cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124559.v1
title: Supplementary Material for: Prenatal Diagnosis of Congenital Epulis by 2D/3D Ultrasound and Magnetic Resonance

description: Congenital epulis is a rare benign oral cavity tumor that usually arises from the maxillary alveolar mucosa. It is also known as congenital gingival granular cell tumor. Prenatal diagnosis is uncommon and mostly confined to the third trimester. We report a case of congenital epulis, which was referred to our department at 35 weeks of gestation. Both images from our prenatal 2D/3D ultrasound (including Doppler technique) and magnetic resonance examination are presented. A baby girl weighing 2,800 g was delivered spontaneously at 36 weeks and 1 day. The newborn had to be intubated immediately after delivery. A simple excision of the mass was performed on the first day of neonatal life after clinical examination by our pediatric stomatologists confirmed the presence of a tumor resembling epulis. The correctness of this diagnosis was subsequently confirmed by histogenesis. Photographs from the operating room show the postnatal appearance of the tumor. The baby was discharged at the age of 19 days and has remained well at follow-up controls.
DOI: 10.6084/m9.figshare.5124553
title: Supplementary Material for: Visual Reproduction on the Wechsler Memory Scale-Revised as a Predictor of Alzheimer’s Disease in Japanese Patients with Mild Cognitive Impairments

description: <b><i>Background:</i></b> The Visual Reproduction (VR) test is used to assess mild cognitive impairment (MCI), but the characteristics of visual memory in Japanese MCI patients remain unclear. <b><i>Methods:</i></b> VR scores of 27 MCI patients were evaluated using the Wechsler Memory Scale-Revised. Scores of MCI, no-dementia, and Alzheimer’s disease (AD) groups were then compared. <b><i>Results:</i></b> The annual conversion rate of MCI to AD was 18.8%. Mean VR-I and VR-II baseline scores for MCI patients were 33.3 ± 5.6 and 20.5 ± 14.0, respectively. Mean VR-II scores for converted and nonconverted MCI patients were 7.2 ± 8.7 and 29.8 ± 9.3, respectively. <b><i>Conclusions:</i></b> It is likely that VR-II and VR-II/I scores are more sensitive for predicting conversion to AD in Japanese than in American MCI patients. Our results indicate that VR is a sensitive and useful measure for predicting the conversion of Japanese MCI patients to AD within 2 years.
DOI: 10.6084/m9.figshare.5124556.v1
title: Supplementary Material for: Could Inbred Cases Identified in GWAS Data Succeed in Detecting Rare Recessive Variants Where Affected Sib-Pairs Have Failed?

description: To detect fully penetrant rare recessive variants that could constitute Mendelian subentities of complex diseases, we propose a novel strategy, the HBD-GWAS strategy, which can be applied to genome-wide association study (GWAS) data. This strategy first involves the identification of inbred individuals among cases using the genome-wide SNP data and then focuses on these inbred affected individuals and searches for genomic regions of shared homozygosity by descent that could harbor rare recessive disease-causing variants. In this second step, analogous to homozygosity mapping, a heterogeneity lod-score, HFLOD, is computed to quantify the evidence of linkage provided by the data. In this paper, we evaluate this strategy theoretically under different scenarios and compare its performances with those of linkage analysis using affected sib-pair (ASP) data. If cases affected by these Mendelian subentities are not enriched in the sample of cases, the HBD-GWAS strategy has almost no power to detect them, unless they explain an important part of the disease prevalence. The HBD-GWAS strategy outperforms the ASP linkage strategy only in a very limited number of situations where there exists a strong allelic heterogeneity. When several rare recessive variants within the same gene are involved, the ASP design indeed often fails to detect the gene, whereas, by focusing on inbred individuals using the HBD-GWAS strategy, the gene might be detected provided very large samples of cases are available.
DOI: 10.6084/m9.figshare.5124547
title: Supplementary Material for: Highly Pathogenic Influenza Viruses Inhibit Inflammatory Response in Monocytes via Activation of Rar-Related Orphan Receptor RORa

