cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3384916.v1
title: The impact of supervised weight loss and intentional weight regain on sex hormone binding globulin and testosterone in premenopausal women

description: What is the impact of intentional weight loss and regain on serum androgens in women? We conducted an ancillary analysis of prospectively collected samples from a randomized controlled trial. The trial involved supervised 10% weight loss (8.5 kg on average) with diet and exercise over 4-6 months followed by supervised intentional regain of 50% of the lost weight (4.6 kg on average) over 4-6 months. Participants were randomized prior to the partial weight regain component to either continuation or cessation of endurance exercise. Analytic sample included 30 obese premenopausal women (mean age of 40 ± 5.9 years, mean baseline body mass index (BMI) of 32.9 ± 4.2 kg/m<sup>2</sup>) with metabolic syndrome. We evaluated sex hormone binding globulin (SHBG), total testosterone (T), free androgen index (FAI), and high molecular weight adiponectin (HMWAdp). Insulin, homeostasis model assessment (HOMA), and quantitative insulin sensitivity check index (QUICKI), and visceral adipose tissue (VAT) measured in the original trial were reanalyzed for the current analytic sample. Insulin, HOMA, and QUICKI improved with weight loss and were maintained despite weight regain. Log-transformed SHBG significantly increased from baseline to weight loss, and then significantly decreased with weight regain. LogFAI and logVAT decreased similarly and increased with weight loss followed by weight regain. No changes were found in logT and LogHMWAdp. There was no significant difference in any tested parameters by exercise between the groups. SHBG showed prominent sensitivity to body mass fluctuations, as reduction with controlled intentional weight regain showed an inverse relationship to VAT and occurred despite stable HMWAdp and sustained improvements with insulin resistance. FAI showed opposite changes to SHBG, while T did not change significantly with weight. Continued exercise during weight regain did not appear to impact these findings.
DOI: 10.6084/m9.figshare.3384892
title: A Mixed Model to Disentangle Variance and Serial Autocorrelation in Affective Instability Using Ecological Momentary Assessment Data

description: Affective instability, the tendency to experience emotions that fluctuate frequently and intensively over time, is a core feature of several mental disorders including borderline personality disorder. Currently, affect is often measured with Ecological Momentary Assessment protocols, which yield the possibility to quantify the instability of affect over time. A number of linear mixed models are proposed to examine (diagnostic) group differences in affective instability. The models contribute to the existing literature by estimating simultaneously both the variance and serial dependency component of affective instability when observations are unequally spaced in time with the serial autocorrelation (or emotional inertia) declining as a function of the time interval between observations. In addition, the models can eliminate systematic trends, take between subject differences into account and test for (diagnostic) group differences in serial autocorrelation, short-term as well as long-term affective variability. The usefulness of the models is illustrated in a study on diagnostic group differences in affective instability in the domain of eating disorders. Limitations of the model are that they pertain to group (and not individual) differences and do not focus explicitly on circadian rhythms or cycles in affect.
DOI: 10.6084/m9.figshare.3384892.v2
title: A Mixed Model to Disentangle Variance and Serial Autocorrelation in Affective Instability Using Ecological Momentary Assessment Data

description: Affective instability, the tendency to experience emotions that fluctuate frequently and intensively over time, is a core feature of several mental disorders including borderline personality disorder. Currently, affect is often measured with Ecological Momentary Assessment protocols, which yield the possibility to quantify the instability of affect over time. A number of linear mixed models are proposed to examine (diagnostic) group differences in affective instability. The models contribute to the existing literature by estimating simultaneously both the variance and serial dependency component of affective instability when observations are unequally spaced in time with the serial autocorrelation (or emotional inertia) declining as a function of the time interval between observations. In addition, the models can eliminate systematic trends, take between subject differences into account and test for (diagnostic) group differences in serial autocorrelation, short-term as well as long-term affective variability. The usefulness of the models is illustrated in a study on diagnostic group differences in affective instability in the domain of eating disorders. Limitations of the model are that they pertain to group (and not individual) differences and do not focus explicitly on circadian rhythms or cycles in affect.
DOI: 10.6084/m9.figshare.3384820
title: Multipotent neurogenic fate of mesenchymal stem cell is determined by Cdk4-mediated hypophosphorylation of Smad-STAT3

