cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124973
title: Supplementary Material for: Optimizing the Use of a Skin Prick Test Device on Children

description: <b><i>Background:</i></b> Studies comparing skin prick test (SPT) devices have revealed varying results in performance and there is little known about their use on children. <b><i>Methods:</i></b> We performed 2 complementary studies to test the sensitivity, reproducibility and acceptability of commercially available SPT devices (Stallerpoint, Antony, France) using different application techniques. In the first part, histamine/saline was put on as a drop by use of a vial (V), and in the second part it was transferred from a well with the aid of the test device (W). The techniques were as follows: apply vertical pressure (Stallerpoint-VP or Stallerpoint-WP), apply vertical pressure with 90° clockwise rotation (Stallerpoint-VC or Stallerpoint-WC) and apply vertical pressure with 90° clockwise and counter-clockwise rotations (Stallerpoint-VCC or Stallerpoint-WCC). For comparison, ALK Lancet was used with a technique of ‘drop and apply vertical pressure'. <b><i>Results:</i></b> In the first part, sensitivities of the Stallerpoint-VC (96.6%), Stallerpoint-VCC (95.5%) and ALK Lancet (93.2%) techniques were superior (p &lt; 0.001) to the other Stallerpoint-VP and Stallerpoint-WP techniques (76.1 and 46.6%). Intrapatient coefficient of variation (CV) values were 15.0, 18.9, 15.4, 22.4 and 48.5%, respectively. Interpatient CV ranged between 22.8 and 55.1%. In the second part, the Stallerpoint-WC (98.8%), WCC (97.5%) and ALK Lancet (98.8%) techniques yielded high sensitivities, whereas the sensitivity of Stallerpoint-WP (28.7%) was very low. There were false-positive reactions in the Stallerpoint-VCC and WCC techniques. <b><i>Conclusion:</i></b> In children, the SPT technique was found to be as important as the testing device. Stallerpoint-VC and WC techniques are reliable, tolerable and comparable with the ALK Lancet technique.
DOI: 10.6084/m9.figshare.5124979
title: Supplementary Material for: Macrolide Therapy Decreases Chronic Obstructive Pulmonary Disease Exacerbation: A Meta-Analysis

description: <b><i>Background:</i></b> Macrolide antibiotics have anti-inflammatory effects, and long-term administration may reduce chronic obstructive pulmonary disease (COPD) exacerbations. <b><i>Objective:</i></b> To investigate the effects of long-term treatment of macrolide therapy for COPD. <b><i>Methods:</i></b> We searched the PubMed and Embase databases to identify randomized controlled trials that evaluated the effect of macrolide therapy (of at least 2 weeks) for COPD. The primary outcome assessed was the frequency of acute exacerbations during follow-up. <b><i>Results:</i></b> Six trials involving 1,485 COPD patients were included in the analysis. Analysis of the pooled data of all 6 trials showed that macrolide administration reduced the frequency of acute exacerbations of COPD [risk ratio (RR) = 0.62; 95% CI 0.43-0.89, p = 0.01]. Subgroup analysis showed that only erythromycin might be associated with decreased COPD exacerbations (erythromycin: p = 0.04, azithromycin: p<i> = </i>0.22, clarithromycin: p<i> = </i>0.18). Moreover, macrolide therapy for 3 months did not significantly reduce the number of exacerbations (p<i> = </i>0.18), whereas a beneficial effect was conclusive in the 6-month (p<i> = </i>0.009) and 12-month (p<i> = </i>0.03) treatment subgroups. In addition, nonfatal adverse events were more frequent in the macrolide treatment groups than in the controls (RR = 1.32; 95% CI 1.06-1.64, p<i> = </i>0.01). However, related clinical factors had no influence on the overall result (p<i> = </i>0.19). There was no publication bias among the included trials. <b><i>Conclusions:</i></b> Macrolide therapy was effective and safe in decreasing the frequency of exacerbations in patients with COPD. Treatment might provide a significant benefit but only when therapy lasts more than 6 months.
DOI: 10.6084/m9.figshare.5125087.v7
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.v1
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.5124979.v1
title: Supplementary Material for: Macrolide Therapy Decreases Chronic Obstructive Pulmonary Disease Exacerbation: A Meta-Analysis