description: Infections with highly pathogenic avian influenza viruses (HPAIV) in humans lead to systemic disease associated with cytokine storm and multiorgan failure. In this study we aimed to identify the role of monocytes for the host response to HPAIV infection. Using genome-wide microarray analysis, we surprisingly demonstrate a reduced immune response of human monocytes to HPAIV H5N1 compared to human influenza A viruses. In bioinformatic analyses we could reveal a potential role of the Rar-related orphan receptor alpha (RORa) for the gene expression pattern induced by H5N1. RORa is known as an inhibitor of NF-κB signaling. We provide evidence that in monocytes RORa is activated by H5N1, resulting in inhibited NF-κB signaling. Using murine Hoxb8-immortalized RORa<sup>-/-</sup>, monocytes rescued NF-κB signaling upon H5N1 infection, confirming the biological relevance of RORa as an H5N1-induced mediator of monocytic immunosuppression. In summary, our study reveals a novel RORa-dependent escape mechanism by which H5N1 prevents an effective inflammatory response of monocytes blocking NF-κB-dependent gene expression.
DOI: 10.6084/m9.figshare.5124550
title: Supplementary Material for: Healthy Behaviors, Risk Factor Control and Awareness of Chronic Kidney Disease

description: <b><i>Background/Aims:</i></b> The association between chronic kidney disease (CKD) awareness and healthy behaviors is unknown. We examined whether CKD self-recognition is associated with healthy behaviors and achieving risk-reduction targets known to decrease risk of cardiovascular morbidity and CKD progression. <b><i>Methods:</i></b> CKD awareness, defined as a ‘yes’ response to ‘Has a doctor or other health professional ever told you that you had kidney disease?’, was examined among adults with CKD (eGFR &lt;60 ml/min/1.73 m<sup>2</sup>) who participated in the REasons for Geographic And Racial Differences in Stroke (REGARDS) study. Odds of participation in healthy behaviors (tobacco avoidance, avoidance of regular nonsteroidal anti-inflammatory drug use, and physical activity) and achievement of risk-reduction targets (angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, systolic blood pressure control and glycemic control among those with diabetes) among those aware versus unaware of their CKD were determined by logistic regression, controlling for sociodemographics, access to care and comorbid conditions. Systolic blood pressure control was defined as &lt;130 mm Hg (primary definition) or &lt;140 mm Hg (secondary definition). <b><i>Results:</i></b> Of 2,615 participants, only 6% (n = 166) were aware of having CKD. Those who were aware had 82% higher odds of tobacco avoidance compared to those unaware (adjusted OR = 1.82, 95% CI 1.02–3.24). CKD awareness was not associated with other healthy behaviors or achievement of risk-reduction targets. <b><i>Conclusions:</i></b> Awareness of CKD was only associated with participation in one healthy behavior and was not associated with achievement of risk-reduction targets. To encourage adoption of healthy behaviors, a better understanding of barriers to participation in CKD-healthy behaviors is needed.
DOI: 10.6084/m9.figshare.5124547.v1
title: Supplementary Material for: Highly Pathogenic Influenza Viruses Inhibit Inflammatory Response in Monocytes via Activation of Rar-Related Orphan Receptor RORa

description: Infections with highly pathogenic avian influenza viruses (HPAIV) in humans lead to systemic disease associated with cytokine storm and multiorgan failure. In this study we aimed to identify the role of monocytes for the host response to HPAIV infection. Using genome-wide microarray analysis, we surprisingly demonstrate a reduced immune response of human monocytes to HPAIV H5N1 compared to human influenza A viruses. In bioinformatic analyses we could reveal a potential role of the Rar-related orphan receptor alpha (RORa) for the gene expression pattern induced by H5N1. RORa is known as an inhibitor of NF-κB signaling. We provide evidence that in monocytes RORa is activated by H5N1, resulting in inhibited NF-κB signaling. Using murine Hoxb8-immortalized RORa<sup>-/-</sup>, monocytes rescued NF-κB signaling upon H5N1 infection, confirming the biological relevance of RORa as an H5N1-induced mediator of monocytic immunosuppression. In summary, our study reveals a novel RORa-dependent escape mechanism by which H5N1 prevents an effective inflammatory response of monocytes blocking NF-κB-dependent gene expression.
DOI: 10.6084/m9.figshare.5124550.v1
title: Supplementary Material for: Healthy Behaviors, Risk Factor Control and Awareness of Chronic Kidney Disease