description: Cyclin-dependent kinase (Cdk) in complex with a corresponding cyclin plays a pivotal role in neurogenic differentiation. In particular, Cdk4 activity acts as a signaling switch to direct human mesenchymal stem cells (MSCs) to neural transdifferentiation. However, the molecular evidence of how Cdk4 activity converts MSCs to neurogenic lineage remains unknown. Here, we found that Cdk4 inhibition in human MSCs enriches the populations of neural stem and progenitor pools rather than differentiated glial and neuronal cell pools. Interestingly, Cdk4 inhibition directly inactivates Smads and subsequently STAT3 signaling by hypophosphorylation, and both Cdk4 and Smads levels are linked during the processes of neural transdifferentiation and differentiation. In summary, our results provide novel molecular evidence in which Cdk4 inhibition leads to directing human MSCs to a multipotent neurogenic fate by inactivating Smads-STAT3 signaling.
DOI: 10.6084/m9.figshare.3384820.v1
title: Multipotent neurogenic fate of mesenchymal stem cell is determined by Cdk4-mediated hypophosphorylation of Smad-STAT3

description: Cyclin-dependent kinase (Cdk) in complex with a corresponding cyclin plays a pivotal role in neurogenic differentiation. In particular, Cdk4 activity acts as a signaling switch to direct human mesenchymal stem cells (MSCs) to neural transdifferentiation. However, the molecular evidence of how Cdk4 activity converts MSCs to neurogenic lineage remains unknown. Here, we found that Cdk4 inhibition in human MSCs enriches the populations of neural stem and progenitor pools rather than differentiated glial and neuronal cell pools. Interestingly, Cdk4 inhibition directly inactivates Smads and subsequently STAT3 signaling by hypophosphorylation, and both Cdk4 and Smads levels are linked during the processes of neural transdifferentiation and differentiation. In summary, our results provide novel molecular evidence in which Cdk4 inhibition leads to directing human MSCs to a multipotent neurogenic fate by inactivating Smads-STAT3 signaling.
DOI: 10.6084/m9.figshare.3384802
title: Multilabel classification with R package mlr

description: This is the code that is used for the benchmark study in the paper "Multilabel classification with R package mlr".<br>
DOI: 10.6084/m9.figshare.3384802.v1
title: Multilabel classification with R package mlr

description: This is the code and the datasets that were used in the paper "Multilabel classification with R package mlr".<br>
DOI: 10.6084/m9.figshare.3384802.v2
title: Multilabel classification with R package mlr

description: This is the code and the datasets that are used in the paper "Multilabel classification with R package mlr".<br>
DOI: 10.6084/m9.figshare.3384802.v3
title: Multilabel classification with R package mlr

description: This is the code and the datasets that are used in the paper "Multilabel classification with R package mlr".<br>
DOI: 10.6084/m9.figshare.3384802.v4
title: Multilabel classification with R package mlr

description: This is the code and the datasets that are used in the paper "Multilabel classification with R package mlr".<br>
DOI: 10.6084/m9.figshare.12251342
title: Clinical features of 57 patients with lipoid congenital adrenal hyperplasia.

description: <b>A supplemental material for a clinical research paper of </b>doi.org/10.1210/clinem/dgaa557.<br>
DOI: 10.6084/m9.figshare.3384745
title: Aurora-A regulates MCRS1 function during mitosis

description: The mitotic spindle is made of microtubules (MTs) nucleated through different pathways involving the centrosomes, the chromosomes or the walls of pre-existing MTs. MCRS1 is a RanGTP target that specifically associates with the chromosome-driven MTs protecting them from MT depolymerases. MCRS1 is also needed for the control of kinetochore fiber (K-fiber) MT minus-ends dynamics in metaphase. Here, we investigated the regulation of MCRS1 activity in M-phase. We show that MCRS1 is phosphorylated by the Aurora-A kinase in mitosis on Ser35/36. Although this phosphorylation has no role on MCRS1 localization to chromosomal MTs and K-fiber minus-ends, we show that it regulates MCRS1 activity in mitosis. We conclude that Aurora-A activity is particularly important in the tuning of K-fiber minus-ends dynamics in mitosis.
DOI: 10.6084/m9.figshare.3384745.v1
title: Aurora-A regulates MCRS1 function during mitosis

