cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125009.v1
title: Supplementary Material for: The Use of Haplotypes in the Identification of Interaction between SNPs

description: Although haplotypes can provide great insight into the complex relationships between functional polymorphisms at a locus, their use in modern association studies has been limited. This is due to our inability to directly observe haplotypes in studies of unrelated individuals, but also to the extra complexity involved in their analysis and the difficulty in identifying which is the truly informative haplotype. Using a series of simulations, we tested a number of different models of a haplotype carrying two functional single nucleotide polymorphisms (SNPs) to assess the ability of haplotypic analysis to identify functional interactions between SNPs at the same locus. We found that, when phase is known, analysis of the haplotype is more powerful than analysis of the individual SNPs. The difference between the two approaches becomes less either as an increasing number of non-informative SNPs are included, or when the haplotypic phase is unknown, while in both cases the SNP association becomes progressively better at identifying the association. Our results suggest that when novel genotyping and bioinformatics methods are available to reconstruct haplotypic phase, this will permit the emergence of a new wave of haplotypic analysis able to consider interactions between SNPs with increased statistical power.
DOI: 10.6084/m9.figshare.5125006.v1
title: Supplementary Material for: Comparison of Exhaled Endogenous Particles from Smokers and Non-Smokers Using Multivariate Analysis

description: <b><i>Background:</i></b> Smoking, along with many respiratory diseases, has been shown to induce airway inflammation and alter the composition of the respiratory tract lining fluid (RTLF). We have previously shown that the phospholipid and protein composition of particles in exhaled air (PEx) reflects that of RTLF. In this study, we hypothesized that the composition of PEx differs between smokers and non-smokers, reflecting inflammation in the airways. <b><i>Objective:</i></b> It was the aim of this study to identify differences in the phospholipid composition of PEx from smokers and non-smokers. <b><i>Methods:</i></b> PEx from 12 smokers and 13 non-smokers was collected using a system developed in-house. PEx was analysed using time-of-flight secondary ion mass spectrometry, and the mass spectral data were evaluated using multivariate analysis. Orthogonal partial least squares (OPLS) was used to relate smoking status, lung function and pack years to the chemical composition of RTLF. The discriminating ions identified by OPLS were then used as explanatory variables in traditional regression analysis. <b><i>Results:</i></b> There was a clear discrimination between smokers and non-smokers according to the chemical composition, where phospholipids from smokers were protonated and sodiated to a larger extent. Poor lung function showed a strong association with higher response from all molecular phosphatidylcholine species in the samples. Furthermore, the accumulated amount of tobacco consumed was associated with variations in mass spectra, indicating a dose-response relationship. <b><i>Conclusion:</i></b> The chemical composition of PEx differs between smokers and non-smokers, reflecting differences in the RTLF. The results from this study may suggest that the composition of RTLF is affected by smoking and may be of importance for lung function.
DOI: 10.6084/m9.figshare.5124994
title: Supplementary Material for: Gehirn ohne Geist? - armes reiches Europa!

description: Medicine
DOI: 10.6084/m9.figshare.5124994.v1
title: Supplementary Material for: Gehirn ohne Geist? - armes reiches Europa!

description: Medicine
DOI: 10.6084/m9.figshare.5125000
title: Supplementary Material for: Are Transrectal Prostate Biopsies Routinely Indicated in Patients with Incidentally Diagnosed Prostate Cancer following Transurethral Resection of the Prostate for Benign Disease?

