cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6590903.v2
title: DNMT1 modulates interneuron morphology by regulating <i>Pak6</i> expression through crosstalk with histone modifications

description: Epigenetic mechanisms of gene regulation, including DNA methylation and histone modifications, call increasing attention in the context of development and human health. Thereby, interactions between DNA methylating enzymes and histone modifications tremendously multiply the spectrum of potential regulatory functions. Epigenetic networks are critically involved in the establishment and functionality of neuronal circuits that are composed of gamma-aminobutyric acid (GABA)-positive inhibitory interneurons and excitatory principal neurons in the cerebral cortex. We recently reported a crucial role of the DNA methyltransferase 1 (DNMT1) during the migration of immature POA-derived cortical interneurons by promoting the migratory morphology through repression of <i>Pak6</i>. However, the DNMT1-dependent regulation of <i>Pak6</i> expression appeared to occur independently of direct DNA methylation. Here, we show that in addition to its DNA methylating activity, DNMT1 can act on gene transcription by modulating permissive H3K4 and repressive H3K27 trimethylation in developing inhibitory interneurons, similar to what was found in other cell types. In particular, the transcriptional control of <i>Pak6</i>, interactions of DNMT1 with the Polycomb-repressor complex 2 (PCR2) core enzyme EZH2, mediating repressive H3K27 trimethylations at regulatory regions of the <i>Pak6</i> gene locus. Similar to what was observed upon <i>Dnmt1</i> depletion, inhibition of EZH2 caused elevated <i>Pak6</i> expression levels accompanied by increased morphological complexity, which was rescued by siRNA-mediated downregulation of <i>Pak6</i> expression. Together, our data emphasise the relevance of DNMT1-dependent crosstalk with histone tail methylation for transcriptional control of genes like <i>Pak6</i> required for proper cortical interneuron migration.
DOI: 10.6084/m9.figshare.6590903.v1
title: DNMT1 modulates interneuron morphology by regulating <i>Pak6</i> expression through crosstalk with histone modifications

description: Epigenetic mechanisms of gene regulation, including DNA methylation and histone modifications, call increasing attention in the context of development and human health. Thereby, interactions between DNA methylating enzymes and histone modifications tremendously multiply the spectrum of potential regulatory functions. Epigenetic networks are critically involved in the establishment and functionality of neuronal circuits that are composed of gamma-aminobutyric acid (GABA)-positive inhibitory interneurons and excitatory principal neurons in the cerebral cortex. We recently reported a crucial role of the DNA methyltransferase 1 (DNMT1) during the migration of immature POA-derived cortical interneurons by promoting the migratory morphology through repression of <i>Pak6</i>. However, the DNMT1-dependent regulation of <i>Pak6</i> expression seemed independent of direct DNA methylation. Here, we show that, in addition to its DNA methylating activity, DNMT1 can act on gene transcription by modulating permissive H3K4 and repressive H3K27 trimethylation in developing inhibitory interneurons similar to what was found in other cell types. In particular, the transcriptional control of <i>Pak6</i> was accomplished by interactions of DNMT1 with the Polycomb-repressor complex 2 (PCR2) core enzyme EZH2, mediating repressive H3K27 trimethylation at regulatory regions of the <i>Pak6</i> gene locus. Similar to what was observed upon <i>Dnmt1</i> depletion, inhibition of EZH2 caused elevated <i>Pak6</i> expression levels accompanied by increased morphological complexity, which was rescued by siRNA-mediated downregulation of <i>Pak6</i> expression. Together, our data emphasize the important function of DNMT1 in promoting interneuron migration through the transcriptional control over key genes like <i>Pak6</i> achieved by a crosstalk with histone tail methylation.
DOI: 10.6084/m9.figshare.6590867
title: Insights into how predator diversity, population density and habitat type may affect defensive behaviour in a Mediterranean lizard

