cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9318851.v3
title: DEN-IM: Dengue virus genotyping from shotgun and targeted metagenomics - HTML reports

description: To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021. The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.The third dataset contains publicly available sequences, both from shotgun and targeted metagenomics, containing 4 CHIKV, 16 ZKV, and 21 YFV samplesThe analyses were executed with the default resources and parameters, with the option to include NCBI references and the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for all analysis are available as compressed files. To open the report in your default browser uncompress the folders and open the pipeline_report.html file inside.
DOI: 10.6084/m9.figshare.9316610
title: SNP set of four Chinese indigenous rabbit breeds

description: <b>Genetic diversity of four Chinese indigenous rabbit breeds</b><br>
DOI: 10.6084/m9.figshare.9316610.v1
title: SNP set of four Chinese indigenous rabbit breeds

description: <b>Genetic diversity of four Chinese indigenous rabbit breeds</b><br>
DOI: 10.6084/m9.figshare.9312206
title: Non-alcoholic fatty liver disease (NAFLD) is associated with dynamic changes in DNA hydroxymethylation

description: Non-alcoholic fatty liver disease (NAFLD) is now the commonest cause of liver disease in developed countries affecting 25–33% of the general population and up to 75% of those with obesity. Recent data suggest that alterations in DNA methylation may be related to NAFLD pathogenesis and progression and we have previously shown that dynamic changes in the cell lineage identifier 5-hydroxymethylcytosine (5hmC) may be important in the pathogenesis of liver disease. We used a model of diet-induced obesity, maintaining male mice on a high-fat diet (HFD) to generate hepatic steatosis. We profiled hepatic gene expression, global and locus-specific 5hmC and additionally investigated the effects of weight loss on the phenotype. HFD led to increased weight gain, fasting hyperglycaemia, glucose intolerance, insulin resistance and hepatic periportal macrovesicular steatosis. Diet-induced hepatic steatosis associated with reversible 5hmC changes at a discrete number of functionally important genes. We propose that 5hmC profiles are a useful signature of gene transcription and a marker of cell state in NAFLD and suggest that 5hmC profiles hold potential as a biomarker of abnormal liver physiology.
DOI: 10.6084/m9.figshare.9312107
title: Supplementary Material for: Age Differences in Emotion Regulation and Facial Muscle Reactivity to Emotional Films

description: <b><i>Background:</i></b> Age-related declines in many cognitive abilities are common in healthy aging. However, the ability to effectively regulate emotions is preserved, and possibly even enhanced, in late adulthood. This capacity has been examined most commonly in relation to low-intensity emotional stimuli that typically involve static pictures. Evidence is suggesting that older adults may become overwhelmed when exposed to emotional cues of heightened intensity. <b><i>Objective:</i></b> In the current study, we assessed whether older adults retain the ability to regulate emotions successfully when exposed to more emotionally evocative (e.g., dynamic) stimuli. <b><i>Methods:</i></b> Young and older adults were instructed to regulate, using expressive suppression, their outward behavioral expression of emotions while viewing dynamic stimuli involving amusing and sad films. Facial reactivity, as indexed using electromyography, self-rated emotional experience, and memory for the stimuli were assessed. <b><i>Results:</i></b> The results showed that, relative to young adults, older adults were unable to suppress <i>zygomaticus</i> (cheek) activity to amusing films or <i>corrugator</i> (brow) reactivity to sad films, which is likely due to their relatively reduced facial muscle reactivity. Expressive suppression did not affect young or older adults’ subjective feelings or memory for the stimuli. <b><i>Conclusion:</i></b> Our findings suggest that there are age differences in facial muscle reactivity to amusing and sad cues of heightened intensity. These findings suggest that older adults’ ability to effectively regulate emotions may be limited, at least with expressive suppression, in the context of high-intensity emotional cues. Further research is needed to investigate possible exceptions the preservation of emotion regulation in older adults.
DOI: 10.6084/m9.figshare.9312206.v2
title: Non-alcoholic fatty liver disease (NAFLD) is associated with dynamic changes in DNA hydroxymethylation

