cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6452117
title: Data from Habitat partitioning during character displacement between the sexes

description: Ecological differences between the sexes are often interpreted as evidence of within-species ecological character displacement (ECD), a hypothesis with almost no direct tests. Here, we experimentally test two predictions that are direct corollaries of ECD between the sexes, in a salamander. First, we find support for the prediction that each sex has a growth rate advantage in the aquatic microhabitat where it is most commonly found. Second, we test the prediction that selection for ECD in the breeding environment may affect partial migration out of this environment. We found that phenotype-dependent migration resulted in a shift in the phenotypic distribution across treatments, with the highest sexual dimorphism occurring among residents at high founding density, suggesting that migration and ECD can both be driven by competition. Our work illustrates how complex patterns of habitat partitioning evolve during ECD between the sexes and suggest ECD and partial migration can interact to effect both ecological dynamics and evolution of sexual dimorphism.
DOI: 10.6084/m9.figshare.6452117.v1
title: Data from Habitat partitioning during character displacement between the sexes

description: Ecological differences between the sexes are often interpreted as evidence of within-species ecological character displacement (ECD), a hypothesis with almost no direct tests. Here, we experimentally test two predictions that are direct corollaries of ECD between the sexes, in a salamander. First, we find support for the prediction that each sex has a growth rate advantage in the aquatic microhabitat where it is most commonly found. Second, we test the prediction that selection for ECD in the breeding environment may affect partial migration out of this environment. We found that phenotype-dependent migration resulted in a shift in the phenotypic distribution across treatments, with the highest sexual dimorphism occurring among residents at high founding density, suggesting that migration and ECD can both be driven by competition. Our work illustrates how complex patterns of habitat partitioning evolve during ECD between the sexes and suggest ECD and partial migration can interact to effect both ecological dynamics and evolution of sexual dimorphism.
DOI: 10.6084/m9.figshare.6450743
title: Mental health and behavioral screening in pediatric type 1 and type 2 diabetes mellitus

description: Data from Strengths and Differences Questionnaire (SDQ) screening tool used in patients with type 1 and type 2 diabetes aged 11 - 17 years.
DOI: 10.6084/m9.figshare.12893405
title: R0189_20171003a_videos

description: Rat 0189, skilled reaching data collected on 10/3/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12893405.v1
title: R0189_20171003a_videos

description: Rat 0189, skilled reaching data collected on 10/3/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.6450695
title: crater excavation omega=3

description: crater excavation omega=3
DOI: 10.6084/m9.figshare.6450695.v1
title: crater excavation omega=3

description: crater excavation omega=3
DOI: 10.6084/m9.figshare.6450632
title: Differentially expressed gene lists - Repeats

description: Files for 13 mutant lines, investigated for differentially expressed repeats, containing the repeat instances determined to be differentially expressed (using DESeq2).<br>see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450632.v1
title: Differentially expressed gene lists - Repeats

description: Files for 13 mutant lines, investigated for differentially expressed repeats, containing the repeat instances determined to be differentially expressed (using DESeq2).<br>see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450629
title: Differentially expressed gene lists - Dhx35/Morc2a mapped without transcriptome

description: Files of differentially expressed genes (using DESeq2) from two lines (Dhx35 and Morc2a). The reads for these lines were mapped without using a reference transcriptome.<br>see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450629.v1
title: Differentially expressed gene lists - Dhx35/Morc2a mapped without transcriptome

description: Files of differentially expressed genes (using DESeq2) from two lines (Dhx35 and Morc2a). The reads for these lines were mapped without using a reference transcriptome.<br>see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450443
title: Toxic and genotoxic effects of graphene and multi-walled carbon nanotubes