description: Various factors may alter anti-predatory responses among conspecifics. Here we assess some of these factors using three populations of a Mediterranean lizard (<i>Acanthodactylus schreiberi</i>) in Cyprus that differ in their habitat type, predator diversity and population density. We expected that predation would affect flight initiation distance (FID; the approach distance allowed to an observer before the lizard flees), escape distance (ED; the distance covered by the lizard from the point an escape attempt starts to the first place the lizard stops) and tail autotomy (autotomy rates, economy of autotomy, post-autotomy tail movement). We also predicted that juveniles, being more exposed to predators, would be more effective in their defensive responses. Our findings suggest that predation and population density appear to be associated with most autotomy traits but were not associated with FID and ED, which are better explained by refuge availability. The only ontogenetic difference was detected in the economy of autotomy: juveniles are more prone to autotomise, possibly because they do not experience such high costs as tailless adult individuals. Our results suggest that anti-predatory responses are influenced by a variety of factors. Unravelling the compound effects of all the factors involved should be the focus of future research.
DOI: 10.6084/m9.figshare.6590867.v1
title: Insights into how predator diversity, population density and habitat type may affect defensive behaviour in a Mediterranean lizard

description: Various factors may alter anti-predatory responses among conspecifics. Here we assess some of these factors using three populations of a Mediterranean lizard (<i>Acanthodactylus schreiberi</i>) in Cyprus that differ in their habitat type, predator diversity and population density. We expected that predation would affect flight initiation distance (FID; the approach distance allowed to an observer before the lizard flees), escape distance (ED; the distance covered by the lizard from the point an escape attempt starts to the first place the lizard stops) and tail autotomy (autotomy rates, economy of autotomy, post-autotomy tail movement). We also predicted that juveniles, being more exposed to predators, would be more effective in their defensive responses. Our findings suggest that predation and population density appear to be associated with most autotomy traits but were not associated with FID and ED, which are better explained by refuge availability. The only ontogenetic difference was detected in the economy of autotomy: juveniles are more prone to autotomise, possibly because they do not experience such high costs as tailless adult individuals. Our results suggest that anti-predatory responses are influenced by a variety of factors. Unravelling the compound effects of all the factors involved should be the focus of future research.
DOI: 10.6084/m9.figshare.6590849
title: Athlete_MetaData_for_Microbiome-MBIO-D-18-00326.zip

description: Support for Manuscript Microbiome-MBIO-D-18-00326 Lauren Petersen et al 2018<br>
DOI: 10.6084/m9.figshare.6590849.v1
title: Athlete_MetaData_for_Microbiome-MBIO-D-18-00326.zip

description: Support for Manuscript Microbiome-MBIO-D-18-00326 Lauren Petersen et al 2018<br>
DOI: 10.6084/m9.figshare.6590846.v1
title: Introducing Agroecology Presentations

description: These presentations accompany the Introducing Agroecology website: https://trec-agroecology.github.io/introducing-agroecology/<br>The presentations and website are indented for Extension workshops and public outreach developed by the Agroecology Lab (https://trec.ifas.ufl.edu/agroecology/) at the Tropical Research and Education Center of the University of Florida<br>
DOI: 10.6084/m9.figshare.6590426
title: Phylogenetic and population studies of geophytic <i>Euphorbia</i> species (subgenus <i>Euphorbia</i>) from some deciduous forests and hill top plateaus in India

description: Geophytic <i>Euphorbia</i> species are distributed across four sections in subgenus <i>Euphorbia</i> of genus <i>Euphorbia</i>. At least nine Indian geophytic <i>Euphorbia</i> species have been identified, but delimitation of these species is controversial. Phylogenetic studies using nuclear ribosomal internal transcribed spacers (nrITS) and <i>matK</i> sequences showed that the Indian geophytic <i>Euphorbia</i> species lie within the section <i>Euphorbia</i> clade that includes African and Indian non-geophytic species. Ribotype/ haplotype analysis of nrITS and <i>matK</i> sequences revealed that the populations of <i>Euphorbia fusiformis</i> and <i>Euphorbia nana</i> could not be distinguished on this basis. Population studies based on nrITS sequences showed significant gene differentiation between the populations from different localities. The Indian geophytic <i>Euphorbia</i> species showed morphological variation in their leaf and cyathial characters, which correlated with the variation in soil composition of their habitats. Our studies suggest that local adaptation and phenotypic plasticity are responsible for taxonomic ambiguities in the classification of Indian geophytic <i>Euphorbia</i> species.
DOI: 10.6084/m9.figshare.6590426.v1
title: Phylogenetic and population studies of geophytic <i>Euphorbia</i> species (subgenus <i>Euphorbia</i>) from some deciduous forests and hill top plateaus in India