description: <b><i>Objective:</i></b> To determine the indication of routine transrectal ultrasound-guided needle biopsy (TRUSBx) of the prostate gland following incidental cancer diagnosis after transurethral resection of the prostate (TURP) for benign prostatic hyperplasia. <b><i>Materials and Methods:</i></b> A multi-institutional search identified 63 patients with incidental TURP-diagnosed prostate cancer from 2001 to 2010, who underwent subsequent TRUSBx or radical prostatectomy (RP). The Gleason scores from TURP were compared to those from TRUSBx or RP. Whole mount maps from RP were analysed to provide an anatomical basis for the correlation observed. To determine the clinical impact of this problem, the incidence of TURP-diagnosed prostate cancer in the population was also determined. <b><i>Results:</i></b> Of 22 patients who underwent TRUSBx, the rates of Gleason score concordance, upgrading and downgrading were 32, 14 and 54% respectively (Spearman correlation coefficient 0.20). Most cases of pathological downgrading consisted of benign cores at biopsy. Therefore, TRUSBx did not give additional Gleason score (GS) information in 86% of patients. Of 41 RP patients, the respective rates were 61, 22 and 17% (Spearman correlation coefficient 0.15). The majority of them retained a similar or lower GS between TURP and RP. Of 13 whole mount maps analysed, 6 (46%) were found with anterior/transitional zone (AZ/TZ) tumours, 6 (46%) with multifocal tumours and 1 (8%) with a large peripheral zone (PZ) tumour extending into the TZ. Regional population data show that despite a gradual reduction in the proportion of TURP-diagnosed cases over the past decade, they still account for 8.5-13% of all new cases. <b><i>Conclusion:</i></b> TURP-diagnosed prostate cancers represent predominantly AZ tumours. A TRUSBx does not give additional GS information in a majority of cases, and therefore is not routinely indicated. It may be selectively useful prior to active surveillance, but not in all pursuing radical treatment. These findings may help reduce unnecessary TRUSBx in the population.
DOI: 10.6084/m9.figshare.5125003.v1
title: Supplementary Material for: A Systematic Review of the Association between Pulmonary Tuberculosis and the Development of Chronic Airflow Obstruction in Adults

description: <b><i>Background:</i></b> Chronic obstructive pulmonary disease (COPD) is a major public health concern, accounting for 3 million deaths annually, 90% of which occur in low- and middle-income countries. Pulmonary tuberculosis (PTB) as a contributory factor in the aetiology of COPD is under debate, with most epidemiologic evidence suggesting a positive association. <b><i>Objectives:</i></b> To compile a systematic review of evidence for an association between PTB and the development of chronic airflow obstruction (CAO). <b><i>Methods:</i></b> We performed a systematic review of original English-language, peer-reviewed literature using the PubMed/MEDLINE database. CAO was defined by spirometry [FEV<sub>1</sub>:FVC ratio &lt;0.70 or <i>Results:</i> Nineteen studies (1 case series, 3 case-control studies, 4 cohort studies, 8 single-centre cross-sectional studies and 3 multi-centre cross-sectional studies) met the eligibility criteria. All but 2 reported a positive association between PTB and CAO. Three of 4 large population-based surveys (n = 4,291-8,066) confirmed a significant association between PTB and CAO (OR 1.37 - 2.94). A formal meta-analysis was not possible owing to marked heterogeneity between studies. <b><i>Conclusions: </i></b>This systematic review confirms evidence for a positive association between a past history of tuberculosis and the presence of CAO. The association is independent of cigarette smoking. Causality is likely but cannot be assumed.
DOI: 10.6084/m9.figshare.5125087.v5
title: Inferring the effects of sink strength on plant carbon balance processes from experimental measurements

description: This folder consists of existing dataset from the container volume experiment which was carried out at the Hawkesbury Forest Experiment site (33°37'S 150°44'E) in Richmond, NSW, Australia. The site and experimental setup have been explained in detail by Campany et al. (2017). <br>In brief, 20 weeks old Eucalyptus tereticornis seedlings in tube stock were chosen from a single local Cumberland plain cohort. Ten additional seedlings of similar age and growth were harvested to measure initial leaf area and dry mass of leaves, stems and roots. A total of 49 Eucalyptus tereticornis seedlings were grown in a range of container sizes (5 L to 35 L) in field conditions, using freely-rooted seedlings as a control for the container size treatments, with the goal to examine how the C balance of the plants are affected to belowground sink limitations. Six container sizes were used with each container experiment had a complete replicate set of six container volumes along with a free seedling. Similar notations are used here as Campany et al. (2017) for the treatments in different pots as 5 L, 10 L, 15 L, 20 L, 25 L and 35 L in respect of their pot sizes. The experiment tracked leaf-level gas exchange, leaf carbohydrate accumulation and seedling allometry over the course of 4 months for all 7 treatments.
DOI: 10.6084/m9.figshare.5124991
title: Supplementary Material for: Physical Mapping of 20 Unmapped Fragments of the Btau_4.0 Genome Assembly in Cattle, Sheep and River Buffalo

