cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5813529.v1
title: A role for endothelial cells in radiation-induced inflammation

description: <b>Purpose:</b> To unravel the role of the vasculature in radiation-induced brain tissue damage. <b>Materials and methods:</b> Postnatal day 14 mice received a single dose of 10 Gy cranial irradiation and were sacrificed 6 h, 24 h or 7 days post-irradiation. Endothelial cells were isolated from the hippocampus and cerebellum using fluorescence-activated cell sorting, followed by cell cycle analysis and gene expression profiling. <b>Results:</b> Flow cytometric analysis revealed that irradiation increased the percentage of endothelial cells, relative to the whole cell population in both the hippocampus and the cerebellum. This change in cell distribution indicates that other cell types are more susceptible to irradiation-induced cell death, compared to endothelial cells. This was supported by data showing that genes involved in endothelial cell-specific apoptosis (e.g. <i>Smpd1</i>) were not induced at any time point investigated but that genes involved in cell-cycle arrest (e.g. <i>Cdkn1a</i>) were upregulated at all investigated time points, indicating endothelial cell repair. Inflammation-related genes, on the other hand, were strongly induced, such as <i>Ccl2</i>, <i>Ccl11</i> and <i>Il6</i>. <b>Conclusions:</b> We conclude that endothelial cells are relatively resistant to ionizing radiation but that they play an active, hitherto unknown, role in the inflammatory response after irradiation. In the current study, this was shown in both the hippocampus, where neurogenesis and extensive cell death after irradiation occurs, and in the cerebellum, where neurogenesis no longer occurs at this developmental age.
DOI: 10.6084/m9.figshare.5813526
title: Reproducible Document Stack project (ELIXIR UK meeting)

description: Presentation given by Giuliano Maciocci for ELIXIR UK meeting, January 24 2018.<br>This slide deck describes the Reproducible Document Stack project. More information can be found at https://elifesciences.org/for-the-press/e6038800/elife-supports-development-of-open-technology-stack-for-publishing-reproducible-manuscripts-online.
DOI: 10.6084/m9.figshare.5813526.v1
title: Reproducible Document Stack project (ELIXIR UK meeting)

description: Presentation given by Giuliano Maciocci for ELIXIR UK meeting, January 24 2018.<br>This slide deck describes the Reproducible Document Stack project. More information can be found at https://elifesciences.org/for-the-press/e6038800/elife-supports-development-of-open-technology-stack-for-publishing-reproducible-manuscripts-online.
DOI: 10.6084/m9.figshare.5813514
title: Supporting authors to bring data to the forefront: a case study on Springer Nature’s past, present, and future interest in research data

description: A case study explaining Springer Nature's figshare implementation and future plans for Research Data Support.
DOI: 10.6084/m9.figshare.5813514.v3
title: Supporting authors to bring data to the forefront: a case study on Springer Nature’s past, present, and future interest in research data

description: A case study explaining Springer Nature's figshare implementation and future plans for Research Data Support.
DOI: 10.6084/m9.figshare.5813514.v2
title: Supporting authors to bring data to the forefront: a case study on Springer Nature’s past, present, and future interest in research data

description: A case study explaining Springer Nature's figshare implementation and future plans for Research Data Support.
DOI: 10.6084/m9.figshare.5813475
title: Evolutionary crop ecology: trends in root architecture during wheat breeding

description: Plants were grown in agar gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resources treatments for fractal analysis of root system architecture. Yield in the field was tested at standard and low planting densities.
DOI: 10.6084/m9.figshare.5813475.v1
title: Evolutionary crop ecology: trends in root architecture during wheat breeding

description: Plants were grown in agar gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resources treatments for fractal analysis of root system architecture. Yield in the field was tested at standard and low planting densities.
DOI: 10.6084/m9.figshare.5813475.v2
title: Evolutionary crop ecology: trends in root architecture during wheat breeding

description: Plants were grown in agar gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resources treatments for fractal analysis of root system architecture. Yield in the field was tested at standard and low planting densities.
DOI: 10.6084/m9.figshare.5813475.v4
title: Evolutionary crop ecology: trends in root architecture during wheat breeding