description: Geophytic <i>Euphorbia</i> species are distributed across four sections in subgenus <i>Euphorbia</i> of genus <i>Euphorbia</i>. At least nine Indian geophytic <i>Euphorbia</i> species have been identified, but delimitation of these species is controversial. Phylogenetic studies using nuclear ribosomal internal transcribed spacers (nrITS) and <i>matK</i> sequences showed that the Indian geophytic <i>Euphorbia</i> species lie within the section <i>Euphorbia</i> clade that includes African and Indian non-geophytic species. Ribotype/ haplotype analysis of nrITS and <i>matK</i> sequences revealed that the populations of <i>Euphorbia fusiformis</i> and <i>Euphorbia nana</i> could not be distinguished on this basis. Population studies based on nrITS sequences showed significant gene differentiation between the populations from different localities. The Indian geophytic <i>Euphorbia</i> species showed morphological variation in their leaf and cyathial characters, which correlated with the variation in soil composition of their habitats. Our studies suggest that local adaptation and phenotypic plasticity are responsible for taxonomic ambiguities in the classification of Indian geophytic <i>Euphorbia</i> species.
DOI: 10.6084/m9.figshare.6588164
title: Signal-anchor sequences are an essential factor for the Golgi-plasma membrane localization of type II membrane proteins

description: Despite studies of the mechanism underlying the intracellular localization of membrane proteins, the specific mechanisms by which each membrane protein localizes to the endoplasmic reticulum, Golgi apparatus, and plasma membrane in the secretory pathway are unclear. In this study, a discriminant analysis of endoplasmic reticulum, Golgi apparatus and plasma membrane-localized type II membrane proteins was performed using a position-specific scoring matrix derived from the amino acid propensity of the sequences around signal-anchors. The possibility that the sequence around the signal-anchor is a factor for identifying each localization group was evaluated. The discrimination accuracy between the Golgi apparatus and plasma membrane-localized type II membrane proteins was as high as 90%, indicating that, in addition to other factors, the sequence around signal-anchor is an essential component of the selection mechanism for the Golgi and plasma membrane localization. These results may improve the use of membrane proteins for drug delivery and therapeutic applications. The sequence around the signal-anchor is an essential component of the selection mechanism for Golgi and plasma membrane protein localization.
DOI: 10.6084/m9.figshare.6588164.v1
title: Signal-anchor sequences are an essential factor for the Golgi-plasma membrane localization of type II membrane proteins

description: Despite studies of the mechanism underlying the intracellular localization of membrane proteins, the specific mechanisms by which each membrane protein localizes to the endoplasmic reticulum, Golgi apparatus, and plasma membrane in the secretory pathway are unclear. In this study, a discriminant analysis of endoplasmic reticulum, Golgi apparatus and plasma membrane-localized type II membrane proteins was performed using a position-specific scoring matrix derived from the amino acid propensity of the sequences around signal-anchors. The possibility that the sequence around the signal-anchor is a factor for identifying each localization group was evaluated. The discrimination accuracy between the Golgi apparatus and plasma membrane-localized type II membrane proteins was as high as 90%, indicating that, in addition to other factors, the sequence around signal-anchor is an essential component of the selection mechanism for the Golgi and plasma membrane localization. These results may improve the use of membrane proteins for drug delivery and therapeutic applications. The sequence around the signal-anchor is an essential component of the selection mechanism for Golgi and plasma membrane protein localization.
DOI: 10.6084/m9.figshare.6588023
title: Athlete_Data_for_Microbiome-MBIO-D-18-00326.tar.gz

description: Support for Manuscript Microbiome-MBIO-D-18-00326 Lauren Petersen et al 2018<br>
DOI: 10.6084/m9.figshare.6588023.v1
title: Athlete_Data_for_Microbiome-MBIO-D-18-00326.tar.gz

description: Support for Manuscript Microbiome-MBIO-D-18-00326 Lauren Petersen et al 2018<br>
DOI: 10.6084/m9.figshare.6587684
title: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals

description: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals. <br><br>Data files:Aconitase measurements = acon.csvAconitase standard = acon_calib.csvSummary Stats of Aconitase measurements = acon summary for fig.csv<br>Protein measurements = protein.csvProtein standard = protein_calib.csvSurvival data = surv.csvIron measurements = iron.csv<br>
DOI: 10.6084/m9.figshare.6587684.v1
title: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals

