cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5128303
title: Supplementary Material for: A Recombinant Sal k 1 Isoform as an Alternative to the Polymorphic Allergen from <b><i>Salsola kali</i></b> Pollen for Allergy Diagnosis

description: <b><i>Background:</i></b> The incidence of Amaranthaceae pollen allergy has increased due to the desertification occurring in many countries. In some regions of Spain, <i>Salsola kali </i>is the main cause of pollinosis, at almost the same level as olive and grass pollen. Sal k 1 - the sensitization marker of <i>S. kali </i>pollinosis - is used in clinical diagnosis, but is purified at a low yield from pollen. We aimed to produce a recombinant (r)Sal k 1 able to span the structural and immunological properties of the natural isoforms from pollen, and validate its potential use for diagnosis. <b><i>Methods:</i></b> Specific cDNA was amplified by PCR, cloned into the pET41b vector and used to transform BL21 (DE3) <i>Escherichia coli </i>cells. Immunoblotting, ELISA, basophil activation and skin-prick tests were used to validate the recombinant protein against Sal k 1 isolated from pollen. Sera and blood cells from <i>S. kali </i>pollen-sensitized patients and specific monoclonal and polyclonal antisera were used. <b><i>Results:</i></b> rSal k 1 was produced in bacteria with a yield of 7.5 mg/l of cell culture. The protein was purified to homogeneity and structural and immunologically validated against the natural form. rSal k 1 exhibited a higher IgE cross-reactivity with plant-derived food extracts such as peanut, almond or tomato than with pollen sources such as <i>Platanus acerifolia</i> and Oleaceae members. <b><i>Conclusions:</i></b> rSal k 1 expressed in bacteria retains intact structural and immunological properties in comparison to the pollen-derived allergen. It spans the immunological properties of most of the isoforms found in pollen, and it might substitute natural Sal k 1 in clinical diagnosis.
DOI: 10.6084/m9.figshare.5128297
title: Supplementary Material for: Transmission Disequilibrium Tests Based on Read Counts for Low-Coverage Next-Generation Sequence Data

description: The purpose of this paper is the introduction of new statistical methods for case-parent trio association studies based on the read counts that can be obtained from next-generation sequencing (NGS) experiments. This work focuses on the inclusion of low-coverage data into the case-parent trio design without genotype classification or imputation. Two different approaches are considered: (1) a likelihood-based approach implementing a 15-component parametric mixture model and (2) a model-free approach that applies non-parametric statistical methods to the ratios of the read counts to coverage. Simulation studies are conducted to evaluate the performances of the proposed tests. In addition, the non-centrality parameters of the mixture likelihood-based tests are derived to determine sample sizes and coverage for a NGS experimental design. As an example, the sample sizes to maintain specified powers of a published adolescent idiopathic scoliosis (AIS) study are presented. The simulation results show that the tests using the genotypes classified by the maximum Bayesian posterior probability have significantly inflated type I error rates for low-coverage data. The tests using the posterior probabilities instead of the classified genotypes show lower power than the proposed tests. Generally, power for the likelihood-based approach is higher than that for the non-parametric ratio-based approach. For the AIS example, approximately 654 trios with 4× coverage are necessary to maintain 90% power when detecting an association of odds ratio 2 at a locus with a minor allele frequency of 0.35 at the level of significance <i>α</i> = 5 × 10<sup>-8</sup>. By comparison, approximately 416 trios with 25× coverage are required to maintain the same power with the same settings. The R and C source codes to calculate the proposed test statistics, the sample sizes and power can be obtained by contacting the author (wkim@cau.ac.kr).
DOI: 10.6084/m9.figshare.5128300
title: Supplementary Material for: Die Schrott-Schwemme und fünf Gründe, warum wir nicht dazugehören

description: Medicine
DOI: 10.6084/m9.figshare.5128294
title: Supplementary Material for: Dietary Fiber Consumption Decreases the Risks of Overweight and Hypercholesterolemia in Japanese Children

