.com/mg).
DOI: 10.6084/m9.figshare.9891398.v1
title: PASS-based prediction of metabolites detection in biological systems

description: Metabolite identification is an essential part of the drug discovery and development process. Experimental methods allow identifying metabolites and estimating their relative amount, but they require cost-intensive and time-consuming techniques. Computational methods for metabolite prediction are devoid of these shortcomings and may be applied at the early stage of drug discovery. In this study, we investigated the possibility of creating SAR models for the prediction of the qualitative metabolite yield (‘major’, ‘minor’, ”trace” and ”negligible”) depending on species and biological experimental systems. In addition, we have created models for prediction of xenobiotic excretion depending on its administration route for different species. The prediction is based on an algorithm of naïve Bayes classifier implemented in PASS software. The average accuracy of prediction was 0.91 for qualitative metabolite yield prediction and 0.89 for prediction of xenobiotic excretion. The created models were included as a component of MetaTox web application, which allows predicting the xenobiotic metabolism pathways (http://www.way2drug.com/mg).
DOI: 10.6084/m9.figshare.9891371
title: Teachers: Beliefs and practice change

description: The excel documents contain data sets for the beliefs rating provided by teachers participating in LTMI and those in an INSET training programme taking place during the same period. Analysis shows beliefsaccording to three different constructs - transmission, discovery and connectionist (see Askew et al., 1997 for more details about these).<br>The two pdf documents show teachers' practices according to the list of "classroom actions" - both teacher and student actions - and the pen portraits of each of the three case study teachers.<br>
DOI: 10.6084/m9.figshare.9891371.v1
title: Teachers: Beliefs and practice change

description: The excel documents contain data sets for the beliefs rating provided by teachers participating in LTMI and those in an INSET training programme taking place during the same period. Analysis shows beliefsaccording to three different constructs - transmission, discovery and connectionist (see Askew et al., 1997 for more details about these).<br>The pdf document shows teachers' practices according to the list of "classroom actions" - both teacher and student actions.
DOI: 10.6084/m9.figshare.9891317
title: Molecular modelling and dynamics of CA2 missense mutations causative to carbonic anhydrase 2 deficiency syndrome

description: Carbonic anhydrase 2 (CA2) enzyme deficiency caused by CA2 gene mutations is an inherited disorder characterized by symptoms like osteopetrosis, renal tubular acidosis, and cerebral calcification. This study has collected the CA2 deficiency causal missense mutations and assessed their pathogenicity using diverse computational programs. The 3D protein models for all missense mutations were built, and analyzed for structural divergence, protein stability, and molecular dynamics properties. We found M-CAP as the most sensitive prediction method to measure the deleterious potential of CA2 missense mutations. Free energy dynamics of tertiary structure models of CA2 mutants with DUET, mCSM, and SDM based consensus methods predicted only 50% of the variants as destabilizing. Superimposition of native and mutant CA2 models revealed the minor structural fluctuations at the amino acid residue level but not at the whole protein structure level. Near native molecular dynamic simulation analysis indicated that CA2 causative missense variants result in residue level fluctuation pattern in the protein structure. This study expands the understanding of genotype-protein phenotype correlations underlying CA2 variant pathogenicity and presents a potential avenue for modifying the CA2 deficiency by targeting biophysical structural features of CA2 protein. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9891317.v2
title: Molecular modelling and dynamics of CA2 missense mutations causative to carbonic anhydrase 2 deficiency syndrome

description: Carbonic anhydrase 2 (CA2) enzyme deficiency caused by CA2 gene mutations is an inherited disorder characterized by symptoms like osteopetrosis, renal tubular acidosis, and cerebral calcification. This study has collected the CA2 deficiency causal missense mutations and assessed their pathogenicity using diverse computational programs. The 3D protein models for all missense mutations were built, and analyzed for structural divergence, protein stability, and molecular dynamics properties. We found M-CAP as the most sensitive prediction method to measure the deleterious potential of CA2 missense mutations. Free energy dynamics of tertiary structure models of CA2 mutants with DUET, mCSM, and SDM based consensus methods predicted only 50% of the variants as destabilizing. Superimposition of native and mutant CA2 models revealed the minor structural fluctuations at the amino acid residue level but not at the whole protein structure level. Near native molecular dynamic simulation analysis indicated that CA2 causative missense variants result in residue level fluctuation pattern in the protein structure. This study expands the understanding of genotype-protein phenotype correlations underlying CA2 variant pathogenicity and presents a potential avenue for modifying the CA2 deficiency by targeting biophysical structural features of CA2 protein. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9891293
title: Bb_copper rep.xls

