cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127214
title: Supplementary Material for: Four-Copy Number Intervals in SNP Microarray Analysis: Unique Patterns and Positions

description: Over the past several years, the utility of microarray technology in delineating copy number changes has become well established. In the past 4 years, we have used the SNP array to detect and analyze allele ratios in 150 cases with 4-copy intervals, confirmed by FISH, offering insight into the underlying mechanisms of formation. These cases may be divided into 5 allele patterns - the first 4 of which involve a single homologue - as detected by the genotyping aspects of the microarray: (1) triplications combining homozygous and heterozygous alleles, with a 3:1 ratio of heterozygotes; (2) triplications with allele patterns combining homozygous and heterozygous alleles, with heterozygote ratios of both 3:1 and 2:2; (3) triplications that have homozygous alleles combined with only 2:2 heterozygous alleles; (4) triplications that are completely homozygous; and (5) homozygous duplications on each homologue with no heterozygous alleles. The implications of copy number variants with diverse allelic segregations are presented in this study.
DOI: 10.6084/m9.figshare.5127214.v1
title: Supplementary Material for: Four-Copy Number Intervals in SNP Microarray Analysis: Unique Patterns and Positions

description: Over the past several years, the utility of microarray technology in delineating copy number changes has become well established. In the past 4 years, we have used the SNP array to detect and analyze allele ratios in 150 cases with 4-copy intervals, confirmed by FISH, offering insight into the underlying mechanisms of formation. These cases may be divided into 5 allele patterns - the first 4 of which involve a single homologue - as detected by the genotyping aspects of the microarray: (1) triplications combining homozygous and heterozygous alleles, with a 3:1 ratio of heterozygotes; (2) triplications with allele patterns combining homozygous and heterozygous alleles, with heterozygote ratios of both 3:1 and 2:2; (3) triplications that have homozygous alleles combined with only 2:2 heterozygous alleles; (4) triplications that are completely homozygous; and (5) homozygous duplications on each homologue with no heterozygous alleles. The implications of copy number variants with diverse allelic segregations are presented in this study.
DOI: 10.6084/m9.figshare.5127217
title: Supplementary Material for: Intestinal Vascular Endothelial Growth Factor Is Decreased in Necrotizing Enterocolitis

description: <b><i>Background:</i></b> Decreased intestinal perfusion may contribute to the development of necrotizing enterocolitis (NEC). Vascular endothelial growth factor (VEGF) is an angiogenic protein necessary for the development and maintenance of capillary networks. Whether VEGF is dysregulated in NEC remains unknown. <b><i>Objectives:</i></b> The objective of this study was to determine whether intestinal VEGF expression is altered in a neonatal mouse model of NEC and in human NEC patients. <b><i>Methods:</i></b> We first assessed changes of intestinal VEGF mRNA and protein in a neonatal mouse NEC model before significant injury occurs. We then examined whether exposure to formula feeding, bacterial inoculation, cold stress and/or intermittent hypoxia affected intestinal VEGF expression. Last, we visualized VEGF protein in intestinal tissues of murine and human NEC and control cases by immunohistochemistry. <b><i>Results:</i></b> Intestinal VEGF protein and mRNA were significantly decreased in pups exposed to the NEC protocol compared to controls. Hypoxia, cold stress and commensal bacteria, when administered together, significantly downregulated intestinal VEGF expression, while they had no significant effect when given alone. VEGF was localized to a few single intestinal epithelial cells and some cells of the lamina propria and myenteric plexus. VEGF staining was decreased in murine and human NEC intestines when compared to control tissues. <b><i>Conclusion:</i></b> Intestinal VEGF protein is reduced in human and experimental NEC. Decreased VEGF production might contribute to NEC pathogenesis.
DOI: 10.6084/m9.figshare.5127211
title: Supplementary Material for: Autophagic Markers BECLIN 1 and LC3 Are Associated with Prognosis of Multiple Myeloma