description: Graphene and multi-walled carbon nanotubes (MWCNT) are widely used in nanomedicine, and other fields, due to their unique physicochemical properties including high tensile strength, ultra-light weight, thermal and chemical stability, and reliable semi-conductive electronic properties. Although extensive amount of data exist describing their adverse effects including potential genotoxicity, few studies using gene mutation detection approaches in mammalian cells are available, which represents an important gap for risk estimations. The aim of the present study was to determine the effects of graphene or MWCNT [as pure, carboxyl (COOH) functionalized, and amide (NH<sub>2</sub>) functionalized] on cytotoxicity, intracellular levels of reactive oxygen species, apoptosis, gene expression changes, and gene mutation induction in L5178Y/<i>Tk<sup>+/–</sup></i>3.7.2C mouse lymphoma cell line. Although some adverse effects were observed at concentrations of 350 and 450 µg/ml, which are excessive and not environmentally relevant levels, no marked effects were detected at concentrations of 250 µg/ml and lower. This is the first study reporting cytotoxicity, mutagenicity, and gene expression findings in the mouse lymphoma cell line for graphene and different MWCNT forms at high concentrations; however, the biological relevance of these observations needs to be assessed following chronic <i>in vivo</i> exposure.
DOI: 10.6084/m9.figshare.6450443.v1
title: Toxic and genotoxic effects of graphene and multi-walled carbon nanotubes

description: Graphene and multi-walled carbon nanotubes (MWCNT) are widely used in nanomedicine, and other fields, due to their unique physicochemical properties including high tensile strength, ultra-light weight, thermal and chemical stability, and reliable semi-conductive electronic properties. Although extensive amount of data exist describing their adverse effects including potential genotoxicity, few studies using gene mutation detection approaches in mammalian cells are available, which represents an important gap for risk estimations. The aim of the present study was to determine the effects of graphene or MWCNT [as pure, carboxyl (COOH) functionalized, and amide (NH<sub>2</sub>) functionalized] on cytotoxicity, intracellular levels of reactive oxygen species, apoptosis, gene expression changes, and gene mutation induction in L5178Y/<i>Tk<sup>+/–</sup></i>3.7.2C mouse lymphoma cell line. Although some adverse effects were observed at concentrations of 350 and 450 µg/ml, which are excessive and not environmentally relevant levels, no marked effects were detected at concentrations of 250 µg/ml and lower. This is the first study reporting cytotoxicity, mutagenicity, and gene expression findings in the mouse lymphoma cell line for graphene and different MWCNT forms at high concentrations; however, the biological relevance of these observations needs to be assessed following chronic <i>in vivo</i> exposure.
DOI: 10.6084/m9.figshare.6450371
title: Differentially expressed gene lists - unfiltered

description: Files of differentially expressed genes (using DESeq2) from different mutant lines.see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450371.v1
title: Differentially expressed gene lists - unfiltered

description: Files of differentially expressed genes (using DESeq2) from different mutant lines.see the README for more detail.<br>
DOI: 10.6084/m9.figshare.6450356
title: Supplementary Material for: Breathlessness and Restrictive Lung Disease: An Important Diabetes-Related Feature in Patients with Type 2 Diabetes

description: <b><i>Background:</i></b> Diabetes mellitus is a significant comorbidity of interstitial lung disease (ILD). <b><i>Objectives:</i></b> The aim of this study was to investigate the incidence of restrictive lung disease (RLD) and ILD in patients with prediabetes and type 2 diabetes (T2D). <b><i>Methods:</i></b> Forty-eight nondiabetics, 68 patients with prediabetes, 29 newly diagnosed T2D, and 110 patients with long-term T2D were examined for metabolic control, diabetes-related complications, breathlessness, and lung function. Five participants with T2D, breathlessness, and RLD underwent multidetector computed tomography (MDCT) and a Six-Minute Walk Test (6MWT). Lung tissue from 4 patients without diabetes and from 3 patients with T2D was histologically examined for presence of pulmonary fibrosis. <b><i>Results:</i></b> Breathlessness in combination with RLD was significantly increased in patients with prediabetes and T2D (<i>p</i> &lt; 0.01). RLD was found in 9% of patients with prediabetes, in 20% of patients with newly diagnosed T2D, and in 27% of patients with long-term T2D. Thus, patients with long-term T2D had an increased risk of RLD (OR 5.82 [95% CI 1.71–20.5], <i>p</i> &lt; 0.01). RLD was significantly associated with glucose metabolism and albuminuria (<i>p</i> &lt; 0.01); furthermore, presence of nephropathy increased the risk of RLD (OR 8.57 [95% CI 3.4–21.9], <i>p</i> &lt; 0.01) compared to nondiabetics. MDCT revealed ILD in 4 patients, the 6MWT correlated with the extent of ILD, and histological analysis showed fibrosing ILD in patients with T2D. <b><i>Conclusions:</i></b> This study demonstrates increased breathlessness and a high prevalence of RLD in patients with T2D, indicating an association between diabetes and fibrosing ILD.
DOI: 10.6084/m9.figshare.6450320
title: The Chaetophorales (Chlorophyceae) – a taxonomic revision at family level