description: The recent advances in sequencing technology and bioinformatics have revolutionized genomic research, making the decoding of the genome an easier task. Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (<i>Bos taurus</i>, 2n = 60), sheep (<i>Ovis aries</i>, 2n = 54) and river buffalo (<i>Bubalus bubalis</i>, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. Finally, the results presented here suggest that FISH was, and still is, a useful technology to validate the data produced by genome sequencing programs.
DOI: 10.6084/m9.figshare.5124982
title: Supplementary Material for: Associations between Pituitary Imaging Abnormalities and Clinical and Biochemical Phenotypes in Children with Congenital Growth Hormone Deficiency: Data from an International Observational Study

description: <b><i>Background/Aims:</i></b> Magnetic resonance imaging (MRI) is used to investigate the etiology of growth hormone deficiency (GHD). This study examined relationships between MRI findings and clinical/hormonal phenotypes in children with GHD in the observational Genetics and Neuroendocrinology of Short Stature International Study, GeNeSIS. <b><i>Methods:</i></b> Clinical presentation, hormonal status and first-year GH response were compared between patients with pituitary imaging abnormalities (n = 1,071), patients with mutations in genes involved in pituitary development/GH secretion (n = 120) and patients with idiopathic GHD (n = 7,039). <b><i>Results:</i></b> Patients with hypothalamic-pituitary abnormalities had more severe phenotypes than patients with idiopathic GHD. Additional hormonal deficiencies were found in 35% of patients with structural abnormalities (thyroid-stimulating hormone &gt; adrenocorticotropic hormone &gt; luteinizing hormone/follicle-stimulating hormone &gt; antidiuretic hormone), most frequently in patients with septo-optic dysplasia (SOD). Patients with the triad [ectopic posterior pituitary (EPP), pituitary aplasia/hypoplasia and stalk defects] had a more severe phenotype and better response to GH treatment than patients with isolated abnormalities. The sex ratio was approximately equal for patients with SOD, but there was a significantly higher proportion of males (approximately 70%) in the EPP, pituitary hypoplasia, stalk defects, and triad categories. <b><i>Conclusion:</i></b> This large, international database demonstrates the value of classification of GH-deficient patients by the presence and type of hypothalamic-pituitary imaging abnormalities. This information may assist family counseling and patient management.
DOI: 10.6084/m9.figshare.5124985
title: Supplementary Material for: Bevacizumab with Erlotinib as First-line Therapy in Asian Patients with Advanced Hepatocellular Carcinoma: A Multicenter Phase II Study

description: <b><i>Objectives:</i></b> The bevacizumab/erlotinib combination was reported with high clinical activity for advanced hepatocellular carcinoma (HCC) by a phase II study conducted in the USA. This multicenter study across several Asian countries was to evaluate the safety and efficacy of the combination in this population. <b><i>Methods:</i></b> Patients with histology-proven HCC, advanced disease and Child-Pugh class A liver function received bevacizumab 5 mg/kg intravenously every 2 weeks and erlotinib 150 mg/day orally as first-line therapy. The primary end point was progression-free survival at 16 weeks (PFS-16W). The expression of epidermal growth factor receptor (EGFR), phospho-AKT and vascular endothelial growth factor, the microvessel density and the EGFR gene copy number in HCC tissues were correlated with treatment efficacy. <b><i>Results:</i></b> Fifty-one patients were enrolled. The PFS-16W was 35.3% (95% CI 22.4-49.9), the median PFS was 2.9 months (95% CI, 1.3-4.4) and the median overall survival was 10.7 months (95% CI, 6.2-15.2). Grade 3/4 toxicities were uncommon, including rash, acne (10% each), diarrhea (6%) and gastrointestinal bleeding (4%). None of the evaluated biomarkers correlated with disease control or PFS. <b><i>Conclusions:</i></b> Bevacizumab plus erlotinib showed good tolerability and modest activity in this Asian cohort. Further studies are warranted to identify the predictive biomarkers of this combination.
DOI: 10.6084/m9.figshare.5124991.v1
title: Supplementary Material for: Physical Mapping of 20 Unmapped Fragments of the Btau_4.0 Genome Assembly in Cattle, Sheep and River Buffalo