description: <b><i>Background/Aims:</i></b> Autophagy is crucial for the survival and function of plasma cells including protection from toxic misfolded immunoglobulin and proper energy metabolism. Multiple myeloma (MM) is an indolent but eventually fatal neoplasm of plasma cells. Autophagy may play a critical role in the survival of MM cells and their response to chemotherapeutic agents. In this study, we correlated the expression of autophagy-related proteins with the prognosis of MM. <b><i>Methods:</i></b> In this retrospective cohort study, we examined the expression of the autophagic markers BECLIN 1 and microtubule-associated protein light chain 3 (LC3) in 89 cases of MM biopsied from 2001 to 2004 at the Asan Medical Center. The association of the expression scores of these markers with clinical outcomes was assessed. <b><i>Results:</i></b> Patients with strong immunoreactivity to BECLIN 1 or LC3 had a significantly better overall survival (OS) than patients with negative to moderate immunoreactivity (p = 0.036 and 0.018, respectively). This was also true for disease-specific survival (DSS; p = 0.051 and 0.043, respectively). In addition, LC3 immunostaining remained an independent factor impacting OS (p = 0.028) and DSS (p = 0.020) after multivariate analysis. <b><i>Conclusions:</i></b> The results of this study suggest that higher immunoreactivity for autophagic markers in MM is associated with superior patient survival.
DOI: 10.6084/m9.figshare.5127217.v1
title: Supplementary Material for: Intestinal Vascular Endothelial Growth Factor Is Decreased in Necrotizing Enterocolitis

description: <b><i>Background:</i></b> Decreased intestinal perfusion may contribute to the development of necrotizing enterocolitis (NEC). Vascular endothelial growth factor (VEGF) is an angiogenic protein necessary for the development and maintenance of capillary networks. Whether VEGF is dysregulated in NEC remains unknown. <b><i>Objectives:</i></b> The objective of this study was to determine whether intestinal VEGF expression is altered in a neonatal mouse model of NEC and in human NEC patients. <b><i>Methods:</i></b> We first assessed changes of intestinal VEGF mRNA and protein in a neonatal mouse NEC model before significant injury occurs. We then examined whether exposure to formula feeding, bacterial inoculation, cold stress and/or intermittent hypoxia affected intestinal VEGF expression. Last, we visualized VEGF protein in intestinal tissues of murine and human NEC and control cases by immunohistochemistry. <b><i>Results:</i></b> Intestinal VEGF protein and mRNA were significantly decreased in pups exposed to the NEC protocol compared to controls. Hypoxia, cold stress and commensal bacteria, when administered together, significantly downregulated intestinal VEGF expression, while they had no significant effect when given alone. VEGF was localized to a few single intestinal epithelial cells and some cells of the lamina propria and myenteric plexus. VEGF staining was decreased in murine and human NEC intestines when compared to control tissues. <b><i>Conclusion:</i></b> Intestinal VEGF protein is reduced in human and experimental NEC. Decreased VEGF production might contribute to NEC pathogenesis.
DOI: 10.6084/m9.figshare.5127223.v1
title: Supplementary Material for: Factors Affecting Recall of Different Types of Personal Genetic Information about Alzheimer's Disease Risk: The REVEAL Study

description: <b><i>Methods:</i></b> Data were obtained through a multisite clinical trial in which different types of genetic risk-related information were disclosed to individuals (n = 246) seeking a risk assessment for Alzheimer's disease. <b><i>Results:</i></b> Six weeks after disclosure, 83% of participants correctly recalled the number of risk-increasing <i>APOE </i>alleles they possessed, and 74% correctly recalled their <i>APOE </i>genotype. While 84% of participants recalled their lifetime risk estimate to within 5 percentage points, only 51% correctly recalled their lifetime risk estimate exactly. Correct recall of the number of <i>APOE </i>risk-increasing alleles was independently associated with higher education (p &lt; 0.001), greater numeracy (p &lt; 0.05) and stronger family history of Alzheimer's disease (p &lt; 0.05). Before adjustments for confounding, correct recall of <i>APOE </i>genotype was also associated with higher education, greater numeracy and stronger family history of Alzheimer's disease, as well as with higher comfort with numbers and European American ethnicity (all p &lt; 0.05). Correct recall of the lifetime risk estimate was independently associated only with younger age (p &lt; 0.05). <b><i>Conclusions:</i></b> Recall of genotype-specific information is high, but recall of exact risk estimates is lower. Incorrect recall of numeric risk may lead to distortions in understanding risk. Further research is needed to determine how best to communicate different types of genetic risk information to patients, particularly to those with lower educational levels and lower numeracy. Health-care professionals should be aware that each type of genetic risk information may be differentially interpreted and retained by patients and that some patient subgroups may have more problems with recall than others.
DOI: 10.6084/m9.figshare.5127202
title: Supplementary Material for: Birch Pollen Immunotherapy in Mice: Inhibition of Th2 Inflammation Is Not Sufficient to Decrease Airway Hyper-Reactivity