description: Non-alcoholic fatty liver disease (NAFLD) is now the commonest cause of liver disease in developed countries affecting 25–33% of the general population and up to 75% of those with obesity. Recent data suggest that alterations in DNA methylation may be related to NAFLD pathogenesis and progression and we have previously shown that dynamic changes in the cell lineage identifier 5-hydroxymethylcytosine (5hmC) may be important in the pathogenesis of liver disease. We used a model of diet-induced obesity, maintaining male mice on a high-fat diet (HFD) to generate hepatic steatosis. We profiled hepatic gene expression, global and locus-specific 5hmC and additionally investigated the effects of weight loss on the phenotype. HFD led to increased weight gain, fasting hyperglycaemia, glucose intolerance, insulin resistance and hepatic periportal macrovesicular steatosis. Diet-induced hepatic steatosis associated with reversible 5hmC changes at a discrete number of functionally important genes. We propose that 5hmC profiles are a useful signature of gene transcription and a marker of cell state in NAFLD and suggest that 5hmC profiles hold potential as a biomarker of abnormal liver physiology.
DOI: 10.6084/m9.figshare.9311927
title: The bryophyte flora of northern Iturup (north-west Pacific): between the circumboreal and East Asian floristic regions

description: <b>Introduction.</b> The Kuril Islands Chain demarcates the boundary between the circumpolar and East Asian floras in the amphi-Pacific and is a trans-Oceanic migration route from warm-temperate insular East Asia to north-east Asia and Beringia. This paper reviews the flora of the northern part of Iturup Island in regards to its bryogeography and taxonomic diversity, as well as its relative position among other bryophyte floras of north-east and East Asia. <b>Methods.</b> The paper uses morphological methods to identify the species composition and detrended correspondence analysis to identify the position of the northern Iturup Island in the system of local floras of the eastern, extra-tropical, Pacific. <b>Key results.</b> The flora is closely related to the bryophyte floras of the southern Kurils and Hokkaido Island, but has been found to be distinctly distant from the ‘true’ cool-temperate East Asian floras, as well as from the boreal and hemiarctic floras of north-east Asia. Instead, the floras of the south Kurils and northern Hokkaido Island belong to a peculiar intermediate phytogeographic province that cannot be unambiguously placed in either the East Asian or circumboreal floristic regions. The hemiboreal character of the bryophyte flora of northern Iturup Island is in contrast to the general appearance of many of the dominant vegetation communities on the island, which are more characteristic of the hemiarctic. <b>Conclusion.</b> There is no robust evidence to refer the bryophyte flora of northern Iturup either to the circumboreal or East Asian Floristic Region, the flora belongs to a unique intermediate province between the two regions.
DOI: 10.6084/m9.figshare.9312206.v1
title: Non-alcoholic fatty liver disease (NAFLD) is associated with dynamic changes in DNA hydroxymethylation

description: Non-alcoholic fatty liver disease (NAFLD) is now the commonest cause of liver disease in developed countries affecting 25–33% of the general population and up to 75% of those with obesity. Recent data suggest that alterations in DNA methylation may be related to NAFLD pathogenesis and progression and we have previously shown that dynamic changes in the cell lineage identifier 5-hydroxymethylcytosine (5hmC) may be important in the pathogenesis of liver disease. We used a model of diet-induced obesity, maintaining male mice on a high-fat diet (HFD) to generate hepatic steatosis. We profiled hepatic gene expression, global and locus-specific 5hmC and additionally investigated the effects of weight loss on the phenotype. HFD led to increased weight gain, fasting hyperglycaemia, glucose intolerance, insulin resistance and hepatic periportal macrovesicular steatosis. Diet-induced hepatic steatosis associated with reversible 5hmC changes at a discrete number of functionally important genes. We propose that 5hmC profiles are a useful signature of gene transcription and a marker of cell state in NAFLD and suggest that 5hmC profiles hold potential as a biomarker of abnormal liver physiology.
DOI: 10.6084/m9.figshare.9311813
title: Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum

description: Data from Q-PCR analysis of equine mesenteric lymph nodes (LN) and Ileum mucosa (IL)
DOI: 10.6084/m9.figshare.9311888
title: Supplementary Material for: Audiovestibular Phenotypes and Advanced Magnetic Resonance Imaging Features of Cochlin Gene Mutation Carriers