description: Plants were grown in agar gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resources treatments for fractal analysis of root system architecture. Yield in the field was tested at standard and low planting densities.
DOI: 10.6084/m9.figshare.5813475.v3
title: Evolutionary crop ecology: trends in root architecture during wheat breeding

description: Plants were grown in agar gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resources treatments for fractal analysis of root system architecture. Yield in the field was tested at standard and low planting densities.
DOI: 10.6084/m9.figshare.5813460.v1
title: Text and Data Mining taxonomy

description: This taxonomy was created as part of the OpenMinTeD project http://openminted.eu/
DOI: 10.6084/m9.figshare.5813151.v1
title: Editorial: Ética profissional, sustentabilidade e informação científica

description: Este é o editorial do primeiro fascículo de 2018, com a temática "ÉTICA PROFISSIONAL, SUSTENTABILIDADE E INFORMAÇÃO CIENTÍFICA", que objetiva argumentar os trabalhos submetidos com essa proposta.
DOI: 10.6084/m9.figshare.5813016
title: Data from: A diverse assemblage of moths feeding on aphid honeydew

description: Sakagami, K., Sugiura, S., 2018. A diverse assemblage of moths feeding on aphid honeydew. Journal of Asia-Pacific Entomology DOI: 10.1016/j.aspen.2018.01.019
DOI: 10.6084/m9.figshare.5812986
title: Glyphosate residues in Swiss market foods: monitoring and risk evaluation

description: A total of 243 samples of diverse foodstuffs were analysed for glyphosate and aminomethylphosphonic acid (AMPA) using a liquid chromatography triple quadrupole mass spectrometry (LC/MS/MS) method with a relatively low limit of quantification in the range of 0.0005–0.0025 mg kg<sup>−1</sup>. Main contributors for dietary glyphosate and AMPA intake were cereals and pulses. The results suggest that pasta is a very important foodstuff for dietary glyphosate residue intake in Switzerland. Interestingly all samples of wine, fruit juice and nearly all samples of honey tested positive for glyphosate although at very low levels. A dietary risk assessment was conducted. Food products for analysis were not selected purely at random, rather products were selected for which high levels of glyphosate residues were suspected. However, even in samples where high residue levels were expected, no exceedances of maximum residue levels were found. Consequently, human exposure did not exceed neither acceptable daily intake nor acute reference dose. Therefore, glyphosate residues found in the sampled foodstuffs from the Swiss market were of no concern for human health.
DOI: 10.6084/m9.figshare.5812986.v1
title: Glyphosate residues in Swiss market foods: monitoring and risk evaluation

description: A total of 243 samples of diverse foodstuffs were analysed for glyphosate and aminomethylphosphonic acid (AMPA) using a liquid chromatography triple quadrupole mass spectrometry (LC/MS/MS) method with a relatively low limit of quantification in the range of 0.0005–0.0025 mg kg<sup>−1</sup>. Main contributors for dietary glyphosate and AMPA intake were cereals and pulses. The results suggest that pasta is a very important foodstuff for dietary glyphosate residue intake in Switzerland. Interestingly all samples of wine, fruit juice and nearly all samples of honey tested positive for glyphosate although at very low levels. A dietary risk assessment was conducted. Food products for analysis were not selected purely at random, rather products were selected for which high levels of glyphosate residues were suspected. However, even in samples where high residue levels were expected, no exceedances of maximum residue levels were found. Consequently, human exposure did not exceed neither acceptable daily intake nor acute reference dose. Therefore, glyphosate residues found in the sampled foodstuffs from the Swiss market were of no concern for human health.
DOI: 10.6084/m9.figshare.5812956
title: Supplementary Material for: Body Composition following Necrotising Enterocolitis in Preterm Infants

