cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5584489
title: Supplementary Material for: A Prospective Study to Evaluate a Diagnostic Algorithm for the Use of Fluid Lymphocyte Subset Analysis in Undiagnosed Unilateral Pleural Effusions

description: <b><i>Background:</i></b> Haematological malignancy is an important cause of pleural effusion. Pleural effusions secondary to haematological malignancy are usually lymphocyte predominant. However, several other conditions such as carcinoma, tuberculosis, and chronic heart failure also cause lymphocytic effusions. Lymphocyte subset (LS) analysis may be a useful test to identify haematological malignancy in patients with lymphocytic effusions. However, research into their utility in pleural effusion diagnostic algorithms has not yet been published. <b><i>Objectives:</i></b> We aimed to determine the clinical utility of pleural fluid LS analysis and whether it can be applied to a diagnostic algorithm to identify effusions secondary to haematological malignancy. The secondary aim was to evaluate the diagnostic value of pleural fluid differential cell count. <b><i>Methods:</i></b> Consecutive consenting patients presenting to our pleural service between 2008 and 2013 underwent thoracentesis and differential cell count analysis. We proposed an algorithm which selected patients with lymphocytic effusions (&gt;50%) to have further fluid sent for LS analysis. Two independent consultants agreed on the cause of the original effusion after a 12-month follow-up period. <b><i>Results:</i></b> A total of 60 patients had samples sent for LS analysis. LS analysis had an 80% sensitivity (8/10) and a 100% specificity for the diagnosis of haematological malignancy. The positive and negative predictive values were 100 and 96.1%, respectively. Overall 344 differential cell counts were analysed; 16% of pleural effusions with a malignant aetiology were neutrophilic or eosinophilic at presentation. A higher neutrophil and eosinophil count was associated with benign diagnoses, whereas a higher lymphocyte count was associated with malignant diagnoses. <b><i>Conclusions:</i></b> LS analysis may identify haematological malignancy in a specific cohort of patients with undiagnosed pleural effusions. A pleural fluid differential cell count provides useful additional information to streamline patient pathway decisions.
DOI: 10.6084/m9.figshare.5584477
title: MLDP-InstanceSet

description: Instance set tested for MLDP PhD research
DOI: 10.6084/m9.figshare.5584477.v1
title: MLDP-InstaceSet

description: Instance set tested for MLDP PhD research
DOI: 10.6084/m9.figshare.5584489.v1
title: Supplementary Material for: A Prospective Study to Evaluate a Diagnostic Algorithm for the Use of Fluid Lymphocyte Subset Analysis in Undiagnosed Unilateral Pleural Effusions

description: <b><i>Background:</i></b> Haematological malignancy is an important cause of pleural effusion. Pleural effusions secondary to haematological malignancy are usually lymphocyte predominant. However, several other conditions such as carcinoma, tuberculosis, and chronic heart failure also cause lymphocytic effusions. Lymphocyte subset (LS) analysis may be a useful test to identify haematological malignancy in patients with lymphocytic effusions. However, research into their utility in pleural effusion diagnostic algorithms has not yet been published. <b><i>Objectives:</i></b> We aimed to determine the clinical utility of pleural fluid LS analysis and whether it can be applied to a diagnostic algorithm to identify effusions secondary to haematological malignancy. The secondary aim was to evaluate the diagnostic value of pleural fluid differential cell count. <b><i>Methods:</i></b> Consecutive consenting patients presenting to our pleural service between 2008 and 2013 underwent thoracentesis and differential cell count analysis. We proposed an algorithm which selected patients with lymphocytic effusions (&gt;50%) to have further fluid sent for LS analysis. Two independent consultants agreed on the cause of the original effusion after a 12-month follow-up period. <b><i>Results:</i></b> A total of 60 patients had samples sent for LS analysis. LS analysis had an 80% sensitivity (8/10) and a 100% specificity for the diagnosis of haematological malignancy. The positive and negative predictive values were 100 and 96.1%, respectively. Overall 344 differential cell counts were analysed; 16% of pleural effusions with a malignant aetiology were neutrophilic or eosinophilic at presentation. A higher neutrophil and eosinophil count was associated with benign diagnoses, whereas a higher lymphocyte count was associated with malignant diagnoses. <b><i>Conclusions:</i></b> LS analysis may identify haematological malignancy in a specific cohort of patients with undiagnosed pleural effusions. A pleural fluid differential cell count provides useful additional information to streamline patient pathway decisions.
DOI: 10.6084/m9.figshare.5584438
title: Supplementary Material for: Recurrent Copy Number Variants Associated with Syndromic Short Stature of Unknown Cause