description: <b><i>Objective:</i></b> To describe clinical and imaging findings in a group of patients affected by nonsyndromic deafness A9 (DFNA9), using advanced magnetic resonance imaging (MRI) with 3-dimensional (3D) fluid-attenuated inversion recovery (FLAIR) sequence. <b><i>Method:</i></b> A retrospective case review was conducted in a tertiary referral center in Italy. Four sequential adult DFNA9-affected patients, who had undergone MRI at our Department between January 2017 and June 2018, were enrolled (male = 2, female = 2; median age: 65.6 years; 8 diseased ears analyzed). Three patients were relatives; the fourth was unrelated. The main outcome measures – age, sex, records of audiological and vestibular testing, genetic assessment, MRI findings – were analyzed. <b><i>Results:</i></b> All subjects suffered from bilateral progressive sensorineural hearing loss, more severely at the high frequencies and with a typical clinical pattern of bilateral chronic degenerative cochleovestibular deficit. Aural fullness was reported at the onset of the disease. All patients revealed a pathogenic heterozygous mutation in the Limulus factor C, Coch-5b2 and Lgl1 domain of cochlin. None of the patients showed a significant vestibular and cochlear endolymphatic hydrops at MRI, while high bilateral contrast enhancement on 4-h delayed postcontrast 3D FLAIR sequence was observed in all ears. <b><i>Conclusions:</i></b> Increased perilymph enhancement on 4-h delayed postcontrast 3D FLAIR sequence is the common imaging feature of DFNA9 ears, suggesting that blood-labyrinthine barrier breakdown may play the main role in the pathophysiology of this disease. Significant hydrops has been excluded by MRI. This finding might be clinically useful in differentiating DFNA9 disease from other pathologies with similar clinical findings like Ménière’s disease.
DOI: 10.6084/m9.figshare.9311927.v1
title: The bryophyte flora of northern Iturup (north-west Pacific): between the circumboreal and East Asian floristic regions

description: <b>Introduction.</b> The Kuril Islands Chain demarcates the boundary between the circumpolar and East Asian floras in the amphi-Pacific and is a trans-Oceanic migration route from warm-temperate insular East Asia to north-east Asia and Beringia. This paper reviews the flora of the northern part of Iturup Island in regards to its bryogeography and taxonomic diversity, as well as its relative position among other bryophyte floras of north-east and East Asia. <b>Methods.</b> The paper uses morphological methods to identify the species composition and detrended correspondence analysis to identify the position of the northern Iturup Island in the system of local floras of the eastern, extra-tropical, Pacific. <b>Key results.</b> The flora is closely related to the bryophyte floras of the southern Kurils and Hokkaido Island, but has been found to be distinctly distant from the ‘true’ cool-temperate East Asian floras, as well as from the boreal and hemiarctic floras of north-east Asia. Instead, the floras of the south Kurils and northern Hokkaido Island belong to a peculiar intermediate phytogeographic province that cannot be unambiguously placed in either the East Asian or circumboreal floristic regions. The hemiboreal character of the bryophyte flora of northern Iturup Island is in contrast to the general appearance of many of the dominant vegetation communities on the island, which are more characteristic of the hemiarctic. <b>Conclusion.</b> There is no robust evidence to refer the bryophyte flora of northern Iturup either to the circumboreal or East Asian Floristic Region, the flora belongs to a unique intermediate province between the two regions.
DOI: 10.6084/m9.figshare.9311813.v1
title: Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum

description: Data from Q-PCR analysis of equine mesenteric lymph nodes (LN) and Ileum mucosa (IL)
DOI: 10.6084/m9.figshare.9307814
title: Habitat use models of spatially auto-correlated data: a case study of the common bottlenose dolphin, <i>Tursiops truncatus truncatus</i>, in southeastern Brazil