description: The recent advances in sequencing technology and bioinformatics have revolutionized genomic research, making the decoding of the genome an easier task. Genome sequences are currently available for many species, including cattle, sheep and river buffalo. The available reference genomes are very accurate, and they represent the best possible order of loci at this time. In cattle, despite the great accuracy achieved, a part of the genome has been sequenced but not yet assembled: these genome fragments are called unmapped fragments. In the present study, 20 unmapped fragments belonging to the Btau_4.0 reference genome have been mapped by FISH in cattle (<i>Bos taurus</i>, 2n = 60), sheep (<i>Ovis aries</i>, 2n = 54) and river buffalo (<i>Bubalus bubalis</i>, 2n = 50). Our results confirm the accuracy of the available reference genome, though there are some discrepancies between the expected localization and the observed localization. Moreover, the available data in the literature regarding genomic homologies between cattle, sheep and river buffalo are confirmed. Finally, the results presented here suggest that FISH was, and still is, a useful technology to validate the data produced by genome sequencing programs.
DOI: 10.6084/m9.figshare.5124982.v1
title: Supplementary Material for: Associations between Pituitary Imaging Abnormalities and Clinical and Biochemical Phenotypes in Children with Congenital Growth Hormone Deficiency: Data from an International Observational Study

description: <b><i>Background/Aims:</i></b> Magnetic resonance imaging (MRI) is used to investigate the etiology of growth hormone deficiency (GHD). This study examined relationships between MRI findings and clinical/hormonal phenotypes in children with GHD in the observational Genetics and Neuroendocrinology of Short Stature International Study, GeNeSIS. <b><i>Methods:</i></b> Clinical presentation, hormonal status and first-year GH response were compared between patients with pituitary imaging abnormalities (n = 1,071), patients with mutations in genes involved in pituitary development/GH secretion (n = 120) and patients with idiopathic GHD (n = 7,039). <b><i>Results:</i></b> Patients with hypothalamic-pituitary abnormalities had more severe phenotypes than patients with idiopathic GHD. Additional hormonal deficiencies were found in 35% of patients with structural abnormalities (thyroid-stimulating hormone &gt; adrenocorticotropic hormone &gt; luteinizing hormone/follicle-stimulating hormone &gt; antidiuretic hormone), most frequently in patients with septo-optic dysplasia (SOD). Patients with the triad [ectopic posterior pituitary (EPP), pituitary aplasia/hypoplasia and stalk defects] had a more severe phenotype and better response to GH treatment than patients with isolated abnormalities. The sex ratio was approximately equal for patients with SOD, but there was a significantly higher proportion of males (approximately 70%) in the EPP, pituitary hypoplasia, stalk defects, and triad categories. <b><i>Conclusion:</i></b> This large, international database demonstrates the value of classification of GH-deficient patients by the presence and type of hypothalamic-pituitary imaging abnormalities. This information may assist family counseling and patient management.
DOI: 10.6084/m9.figshare.5125087.v6
title: Inferring the effects of sink strength on plant carbon balance processes from experimental measurements