description: The mitotic spindle is made of microtubules (MTs) nucleated through different pathways involving the centrosomes, the chromosomes or the walls of pre-existing MTs. MCRS1 is a RanGTP target that specifically associates with the chromosome-driven MTs protecting them from MT depolymerases. MCRS1 is also needed for the control of kinetochore fiber (K-fiber) MT minus-ends dynamics in metaphase. Here, we investigated the regulation of MCRS1 activity in M-phase. We show that MCRS1 is phosphorylated by the Aurora-A kinase in mitosis on Ser35/36. Although this phosphorylation has no role on MCRS1 localization to chromosomal MTs and K-fiber minus-ends, we show that it regulates MCRS1 activity in mitosis. We conclude that Aurora-A activity is particularly important in the tuning of K-fiber minus-ends dynamics in mitosis.
DOI: 10.6084/m9.figshare.3384730
title: Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in <i>Tetrahymena thermophila</i>

description: Although the role of cyclins in controlling nuclear division is well established, their function in ciliate meiosis remains unknown. In ciliates, the cyclin family has undergone massive expansion which suggests that diverse cell cycle systems exist, and this warrants further investigation. A screen for cyclins in the model ciliate <i>Tetrahymena thermophila</i> showed that there are 34 cyclins in this organism. Only 1 cyclin, Cyc17, contains the complete cyclin core and is specifically expressed during meiosis. Deletion of <i>CYC17</i> led to meiotic arrest at the diakinesis-like metaphase I stage. Expression of genes involved in DNA metabolism and chromosome organization (chromatin remodeling and basic chromosomal structure) was repressed in <i>cyc17</i> knockout matings. Further investigation suggested that Cyc17 is involved in regulating spindle pole attachment, and is thus essential for chromosome segregation at meiosis. These findings suggest a simple model in which chromosome segregation is influenced by Cyc17.
DOI: 10.6084/m9.figshare.3384730.v2
title: Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in <i>Tetrahymena thermophila</i>

description: Although the role of cyclins in controlling nuclear division is well established, their function in ciliate meiosis remains unknown. In ciliates, the cyclin family has undergone massive expansion which suggests that diverse cell cycle systems exist, and this warrants further investigation. A screen for cyclins in the model ciliate <i>Tetrahymena thermophila</i> showed that there are 34 cyclins in this organism. Only 1 cyclin, Cyc17, contains the complete cyclin core and is specifically expressed during meiosis. Deletion of <i>CYC17</i> led to meiotic arrest at the diakinesis-like metaphase I stage. Expression of genes involved in DNA metabolism and chromosome organization (chromatin remodeling and basic chromosomal structure) was repressed in <i>cyc17</i> knockout matings. Further investigation suggested that Cyc17 is involved in regulating spindle pole attachment, and is thus essential for chromosome segregation at meiosis. These findings suggest a simple model in which chromosome segregation is influenced by Cyc17.
DOI: 10.6084/m9.figshare.3384730.v1
title: Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila

description: Although the role of cyclins in controlling nuclear division is well established, their function in ciliate meiosis remains unknown. In ciliates, the cyclin family has undergone massive expansion which suggests that diverse cell cycle systems exist, and this warrants further investigation. A screen for cyclins in the model ciliate <i>Tetrahymena thermophila</i> showed that there are 34 cyclins in this organism. Only one cyclin, Cyc17, contains the complete cyclin core and is specifically expressed during meiosis. Deletion of <i>CYC17</i> led to meiotic arrest at the diakinesis-like metaphase I stage. Expression of genes involved in DNA metabolism and chromosome organization (chromatin remodeling and basic chromosomal structure) was repressed in <i>cyc17</i> knockout matings. Further investigation suggested that Cyc17 is involved in regulating spindle pole attachment, and is thus essential for chromosome segregation at meiosis. These findings suggest a simple model in which chromosome segregation is influenced by Cyc17.
DOI: 10.6084/m9.figshare.3384727
title: Bursicon-α subunit modulates dLGR2 activity in the adult <i>Drosophila melanogaster</i> midgut independently to Bursicon-β