description: <b><i>Background:</i></b> Macrolide antibiotics have anti-inflammatory effects, and long-term administration may reduce chronic obstructive pulmonary disease (COPD) exacerbations. <b><i>Objective:</i></b> To investigate the effects of long-term treatment of macrolide therapy for COPD. <b><i>Methods:</i></b> We searched the PubMed and Embase databases to identify randomized controlled trials that evaluated the effect of macrolide therapy (of at least 2 weeks) for COPD. The primary outcome assessed was the frequency of acute exacerbations during follow-up. <b><i>Results:</i></b> Six trials involving 1,485 COPD patients were included in the analysis. Analysis of the pooled data of all 6 trials showed that macrolide administration reduced the frequency of acute exacerbations of COPD [risk ratio (RR) = 0.62; 95% CI 0.43-0.89, p = 0.01]. Subgroup analysis showed that only erythromycin might be associated with decreased COPD exacerbations (erythromycin: p = 0.04, azithromycin: p<i> = </i>0.22, clarithromycin: p<i> = </i>0.18). Moreover, macrolide therapy for 3 months did not significantly reduce the number of exacerbations (p<i> = </i>0.18), whereas a beneficial effect was conclusive in the 6-month (p<i> = </i>0.009) and 12-month (p<i> = </i>0.03) treatment subgroups. In addition, nonfatal adverse events were more frequent in the macrolide treatment groups than in the controls (RR = 1.32; 95% CI 1.06-1.64, p<i> = </i>0.01). However, related clinical factors had no influence on the overall result (p<i> = </i>0.19). There was no publication bias among the included trials. <b><i>Conclusions:</i></b> Macrolide therapy was effective and safe in decreasing the frequency of exacerbations in patients with COPD. Treatment might provide a significant benefit but only when therapy lasts more than 6 months.
DOI: 10.6084/m9.figshare.5124964
title: Supplementary Material for: Mycophenolate as Maintenance Therapy for Lupus Nephritis with Impaired Renal Function

description: <b><i>Background:</i></b> Mycophenolate (MF) is effective as a maintenance therapy after induction therapy in patients with lupus nephritis (LN). However, little is known about its role in patients with impaired renal function. The purpose of this study was to evaluate the efficacy and safety of MF as a maintenance therapy for LN and its association with renal function. <b><i>Methods:</i></b> Data were obtained for 56 Spanish patients who were receiving MF as a maintenance therapy for LN. Patients were classified into two groups according to renal function at the initiation of MF treatment: group 1 [estimated glomerular filtration rate (eGFR) ≥60 ml/min/1.73 m<sup>2</sup>] and group 2 (eGFR &lt;60 ml/min/1.73 m<sup>2</sup>). The primary endpoints of the study were the rates of renal relapse and responses, and their relationship with baseline renal function. Secondary outcomes were the appearance of side effects during treatment. <b><i>Results:</i></b> At initiation of MF treatment, the only differences between the groups were for age, hemoglobin levels, anti-DNA antibody titer, proteinuria, and renal function. In group 1 (n = 38), the eGFR was 98 ± 34 ml/min/1.73 m<sup>2</sup> and in group 2 (n = 18) the eGFR was 43 ± 14 ml/min/1.73 m<sup>2</sup>. Only 3 cases had an eGFR &lt;30 ml/min/1.73 m<sup>2</sup>. No significant differences were observed in the rate of relapse at 6 months (group 1: 20%; group 2: 23%) or at 12 months (group 1: 25%; group 2: 17%). Response rates were also similar in both groups. Side effects were unremarkable. <b><i>Conclusions:</i></b> MF is effective and safe as a maintenance therapy for LN both in patients with normal renal function and in those with renal impairment.
DOI: 10.6084/m9.figshare.5124976.v1
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.
DOI: 10.6084/m9.figshare.5124955
title: Supplementary Material for: Epidemiology of Traumatic Spinal Cord Injury in Developing Countries: A Systematic Review