description: <b><i>Background/Aims:</i></b> Genetic imbalances are responsible for many cases of short stature of unknown etiology. This study aims to identify recurrent pathogenic copy number variants (CNVs) in patients with syndromic short stature of unknown cause. <b><i>Methods:</i></b> We selected 229 children with short stature and dysmorphic features, developmental delay, and/or intellectual disability, but without a recognized syndrome. All patients were evaluated by chromosomal microarray (array-based comparative genomic hybridization/single nucleotide polymorphism array). Additionally, we searched databases and previous studies to recover recurrent pathogenic CNVs associated with short stature. <b><i>Results:</i></b> We identified 32 pathogenic/probably pathogenic CNVs in 229 patients. By reviewing the literature, we selected 4 previous studies which evaluated CNVs in cohorts of patients with short stature. Taken together, there were 671 patients with short stature of unknown cause evaluated by chromosomal microarray. Pathogenic/probably pathogenic CNVs were identified in 87 patients (13%). Seven recurrent CNVs, 22q11.21, 15q26, 1p36.33, Xp22.33, 17p13.3, 1q21.1, 2q24.2, were observed. They are responsible for about 40% of all pathogenic/probably pathogenic genomic imbalances found in short stature patients of unknown cause. <b><i>Conclusion:</i></b> CNVs seem to play a significant role in patients with short stature. Chromosomal microarray should be used as a diagnostic tool for evaluation of growth disorders, especially for syndromic short stature of unknown cause.
DOI: 10.6084/m9.figshare.5584438.v1
title: Supplementary Material for: Recurrent Copy Number Variants Associated with Syndromic Short Stature of Unknown Cause

description: <b><i>Background/Aims:</i></b> Genetic imbalances are responsible for many cases of short stature of unknown etiology. This study aims to identify recurrent pathogenic copy number variants (CNVs) in patients with syndromic short stature of unknown cause. <b><i>Methods:</i></b> We selected 229 children with short stature and dysmorphic features, developmental delay, and/or intellectual disability, but without a recognized syndrome. All patients were evaluated by chromosomal microarray (array-based comparative genomic hybridization/single nucleotide polymorphism array). Additionally, we searched databases and previous studies to recover recurrent pathogenic CNVs associated with short stature. <b><i>Results:</i></b> We identified 32 pathogenic/probably pathogenic CNVs in 229 patients. By reviewing the literature, we selected 4 previous studies which evaluated CNVs in cohorts of patients with short stature. Taken together, there were 671 patients with short stature of unknown cause evaluated by chromosomal microarray. Pathogenic/probably pathogenic CNVs were identified in 87 patients (13%). Seven recurrent CNVs, 22q11.21, 15q26, 1p36.33, Xp22.33, 17p13.3, 1q21.1, 2q24.2, were observed. They are responsible for about 40% of all pathogenic/probably pathogenic genomic imbalances found in short stature patients of unknown cause. <b><i>Conclusion:</i></b> CNVs seem to play a significant role in patients with short stature. Chromosomal microarray should be used as a diagnostic tool for evaluation of growth disorders, especially for syndromic short stature of unknown cause.
DOI: 10.6084/m9.figshare.5584420
title: Variations in physiological, biochemical, and structural traits of photosynthesis and resource use efficiency in maize and teosintes (NADP-ME-type C<sub>4</sub>)