description: The <i>in vitro </i>fungicidal effects of six commonly used copper fungicides, namely copper oxide, copper hydroxide, copper oxychloride, copper sulfate, dicopper chloride trihydroxide, and tribasic copper sulfate, on mycelial growth, sporulation and conidial germination of the commercial isolate of <i>Beauveria bassiana </i>(ATCC 74040) were investigated. Mycelial growth at 15 and 25˚C were evaluated on PDA plates containing 100, 75, 50, 25, 12.5, 6.25 and 0% of the recommended application rate of each fungicide. Sporulation and conidial germination were checked at the recommended field dosage rate of tested fungicides at 25˚C.
DOI: 10.6084/m9.figshare.9891284
title: Heritable natural variation of light/dark preference in an outbred zebrafish population

description: Anxiety is a fear-like response to stimuli perceived to be threatening. Excessive or uncontrollable anxiety is a debilitating psychiatric disorder which affects many people throughout their lifetime. In unravelling the complex genetic and environmental regulations of anxiety-like phenotypes, models measuring the natural dark avoidance of larval zebrafish have shed light on the individual variation and heritability of this anxiety-related trait. Using the light/dark choice paradigm and selective breeding, this study aims to validate previous findings of the variable (VDA) and strong dark aversion (SDA) heritability in AB-WT larval zebrafish using the outbred zebrafish strain EK, which offers more genetic diversity to aid in future molecular mapping efforts. 190 larvae (6 days post fertilization [dpf] and 7 dpf) were tested across four trials and divided into variable (VDA), medium (MDA) and strong (SDA) dark aversion for further in-crosses. VDA and MDA larvae became more explorative with time, whereas SDA larvae rarely left the preferred light zone. The SDA and VDA in-crosses significantly increased the respective phenotypes in the second generation of larvae, whereas VDA × MDA inter-crosses did not. For the second-generation SDA cohort, dark aversion correlated with increased thigmotaxis, which reinforces SDA as an anxiety-like phenotype. Our finding that the dark aversion trait and SDA and VDA phenotypes are heritable in an outbred zebrafish population lays an important foundation for future studies of genetic underpinnings using whole-genome mapping methods. This conserved fear/anxiety-like response in a highly accessible model organism also allows for further pharmacological and behavioral studies to elucidate the etiology of anxiety and the search for novel therapeutics for anxiety disorders.
DOI: 10.6084/m9.figshare.9891293.v1
title: Bb_copper rep.xls

description: The <i>in vitro </i>fungicidal effects of six commonly used copper fungicides, namely copper oxide, copper hydroxide, copper oxychloride, copper sulfate, dicopper chloride trihydroxide, and tribasic copper sulfate, on mycelial growth, sporulation and conidial germination of the commercial isolate of <i>Beauveria bassiana </i>(ATCC 74040) were investigated. Mycelial growth at 15 and 25˚C were evaluated on PDA plates containing 100, 75, 50, 25, 12.5, 6.25 and 0% of the recommended application rate of each fungicide. Sporulation and conidial germination were checked at the recommended field dosage rate of tested fungicides at 25˚C.
DOI: 10.6084/m9.figshare.9891260
title: Epidemiology of viral hepatitis B and C in Punjab, Pakistan: a multi-center cross-sectional study, 2017-18 (Extended Data File)

description: This is an underlying data sheet for the research work entitled " <br>Epidemiology of viral hepatitis B and C in Punjab, Pakistan: a multi-center cross-sectional study, 2017-18"
DOI: 10.6084/m9.figshare.9891260.v1
title: Epidemiology of viral hepatitis B and C in Punjab, Pakistan: a multi-center cross-sectional study, 2017-18 (Extended Data File)