description: <b><i>Background/Aims:</i></b> To describe the epidemiology of spinal cord injury (SCI) in the developing world. <b><i>Methods:</i></b> Developing countries were selected based on the definition proposed by the International Monetary Fund. A literature search was performed in July 2012 in Medline and Embase. Further article procurement was obtained via the reference lists of the identified articles, websites, and direct contact with the authors of the identified studies. We designed search strategies using the key words: SCI, epidemiology, incidence, and prevalence. According to the inclusion criteria, 64 studies from 28 countries were included. <b><i>Results:</i></b> The incidence of SCI in developing countries is 25.5/million/year (95% CI: 21.7-29.4/million/year) and ranges from 2.1 to 130.7/million/year. Males comprised 82.8% (95% CI: 80.3-85.2) of all SCIs with a mean age of 32.4 years (95% CI: 29.7-35.2). The two leading causes of SCI were found to be motor vehicle crashes (41.4%; 95% CI: 35.4-47.4) and falls (34.9%; 95% CI: 26.7-43.1). Complete SCIs were found to be more common than incomplete injuries (complete SCI: 56.5%; 95% CI: 47.6-65.3; incomplete SCI: 43.0%; 95% CI: 34.1-52.0). Similarly, paraplegia was found to be more common than tetraplegia (paraplegia: 58.7%; 95% CI: 51.5-66.0; tetraplegia: 40.6%; 95% CI: 33.3-48.0). <b><i>Conclusion:</i></b> Through an understanding of the epidemiology of SCI in developing countries, appropriate preventative strategies and resource allocation may decrease the incidence and improve the care of these injuries.
DOI: 10.6084/m9.figshare.5124961
title: Supplementary Material for: Analysis of Sterol-Regulatory Element-Binding Protein 1c Target Genes in Mouse Liver during Aging and High-Fat Diet

description: <b><i>Background:</i></b> The sterol regulatory element-binding protein (SREBP) 1c contributes to the transcriptional coordination of cholesterol, fatty acid, and carbohydrate metabolisms. Alterations in these processes accelerate the progression of hepatic steatosis and insulin resistance during aging and obesity. <b><i>Methods:</i></b> Using an ex vivo chromatin immunoprecipitation coupled to microarray (ChIP-on-chip) technique combined with genome-wide gene expression analysis, we analyzed the transcriptomic adaptations mediated by <i>Srebp-1c</i> binding to gene promoters in the liver of mice fed with a low-fat diet or a high-fat diet (HFD) for either 1 or 12 months. <b><i>Results:</i></b> Aging had a higher transcriptional impact than HFD and modified the expression of genes involved in fatty acid oxidation and oxidative stress. HFD was associated with a marked induction of genes involved in lipid and cholesterol metabolism. The prolonged high-fat feeding together with the aging effects stimulates inflammatory pathways. ChIP-on-chip applied to aging and HFD analyses revealed that the binding of SREBP-1c to a series of promoters accompanied a paralleled modification of gene expression. Therefore, SREBP-1c could play a role in aging and high-fat feeding through the regulation of genes involved in lipid metabolism and inflammatory response. <b><i>Conclusions:</i></b> This study represents an original ex vivo experiment to elucidate the molecular events involved in metabolic disorders.
DOI: 10.6084/m9.figshare.5124958
title: Supplementary Material for: Building a European Consensus on Minimum Quality Standards for Drug Treatment, Rehabilitation and Harm Reduction

description: <b><i>Background/Aims:</i></b> The Study on the Development of an EU Framework for Minimum Quality Standards and Benchmarks in Drug Demand Reduction (EQUS) has set up an inventory of quality standards and initiated a consensus-building process, aiming at establishing a set of European minimum quality standards (MQS) for treatment/rehabilitation and harm reduction in the field of drug abuse and dependence. <b><i>Methods:</i></b> Existing documents were collected by country-specific experts and integrated into a predefined framework of quality standards. Agreement, implementation status and expected implementation problems of the proposed standards were assessed by a survey of European stakeholders and the final lists of European MQS were established at a European conference. <b><i>Results:</i></b> Overall, 349 documents were identified as relevant. Major gaps were identified for ethical and legal standards, and for documents that provide grades of evidence for specific standards. A high level of acceptance was found for the treatment/rehabilitation MQS, while a somewhat lower level was found for the harm reduction MQS. The final lists of MQS were based on at least 80% of acceptance by European experts and stakeholders. <b><i>Conclusion:</i></b> A high consensus of European MQS for treatment/rehabilitation and harm reduction has been achieved. Further implementation and developmental steps are discussed.
DOI: 10.6084/m9.figshare.5124961.v1
title: Supplementary Material for: Analysis of Sterol-Regulatory Element-Binding Protein 1c Target Genes in Mouse Liver during Aging and High-Fat Diet