description: This folder consists of existing dataset from the container volume experiment which was carried out at the Hawkesbury Forest Experiment site (33°37'S 150°44'E) in Richmond, NSW, Australia. The site and experimental setup have been explained in detail by Campany et al. (2017). <br>In brief, 20 weeks old Eucalyptus tereticornis seedlings in tube stock were chosen from a single local Cumberland plain cohort. Ten additional seedlings of similar age and growth were harvested to measure initial leaf area and dry mass of leaves, stems and roots. A total of 49 Eucalyptus tereticornis seedlings were grown in a range of container sizes (5 L to 35 L) in field conditions, using freely-rooted seedlings as a control for the container size treatments, with the goal to examine how the C balance of the plants are affected to belowground sink limitations. Six container sizes were used with each container experiment had a complete replicate set of six container volumes along with a free seedling. Similar notations are used here as Campany et al. (2017) for the treatments in different pots as 5 L, 10 L, 15 L, 20 L, 25 L and 35 L in respect of their pot sizes. The experiment tracked leaf-level gas exchange, leaf carbohydrate accumulation and seedling allometry over the course of 4 months for all 7 treatments.
DOI: 10.6084/m9.figshare.5124970
title: Supplementary Material for: Sex-Biased Expression of Sex-Differentiating Genes <b><i>FOXL2</i></b> and <b><i>FGF9</i></b> in American Alligators, <b><i>Alligator mississippiensis</i></b>

description: Across amniotes, sex-determining mechanisms exhibit great variation, yet the genes that govern sexual differentiation are largely conserved. Studies of evolution of sex-determining and sex-differentiating genes require an exhaustive characterization of functions of those genes such as <i>FOXL2</i> and <i>FGF9</i>. <i>FOXL2</i> is associated with ovarian development, and<i> FGF9</i> is known to play a role in testicular organogenesis in mammals and other amniotes. As a step toward characterization of the evolutionary history of sexual development, we measured expression of <i>FOXL2</i> and <i>FGF9</i> across 3 developmental stages and 8 juvenile tissue types in male and female American alligators, <i>Alligator mississippiensis. </i>We report surprisingly high expression of <i>FOXL2</i> before the stage of embryonic development when sex is determined in response to temperature, and sustained and variable expression of <i>FGF9</i> in juvenile male, but not female tissue types. Novel characterization of gene expression in reptiles with temperature-dependent sex determination such as American alligators may inform the evolution of sex-determining and sex-differentiating gene networks, as they suggest alternative functions from which the genes may have been exapted. Future functional profiling of sex-differentiating genes should similarly follow other genes and other species to enable a broad comparison across sex-determining mechanisms.
DOI: 10.6084/m9.figshare.5124976
title: Supplementary Material for: Mapping of the Immunodominant Regions of Shrimp Tropomyosin Pan b 1 by Human IgE-Binding and IgE Receptor Crosslinking Studies

description: <b><i>Background:</i></b> Epitope mapping of an allergen is generally done by IgE-binding assays with short synthetic peptides, but this provides little information about which domains are responsible for IgE receptor crosslinking on effector cells. Our aim was to map the immunodominant regions of shrimp tropomyosin by both IgE-binding and IgE-receptor crosslinking studies. <b><i>Methods:</i></b> Five overlapping fragments covering <i>Pandalus borealis</i> tropomyosin were cloned, expressed in <i>Escherichia coli</i> and characterized by circular dichroism spectroscopy, native PAGE and bis(sulfosuccinimidyl) suberate-crosslinking. IgE binding was detected by Western blot, indirect ELISA and inhibition ELISA, and IgE receptor crosslinking was investigated by basophil activation test and skin prick test with Norwegian shrimp allergic adults. <b><i>Results:</i></b> The N- and C-terminal fragments of tropomyosin showed the highest amount of secondary structure. Western blot studies showed preferential binding to the terminal fragments, while indirect and inhibition ELISA studies showed binding to all fragments, but with individual variations. Basophil CD63 expression was upregulated by all fragments at high concentrations (1 µg/ml) and showed individual variations comparable to ELISA results. A mixture of the fragments with equal molar ratios induced comparably strong CD63 activation as for tropomyosin. Skin prick test studies showed positive responses to the terminal and middle fragments and increased responses to the fragment mixture compared to whole tropomyosin. <b><i>Conclusions:</i></b> The terminal and middle fragments of tropomyosin had the highest IgE reactivity, but overall no clear immunodominant region was observed in this study. These results correlated well with previous studies with short peptides. Dividing shrimp tropomyosin into five fragments did not reduce the allergenicity of the protein.