description: <b><i>Background:</i></b> Suppression of Th2 cytokine production by allergen-specific Th2 cells is considered to be critical for the suppression of allergic symptoms by subcutaneous immunotherapy. The aim of this study was to develop a mouse model for birch pollen (BP) immunotherapy to elucidate the underlying mechanisms that contribute to the improvement of clinical symptoms. <b><i>Methods:</i></b> Mice with BP-induced allergic airway inflammation received weekly subcutaneous immunotherapy (SCIT) injections with BP extract (BPE) adsorbed to alum. The effect of an increasing dose of BPE adsorbed to a fixed concentration of alum on the suppression of airway inflammation and airway hyper-responsiveness (AHR) was determined. After 2, 4, 6 or 8 immunotherapy injections, the mice were rechallenged with the same allergen and all hallmarks of allergic asthma were evaluated. <b><i>Results:</i></b> Suppression of the immunological parameters by immunotherapy was dependent on the BPE dose. Two injections were sufficient to suppress IL-4, IL-5, IL-13, IL-10 and IFN-G production, eosinophil recruitment and peribronchial inflammatory infiltrates. BP-specific immunoglobulins were upregulated, but this was not sufficient to reduce AHR. Eight injections were needed to suppress AHR. The gradual reduction in AHR was inversely associated with the increase of BP IgG2a. <b><i>Conclusions:</i></b> BP SCIT induces an early suppression of Th2-mediated eosinophilic airway inflammation, but AHR is only effectively reduced after continued SCIT conceivably by allowing IgG2a antibody titres to build up. i 2014 S. Karger AG, Basel
DOI: 10.6084/m9.figshare.5127205
title: Supplementary Material for: The Temporal Dynamics of Cognitive Reactivity and Their Association with the Depression Risk: An Exploratory Study

description: <b><i>Background:</i></b> Cognitive reactivity is the change in depressive thinking in response to negative mood. Previous research indicates that cognitive reactivity is an important variable in the etiology and course of depression. The present study tested which time interval after a negative mood induction is critical for the prediction of the depression risk. <b><i>Methods:</i></b> Participants suffering from a major depressive disorder were recruited when entering inpatient treatment. At the end of inpatient treatment they completed an experimental procedure to assess their depressive thinking once before and twice after a negative mood induction. Subsequently, patients were followed up for 26 weeks. <b><i>Results:</i></b> The immediate change in depressive thinking in response to the negative mood induction was negatively associated with future depression. The delayed change did not predict the depression risk. <b><i>Conclusion:</i></b> The negative association between the immediate change in depressive thinking and the depression risk is not in line with results from previous studies on cognitive reactivity. Previous research on emotion context insensitivity and the avoidance of negative thoughts offers hypotheses which could account for this result. Further research is needed to shed light on the processes underlying cognitive reactivity.
DOI: 10.6084/m9.figshare.5127208
title: Supplementary Material for: Association of Genetic Polymorphisms for Glutathione Peroxidase Genes with Obesity in Spanish Children

description: <b><i>Background/Aims:</i></b> Altered expression and activity of the antioxidant enzymes glutathione peroxidases (GPXs) have been observed in obesity in human and animal studies. We aimed to study 59 single nucleotide polymorphisms (SNPs) for <i>GPX1-7</i> genes and to characterize their association with prepubertal childhood obesity and its associated biomarkers. <b><i>Methods:</i></b> This case-control study included 193 obese and 191 normal-weight prepubertal Spanish children, in whom anthropometry, biochemical parameters, adipokines, antioxidant enzyme erythrocyte activities and biomarkers of oxidative stress, inflammation and cardiovascular risk were measured. The genotype analysis was performed in the Illumina platform. PLINK and SPSS were used for statistical analyses. <b><i>Results:</i></b> We found SNPs rs757228 and rs8103188 <i>(GPX4) </i>to be negatively associated and rs445870 <i>(GPX5)</i> and rs406113 <i>(GPX6)</i> to be positively associated with obesity in children. The variant rs2074451 (<i>GPX4</i>) increased GPX activity in erythrocytes. Although we did not find significant differences in erythrocyte GPX activity between obese and normal-weight children, GPX activity was found to be positively and significantly correlated with blood pressure, adipocyte fatty acid-binding protein and high-sensitivity C-reactive protein. <b><i>Conclusions:</i></b> The GPX variants rs757228, rs8103188, rs445870 and rs406113 were associated with prepubertal childhood obesity. However, erythrocyte GPX activity was not altered in obese prepubertal Spanish children.
DOI: 10.6084/m9.figshare.5127211.v1
title: Supplementary Material for: Autophagic Markers BECLIN 1 and LC3 Are Associated with Prognosis of Multiple Myeloma