description: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals. <br><br>Data files:Aconitase measurements = acon.csvAconitase standard = acon_calib.csvProtein measurements = protein.csvProtein standard = protein_calib.csvSurvival data = surv.csvIron measurements = iron.csv<br>
DOI: 10.6084/m9.figshare.6587684.v2
title: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals

description: Data and Code from: An in vivo test of the biologically relevant roles of carotenoids as antioxidants in animals. <br><br>Data files:Aconitase measurements = acon.csvAconitase standard = acon_calib.csvSummary Stats of Aconitase measurements = acon summary for fig.csv<br>Protein measurements = protein.csvProtein standard = protein_calib.csvSurvival data = surv.csvIron measurements = iron.csv<br>
DOI: 10.6084/m9.figshare.6587666
title: Raw data of spiked and unspiked water samples from Formulation of chelating agent with surfactant in cloud point extraction for the extraction of methylphenol in water

description: Cloud point extraction (CPE) is a separation and preconcentration of non-ionic surfactant from one liquid phase to another. In this study, Sylgard-309 and three different types of additives for CPE, namely CPE-Sylgard, CPE-Sylgard-BMIMBr and CPE-Sylgard-GLDA, are investigated to extract methylphenol from water samples. The methylphenols are well separated on a reversed-phase high-performance liquid chromatography (HPLC) with isocratic elution of acetonitrile:water; 60:40 (v/v) and detection at 260 nm. The optimized parameters of the effect of salt, surfactant, temperature, time of extraction, pH, interference study and the performance of different additives on methylphenol extraction are investigated. CPE-Sylgard-GLDA is chosen because it gives us the high and good peak area compared with CPE-Sylgard and CPE-Sylgard-BMIMBr. The recovery extractions of CPE-Sylgard-GLDA are obtained in the range of 80–99% as the percentage of relative standard deviation (RSD) is less than 10. The LOD and LOQ are 0.05 ppm and 0.18 ppm, respectively. The method developed for CPE-Sylgard-GLDA coupled with HPLC is feasible for the determination of methylphenol because it is simple, effective, cheap, and produces a high percentage of recovery.
DOI: 10.6084/m9.figshare.6587666.v1
title: Raw data of spiked and unspiked water samples from Formulation of chelating agent with surfactant in cloud point extraction for the extraction of methylphenol in water

description: Cloud point extraction (CPE) is a separation and preconcentration of non-ionic surfactant from one liquid phase to another. In this study, Sylgard-309 and three different types of additives for CPE, namely CPE-Sylgard, CPE-Sylgard-BMIMBr and CPE-Sylgard-GLDA, are investigated to extract methylphenol from water samples. The methylphenols are well separated on a reversed-phase high-performance liquid chromatography (HPLC) with isocratic elution of acetonitrile:water; 60:40 (v/v) and detection at 260 nm. The optimized parameters of the effect of salt, surfactant, temperature, time of extraction, pH, interference study and the performance of different additives on methylphenol extraction are investigated. CPE-Sylgard-GLDA is chosen because it gives us the high and good peak area compared with CPE-Sylgard and CPE-Sylgard-BMIMBr. The recovery extractions of CPE-Sylgard-GLDA are obtained in the range of 80–99% as the percentage of relative standard deviation (RSD) is less than 10. The LOD and LOQ are 0.05 ppm and 0.18 ppm, respectively. The method developed for CPE-Sylgard-GLDA coupled with HPLC is feasible for the determination of methylphenol because it is simple, effective, cheap, and produces a high percentage of recovery.
DOI: 10.6084/m9.figshare.6587519
title: Faecal secretogranin and chromogranin levels persist over time and are unrelated to disease history and outcome in patients with ulcerative colitis