description: Bursicon is the main regulator of post molting and post eclosion processes during arthropod development. The active Bursicon hormone is a heterodimer of Burs-α and Burs-β. However, adult midguts express Burs-α to regulate the intestinal stem cell niche. Here, we examined the potential expression and function of its heterodimeric partner, Burs-β in the adult midgut. Unexpectedly, our evidence suggests that Burs-β is not significantly expressed in the adult midgut. <i>burs</i>-β mutants displayed the characteristic developmental defects but showed wild type-like adult midguts, thus uncoupling the developmental and adult phenotypes seen in <i>burs</i>-α mutants. Gain of function data and <i>ex vivo</i> experiments using a cAMP biosensor, demonstrated that Burs-α is sufficient to drive stem cell quiescence and to activate dLGR2 in the adult midgut. Our evidence suggests that the post developmental transactivation of dLGR2 in the adult midgut is mediated by Burs-α and that the β subunit of Bursicon is dispensable for these activities.
DOI: 10.6084/m9.figshare.3384727.v2
title: Bursicon-α subunit modulates dLGR2 activity in the adult <i>Drosophila melanogaster</i> midgut independently to Bursicon-β

description: Bursicon is the main regulator of post molting and post eclosion processes during arthropod development. The active Bursicon hormone is a heterodimer of Burs-α and Burs-β. However, adult midguts express Burs-α to regulate the intestinal stem cell niche. Here, we examined the potential expression and function of its heterodimeric partner, Burs-β in the adult midgut. Unexpectedly, our evidence suggests that Burs-β is not significantly expressed in the adult midgut. <i>burs</i>-β mutants displayed the characteristic developmental defects but showed wild type-like adult midguts, thus uncoupling the developmental and adult phenotypes seen in <i>burs</i>-α mutants. Gain of function data and <i>ex vivo</i> experiments using a cAMP biosensor, demonstrated that Burs-α is sufficient to drive stem cell quiescence and to activate dLGR2 in the adult midgut. Our evidence suggests that the post developmental transactivation of dLGR2 in the adult midgut is mediated by Burs-α and that the β subunit of Bursicon is dispensable for these activities.
DOI: 10.6084/m9.figshare.3384727.v1
title: Bursicon-α subunit modulates dLGR2 activity in the adult <i>Drosophila</i> melanogaster midgut independently to Bursicon-β

description: Bursicon is the main regulator of post molting and post eclosion processes during arthropod development. The active Bursicon hormone is a heterodimer of Burs-α and Burs- However, adult midguts express Burs-to regulate the intestinal stem cell niche. Here, we examined the potential expression and function of its heterodimeric partner, Burs- in the adult midgut. Unexpectedly, our evidence suggests that in the adult midgut Burs- is not significantly expressed. <i>burs-</i> mutants displayed the characteristic developmental defects but showed wild type-like adult midguts, thus uncoupling the developmental and adult phenotypes seen in <i>burs-</i>α mutants. Gain of function data and <i>ex vivo</i> experiments using a cAMP biosensor, demonstrated that Burs- is sufficient to drive stem cell quiescence and to activate dLGR2 in the adult midgut. Our evidence suggests that the post developmental transactivation of dLGR2 in the adult midgut is mediated by Burs- and that the β subunit of Bursicon is dispensable for these activities.
DOI: 10.6084/m9.figshare.3384712
title: Example_Data.tar.bz2

description: ANGSD-wrapper sample data. Maize Chromosome 10 15000000-25000000
DOI: 10.6084/m9.figshare.3384712.v1
title: Example_Data.tar.bz2

description: ANGSD-wrapper sample data. Maize Chromosome 10 15000000-25000000
DOI: 10.6084/m9.figshare.3384694
title: Glacier_bacteria

description: Mapping file and 454 raw sequence file for 16S rRNA gene sequencing of bacterial communities from deglaciating soil of Mendenhall Glacier (MG) located in southeast Alaska, USA and Easton Glacier (EG) located in the North Cascade mountains of Washington, USA. Sampling was done in late summer or early fall of 2010.
DOI: 10.6084/m9.figshare.3384694.v2
title: Glacier_bacteria