description: <b><i>Aims:</i></b> It remains inconclusive whether high dietary fiber intake decreases the risk of obesity, hypercholesterolemia or high blood pressure during childhood. Therefore, this study investigated the relationships of dietary fiber intake with weight status and related clinical parameters among Japanese children. <b><i>Methods:</i></b> We analyzed the data of 5,600 subjects aged 10-11 years, between 2006 and 2010. Fiber intake was assessed using the Brief-type Diet History Questionnaire. Body height and weight and blood pressure were measured. Serum levels of total cholesterol, low- and high-density lipoprotein cholesterol and triglycerides were analyzed. Fiber intake was categorized into quintiles, and multivariate models were used to adjust for lifestyle factors. <b><i>Results:</i></b> Total fiber intake decreased the risks of overweight and high total cholesterol (OR Quintile 5 vs. Quintile 1 overweight: 0.71 for boys, 0.40 for girls; total cholesterol: 0.60 for boys, 0.66 for girls). Water-soluble fiber intake was associated with a lower risk of high blood pressure, although the ORs were not significant. <b><i>Conclusions:</i></b> Increasing the dietary fiber intake in Japanese children may have favorable effects on overweight and hypercholesterolemia.
DOI: 10.6084/m9.figshare.5128303.v1
title: Supplementary Material for: A Recombinant Sal k 1 Isoform as an Alternative to the Polymorphic Allergen from <b><i>Salsola kali</i></b> Pollen for Allergy Diagnosis

description: <b><i>Background:</i></b> The incidence of Amaranthaceae pollen allergy has increased due to the desertification occurring in many countries. In some regions of Spain, <i>Salsola kali </i>is the main cause of pollinosis, at almost the same level as olive and grass pollen. Sal k 1 - the sensitization marker of <i>S. kali </i>pollinosis - is used in clinical diagnosis, but is purified at a low yield from pollen. We aimed to produce a recombinant (r)Sal k 1 able to span the structural and immunological properties of the natural isoforms from pollen, and validate its potential use for diagnosis. <b><i>Methods:</i></b> Specific cDNA was amplified by PCR, cloned into the pET41b vector and used to transform BL21 (DE3) <i>Escherichia coli </i>cells. Immunoblotting, ELISA, basophil activation and skin-prick tests were used to validate the recombinant protein against Sal k 1 isolated from pollen. Sera and blood cells from <i>S. kali </i>pollen-sensitized patients and specific monoclonal and polyclonal antisera were used. <b><i>Results:</i></b> rSal k 1 was produced in bacteria with a yield of 7.5 mg/l of cell culture. The protein was purified to homogeneity and structural and immunologically validated against the natural form. rSal k 1 exhibited a higher IgE cross-reactivity with plant-derived food extracts such as peanut, almond or tomato than with pollen sources such as <i>Platanus acerifolia</i> and Oleaceae members. <b><i>Conclusions:</i></b> rSal k 1 expressed in bacteria retains intact structural and immunological properties in comparison to the pollen-derived allergen. It spans the immunological properties of most of the isoforms found in pollen, and it might substitute natural Sal k 1 in clinical diagnosis.
DOI: 10.6084/m9.figshare.5128288
title: Supplementary Material for: A Key Role of Autophagy in Osteoblast Differentiation on Titanium-Based Dental Implants