description: The Chaetophorales (Chlorophyceae) consist of filamentous green algae that were mostly described directly from natural samples by light microscopy. However, the descriptions were often based on morphological characters that are either homoplasious or sensitive to environmental factors. This clearly prevents proper identification of several chaetophoralean taxa and highlights the need for taxonomic revision at different taxonomic levels. In the present study, we focused on revision of the Chaetophorales at the family level. We used a well-resolved molecular phylogeny to re-evaluate morphological characters in the Chaetophorales under clearly defined laboratory conditions. We identified five morphological characters that permitted unambiguous identification of most chaetophoralean families, and used these characters to establish a new family, the Fritschiellaceae (fam. nov.), and emend the Chaetophoraceae Greville 1824. Knowledge gained from this study lends additional weight to the current classification of the Chaetophorales and may serve as an example for taxonomic revisions of other complex filamentous algae.
DOI: 10.6084/m9.figshare.6450320.v1
title: The Chaetophorales (Chlorophyceae) – a taxonomic revision at family level

description: The Chaetophorales (Chlorophyceae) consist of filamentous green algae that were mostly described directly from natural samples by light microscopy. However, the descriptions were often based on morphological characters that are either homoplasious or sensitive to environmental factors. This clearly prevents proper identification of several chaetophoralean taxa and highlights the need for taxonomic revision at different taxonomic levels. In the present study, we focused on revision of the Chaetophorales at the family level. We used a well-resolved molecular phylogeny to re-evaluate morphological characters in the Chaetophorales under clearly defined laboratory conditions. We identified five morphological characters that permitted unambiguous identification of most chaetophoralean families, and used these characters to establish a new family, the Fritschiellaceae (fam. nov.), and emend the Chaetophoraceae Greville 1824. Knowledge gained from this study lends additional weight to the current classification of the Chaetophorales and may serve as an example for taxonomic revisions of other complex filamentous algae.
DOI: 10.6084/m9.figshare.6450311
title: Supplementary Material for: Acceptance and Commitment Therapy for the Management of Suicidal Patients: A Randomized Controlled Trial

description: <b><i>Background:</i></b> The management of suicidal crisis remains a major issue for clinicians, driving the development of new strategies to improve suicide prevention. <b><i>Methods:</i></b> We conducted a randomized controlled trial comparing a 7-week acceptance and commitment therapy (ACT) versus relaxation group, as adjunct to treatment as usual for adult outpatients suffering from a current suicidal behavior disorder. The primary outcome was the rate of change in the Columbia Suicide Severity Rating Scale suicidal ideation subscore (adding severity and intensity subscores). Secondary outcomes were the rates of change for depressive symptomatology, psychological pain, anxiety, hopelessness, anger, quality of life, and therapeutic processes. Assessments were performed in the 2 weeks preceding the beginning of the treatment (pretreatment assessment), and within 1 week (posttherapy assessment) and 3 months (follow-up assessment) after therapy completion. <b><i>Results:</i></b> Forty adults were included and randomized. The rate of change in ACT for suicidal ideation at the posttherapy assessment was higher than in the relaxation group (β [SE] = –1.88 [0.34] vs. –0.79 [0.37], respectively; <i>p</i> = 0.03). ACT effectiveness remained stable at the 3-month follow-up. We found a similar pattern of change for depressive symptomatology and anxiety, psychological pain, hopelessness, anger, and quality of life. Therapeutic processes improved more in the ACT group than in the relaxation group. Treatment adherence was high in the ACT group, all participants reported satisfaction with the program. <b><i>Conclusions:</i></b> Through its effectiveness in reducing suicidal ideation and improving the clinical dimensions associated with suicidal risk in patients suffering from a suicidal behavior disorder, ACT could be developed as an adjunctive strategy in programs for suicide prevention.
DOI: 10.6084/m9.figshare.6450311.v1
title: Supplementary Material for: Acceptance and Commitment Therapy for the Management of Suicidal Patients: A Randomized Controlled Trial