description: C<sub>4</sub> plants show higher photosynthetic capacity and resource use efficiency than C<sub>3</sub> plants. However, the genetic variations of these traits and their regulatory factors in C<sub>4</sub> plants still remain to be resolved. We investigated physiological, biochemical, and structural traits involved in photosynthesis and photosynthetic water and nitrogen use efficiencies (PWUE and PNUE) in 22 maize lines and four teosinte lines from various regions of the world. Net photosynthetic rate (<i>P</i><sub><i>N</i></sub>) ranged from 32.1 to 46.5 μmol m<sup>−2</sup> s<sup>−1</sup>. <i>P</i><sub><i>N</i></sub> was positively correlated with stomatal conductance, transpiration rate, and chlorophyll, nitrogen and soluble protein contents of leaves, but not with specific leaf weight. <i>P</i><sub><i>N</i></sub> was positively correlated with the activities of ribulose-1,5-bisphosphate carboxylase/oxygenase and the C<sub>4</sub>-acid decarboxylases, NADP-malic enzyme and phospho<i>enol</i>pyruvate carboxykinase, but not with the activity of phospho<i>enol</i>pyruvate carboxylase. Leaf structural traits (stomatal parameters, leaf thickness, and interveinal distance) were not correlated with <i>P</i><sub><i>N</i></sub>. These data suggest that physiological and biochemical traits are involved in the genetic variation of <i>P</i><sub><i>N</i></sub>, but structural traits are not directly involved. PWUE is in the lower class of values reported for C<sub>4</sub> plants, whereas PNUE is in the highest class of values reported for C<sub>4</sub> plants. PNUE was negatively correlated with leaf nitrogen content but not significantly correlated with <i>P</i><sub><i>N</i></sub>. PWUE was not correlated with <i>δ</i><sup>13</sup>C values of leaves, indicating difficulty in using <i>δ</i><sup>13</sup>C values as an indicator of PWUE of maize. In general, teosinte lines showed lower <i>P</i><sub><i>N</i></sub> but higher PWUE than maize lines.
DOI: 10.6084/m9.figshare.5584420.v1
title: Variations in physiological, biochemical, and structural traits of photosynthesis and resource use efficiency in maize and teosintes (NADP-ME-type C<sub>4</sub>)

description: C<sub>4</sub> plants show higher photosynthetic capacity and resource use efficiency than C<sub>3</sub> plants. However, the genetic variations of these traits and their regulatory factors in C<sub>4</sub> plants still remain to be resolved. We investigated physiological, biochemical, and structural traits involved in photosynthesis and photosynthetic water and nitrogen use efficiencies (PWUE and PNUE) in 22 maize lines and four teosinte lines from various regions of the world. Net photosynthetic rate (<i>P</i><sub><i>N</i></sub>) ranged from 32.1 to 46.5 μmol m<sup>−2</sup> s<sup>−1</sup>. <i>P</i><sub><i>N</i></sub> was positively correlated with stomatal conductance, transpiration rate, and chlorophyll, nitrogen and soluble protein contents of leaves, but not with specific leaf weight. <i>P</i><sub><i>N</i></sub> was positively correlated with the activities of ribulose-1,5-bisphosphate carboxylase/oxygenase and the C<sub>4</sub>-acid decarboxylases, NADP-malic enzyme and phospho<i>enol</i>pyruvate carboxykinase, but not with the activity of phospho<i>enol</i>pyruvate carboxylase. Leaf structural traits (stomatal parameters, leaf thickness, and interveinal distance) were not correlated with <i>P</i><sub><i>N</i></sub>. These data suggest that physiological and biochemical traits are involved in the genetic variation of <i>P</i><sub><i>N</i></sub>, but structural traits are not directly involved. PWUE is in the lower class of values reported for C<sub>4</sub> plants, whereas PNUE is in the highest class of values reported for C<sub>4</sub> plants. PNUE was negatively correlated with leaf nitrogen content but not significantly correlated with <i>P</i><sub><i>N</i></sub>. PWUE was not correlated with <i>δ</i><sup>13</sup>C values of leaves, indicating difficulty in using <i>δ</i><sup>13</sup>C values as an indicator of PWUE of maize. In general, teosinte lines showed lower <i>P</i><sub><i>N</i></sub> but higher PWUE than maize lines.
DOI: 10.6084/m9.figshare.5584231
title: data

description: Data from manuscript titled "The Reciprocal Relations between Experiential Avoidance, School Stressor, and Psychological Stress Response among Japanese Adolescents" <br>
DOI: 10.6084/m9.figshare.5584231.v1
title: data

description: Data from manuscript titled "The Reciprocal Relations between Experiential Avoidance, School Stressor, and Psychological Stress Response among Japanese Adolescents" <br>
DOI: 10.6084/m9.figshare.5584216
title: Data from Incubation environment impacts the social cognition of adult lizards

description: The data associated with this publication
DOI: 10.6084/m9.figshare.5584216.v1
title: Data from Incubation environment impacts the social cognition of adult lizards

description: The data associated with this publication
DOI: 10.6084/m9.figshare.5584183
title: Using the EM algorithm for Bayesian variable selection in logistic regression models with related covariates