description: <b>Objectives</b>: Chromogranins (Cg) and secretogranins (Sg) are expressed by endocrine cells and may be important for the pathophysiology of ulcerative colitis (UC). We investigated dynamics of faecal granin expression in patients with UC during a period of 18 months, both during remission and relapse, and association to disease outcome the following 3 years. <b>Materials and methods</b>: Secretoneurin (SN), Sg3, CgA and CgB were measured in three to seven serial faecal samples from UC patients who did not (n = 20) or did (n = 20) relapse during study time. All patients were in remission at baseline and disease characteristic were monitored during sampling and 3 years after the final sample. <b>Results</b>: Faecal SN, Sg3, CgA and CgB levels showed no association to patient characteristic or disease history at baseline. Faecal granin levels showed low intra-patient variability and levels stayed constant during short and long intervals at remission, did not alter during or after clinical relapse and were not associated to medical therapy. In contrast, high inter-patient variability was detected and multivariate analysis revealed three distinct patient groups, where extensive disease was more common in patients with high levels of SN and CgA as compared to patients with low levels of all granins or patients with high levels of Sg3 and CgB. These patient subgroups did, however, not differ in patient characteristics, disease history or future disease course. <b>Conclusions</b>: Faecal granin levels are stable over time but are unrelated to disease history, activity and outcome and are thus not valuable markers for disease activity in UC patients.
DOI: 10.6084/m9.figshare.6587519.v1
title: Faecal secretogranin and chromogranin levels persist over time and are unrelated to disease history and outcome in patients with ulcerative colitis

description: <b>Objectives</b>: Chromogranins (Cg) and secretogranins (Sg) are expressed by endocrine cells and may be important for the pathophysiology of ulcerative colitis (UC). We investigated dynamics of faecal granin expression in patients with UC during a period of 18 months, both during remission and relapse, and association to disease outcome the following 3 years. <b>Materials and methods</b>: Secretoneurin (SN), Sg3, CgA and CgB were measured in three to seven serial faecal samples from UC patients who did not (n = 20) or did (n = 20) relapse during study time. All patients were in remission at baseline and disease characteristic were monitored during sampling and 3 years after the final sample. <b>Results</b>: Faecal SN, Sg3, CgA and CgB levels showed no association to patient characteristic or disease history at baseline. Faecal granin levels showed low intra-patient variability and levels stayed constant during short and long intervals at remission, did not alter during or after clinical relapse and were not associated to medical therapy. In contrast, high inter-patient variability was detected and multivariate analysis revealed three distinct patient groups, where extensive disease was more common in patients with high levels of SN and CgA as compared to patients with low levels of all granins or patients with high levels of Sg3 and CgB. These patient subgroups did, however, not differ in patient characteristics, disease history or future disease course. <b>Conclusions</b>: Faecal granin levels are stable over time but are unrelated to disease history, activity and outcome and are thus not valuable markers for disease activity in UC patients.
DOI: 10.6084/m9.figshare.6587153
title: Metabolome profiling of fish muscle tissue exposed to benzo[a]pyrene using in vivo solid-phase microextraction

description: This is the raw data and R script for this research.
DOI: 10.6084/m9.figshare.6587153.v1
title: Metabolome profiling of fish muscle tissue exposed to benzo[a]pyrene using in vivo solid-phase microextraction

description: This is the raw data and R script for this research.
DOI: 10.6084/m9.figshare.6587141
title: A systematic review and combined analysis of therapeutic drug monitoring studies for oral paliperidone

description: <b>Introduction</b>: This article includes a combined analysis of therapeutic drug monitoring (TDM) studies and a review of the marketer’s data on pharmacological mechanisms. <b>Areas covered</b>: An article search led to the inclusion of 21 paliperidone studies in the systematic review plus 2 case reports. Paliperidone clearance was calculated from: 1) steady-state studies using concentration/dose (C/D) ratios, and 2) single-dose studies describing 24-h area under the curve calculations. The marketed extended-release formulation has 28% bioavailability. Calculated mean C/D ratios (ng/ml/mg/d) were: 1) 4.09 in 6 studies of 221 non-Korean and non-geriatric adult patients, 2) 2.59 in 2 studies of 100 Korean adult patients, and 3) 6.89 in 1 study with 15 elderly Japanese patients. The limited drug–drug interaction studies indicated that carbamazepine is a clinically relevant inducer requiring three times the dosage, and that valproate, probably an inhibitor, requires half the dosage. Renal impairment markedly decreased paliperidone elimination, and other antipsychotics should be considered. <b>Expert Commentary</b>: We recommend more use of: 1) paliperidone TDM in clinical practice, 2) TDM when moving from oral to long-acting paliperidone, 3) better designs for paliperidone TDM studies, 4) laboratory studies on paliperidone pharmacokinetic mechanisms, and 5) TDM studies comparing paliperidone and risperidone dosing.