description: A common approach to studying habitat use in cetaceans is to conduct line-transect surveys, to investigate their distribution. In developing countries, there are limited resources for data collection. One solution is to employ field surveys to collect a wide range of ecological and behavioural data, for which a haphazard sampling schedule is adopted, to optimize the cost–benefit ratio. As with line-transect surveys, the haphazard sampling may lead to spatial autocorrelation (SAC), an overlooked problem in ecology. Here, we investigated common bottlenose dolphins (<i>Tursiops truncatus truncatus</i>) habitat use on an upwelling area and tested an approach that can improve model-based inference on auto-correlated data. We collected data in Cabo Frio, Rio de Janeiro, photo-identified 429 individuals and compared the predictions and model coefficients of standard generalized linear model (GLM) without correcting for spatial autocorrelation with a spatial eigenvector generalized linear model (SEV-GLM) which compensates for SAC. Our best SEV-GLM predicted dolphins are more likely to occur on cold waters with increased chlorophyll concentration, indicating dolphins are influenced by the upwelling. Moreover, by correcting for SAC, our models had a better fit to data, magnified the relevance of significant variables and showed smaller and less clumped residuals than when not correcting.
DOI: 10.6084/m9.figshare.9306854
title: Absence of correlation between follicular fluid volume and follicular granulocyte colony-stimulating factor, a predictor of embryo implantation and successful delivery

description: Follicular granulocyte colony-stimulating factor (G-CSF) is a documented marker of embryo implantation potential. The primary objective was to determine whether follicular G-CSF levels correlate with follicular fluid volume. The secondary objectives were to assess whether follicular G-CSF is associated with oocyte maturity at the time of harvest and with delivery rate after fresh or frozen embryo transfer. Thirty-two patients undergoing intracytoplasmic sperm injection (ICSI) cycles were recruited (Centre de Procréation Médicalement Assistée (CPMA), University of Liège, Belgium). A total of 211 follicular fluid (FF) samples were individually collected at the time of oocyte harvest. FF volume was recorded, and G-CSF concentration was assessed by ELISA. The embryos were individually cultured <i>in vitro</i>. Their implantation and live birth rates were recorded after fresh and frozen embryo transfers. The follicular fluid volume did not correlate with the follicular G-CSF concentration. There were no differences in follicular G-CSF levels between mature and immature oocytes. The probability of successful implantation and delivery was increased for embryos with FF containing a high G-CSF concentration. There was a trend toward lower follicular G-CSF levels in cases of miscarriage. Therefore, follicular fluid volume cannot be a substitute for follicular G-CSF as a marker of embryo implantation ability.
DOI: 10.6084/m9.figshare.9306854.v1
title: Absence of correlation between follicular fluid volume and follicular granulocyte colony-stimulating factor, a predictor of embryo implantation and successful delivery

description: Follicular granulocyte colony-stimulating factor (G-CSF) is a documented marker of embryo implantation potential. The primary objective was to determine whether follicular G-CSF levels correlate with follicular fluid volume. The secondary objectives were to assess whether follicular G-CSF is associated with oocyte maturity at the time of harvest and with delivery rate after fresh or frozen embryo transfer. Thirty-two patients undergoing intracytoplasmic sperm injection (ICSI) cycles were recruited (Centre de Procréation Médicalement Assistée (CPMA), University of Liège, Belgium). A total of 211 follicular fluid (FF) samples were individually collected at the time of oocyte harvest. FF volume was recorded, and G-CSF concentration was assessed by ELISA. The embryos were individually cultured <i>in vitro</i>. Their implantation and live birth rates were recorded after fresh and frozen embryo transfers. The follicular fluid volume did not correlate with the follicular G-CSF concentration. There were no differences in follicular G-CSF levels between mature and immature oocytes. The probability of successful implantation and delivery was increased for embryos with FF containing a high G-CSF concentration. There was a trend toward lower follicular G-CSF levels in cases of miscarriage. Therefore, follicular fluid volume cannot be a substitute for follicular G-CSF as a marker of embryo implantation ability.
DOI: 10.6084/m9.figshare.9307814.v2
title: Habitat use models of spatially auto-correlated data: a case study of the common bottlenose dolphin, <i>Tursiops truncatus truncatus</i>, in southeastern Brazil