description: We develop a Bayesian variable selection method for logistic regression models that can simultaneously accommodate qualitative covariates and interaction terms under various heredity constraints. We use expectation-maximization variable selection (EMVS) with a deterministic annealing variant as the platform for our method, due to its proven flexibility and efficiency. We propose a variance adjustment of the priors for the coefficients of qualitative covariates, which controls false-positive rates, and a flexible parameterization for interaction terms, which accommodates user-specified heredity constraints. This method can handle all pairwise interaction terms as well as a subset of specific interactions. Using simulation, we show that this method selects associated covariates better than the grouped LASSO and the LASSO with heredity constraints in various exploratory research scenarios encountered in epidemiological studies. We apply our method to identify genetic and non-genetic risk factors associated with smoking experimentation in a cohort of Mexican-heritage adolescents.
DOI: 10.6084/m9.figshare.5584183.v1
title: Using the EM algorithm for Bayesian variable selection in logistic regression models with related covariates

description: We develop a Bayesian variable selection method for logistic regression models that can simultaneously accommodate qualitative covariates and interaction terms under various heredity constraints. We use expectation-maximization variable selection (EMVS) with a deterministic annealing variant as the platform for our method, due to its proven flexibility and efficiency. We propose a variance adjustment of the priors for the coefficients of qualitative covariates, which controls false-positive rates, and a flexible parameterization for interaction terms, which accommodates user-specified heredity constraints. This method can handle all pairwise interaction terms as well as a subset of specific interactions. Using simulation, we show that this method selects associated covariates better than the grouped LASSO and the LASSO with heredity constraints in various exploratory research scenarios encountered in epidemiological studies. We apply our method to identify genetic and non-genetic risk factors associated with smoking experimentation in a cohort of Mexican-heritage adolescents.
DOI: 10.6084/m9.figshare.5584138
title: Data for Davies, Gaylard & Asner, Ecological Applications

description: Data files (CSV and TXT) supporting the analyses in the paper: Megafaunal effects on vegetation structure throughout a densely wooded African landscape
DOI: 10.6084/m9.figshare.5584138.v1
title: Data for Davies, Gaylard & Asner, Ecological Applications

description: Data files (CSV and TXT) supporting the analyses in the paper: Megafaunal effects on vegetation structure throughout a densely wooded African landscape
DOI: 10.6084/m9.figshare.5584099
title: I hardly see my baby: challenges and highlights of being a New Zealand working mother of an infant

description: Combining motherhood and paid work presents a significant challenge for many women. We asked 2388 working New Zealand mothers of infants about their biggest highlight and challenge since the birth of their child. Thematic analysis revealed the top three reported highlights were Enjoyment of the Child (40%), Child Development (29%) and Attributes of the Child (16%). The top three challenges included Time Management (24%), difficulties with maternal role and responsibilities (21%) and work-related challenges (18%). Using logistic regression, working was more likely to be reported as a challenge by mothers who worked longer hours, returned to work when their infants were younger, had greater household incomes, or expressed concern about negative career consequences if they stayed on leave. Working was less likely to be reported as a challenge for mothers whose infants had health or developmental problems and who ‘wanted to get out of the house’. Practical implications are explored.
DOI: 10.6084/m9.figshare.5584099.v1
title: I hardly see my baby: challenges and highlights of being a New Zealand working mother of an infant

description: Combining motherhood and paid work presents a significant challenge for many women. We asked 2388 working New Zealand mothers of infants about their biggest highlight and challenge since the birth of their child. Thematic analysis revealed the top three reported highlights were Enjoyment of the Child (40%), Child Development (29%) and Attributes of the Child (16%). The top three challenges included Time Management (24%), difficulties with maternal role and responsibilities (21%) and work-related challenges (18%). Using logistic regression, working was more likely to be reported as a challenge by mothers who worked longer hours, returned to work when their infants were younger, had greater household incomes, or expressed concern about negative career consequences if they stayed on leave. Working was less likely to be reported as a challenge for mothers whose infants had health or developmental problems and who ‘wanted to get out of the house’. Practical implications are explored.
DOI: 10.6084/m9.figshare.5583760
title: Data S1.zip

description: Candidate model set constructed to investigate drivers of vegetation height across two elephant treatments in Addo Elephant National Park, South Africa.
DOI: 10.6084/m9.figshare.5583760.v1
title: Data S1.zip

description: Candidate model set constructed to investigate drivers of vegetation height across two elephant treatments in Addo Elephant National Park, South Africa.
DOI: 10.6084/m9.figshare.5581249
title: Appendix to The OA Effect (PDF)

description: Appendix to The OA Effect (PDF)
DOI: 10.6084/m9.figshare.5581252
title: Appendix to The OA Effect (spreadsheet)