description: Mapping file and 454 raw sequence file for 16S rRNA gene sequencing of bacterial communities from deglaciating soil of Mendenhall Glacier (MG) located in southeast Alaska, USA and Easton Glacier (EG) located in the North Cascade mountains of Washington, USA. Sampling was done in late summer or early fall of 2010.
DOI: 10.6084/m9.figshare.3384673
title: Effect of cholecalciferol supplementation on arterial stiffness: a systematic review and meta-analysis

description: <b>Background:</b> Vitamin D deficiency increases risk of cardiovascular diseases, arterial stiffness, and endothelial dysfunction. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) investigating the impact of vitamin D supplementation on arterial stiffness. <b>Methods:</b> A comprehensive search of the databases of the Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE was performed from inception through November 2015. The inclusion criterion was RCTs that assessed the impact of cholecalciferol supplementation in adults on the surrogate markers of arterial stiffness (aortic pulse wave velocity (PWV) and augmentation index (AIx)). Outcome was the pooled mean difference (MD) of PWV and AIx between the vitamin D supplementation (intervention) group and placebo. <b>Results:</b> The initial search yielded 1164 articles. Twenty-eight articles underwent full-length review and data were extracted from seven RCTs involving totally 547 participants. Dose of cholecalciferol supplementation varied from 1000 IU/day to 120,000 IU/month of cholecalciferol. Duration of treatment ranged from 2 to 12 months. There was no significant difference in the change of PWV (pooled MD = 0.18, 95% CI: −0.17 to 0.52 or AIx (pooled MD = 2.39, 95% CI: −4.43 to 4.92) between the intervention group and placebo. <b>Conclusions:</b> There was no improvement of markers of arterial stiffness after vitamin D supplementation.
DOI: 10.6084/m9.figshare.3384673.v1
title: Effect of cholecalciferol supplementation on arterial stiffness: a systematic review and meta-analysis

description: <b>Background:</b> Vitamin D deficiency increases risk of cardiovascular diseases, arterial stiffness, and endothelial dysfunction. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) investigating the impact of vitamin D supplementation on arterial stiffness. <b>Methods:</b> A comprehensive search of the databases of the Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE was performed from inception through November 2015. The inclusion criterion was RCTs that assessed the impact of cholecalciferol supplementation in adults on the surrogate markers of arterial stiffness (aortic pulse wave velocity (PWV) and augmentation index (AIx)). Outcome was the pooled mean difference (MD) of PWV and AIx between the vitamin D supplementation (intervention) group and placebo. <b>Results:</b> The initial search yielded 1164 articles. Twenty-eight articles underwent full-length review and data were extracted from seven RCTs involving totally 547 participants. Dose of cholecalciferol supplementation varied from 1000 IU/day to 120,000 IU/month of cholecalciferol. Duration of treatment ranged from 2 to 12 months. There was no significant difference in the change of PWV (pooled MD = 0.18, 95% CI: −0.17 to 0.52 or AIx (pooled MD = 2.39, 95% CI: −4.43 to 4.92) between the intervention group and placebo. <b>Conclusions:</b> There was no improvement of markers of arterial stiffness after vitamin D supplementation.
DOI: 10.6084/m9.figshare.3384661
title: Coherent structures in oscillatory flows within the laminar-to-turbulent transition regime for smooth and rough walls

description: We investigate coherent structures present in oscillatory boundary layers over smooth and rough beds for Reynolds numbers between 10<sup>3</sup> and 10<sup>4</sup>, in the transition to turbulence regime. A two-camera 2D- particle image velocimetry (PIV) system was used to visualize coherent structures in an oscillatory-flow tunnel. The obtained results show that smooth-bed flow is populated by vortex-tube structures that are formed due to the Kelvin–Helmholtz instability. Three types of coherent structures are observed in the rough-wall experiments: vortices randomly distributed in space; turbulent bursts – spatial structures without a clear shape compared to vortices but with a longer life than the former; and shear layers of vortices originating due to flow separation from some of the grains on the bed. The reported study contributes to the description of coherent structures in oscillatory flows that are captured with the PIV technique, particularly a new structure in flows over rough beds in the transition to turbulence regime.