description: <b><i>Background:</i></b> The optimal nutritional regimen for preterm infants, including those that develop necrotising enterocolitis (NEC), is unknown. <b><i>Objective:</i></b> The objective here was to evaluate body composition at term in infants following NEC, in comparison with healthy infants. The primary outcome measure was non-adipose tissue mass (non-ATM). <b><i>Methods:</i></b> We compared body composition assessed by magnetic resonance imaging at term in infants born &lt;31 weeks of gestational age that participated in NEON, a trial comparing incremental versus immediate delivery of parenteral amino acids on non-ATM, and SMOF versus intralipid on intrahepatocellular lipid content. There were no differences in the primary outcomes. We compared infants that received surgery for NEC (NEC-surgical), infants with medically managed NEC (NEC-medical), and infants without NEC (reference). <b><i>Results:</i></b> A total of 133 infants were included (8 NEC-surgical; 15 NEC-medical; 110 reference). In comparison with the reference group, infants in the NEC-surgical and NEC-medical groups were significantly lighter [adjusted mean difference (95% CI) NEC-surgical: –630 g (–1,010, –210), <i>p</i> = 0.003; NEC-medical: –440 g (–760, –110), <i>p</i> = 0.009] and the total adipose tissue volume (ATV) was significantly lower [NEC-surgical: –360 cm<sup>3</sup> (–516, –204), <i>p</i> &lt; 0.001; NEC-medical: –127 cm<sup>3</sup> (–251, –4); <i>p</i> = 0.043]. There were no significant differences in non-ATM [adjusted mean difference (95% CI) NEC-surgical: –46 g (–281, 189), <i>p</i> = 0.70; NEC-medical: –122 g (–308, 63), <i>p</i> = 0.20]. <b><i>Conclusion:</i></b> The lower weight at term in preterm infants following surgically and medically managed NEC, in comparison to preterm infants that did not develop the disease, was secondary to a reduction in ATV. This suggests that the nutritional regimen received was adequate to preserve non-ATM but not to support the normal third-trimester deposition of adipose tissue in preterm infants.
DOI: 10.6084/m9.figshare.5812932
title: Supplementary Material for: Quantification of Adipose Tissue and Muscle Mass Based on Computed Tomography Scans: Comparison of Eight Planimetric and Diametric Techniques Including a Step-By-Step Guide

description: <b><i>Background:</i></b> Recent scientific work proved that knowledge about body composition beyond the body mass index is essential. Both adipose tissue and muscular status are determining risk factors of morbidity and mortality. Analysis of single cross-sectional computed tomography (CT) images, acquired during routine care only to prevent additional radiation exposure, provide a detailed insight into the body composition of chronically and critically ill patients. <b><i>Methods:</i></b> This retrospective study included 490 trauma patients of whom a whole-body multiple detector CT scan was acquired at admission. From a single cross-sectional CT, we compared eight diametric and planimetric techniques for the assessment of core muscle mass as well as visceral and subcutaneous adipose tissue. Furthermore, we derived formulas for converting the measurement results of various techniques into each other. <b><i>Results:</i></b> For intra- and interobserver reliability, we obtained intraclass correlation coefficients (ICCs) ranging from 0.947 to 0.997 (intraobserver reliability) and from 0.850 to 0.998 (interobserver reliability) for planimetric measurements. Diametric techniques conferred lower ICCs with 0.851–0.995 and 0.833–0.971, respectively. Overall, area-based measurements of abdominal adipose tissue yielded highly correlated results with diametric measures of obesity. For example, the Pearson correlation of visceral adipose tissue and sagittal abdominal diameter was 0.87 for male and 0.82 for female patients. Planimetric and diametric muscle measurements correlated best for lean psoas area and bilateral diametric measurement of the psoas with a Pearson correlation of 0.90 and 0.93 for male and female patients, respectively. <b><i>Conclusion:</i></b> Planimetric measurements should remain the gold standard to describe fat and muscle compartments. Diametric measurements could however serve as a surrogate if planimetric techniques are not readily available or feasible as for example in large registries.
DOI: 10.6084/m9.figshare.5812929
title: Supplementary Material for: Assessment of Postural Sway in Individuals with Multiple Sclerosis Using a Novel Wearable Inertial Sensor