description: Appendix to The OA Effect (spreadsheet)
DOI: 10.6084/m9.figshare.5581249.v1
title: Appendix to The OA Effect (PDF)

description: Appendix to The OA Effect (PDF)
DOI: 10.6084/m9.figshare.5581252.v1
title: Appendix to The OA Effect (spreadsheet)

description: Appendix to The OA Effect (spreadsheet)
DOI: 10.6084/m9.figshare.5580091
title: GENESIS_ReplicationDataset.csv

description: GENESIS case-control study<br>
DOI: 10.6084/m9.figshare.5580091.v1
title: GENESIS_ReplicationDataset.csv

description: GENESIS case-control study<br>
DOI: 10.6084/m9.figshare.5580061
title: Supplementary Material for: Mechanisms of Targeting the MDM2-p53-FOXM1 Axis in Well-Differentiated Intestinal Neuroendocrine Tumors

description: <b><i>Background/Aims:</i></b> The tumor suppressor p53 is rarely mutated in gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) but they frequently show a strong expression of negative regulators of p53, rendering these tumors excellent targets for a p53 recovery therapy. Therefore, we analyzed the mechanisms of a p53 recovery therapy on intestinal neuroendocrine tumors in vitro and in vivo<i>.</i><b><i>Methods:</i></b> By Western blot and immunohistochemistry, we found that in GEP-NEN biopsy material overexpression of MDM2 was present in intestinal NEN. Therefore, we analyzed the effect of a small-molecule inhibitor, nutlin-3a, in p53 wild-type and mutant GEP-NEN cell lines by proliferation assay, flow cytometry, immunofluorescence, Western blot, and by multiplex gene expression analysis. Finally, we analyzed the antitumor effect of nutlin-3a in a xenograft mouse model in vivo. During the study, the tumor volume was determined. <b><i>Results:</i></b> The midgut wild-type cell line KRJ-I responded to the treatment with cell cycle arrest and apoptosis. By gene expression analysis, we could demonstrate that nutlins reactivated an antiproliferative p53 response. KRJ-I-derived xenograft tumors showed a significantly decreased tumor growth upon treatment with nutlin-3a in vivo. Furthermore, our data suggest that MDM2 also influences the expression of the oncogene FOXM1 in a p53-independent manner. Subsequently, a combined treatment of nutlin-3a and cisplatin (as chemoresistance model) resulted in synergistically enhanced antiproliferative effects. <b><i>Conclusion:</i></b> In summary, MDM2 overexpression is a frequent event in p53 wild-type intestinal neuroendocrine neoplasms and therefore recovery of a p53 response might be a novel personalized treatment approach in these tumors.
DOI: 10.6084/m9.figshare.5579998
title: Supplementary Material for: The Cerebellar-Cerebral Microstructure Is Disrupted at Multiple Sites in Very Preterm Infants with Cerebellar Haemorrhage

description: <b><i>Background:</i></b> Recent advances in magnetic resonance imaging (MRI) techniques have prompted reconsideration of the anatomical correlates of adverse outcomes in preterm infants. The importance of the contribution made by the cerebellum is now increasingly appreciated. The effect of cerebellar haemorrhage (CBH) on the microstructure of the cerebellar-cerebral circuit is largely unexplored. <b><i>Objectives:</i></b> To investigate the effect of CBH on the microstructure of cerebellar-cerebral connections in preterm infants aged &lt;32 gestational weeks. <b><i>Methods:</i></b> Infants underwent diffusion tensor MRI at term-equivalent age. MRI was evaluated for CBH and additional supratentorial brain injury using a validated scoring system. Region of interest-based measures of brain microstructure (fractional anisotropy [FA] and apparent diffusion coefficient) were quantified in 5 vulnerable regions (the centrum semiovale, posterior limb of the internal capsule, corpus callosum, and superior and middle cerebellar peduncles). Group differences between infants with CBH and infants without CBH were assessed. <b><i>Results:</i></b> There were 267 infants included in the study. Infants with CBH (isolated and combined) had significantly lower FA values in all regions investigated. Infants with isolated CBH showed lower FA in the middle and superior cerebellar peduncles and in the posterior limb of the internal capsule. <b><i>Conclusions:</i></b> This study provides evidence that CBH causes alterations in localised and remote WM pathways in the developing brain. The disruption of the cerebellar-cerebral microstructure at multiple sites adds further support for the concept of developmental diaschisis, which is propagated as an explanation for the consequences of early cerebellar injury on cognitive and affective domains.