description: <b><i>Background/Aims:</i></b> The association between chronic kidney disease (CKD) awareness and healthy behaviors is unknown. We examined whether CKD self-recognition is associated with healthy behaviors and achieving risk-reduction targets known to decrease risk of cardiovascular morbidity and CKD progression. <b><i>Methods:</i></b> CKD awareness, defined as a ‘yes’ response to ‘Has a doctor or other health professional ever told you that you had kidney disease?’, was examined among adults with CKD (eGFR &lt;60 ml/min/1.73 m<sup>2</sup>) who participated in the REasons for Geographic And Racial Differences in Stroke (REGARDS) study. Odds of participation in healthy behaviors (tobacco avoidance, avoidance of regular nonsteroidal anti-inflammatory drug use, and physical activity) and achievement of risk-reduction targets (angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, systolic blood pressure control and glycemic control among those with diabetes) among those aware versus unaware of their CKD were determined by logistic regression, controlling for sociodemographics, access to care and comorbid conditions. Systolic blood pressure control was defined as &lt;130 mm Hg (primary definition) or &lt;140 mm Hg (secondary definition). <b><i>Results:</i></b> Of 2,615 participants, only 6% (n = 166) were aware of having CKD. Those who were aware had 82% higher odds of tobacco avoidance compared to those unaware (adjusted OR = 1.82, 95% CI 1.02–3.24). CKD awareness was not associated with other healthy behaviors or achievement of risk-reduction targets. <b><i>Conclusions:</i></b> Awareness of CKD was only associated with participation in one healthy behavior and was not associated with achievement of risk-reduction targets. To encourage adoption of healthy behaviors, a better understanding of barriers to participation in CKD-healthy behaviors is needed.
DOI: 10.6084/m9.figshare.5124553.v1
title: Supplementary Material for: Visual Reproduction on the Wechsler Memory Scale-Revised as a Predictor of Alzheimer’s Disease in Japanese Patients with Mild Cognitive Impairments

description: <b><i>Background:</i></b> The Visual Reproduction (VR) test is used to assess mild cognitive impairment (MCI), but the characteristics of visual memory in Japanese MCI patients remain unclear. <b><i>Methods:</i></b> VR scores of 27 MCI patients were evaluated using the Wechsler Memory Scale-Revised. Scores of MCI, no-dementia, and Alzheimer’s disease (AD) groups were then compared. <b><i>Results:</i></b> The annual conversion rate of MCI to AD was 18.8%. Mean VR-I and VR-II baseline scores for MCI patients were 33.3 ± 5.6 and 20.5 ± 14.0, respectively. Mean VR-II scores for converted and nonconverted MCI patients were 7.2 ± 8.7 and 29.8 ± 9.3, respectively. <b><i>Conclusions:</i></b> It is likely that VR-II and VR-II/I scores are more sensitive for predicting conversion to AD in Japanese than in American MCI patients. Our results indicate that VR is a sensitive and useful measure for predicting the conversion of Japanese MCI patients to AD within 2 years.
DOI: 10.6084/m9.figshare.5124526
title: Supplementary Material for: German Medical Students’ Beliefs about How Best to Treat Alcohol Use Disorder

description: <b><i>Background/Aims:</i></b> A minority of German medical students believe they know how to support smokers willing to quit. This paper examined whether the same would be true for treating alcohol use disorder (AUD), and individual factors associated with incorrect beliefs about the effectiveness of methods to treat AUD. <b><i>Methods:</i></b> In this cross-sectional study, 19,526 undergraduate students from 27 German medical schools completed a survey addressing beliefs about the effectiveness of different methods of overcoming AUD. Beliefs about AUD treatment effectiveness were compared across the 5 years of undergraduate education and predictors identified by means of multiple linear regression. <b><i>Results:</i></b> Even in the fifth year, 28.1% (95% CI: 26.5–29.7) of students believed that willpower alone was more effective for overcoming AUD than a comprehensive treatment program. The only significant predictor of this belief was a similar belief for stopping smoking. <b><i>Conclusion:</i></b> Our results indicate that a considerable proportion of German medical students overestimate the effectiveness of willpower to treat smoking and AUD. The addictive nature of these disorders needs to be stressed during undergraduate medical education to ensure that future physicians will be able and motivated to support patients in their quit attempts.
DOI: 10.6084/m9.figshare.5124532
title: Supplementary Material for: Association between Neuropeptide Y Gene Polymorphisms and Alcohol Dependence: A Case-Control Study in Two Independent Populations