description: <b><i>Background:</i></b> The management of suicidal crisis remains a major issue for clinicians, driving the development of new strategies to improve suicide prevention. <b><i>Methods:</i></b> We conducted a randomized controlled trial comparing a 7-week acceptance and commitment therapy (ACT) versus relaxation group, as adjunct to treatment as usual for adult outpatients suffering from a current suicidal behavior disorder. The primary outcome was the rate of change in the Columbia Suicide Severity Rating Scale suicidal ideation subscore (adding severity and intensity subscores). Secondary outcomes were the rates of change for depressive symptomatology, psychological pain, anxiety, hopelessness, anger, quality of life, and therapeutic processes. Assessments were performed in the 2 weeks preceding the beginning of the treatment (pretreatment assessment), and within 1 week (posttherapy assessment) and 3 months (follow-up assessment) after therapy completion. <b><i>Results:</i></b> Forty adults were included and randomized. The rate of change in ACT for suicidal ideation at the posttherapy assessment was higher than in the relaxation group (β [SE] = –1.88 [0.34] vs. –0.79 [0.37], respectively; <i>p</i> = 0.03). ACT effectiveness remained stable at the 3-month follow-up. We found a similar pattern of change for depressive symptomatology and anxiety, psychological pain, hopelessness, anger, and quality of life. Therapeutic processes improved more in the ACT group than in the relaxation group. Treatment adherence was high in the ACT group, all participants reported satisfaction with the program. <b><i>Conclusions:</i></b> Through its effectiveness in reducing suicidal ideation and improving the clinical dimensions associated with suicidal risk in patients suffering from a suicidal behavior disorder, ACT could be developed as an adjunctive strategy in programs for suicide prevention.
DOI: 10.6084/m9.figshare.6450302
title: BioLayout Data for baseline samples

description: BioLayout input and .layout files for the baseline co-expression correlation networks.
DOI: 10.6084/m9.figshare.6450236
title: Supplementary Material for: Practice Patterns for Chronic Respiratory Diseases in the Asia-Pacific Region: A Cross-Sectional Observational Study

description: <b><i>Background:</i></b> Allergic rhinitis (AR), asthma, chronic obstructive pulmonary disease (COPD), and rhinosinusitis are common and little studied in the Asia-Pacific region. <b><i>Objectives:</i></b> We sought to investigate real-world practice patterns for these respiratory diseases in India, Korea, Malaysia, Singapore, Taiwan, and Thailand. <b><i>Methods:</i></b> This cross-sectional observational study enrolled adults (age ≥18 years) presenting to general practitioners (GP) or specialists for physician-diagnosed AR, asthma, COPD, or rhinosinusitis. Physicians and patients completed study-specific surveys at one visit, recording patient characteristics, health-related quality of life (QoL), work impairment, and healthcare resource use. Findings by country and physician category (GP or specialist) were summarized. <b><i>Results:</i></b> Of the 13,902 patients screened, 7,243 (52%) presented with AR (18%), asthma (18%), COPD (7%), or rhinosinusitis (9%); 5,250 of the 7,243 (72%) patients were eligible for this study. Most eligible patients (70–100%) in India, Korea, Malaysia, and Singapore attended GP, while most (83–85%) in Taiwan and Thailand attended specialists. From 42% (rhinosinusitis) to 67% (AR) of new diagnoses were made by GP. On average, patients with COPD reported the worst health-related QoL, particularly to GP. Median losses of work productivity for each condition and activity impairment, except for asthma, were numerically greater for patients presenting to GP vs. specialists. GP prescribed more antibiotics for AR and asthma, and fewer intranasal corticosteroids for AR, than specialists (<i>p</i> &lt; 0.001 for all comparisons). <b><i>Conclusions:</i></b> Our findings, albeit mostly descriptive and influenced by between-country differences, suggest that practice patterns differ between physician types, and the disease burden may be substantial for patients presenting in general practice.
DOI: 10.6084/m9.figshare.6450215
title: Supplementary Material for: Increased Susceptibility to Allergic Asthma with the Impairment of Respiratory Tolerance Caused by Psychological Stress