description: This is an underlying data sheet for the research work entitled " <br>Epidemiology of viral hepatitis B and C in Punjab, Pakistan: a multi-center cross-sectional study, 2017-18"
DOI: 10.6084/m9.figshare.9891284.v2
title: Heritable natural variation of light/dark preference in an outbred zebrafish population

description: Anxiety is a fear-like response to stimuli perceived to be threatening. Excessive or uncontrollable anxiety is a debilitating psychiatric disorder which affects many people throughout their lifetime. In unravelling the complex genetic and environmental regulations of anxiety-like phenotypes, models measuring the natural dark avoidance of larval zebrafish have shed light on the individual variation and heritability of this anxiety-related trait. Using the light/dark choice paradigm and selective breeding, this study aims to validate previous findings of the variable (VDA) and strong dark aversion (SDA) heritability in AB-WT larval zebrafish using the outbred zebrafish strain EK, which offers more genetic diversity to aid in future molecular mapping efforts. 190 larvae (6 days post fertilization [dpf] and 7 dpf) were tested across four trials and divided into variable (VDA), medium (MDA) and strong (SDA) dark aversion for further in-crosses. VDA and MDA larvae became more explorative with time, whereas SDA larvae rarely left the preferred light zone. The SDA and VDA in-crosses significantly increased the respective phenotypes in the second generation of larvae, whereas VDA × MDA inter-crosses did not. For the second-generation SDA cohort, dark aversion correlated with increased thigmotaxis, which reinforces SDA as an anxiety-like phenotype. Our finding that the dark aversion trait and SDA and VDA phenotypes are heritable in an outbred zebrafish population lays an important foundation for future studies of genetic underpinnings using whole-genome mapping methods. This conserved fear/anxiety-like response in a highly accessible model organism also allows for further pharmacological and behavioral studies to elucidate the etiology of anxiety and the search for novel therapeutics for anxiety disorders.
DOI: 10.6084/m9.figshare.9891284.v1
title: Heritable natural variation of light/dark preference in an outbred zebrafish population

description: Anxiety is a fear-like response to stimuli perceived to be threatening. Excessive or uncontrollable anxiety is a debilitating psychiatric disorder which affects many people throughout their lifetime. In unravelling the complex genetic and environmental regulations of anxiety-like phenotypes, models measuring the natural dark avoidance of larval zebrafish have shed light on the individual variation and heritability of this anxiety-related trait. Using the light/dark choice paradigm and selective breeding, this study aims to validate previous findings of the variable (VDA) and strong dark aversion (SDA) heritability in AB-WT larval zebrafish using the outbred zebrafish strain EK, which offers more genetic diversity to aid in future molecular mapping efforts. 190 larvae (6 days post fertilization [dpf] and 7 dpf) were tested across four trials and divided into variable (VDA), medium (MDA) and strong (SDA) dark aversion for further in-crosses. VDA and MDA larvae became more explorative with time, whereas SDA larvae rarely left the preferred light zone. The SDA and VDA in-crosses significantly increased the respective phenotypes in the second generation of larvae, whereas VDA × MDA inter-crosses did not. For the second-generation SDA cohort, dark aversion correlated with increased thigmotaxis, which reinforces SDA as an anxiety-like phenotype. Our finding that the dark aversion trait and SDA and VDA phenotypes are heritable in an outbred zebrafish population lays an important foundation for future studies of genetic underpinnings using whole-genome mapping methods. This conserved fear/anxiety-like response in a highly accessible model organism also allows for further pharmacological and behavioral studies to elucidate the etiology of anxiety and the search for novel therapeutics for anxiety disorders.
DOI: 10.6084/m9.figshare.9891215
title: Dynamic formation and destruction process of stacking fault tetrahedra in single-crystal Ni during nanoscale cryo-rolling