description: <b><i>Background:</i></b> Alcohol dependence is a chronic, progressive neurobiological brain disorder. Previous research reported an inverse association between ethanol drinking and cerebral neuropeptide Y (NPY) levels. There are conflicting results of studies on <i>NPY</i> gene polymorphisms in association with alcohol dependence in humans. <b><i>Methods:</i></b> To assess the role of the <i>NPY</i> gene in alcohol dependence, we genotyped three polymorphisms - in a sample of 195 subjects from the Kota population (80 alcohol dependence and 115 controls) and 141 subjects from the Badaga population (80 alcohol dependence and 61 controls). Phenotype was defined based on the DSM-IV criteria. Genotyping was performed using sequencing. Association of the <i>NPY</i> gene with alcohol dependence was tested by using logistic regression and haplotype analyses and linkage disequilibrium. <b><i>Results:</i></b> All three polymorphisms were found to be in the Hardy-Weinberg equilibrium in both populations. The results of our study reveal a significant association between G1258A and alcohol dependence in both the Kota and Badaga populations. The linkage disequilibrium between the markers is not strong or significant. Haplotype analysis also did not show significant association between the <i>NPY</i> gene and alcohol dependence. <b><i>Conclusion:</i></b> These data support the hypothesis that alcohol dependence is influenced by the NPY G1258A polymorphism in Indian populations.
DOI: 10.6084/m9.figshare.5124535
title: Supplementary Material for: An Analysis of the Clinical and Cost Effectiveness of Growth Hormone Replacement Therapy before and during Puberty: Should We Increase the Dose?

description: <b><i>Aim:</i></b> To investigate the influence of growth hormone (GH) on linear growth before and during puberty in children with GH deficiency. <b><i>Methods:</i></b> We analysed the relationship between pubertal growth and GH dose in a large dataset of children (n = 236) with GH deficiency using multiple linear regression and multilevel modelling with repeated measures analysis. Additionally, we examined the cost benefit of increasing doses of GH during puberty. <b><i>Results:</i></b> Multilevel modelling revealed a highly significant role for GH dose in the pre-pubertal period (p &lt; 0.001), but a non-significant effect on height gain after pubertal onset (p = 0.32). Important predictors of height gain after puberty onset included gender, age at puberty and number of injections of GH/week. Cost analysis showed that in an average child use of high dose GH, at an extra EUR 5,925 (GBP 4,753/USD 7,538)/year, would produce a height gain of 0.80 cm/year (above baseline growth) pre-pubertally, compared to only 0.20 cm/year post-puberty onset. <b><i>Conclusions:</i></b> The influence of GH dose on height gain after puberty onset is at best a modest one. Cost analysis shows use of high doses of GH post-puberty onset has significant cost implications without providing a worthwhile gain in adult height for children with GH deficiency.
DOI: 10.6084/m9.figshare.5124529
title: Supplementary Material for: Markers CD40, VEGF, AKT, PI3K, and S100 Correlate with Tumor Stage in Gastric Cancer

description: <b><i>Background: </i></b>To better understand gastric cancer occurrence and prognosis, we explored the expression of molecules in the CD40 pathway and their correlation with gastric cancer prognosis. <b><i>Patients and Methods: </i></b>We measured the expression of CD40, VEGF, AKT, PI3K, and S100 in gastric cancer tissues and adjacent normal tissues from 128 patients by immunohistochemistry. <b><i>Results: </i></b>The expression of CD40, VEGF, AKT, and PI3K were significantly higher in tumor tissue than in normal tissue, while S100 expression in dendritic cells (DC) was lower. Expression of CD40, VEGF, AKT, and PI3K significantly increased with T stage, while S100 expression decreased with T stage. Lymph node metastasis was associated with low or negative S100 expression. PI3K expression increased with clinical stage, while negative S100 expression was associated with higher clinical stages. Multivariate analysis did not indicate significant associations between any of these markers and recurrence or mortality. <b><i>Conclusion: </i></b>The correlation between T stage of gastric cancer and the higher expression of CD40, VEGF, AKT, and PI3K, along with lower S100 expression in DC, may provide insights into future targets for more effective immunotherapy for cancer.
DOI: 10.6084/m9.figshare.5124520
title: Supplementary Material for: ICE<b><i>Afe</i></b>1, an Actively Excising Genetic Element from the Biomining Bacterium <b><i>Acidithiobacillus ferrooxidans</i></b>