description: Autophagy plays an important role in embryogenesis, for the maintenance of tissue homeostasis and the elimination of damaged subcellular structures. Furthermore, autophagy could be a mode of physiological cell death and also be implicated in cell differentiation. Thus, we hypothesized that autophagy may have an impact on the differentiation of osteoblast cells influenced by various titanium-based surfaces. Interactions between smooth, commercially available pure titanium (Ti cp), rough Ticer, acid-etched Ti cp (SS) and M1-M3 (comprised of the monoclinic phase of sodium-titanium oxides and rutile; M2 contains amorphous calcium phosphates) and human osteoblast cells were investigated. Immunofluorescent staining was used for detecting autophagy, cell cluster formation and collagen type I (Col-1) expression. Flow cytometry was employed to identify autophagy, the production of endogenous nitric oxide (NO) and the size and granularity of the cells. Rough surfaces caused osteoblast differentiation via the autophagic-dependent PI3/Akt signalling pathway. These surfaces induced the formation of discrete populations of large, granular cells, i.e. mature osteoblasts. In addition, M1-M3 provoked the development of a third population of small, granular cells, responsible for cell cluster formation, which are important for the formation of bone noduli and mineralisation. The same surfaces induced faster osteoblast maturation and enhanced NO production, a hallmark of the already mentioned processes. Neither the mature osteoblasts nor the small cells appeared after the inhibition of autophagy. Inhibition of autophagy also prevented cell cluster formation. We demonstrate that autophagy plays an essential role in the osteoblast differentiation on titanium-based surfaces with rough topography.
DOI: 10.6084/m9.figshare.5128297.v1
title: Supplementary Material for: Transmission Disequilibrium Tests Based on Read Counts for Low-Coverage Next-Generation Sequence Data

description: The purpose of this paper is the introduction of new statistical methods for case-parent trio association studies based on the read counts that can be obtained from next-generation sequencing (NGS) experiments. This work focuses on the inclusion of low-coverage data into the case-parent trio design without genotype classification or imputation. Two different approaches are considered: (1) a likelihood-based approach implementing a 15-component parametric mixture model and (2) a model-free approach that applies non-parametric statistical methods to the ratios of the read counts to coverage. Simulation studies are conducted to evaluate the performances of the proposed tests. In addition, the non-centrality parameters of the mixture likelihood-based tests are derived to determine sample sizes and coverage for a NGS experimental design. As an example, the sample sizes to maintain specified powers of a published adolescent idiopathic scoliosis (AIS) study are presented. The simulation results show that the tests using the genotypes classified by the maximum Bayesian posterior probability have significantly inflated type I error rates for low-coverage data. The tests using the posterior probabilities instead of the classified genotypes show lower power than the proposed tests. Generally, power for the likelihood-based approach is higher than that for the non-parametric ratio-based approach. For the AIS example, approximately 654 trios with 4× coverage are necessary to maintain 90% power when detecting an association of odds ratio 2 at a locus with a minor allele frequency of 0.35 at the level of significance <i>α</i> = 5 × 10<sup>-8</sup>. By comparison, approximately 416 trios with 25× coverage are required to maintain the same power with the same settings. The R and C source codes to calculate the proposed test statistics, the sample sizes and power can be obtained by contacting the author (wkim@cau.ac.kr).
DOI: 10.6084/m9.figshare.5128285
title: Supplementary Material for: Gesundheitsförderung durch Stress- und Burnout-Prophylaxe mit ätherischen Ölen für alle Berufsgruppen im Wiener Otto-Wagner-Spital