description: <b><i>Background/Aims:</i></b> Autophagy is crucial for the survival and function of plasma cells including protection from toxic misfolded immunoglobulin and proper energy metabolism. Multiple myeloma (MM) is an indolent but eventually fatal neoplasm of plasma cells. Autophagy may play a critical role in the survival of MM cells and their response to chemotherapeutic agents. In this study, we correlated the expression of autophagy-related proteins with the prognosis of MM. <b><i>Methods:</i></b> In this retrospective cohort study, we examined the expression of the autophagic markers BECLIN 1 and microtubule-associated protein light chain 3 (LC3) in 89 cases of MM biopsied from 2001 to 2004 at the Asan Medical Center. The association of the expression scores of these markers with clinical outcomes was assessed. <b><i>Results:</i></b> Patients with strong immunoreactivity to BECLIN 1 or LC3 had a significantly better overall survival (OS) than patients with negative to moderate immunoreactivity (p = 0.036 and 0.018, respectively). This was also true for disease-specific survival (DSS; p = 0.051 and 0.043, respectively). In addition, LC3 immunostaining remained an independent factor impacting OS (p = 0.028) and DSS (p = 0.020) after multivariate analysis. <b><i>Conclusions:</i></b> The results of this study suggest that higher immunoreactivity for autophagic markers in MM is associated with superior patient survival.
DOI: 10.6084/m9.figshare.5127199
title: Supplementary Material for: Internet Claims on Dietary and Herbal Supplements in Advanced Nephropathy: Truth or Myth

description: <b><i>Background:</i></b> The use of complementary/alternative medicine has garnered rising interest in recent years. Natural products including herbs, vitamins, and minerals are the most popularly consumed. The Internet is a ubiquitous source of information/market for these supplements. <b><i>Aim:</i></b> To systematically evaluate the dietary and herbal supplement recommended for patients with CKD and ESRD on the Internet, and try to distinguish between the claim of the manufacturer and proven scientific data. <b><i>Methods:</i></b> A questionnaire assessing each website was formulated. Each product ingredient was recorded in the questionnaire by two independent reviewers and statistically analyzed. <b><i>Results:</i></b> Of the 184 websites, 28% claimed to decrease CKD progression, 60% did not advise to consult a doctor before taking the supplement, and &gt;90% did not mention any potential drug interaction, disease interaction, or caution in use during pregnancy or in children. The ten common plant ingredients claiming to be beneficial in kidney diseases were uva ursi, dandelion, parsley, corn silk, juniper, celery, buchu, horsetail, marshmallow, and stinging nettle. In contrast to their claims, these substances were not adequately studied in humans. The available animal studies showed detrimental effects and potential drug interactions with commonly used medications in the CKD/ESRD population. <b><i>Conclusions:</i></b> Nephrologists need to be cognizant of the lack of substantiated proven benefits of these substances and of the potential adverse effects in the animal models that can translate to the patients. Most importantly, the policy needs to change regarding the regulation of these products to prevent patient harm and misinformation. i 2014 S. Karger AG, Basel
DOI: 10.6084/m9.figshare.5127193
title: Supplementary Material for: Intradialytic Exercise in Hemodialysis Patients: A Systematic Review and Meta-Analysis

description: <b><i>Background and Objective:</i></b> Hemodialysis (HD) patients are more inactive, leading to poor functional capacity and quality of life; this may be reversed with intradialytic exercise training. To systematically evaluate the efficacy and safety of intradialytic exercise for HD patients, we conducted a meta-analysis of the published randomized controlled trials. <b><i>Data Sources and Methods:</i></b> Medline, Embase, and Cochrane Central Register of Controlled Trials were systematically searched up to February, 2014. The reference lists of eligible studies and relevant reviews were also checked. <b><i>Results:</i></b> 24 studies of 997 patients were included. Compared with control, intradialytic exercise significantly improve Kt/V (SMD = 0.27, 95% CI 0.01-0.53), peak oxygen consumption (VO<sub>2peak</sub>) (SMD = 0.53, 95% CI 0.30-0.76), and physical performance of physical function of life (SMD = 0.30, 95% CI 0.04-0.55). However, no significant improvements were found in the mental function of life. There was no significant difference with respect to musculoskeletal and cardiovascular complications between the intradialytic exercise groups and control groups. Further subgroup analysis found that, when the trial duration was more than 6 months, the intervention had significant effects on VO<sub>2peak</sub> (SMD = 0.89, 95% CI 0.56-1.22). However, when the trial duration was less than 6 months, the change of VO<sub>2peak</sub> was not significant (SMD = 0.19, 95% CI -0.13 to 0.51). <b><i>Conclusion:</i></b> Intradialytic exercise can improve Kt/V, VO<sub>2peak</sub>, and the physical quality of life, and intradialytic exercise is safe for HD patients. Therefore, we put forward the suggestion that clinical guideline be updated to inform clinicians on the benefits of intradialytic exercise on HD patients. i 2014 S. Karger AG, Basel
DOI: 10.6084/m9.figshare.5127196
title: Supplementary Material for: Impact of Baroreflex Activation Therapy on Renal Function - A Pilot Study