description: Balance impairment is common in individuals with multiple sclerosis (MS). However, objective assessment of balance usually requires clinical expertise and/or the use of expensive and obtrusive measuring equipment. These barriers to the objective assessment of balance may be overcome with the development of a lightweight inertial sensor system. In this study, we examined the concurrent validity of a novel wireless, skin-mounted inertial sensor system (BioStamp®, MC10 Inc.) to measure postural sway in individuals with MS by comparing measurement agreement between this novel sensor and gold standard measurement tools (force plate and externally validated inertial sensor). A total of 39 individuals with MS and 15 healthy controls participated in the study. Participants with MS were divided into groups based on the amount of impairment (MS<sub>Mild</sub>: EDSS 2–4, <i>n</i> = 19; MS<sub>Severe</sub>: EDSS ≥6, <i>n</i> = 20). The balance assessment consisted of two 30-s quiet standing trials in each of three conditions: eyes open/firm surface, eyes closed/firm surface, and eyes open/foam surface. For each trial, postural sway was recorded with a force plate (Bertec) and simultaneously using two accelerometers (BioStamp and Xsens) mounted on the participant’s posterior trunk at L5. Sway metrics (sway area, sway path length, root mean square amplitude, mean velocity, JERK, and total power) were derived to compare the measurement agreement among the measurement devices. Excellent agreement (intraclass correlation coefficients &gt;0.9) between sway metrics derived from the BioStamp and the MTx sensors were observed across all conditions and groups. Good to excellent correlations (<i>r</i> &gt;0.7) between devices were observed in all sway metrics and conditions. Additionally, the acceleration sway metrics were nearly as effective as the force plate sway metrics in differentiating individuals with poor balance from healthy controls. Overall, the BioStamp sensor is a valid and objective measurement tool for postural sway assessment. This novel, lightweight and portable sensor may offer unique advantages in tracking patient’s postural performance.
DOI: 10.6084/m9.figshare.5812917
title: Supplementary Material for: Psychometric Evaluation of the Electronic Pain Assessment Tool: An Innovative Instrument for Individuals with Moderate-to-Severe Dementia

description: <b><i>Background/Aims:</i></b> Pain is common in aged care residents with dementia; yet it often goes undetected. A novel tool, the electronic Pain Assessment Tool (ePAT), was developed to address this challenging problem. We investigated the psychometric properties of the ePAT. <b><i>Methods:</i></b> In a 10-week prospective observational study, the ePAT was evaluated by comparison against the Abbey Pain Scale (APS). Pain assessments were blindly co-performed by the ePAT rater against the nursing staff of two residential aged care facilities. The residents were assessed twice by each rater: at rest and following movement. <b><i>Results:</i></b> The study involved 34 residents aged 85.5 ± 6.3 years, predominantly with severe dementia (Psychogeriatric Assessment Scale – Cognitive Impairment score = 19.7 ± 2.5). Four hundred paired assessments (<i>n</i> = 204 during rest; <i>n</i> = 196 following movement) were performed. Concurrent validity (<i>r</i> = 0.911) and all reliability measures (κ<sub>w</sub> = 0.857; intraclass correlation coefficient = 0.904; α = 0.950) were excellent, while discriminant validity and predictive validity were good. <b><i>Conclusion:</i></b> The ePAT is a suitable tool for the assessment of pain in this vulnerable population.
DOI: 10.6084/m9.figshare.5812917.v1
title: Supplementary Material for: Psychometric Evaluation of the Electronic Pain Assessment Tool: An Innovative Instrument for Individuals with Moderate-to-Severe Dementia

description: <b><i>Background/Aims:</i></b> Pain is common in aged care residents with dementia; yet it often goes undetected. A novel tool, the electronic Pain Assessment Tool (ePAT), was developed to address this challenging problem. We investigated the psychometric properties of the ePAT. <b><i>Methods:</i></b> In a 10-week prospective observational study, the ePAT was evaluated by comparison against the Abbey Pain Scale (APS). Pain assessments were blindly co-performed by the ePAT rater against the nursing staff of two residential aged care facilities. The residents were assessed twice by each rater: at rest and following movement. <b><i>Results:</i></b> The study involved 34 residents aged 85.5 ± 6.3 years, predominantly with severe dementia (Psychogeriatric Assessment Scale – Cognitive Impairment score = 19.7 ± 2.5). Four hundred paired assessments (<i>n</i> = 204 during rest; <i>n</i> = 196 following movement) were performed. Concurrent validity (<i>r</i> = 0.911) and all reliability measures (κ<sub>w</sub> = 0.857; intraclass correlation coefficient = 0.904; α = 0.950) were excellent, while discriminant validity and predictive validity were good. <b><i>Conclusion:</i></b> The ePAT is a suitable tool for the assessment of pain in this vulnerable population.
DOI: 10.6084/m9.figshare.5812839.v1
title: text.tgz