description: <b><i>Hintergrund: </i></b>Mehr als 50% der Menschen leiden an berufsbedingtem und familiärem Stress, der bei hohem Pegel zu körperlichen, mentalen und sozialen Beeinträchtigungen bis hin zum Burnout-Syndrom führen kann. Die regelmäßige Anwendung von hochwertigen ätherischen Ölen vermag den individuellen Stresspegel deutlich zu senken. In einem Projekt zur Gesundheitsförderung durch Stress- und Burnout-Prophylaxe soll die Stressreduktion durch ätherische Öle bestätigt werden. <b><i>Methodik:</i></b> In das Studienprojekt konnten insgesamt 88 Mitarbeiter des Wiener Otto Wagner Spitals mit auswertbaren Aufnahme- und 55 Mitarbeiter mit auswertbaren Abschluss-Fragebögen aufgenommen werden. Die Teilnehmer erhielten einen SOS-Stress-Deoroller mit 12 ätherischen Ölen, der mindestens 3-mal täglich einen Monat lang an den Pulszonen der Handgelenke aufgetragen wurde. <b><i>Ergebnisse: </i></b>Zum Befragungszeitpunkt 1 am Tag der Aufnahme in die Studie betrug der Stresswert bezogen auf eine Stress-Skala von 1 (gar nicht belastet) bis 10 (sehr stark belastet) im Mittel 6,28, am Ende der Beobachtungszeit 5,24. In der Analyse der körperlichen Beeinträchtigungen durch Stress (SK 1-8) zeigte sich beim Pflegepersonal (p = 0,036) und bei Personen über 50 Jahren (p = 0,012 bzw. 0,025) ein signifikanter Benefit der Aromatherapie. Das Belastungsniveau durch körperlichen, psychischen und sozialen Stress zwischen Befragungszeitpunkt 1 und 2 zeigte deutliche, mitunter signifikante positive Veränderung durch die Anwendung der ätherischen Öle. Bei 27 Teilnehmern konnten die Fragebögen von Zeitpunkt 1 und 2 dem jeweiligen Teilnehmer zugeordnet werden. In dieser Personengruppe zeigten sich sowohl in der Gesamtbelastung wie auch in allen Teilbereichen signifikant positive Ergebnisse der Aromatherapie. <b><i>Schlussfolgerung: </i></b>Ein Großteil der Teilnehmer konnte mittels der ätherischen Öle im SOS-Stress-Deoroller seine Stress-assoziierten Beeinträchtigungen deutlich reduzieren. Es konnten keine allergischen Reaktionen oder Unverträglichkeiten beobachtet werden. Ausgewählte hochwertige ätherische Öle können für die Prophylaxe und Behandlung von Stress und Burnout empfohlen werden.
DOI: 10.6084/m9.figshare.5128291
title: Supplementary Material for: Survival in Subcortical Vascular Dementia: Predictors and Comparison to Probable Alzheimer's Disease in a Tertiary Memory Clinic Population

description: <b><i>Background:</i></b> Subcortical vascular dementia (SVaD) is one of the most common dementias, after Alzheimer's disease (AD) dementia. Few survival analyses in SVaD patients have been reported. <b><i>Methods:</i></b> The dates and causes of death of 146 SVaD and 725 AD patients were included. We used the Cox proportional hazards model to compare survival between SVaD and AD patients and to explore possible factors related to survival of SVaD patients. <b><i>Results:</i></b> The median survival time after the onset of SVaD (109 months) was shorter than that recorded for AD (152 months). The most common cause of death in SVaD was stroke (47.1%). Factors associated with shorter survival in SVaD were late onset, male sex, worse baseline cognition, absence of hypertension and a family history of stroke. <b><i>Conclusions:</i></b> Stroke prevention may be important in SVaD treatment because 47.1% of SVaD patients died of stroke. A family history of stroke and absence of hypertension were associated with a shorter survival in SVaD, suggesting the existence of genetic or unknown risk factors.
DOI: 10.6084/m9.figshare.5128300.v1
title: Supplementary Material for: Die Schrott-Schwemme und fünf Gründe, warum wir nicht dazugehören

description: Medicine
DOI: 10.6084/m9.figshare.5128282
title: Supplementary Material for: Transcortical Transventricular Endoscopic Approach and Ommaya Reservoir Placement for Cystic Craniopharyngioma

description: The treatment of craniopharyngioma is varied. It ranges from radical excision to direct radiotherapy. As the morbidity of excision is high, more conservative approaches are used. Placement of a catheter and reservoir is one such option for cystic craniopharyngiomas. The positioning of catheters has been performed by various means. A method of endoscopic reservoir catheter placement is described. Three children with ages ranging from 5 to 12 years presented with clinical features of raised intracranial pressure. They did not have vision impairment. Imaging showed a predominantly cystic craniopharyngioma extending into the third ventricle with hydrocephalus. All underwent precoronal burr hole, transcortical transventricular endoscopic biopsy of craniopharyngioma, and Ommaya reservoir placement. There were no complications. All children did well after surgery and did not require further cyst aspiration.
DOI: 10.6084/m9.figshare.5128285.v1
title: Supplementary Material for: Gesundheitsförderung durch Stress- und Burnout-Prophylaxe mit ätherischen Ölen für alle Berufsgruppen im Wiener Otto-Wagner-Spital