description: <b><i>Background/Aims:</i></b> Resistant hypertension and chronic kidney disease (CKD) are interlinked via sympathetic overdrive. Baroreflex activation therapy (BAT) has been shown to chronically reduce blood pressure (BP) in patients with resistant hypertension. The effect of BAT on renal function in CKD patients with resistant hypertension has not been reported. The aim of this study was to investigate the effect of sympathetic inhibition on renal function in CKD patients. <b><i>Methods:</i></b> 23 CKD patients with resistant hypertension were prospectively treated with BAT. Analyses were performed before and 6 months after the start of BAT. The renal function was analyzed by creatinine, cystatin C, glomerular filtration rate (GFR), renin, aldosterone, fractioned and 24-hour sodium excretion and analyses of urine marker proteins. The purpose of the control group was to investigate the influence of treating patients in a center for hypertension and regression to the mean on investigated variables. <b><i>Results:</i></b> The office mean BP decreased from 116.9 ± 20.9 mm Hg to 104.2 ± 22.2 mm Hg (p &lt; 0.01), while the number of prescribed antihypertensive classes decreased from 6.6 ± 1.6 to 6.1 ± 1.7 (p = 0.02). Proteinuria and albuminuria decreased from a median of 283.9 and 47.7 to 136.5 (p = 0.01) and 45.0 mg/g creatinine (p = 0.01) with pronounced effects in higher CKD stage III + IV compared to I + II (p &lt; 0.01). CKD-EPI cystatin C equation improved from 53.6 ± 22.7 to 60.4 ± 26.1 ml/min (p = 0.02). While creatinine and GFR were impaired after a period of 6 months, no changes of proteinuria, albuminuria, or BP were obtained in control patients. <b><i>Conclusion:</i></b> The data of this prospective trial demonstrate potential nephroprotective effects of BAT in therapy-resistant hypertension in CKD patients by a reduction of BP, proteinuria and moreover, a stabilization of estimated GFR.
DOI: 10.6084/m9.figshare.5127202.v1
title: Supplementary Material for: Birch Pollen Immunotherapy in Mice: Inhibition of Th2 Inflammation Is Not Sufficient to Decrease Airway Hyper-Reactivity

description: <b><i>Background:</i></b> Suppression of Th2 cytokine production by allergen-specific Th2 cells is considered to be critical for the suppression of allergic symptoms by subcutaneous immunotherapy. The aim of this study was to develop a mouse model for birch pollen (BP) immunotherapy to elucidate the underlying mechanisms that contribute to the improvement of clinical symptoms. <b><i>Methods:</i></b> Mice with BP-induced allergic airway inflammation received weekly subcutaneous immunotherapy (SCIT) injections with BP extract (BPE) adsorbed to alum. The effect of an increasing dose of BPE adsorbed to a fixed concentration of alum on the suppression of airway inflammation and airway hyper-responsiveness (AHR) was determined. After 2, 4, 6 or 8 immunotherapy injections, the mice were rechallenged with the same allergen and all hallmarks of allergic asthma were evaluated. <b><i>Results:</i></b> Suppression of the immunological parameters by immunotherapy was dependent on the BPE dose. Two injections were sufficient to suppress IL-4, IL-5, IL-13, IL-10 and IFN-G production, eosinophil recruitment and peribronchial inflammatory infiltrates. BP-specific immunoglobulins were upregulated, but this was not sufficient to reduce AHR. Eight injections were needed to suppress AHR. The gradual reduction in AHR was inversely associated with the increase of BP IgG2a. <b><i>Conclusions:</i></b> BP SCIT induces an early suppression of Th2-mediated eosinophilic airway inflammation, but AHR is only effectively reduced after continued SCIT conceivably by allowing IgG2a antibody titres to build up. i 2014 S. Karger AG, Basel