description: Stacking fault tetrahedra (SFTs) are known to form during the rolling process of face-centered cubic metals and to deteriorate their structural properties. However, the atomistic mechanism of formation and destruction of SFTs during such material processing is still unclear. We have performed molecular dynamics simulations of the nanoscale cryo-rolling process for single-crystal nickel and here report the mechanism behind the formation and collapse of SFTs. It is found that SFTs are formed through dissociation of Shockley partial dislocation loops in the specimen. On the other hand, destruction of SFTs occurs under compressive stress and follows an inverse Silcox-Hirsch mechanism.
DOI: 10.6084/m9.figshare.9891200
title: Raw Data Hygiene Training.xlsx

description: Poor hygiene and sanitation continue to be the main problems in Indonesia, especially in congregate settings such as boarding schools. Having the largest Islamic population in Southeast Asia, a growing number of Islamic boarding schools has been observed. This study addresses a typical problem faced, yet interventions in this specific context are lacking. With the school commitment, it is expected that the intervention can be sustained to improve the health status of students in the boarding school (santris).
DOI: 10.6084/m9.figshare.9891215.v1
title: Dynamic formation and destruction process of stacking fault tetrahedra in single-crystal Ni during nanoscale cryo-rolling

description: Stacking fault tetrahedra (SFTs) are known to form during the rolling process of face-centered cubic metals and to deteriorate their structural properties. However, the atomistic mechanism of formation and destruction of SFTs during such material processing is still unclear. We have performed molecular dynamics simulations of the nanoscale cryo-rolling process for single-crystal nickel and here report the mechanism behind the formation and collapse of SFTs. It is found that SFTs are formed through dissociation of Shockley partial dislocation loops in the specimen. On the other hand, destruction of SFTs occurs under compressive stress and follows an inverse Silcox-Hirsch mechanism.
DOI: 10.6084/m9.figshare.9891125
title: Majiang reservoir

description: We have conducted an integrated magnetic, petrographic, and geochemical investigation of several lithological units in the Majiang paleoreservoir to better understand the destruction of hydrocarbon systems. The manuscript has been accepted in the journal of GRL, and we hope to publish our original data here.
DOI: 10.6084/m9.figshare.9891104
title: Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes

description: Hypersexual disorder (HD) was proposed as a diagnosis in the DSM-5 and the classification ‘Compulsive Sexual Behavior Disorder’ is now presented as an impulse-control disorder in ICD-11. HD incorporates several pathophysiological mechanisms; including impulsivity, compulsivity, sexual desire dysregulation and sexual addiction. No previous study investigated HD in a methylation analysis limited to microRNA (miRNA) associated CpG-sites. The genome wide methylation pattern was measured in whole blood from 60 subjects with HD and 33 healthy volunteers using the Illumina EPIC BeadChip. 8,852 miRNA associated CpG-sites were investigated in multiple linear regression analyses of methylation M-values to a binary independent variable of disease state (HD or healthy volunteer), adjusting for optimally determined covariates. Expression levels of candidate miRNAs were investigated in the same individuals for differential expression analysis. Candidate methylation loci were further studied for an association with alcohol dependence in an independent cohort of 107 subjects. Two CpG-sites were borderline significant in HD – cg18222192 (MIR708)(<i>p</i> &lt; 10E-05,<i>p</i><sub>FDR</sub> = 5.81E-02) and cg01299774 (MIR4456)(p &lt; 10E-06, <i>p</i><sub>FDR</sub> = 5.81E-02). MIR4456 was significantly lower expressed in HD in both univariate (p &lt; 0.0001) and multivariate (p &lt; 0.05) analyses. Cg01299774 methylation levels were inversely correlated with expression levels of MIR4456 (p &lt; 0.01) and were also differentially methylated in alcohol dependence (p = 0.026). Gene target prediction and pathway analysis revealed that MIR4456 putatively targets genes preferentially expressed in brain and that are involved in major neuronal molecular mechanisms thought to be relevant for HD, e.g., the oxytocin signalling pathway. In summary, our study implicates a potential contribution of MIR4456 in the pathophysiology of HD by putatively influencing oxytocin signalling.