description: <b><i>Hintergrund: </i></b>Mehr als 50% der Menschen leiden an berufsbedingtem und familiärem Stress, der bei hohem Pegel zu körperlichen, mentalen und sozialen Beeinträchtigungen bis hin zum Burnout-Syndrom führen kann. Die regelmäßige Anwendung von hochwertigen ätherischen Ölen vermag den individuellen Stresspegel deutlich zu senken. In einem Projekt zur Gesundheitsförderung durch Stress- und Burnout-Prophylaxe soll die Stressreduktion durch ätherische Öle bestätigt werden. <b><i>Methodik:</i></b> In das Studienprojekt konnten insgesamt 88 Mitarbeiter des Wiener Otto Wagner Spitals mit auswertbaren Aufnahme- und 55 Mitarbeiter mit auswertbaren Abschluss-Fragebögen aufgenommen werden. Die Teilnehmer erhielten einen SOS-Stress-Deoroller mit 12 ätherischen Ölen, der mindestens 3-mal täglich einen Monat lang an den Pulszonen der Handgelenke aufgetragen wurde. <b><i>Ergebnisse: </i></b>Zum Befragungszeitpunkt 1 am Tag der Aufnahme in die Studie betrug der Stresswert bezogen auf eine Stress-Skala von 1 (gar nicht belastet) bis 10 (sehr stark belastet) im Mittel 6,28, am Ende der Beobachtungszeit 5,24. In der Analyse der körperlichen Beeinträchtigungen durch Stress (SK 1-8) zeigte sich beim Pflegepersonal (p = 0,036) und bei Personen über 50 Jahren (p = 0,012 bzw. 0,025) ein signifikanter Benefit der Aromatherapie. Das Belastungsniveau durch körperlichen, psychischen und sozialen Stress zwischen Befragungszeitpunkt 1 und 2 zeigte deutliche, mitunter signifikante positive Veränderung durch die Anwendung der ätherischen Öle. Bei 27 Teilnehmern konnten die Fragebögen von Zeitpunkt 1 und 2 dem jeweiligen Teilnehmer zugeordnet werden. In dieser Personengruppe zeigten sich sowohl in der Gesamtbelastung wie auch in allen Teilbereichen signifikant positive Ergebnisse der Aromatherapie. <b><i>Schlussfolgerung: </i></b>Ein Großteil der Teilnehmer konnte mittels der ätherischen Öle im SOS-Stress-Deoroller seine Stress-assoziierten Beeinträchtigungen deutlich reduzieren. Es konnten keine allergischen Reaktionen oder Unverträglichkeiten beobachtet werden. Ausgewählte hochwertige ätherische Öle können für die Prophylaxe und Behandlung von Stress und Burnout empfohlen werden.
DOI: 10.6084/m9.figshare.5128291.v1
title: Supplementary Material for: Survival in Subcortical Vascular Dementia: Predictors and Comparison to Probable Alzheimer's Disease in a Tertiary Memory Clinic Population