description: <b><i>Background:</i></b> Bronchial asthma is characterized by type 2 T helper (Th2) cell inflammation, essentially due to a breakdown of immune tolerance to harmless environmental allergens. Etiologically, experiences of psychological stress can be associated with a heightened prevalence of asthma. However, the mechanisms underlying stress-related asthma development are unclear. In this study, we examined whether psychological stress increases susceptibility to allergic asthma by downregulating immune tolerance. <b><i>Methods:</i></b> Female BALB/c mice were sensitized with ovalbumin/alum, followed by ovalbumin inhalation. Ovalbumin inhalation induced immune tolerance before sensitization occurred. Some mice were exposed to restraint stress during tolerance induction or sensitization. Asthma development was evaluated by airway responsiveness, inflammation, cytokine expression, and IgE synthesis. Sensitization was evaluated by measuring proliferation and cytokine production by splenocytes. The effects of stress exposure on the numbers and functions of dendritic cells and regulatory T (Treg) cells in bronchial lymph nodes and spleens were evaluated. To investigate the role of endogenous glucocorticoid in inhibiting immune tolerance after stress exposure, we examined the effects of (i) a glucocorticoid-receptor antagonist administered prior to stress exposure, and (ii) exogenous gluco­corticoid (instead of stress exposure). <b><i>Results:</i></b> Asthmatic responses and Th2-biased sensitization, which were suppressed in tolerized mice, re-emerged in tolerized mice stressed during tolerance induction in association with decreased tolerogenic dendritic and Treg cell numbers. The effects of stress exposure on tolerized mice were abolished by administering a glucocorticoid-receptor antagonist and reproduced by administering exogenous glucocorticoid without stress. <b><i>Conclusions:</i></b> Our findings suggested that psychological stress can potentially increase allergic asthma susceptibility by inhibiting immune tolerance.
DOI: 10.6084/m9.figshare.6450191
title: Pubertal status and depression

description: Data for paper in PLOS One on associations between pubertal development and depressive symptoms and diagnoses in adolescent females
DOI: 10.6084/m9.figshare.6450149
title: Supplementary Material for: Sleep Disturbance and the Risk of Cognitive Decline or Clinical Conversion in the ADNI Cohort

description: <b><i>Background:</i></b> We investigated the relationship between sleep disturbance and cognitive decline or clinical conversion in individuals with normal cognition (CN), as well as those with mild cognitive impairment (MCI) and dementia due to Alzheimer disease (AD-dementia). <b><i>Methods:</i></b> Secondary analysis of 1,629 adults between 48 and 91 years of age with up to 24 months of follow-up from the ADNI (Alzheimer’s Disease Neuroimaging Initiative), a longitudinal cohort study. <b><i>Results:</i></b> Sleep disturbance was not associated with decline in memory, executive function, or global cognition. The presence of sleep disturbance did not significantly increase the risk of diagnostic conversion in CN, early MCI, or late MCI participants. <b><i>Conclusion:</i></b> This study investigated the effect of sleep disturbance on cognitive decline using several outcomes and does not support the hypothesis that sleep disturbance predicts subsequent cognitive decline.
DOI: 10.6084/m9.figshare.6450098
title: Supplementary Material for: Rapid On-Site Evaluation of Fine-Needle Aspiration by Non-Cytopathologists: A Systematic Review and Meta-Analysis of Diagnostic Accuracy Studies for Adequacy Assessment

description: <b><i>Objective:</i></b> Rapid on-site evaluation (ROSE) has been shown to improve adequacy rates and reduce needle passes. ROSE is often performed by cytopathologists who have limited availability and may be costlier than alternatives. Several recent studies examined the use of alternative evaluators (AEs) for ROSE. A summary of this information could help inform guidelines regarding the use of AEs. The objective was to assess the accuracy of AEs compared to cytopathologists in assessing the adequacy of specimens during ROSE. <b><i>Study Design:</i></b> This was a systematic review and meta-analysis. Reporting and study quality were assessed using the STARD guidelines and QUADAS-2. All steps were performed independently by two evaluators. Summary estimates were obtained using the hierarchal method in Stata v14. Heterogeneity was evaluated using Higgins’ <i>I</i><sup>2</sup> statistic. <b><i>Results:</i></b> The systematic review identified 13 studies that were included in the meta-analysis. Summary estimates of sensitivity and specificity for AEs were 97% (95% CI: 92–99%) and 83% (95% CI: 68–92%). There was wide variation in accuracy statistics between studies (<i>I</i><sup>2</sup> = 0.99). <b><i>Conclusions:</i></b> AEs sometimes have accuracy that is close to cytopathologists. However, there is wide variability between studies, so it is not possible to provide a broad guideline regarding the use of AEs.