description: <b><i>Background:</i></b> The sterol regulatory element-binding protein (SREBP) 1c contributes to the transcriptional coordination of cholesterol, fatty acid, and carbohydrate metabolisms. Alterations in these processes accelerate the progression of hepatic steatosis and insulin resistance during aging and obesity. <b><i>Methods:</i></b> Using an ex vivo chromatin immunoprecipitation coupled to microarray (ChIP-on-chip) technique combined with genome-wide gene expression analysis, we analyzed the transcriptomic adaptations mediated by <i>Srebp-1c</i> binding to gene promoters in the liver of mice fed with a low-fat diet or a high-fat diet (HFD) for either 1 or 12 months. <b><i>Results:</i></b> Aging had a higher transcriptional impact than HFD and modified the expression of genes involved in fatty acid oxidation and oxidative stress. HFD was associated with a marked induction of genes involved in lipid and cholesterol metabolism. The prolonged high-fat feeding together with the aging effects stimulates inflammatory pathways. ChIP-on-chip applied to aging and HFD analyses revealed that the binding of SREBP-1c to a series of promoters accompanied a paralleled modification of gene expression. Therefore, SREBP-1c could play a role in aging and high-fat feeding through the regulation of genes involved in lipid metabolism and inflammatory response. <b><i>Conclusions:</i></b> This study represents an original ex vivo experiment to elucidate the molecular events involved in metabolic disorders.
DOI: 10.6084/m9.figshare.5125087.v8
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.5124943
title: Supplementary Material for: Isolated Hand Paresis: A Case Series

description: <b><i>Background:</i></b> Hand knob infarction is a well-known stroke entity. Based on very limited data, embolic stroke mechanism has been considered the most frequent cause; however, prognosis is considered good. We wanted to shed more light on this phenomenon by assessing a cohort of patients referred to a general hospital stroke unit. <b><i>Methods:</i></b> Every subject admitted to our stroke unit with an acute isolated hand paresis in the period from 2007 to 2012 was identified prospectively. Patients who had suffered from a stroke in the hand motor cortex or an adjacent area explaining the acute loss of hand function were included in the study. The Trial of Org 10172 in Acute Stroke Treatment criteria were used to classify subtypes of stroke according to etiology. The patients were followed up during autumn 2012. <b><i>Results:</i></b> Seventeen subjects were admitted, but in 2 of them symptoms were transitory and magnetic resonance imaging was negative. Two patients were excluded due to persisting sensory deficits. The remaining 13 (11 males and 2 females) patients with an average age of 62.9 (±13.4) years were included, representing 1.5% of all ischemic strokes diagnosed at the stroke unit in the given period. All patients were right-handed, and the dominant hand was affected only in 4 (31%). The average Medical Research Council's scale score was 3.1 (±1.4) on admission, and classified as bad. On follow-up, which occurred on average 29.8 (±19.8) months after the stroke, the score was 4.6 (±0.4) and was classified as fair to good. No patient experienced a new stroke. The outcome was good to excellent in 10 patients (77%). Two patients died (15%), 1 of probable cardiac arrest and 1 of unknown cause. One patient did not participate in the follow-up. The majority of patients had evidence of both small artery (77%) and large artery (85%) disease. On average, there were 1.6 (±0.4) new ischemic lesions per patient. Six patients had a solitary lesion (46%). In 5 of them, small artery occlusion was considered the probable stroke mechanism. In 4 cases, the stroke was of undetermined etiology. Three patients had atrial fibrillation, and in 2 of them cardioembolism was the probable stroke mechanism. Two patients with definite large artery atherosclerosis underwent carotid endarterectomy, and 1 of them had comorbid atrial fibrillation. <b><i>Conclusion:</i></b> Strokes causing isolated hand paresis seem to have a heterogeneous etiology. Prognosis regarding hand function is good, but long-term outcome depends on stroke etiology and secondary prophylaxis.