description: Integrative conjugative elements (ICEs) are self-transferred mobile genetic elements that contribute to horizontal gene transfer. An ICE (ICE<i>Afe</i>1) was identified in the genome of <i>Acidithiobacillus ferrooxidans</i> ATCC 23270. Excision of the element and expression of relevant genes under normal and DNA-damaging growth conditions was analyzed. Bioinformatic tools and DNA amplification methods were used to identify and to assess the excision and expression of genes related to the mobility of the element. Both basal and mitomycin C-inducible excision as well as expression and induction of the genes for integration/excision are demonstrated, suggesting that ICE<i>Afe</i>1 is an actively excising SOS-regulated mobile genetic element. The presence of a complete set of genes encoding self-transfer functions that are induced in response to DNA damage caused by mitomycin C additionally suggests that this element is capable of conjugative transfer to suitable recipient strains. Transfer of ICE<i>Afe</i>1 may provide selective advantages to other acidophiles in this ecological niche through dissemination of gene clusters expressing transfer RNAs, CRISPRs, and exopolysaccharide biosynthesis enzymes, probably by modification of translation efficiency, resistance to bacteriophage infection and biofilm formation, respectively. These data open novel avenues of research on conjugative transformation of biotechnologically relevant microorganisms recalcitrant to genetic manipulation.
DOI: 10.6084/m9.figshare.5124532.v1
title: Supplementary Material for: Association between Neuropeptide Y Gene Polymorphisms and Alcohol Dependence: A Case-Control Study in Two Independent Populations

description: <b><i>Background:</i></b> Alcohol dependence is a chronic, progressive neurobiological brain disorder. Previous research reported an inverse association between ethanol drinking and cerebral neuropeptide Y (NPY) levels. There are conflicting results of studies on <i>NPY</i> gene polymorphisms in association with alcohol dependence in humans. <b><i>Methods:</i></b> To assess the role of the <i>NPY</i> gene in alcohol dependence, we genotyped three polymorphisms - in a sample of 195 subjects from the Kota population (80 alcohol dependence and 115 controls) and 141 subjects from the Badaga population (80 alcohol dependence and 61 controls). Phenotype was defined based on the DSM-IV criteria. Genotyping was performed using sequencing. Association of the <i>NPY</i> gene with alcohol dependence was tested by using logistic regression and haplotype analyses and linkage disequilibrium. <b><i>Results:</i></b> All three polymorphisms were found to be in the Hardy-Weinberg equilibrium in both populations. The results of our study reveal a significant association between G1258A and alcohol dependence in both the Kota and Badaga populations. The linkage disequilibrium between the markers is not strong or significant. Haplotype analysis also did not show significant association between the <i>NPY</i> gene and alcohol dependence. <b><i>Conclusion:</i></b> These data support the hypothesis that alcohol dependence is influenced by the NPY G1258A polymorphism in Indian populations.
DOI: 10.6084/m9.figshare.5124535.v1
title: Supplementary Material for: An Analysis of the Clinical and Cost Effectiveness of Growth Hormone Replacement Therapy before and during Puberty: Should We Increase the Dose?

description: <b><i>Aim:</i></b> To investigate the influence of growth hormone (GH) on linear growth before and during puberty in children with GH deficiency. <b><i>Methods:</i></b> We analysed the relationship between pubertal growth and GH dose in a large dataset of children (n = 236) with GH deficiency using multiple linear regression and multilevel modelling with repeated measures analysis. Additionally, we examined the cost benefit of increasing doses of GH during puberty. <b><i>Results:</i></b> Multilevel modelling revealed a highly significant role for GH dose in the pre-pubertal period (p &lt; 0.001), but a non-significant effect on height gain after pubertal onset (p = 0.32). Important predictors of height gain after puberty onset included gender, age at puberty and number of injections of GH/week. Cost analysis showed that in an average child use of high dose GH, at an extra EUR 5,925 (GBP 4,753/USD 7,538)/year, would produce a height gain of 0.80 cm/year (above baseline growth) pre-pubertally, compared to only 0.20 cm/year post-puberty onset. <b><i>Conclusions:</i></b> The influence of GH dose on height gain after puberty onset is at best a modest one. Cost analysis shows use of high doses of GH post-puberty onset has significant cost implications without providing a worthwhile gain in adult height for children with GH deficiency.