description: A common approach to studying habitat use in cetaceans is to conduct line-transect surveys, to investigate their distribution. In developing countries, there are limited resources for data collection. One solution is to employ field surveys to collect a wide range of ecological and behavioural data, for which a haphazard sampling schedule is adopted, to optimize the cost–benefit ratio. As with line-transect surveys, the haphazard sampling may lead to spatial autocorrelation (SAC), an overlooked problem in ecology. Here, we investigated common bottlenose dolphins (<i>Tursiops truncatus truncatus</i>) habitat use on an upwelling area and tested an approach that can improve model-based inference on auto-correlated data. We collected data in Cabo Frio, Rio de Janeiro, photo-identified 429 individuals and compared the predictions and model coefficients of standard generalized linear model (GLM) without correcting for spatial autocorrelation with a spatial eigenvector generalized linear model (SEV-GLM) which compensates for SAC. Our best SEV-GLM predicted dolphins are more likely to occur on cold waters with increased chlorophyll concentration, indicating dolphins are influenced by the upwelling. Moreover, by correcting for SAC, our models had a better fit to data, magnified the relevance of significant variables and showed smaller and less clumped residuals than when not correcting.
DOI: 10.6084/m9.figshare.9307814.v1
title: Habitat use models of spatially auto-correlated data: a case study of the common bottlenose dolphin, <i>Tursiops truncatus truncatus</i>, in southeastern Brazil

description: A common approach to studying habitat use in cetaceans is to conduct line-transect surveys, to investigate their distribution. In developing countries, there are limited resources for data collection. One solution is to employ field surveys to collect a wide range of ecological and behavioural data, for which a haphazard sampling schedule is adopted, to optimize the cost–benefit ratio. As with line-transect surveys, the haphazard sampling may lead to spatial autocorrelation (SAC), an overlooked problem in ecology. Here, we investigated common bottlenose dolphins (<i>Tursiops truncatus truncatus</i>) habitat use on an upwelling area and tested an approach that can improve model-based inference on auto-correlated data. We collected data in Cabo Frio, Rio de Janeiro, photo-identified 429 individuals and compared the predictions and model coefficients of standard generalized linear model (GLM) without correcting for spatial autocorrelation with a spatial eigenvector generalized linear model (SEV-GLM) which compensates for SAC. Our best SEV-GLM predicted dolphins are more likely to occur on cold waters with increased chlorophyll concentration, indicating dolphins are influenced by the upwelling. Moreover, by correcting for SAC, our models had a better fit to data, magnified the relevance of significant variables and showed smaller and less clumped residuals than when not correcting.
DOI: 10.6084/m9.figshare.9303095
title: Supplementary Material for: Epidemiology and Comorbidities of Psoriasis among Israeli Adolescents: A Large Cross-Sectional Study

description: <b><i>Background and Aims:</i></b> Although psoriasis can develop at any age, the data regarding its characteristics in adolescents are sparse. This study was designed to determine the psoriasis prevalence and its associations with the body mass index (BMI), lipid profile, and comorbidities in adolescents. <b><i>Methods:</i></b> This was a nationwide population-based cross-sectional retrospective study of adolescents (16–18 years old) evaluated for military service between January 1999 and January 2014. <b><i>Results:</i></b> Our database included 887,765 adolescents (57.1% males), of whom 3,112 (0.35%) were diagnosed with psoriasis. During the 15-year study period, the psoriasis prevalence increased by 1.4-fold, from 0.3 to 0.42% (1.25-fold for the males and 1.63-fold for the females). Certain comorbidities, such as contact dermatitis, hyperhidrosis, and arthritis, were significantly associated with psoriasis (odds ratios [ORs] of 2.26, 1.51, and 5.3, respectively). The adolescents with psoriasis had significantly elevated BMI and triglyceride values. We found increased ORs of 1.34 (95% confidence interval [CI] = 1.25–1.56) and 1.56 (95% CI = 1.32–1.83) for the overweight and obese adolescents, respectively, while a lower BMI (&lt;20) had an opposite effect with psoriasis (OR = 0.8). <b><i>Conclusions:</i></b> Based on our results, the psoriasis prevalence in Israeli adolescents is rising. Dermatological comorbidities and an increased BMI were associated with psoriasis in these adolescents. A better understanding of the distinctive epidemiological characteristics of juvenile psoriasis may allow for the early detection of comorbidities and improve its management.