description: <b><i>Background:</i></b> Subcortical vascular dementia (SVaD) is one of the most common dementias, after Alzheimer's disease (AD) dementia. Few survival analyses in SVaD patients have been reported. <b><i>Methods:</i></b> The dates and causes of death of 146 SVaD and 725 AD patients were included. We used the Cox proportional hazards model to compare survival between SVaD and AD patients and to explore possible factors related to survival of SVaD patients. <b><i>Results:</i></b> The median survival time after the onset of SVaD (109 months) was shorter than that recorded for AD (152 months). The most common cause of death in SVaD was stroke (47.1%). Factors associated with shorter survival in SVaD were late onset, male sex, worse baseline cognition, absence of hypertension and a family history of stroke. <b><i>Conclusions:</i></b> Stroke prevention may be important in SVaD treatment because 47.1% of SVaD patients died of stroke. A family history of stroke and absence of hypertension were associated with a shorter survival in SVaD, suggesting the existence of genetic or unknown risk factors.
DOI: 10.6084/m9.figshare.5128276
title: Supplementary Material for: miR-590-3p Is a Novel MicroRNA in Myocarditis by Targeting Nuclear Factor Kappa-B in vivo

description: <b><i>Objective:</i></b> Nuclear factor kappa-B (NF-κB)-induced inflammation leads to myocarditis and heart dysfunction. How microRNAs (miRNAs) contribute to this process is poorly defined. The aim of this study was to investigate whether miRNAs regulate NF-κB-induced inflammation in experimental autoimmune myocarditis (EAM) in vivo. <b><i>Methods and Results:</i></b> NF-κB and its related proinflammatory genes, including interleukin-6 (IL-6) and tumor necrosis factor-a (TNF-a), were activated in EAM. Profiling of NF-κB-related miRNAs revealed that miR-590-3p was strikingly reduced in EAM. We found IL-6-induced proinflammatory signaling via miR-590-3p reduction, p50 induction, NF-κB activation and IL-6/TNF-a expression. Moreover, a luciferase reporter assay demonstrated that miR-590-3p directly interacted with the 3' UTR (untranslated region) of the p50 subunit, and that miR-590-3p overexpression inhibited p50 expression. Finally, miR-590-3p transfection through adeno-associated virus significantly inhibited p50 expression, suppressed NF-κB activity and blocked IL-6/TNF-a expression in vivo, reducing the lesion area and improving cardiac function in EAM. <b><i>Conclusion:</i></b> miR-590-3p is a novel NF-κB-related miRNA that directly targets the p50 subunit. This may provide a novel strategy for the treatment of myocarditis.
DOI: 10.6084/m9.figshare.5128279
title: Supplementary Material for: Characterization of a Novel Mutation in <b><i>SLC1A1 </i></b>Associated with Schizophrenia

description: We have recently described a hemi-deletion on chromosome 9p24.2 at the <i>SLC1A1</i> gene locus and its co-segregation with schizophrenia in an extended Palauan pedigree. This finding represents a point of convergence for several pathophysiological models of schizophrenia. The present report sought to characterize the biological consequences of this hemi-deletion. Dual luciferase assays demonstrated that the partially deleted allele (lacking exon 1 and the native promoter) can drive expression of a 5′-truncated <i>SLC1A1</i> using sequence upstream of exon 2 as a surrogate promoter. However, confocal microscopy and electrophysiological recordings demonstrate that the 5′-truncated <i>SLC1A1</i> lacks normal membrane localization and glutamate transport ability. To identify downstream consequences of the hemi-deletion, we first used a themed qRT-PCR array to compare expression of 84 GABA and glutamate genes in RNA from peripheral blood leukocytes in deletion carriers (n = 11) versus noncarriers (n = 8) as well as deletion carriers with psychosis (n = 5) versus those without (n = 3). Then, targeted RNA-Seq (TREx) was used to quantify expression of 375 genes associated with neuropsychiatric disorders in HEK293 cells subjected to either knockdown of <i>SLC1A1</i> or overexpression of full-length or 5′-truncated <i>SLC1A1</i>. Expression changes of several genes strongly implicated in schizophrenia pathophysiology were detected (e.g. <i>SLC1A2</i>,<i> SLC1A3</i>,<i> SLC1A6</i>,<i> SLC7A11</i>,<i> GRIN2A</i>,<i> GRIA1 </i>and<i> DLX1</i>).