description: Text data of microtremor waveform at three sites <br><br>
DOI: 10.6084/m9.figshare.5812818
title: SimpleQuestions

description: This file contains a linked data version of SimpleQuestions
DOI: 10.6084/m9.figshare.5812806
title: Timelapse 7 - Maximum intensity projections - fused - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5812806.v1
title: Timelapse 7 - Maximum intensity projections - fused - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5812791
title: Supplementary Material for: Predictors of Persistent Milk Allergy in Children: A Retrospective Cohort Study

description: <b><i>Background:</i></b> Cow’s milk (CM) allergy is the second most common food allergy developed during infancy in Japan. To identify predictors of persistent CM allergy, we investigated the tolerance acquisition rate based on an oral food challenge in children under 6 years of age, diagnosed with immediate-type CM allergy. <b><i>Methods:</i></b> This retrospective cohort study included 131 children born in 2005 with a history of immediate allergic reaction to CM, of whom 39 were excluded because of ongoing oral immunotherapy (<i>n</i> = 18) or a lack of follow-up data (<i>n</i> = 21). The 92 remaining participants were followed for 6 years. Tolerance was defined as no adverse reaction to 200 mL of CM and regular intake of milk at home. Subjects were divided into 3 groups based on age at tolerance acquisition: group I (&lt;3 years; <i>n</i> = 31), group II (3–6 years; <i>n</i> = 42), and group III (persistent allergic group; <i>n</i> = 19). <b><i>Results:</i></b> Tolerance acquisition rates by 3, 5, and 6 years of age were 32.6% (30/92), 64.1% (59/92), and 84.8% (70/92), respectively. Age at first hospital visit was significantly higher in groups II and III than in group I (<i>p</i> &lt; 0.001). The incidence of anaphylaxis to other foods was also higher in group III than in group I (<i>p</i> = 0.04), as was CM-induced anaphylaxis (<i>p</i> = 0.03). Furthermore, milk and casein-specific immunoglobulin E (IgE) levels were significantly higher in group III than in group II after birth and remained high thereafter (<i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> The history of anaphylaxis and high milk-specific IgE levels were associated with persistent CM allergy.
DOI: 10.6084/m9.figshare.5812791.v1
title: Supplementary Material for: Predictors of Persistent Milk Allergy in Children: A Retrospective Cohort Study

description: <b><i>Background:</i></b> Cow’s milk (CM) allergy is the second most common food allergy developed during infancy in Japan. To identify predictors of persistent CM allergy, we investigated the tolerance acquisition rate based on an oral food challenge in children under 6 years of age, diagnosed with immediate-type CM allergy. <b><i>Methods:</i></b> This retrospective cohort study included 131 children born in 2005 with a history of immediate allergic reaction to CM, of whom 39 were excluded because of ongoing oral immunotherapy (<i>n</i> = 18) or a lack of follow-up data (<i>n</i> = 21). The 92 remaining participants were followed for 6 years. Tolerance was defined as no adverse reaction to 200 mL of CM and regular intake of milk at home. Subjects were divided into 3 groups based on age at tolerance acquisition: group I (&lt;3 years; <i>n</i> = 31), group II (3–6 years; <i>n</i> = 42), and group III (persistent allergic group; <i>n</i> = 19). <b><i>Results:</i></b> Tolerance acquisition rates by 3, 5, and 6 years of age were 32.6% (30/92), 64.1% (59/92), and 84.8% (70/92), respectively. Age at first hospital visit was significantly higher in groups II and III than in group I (<i>p</i> &lt; 0.001). The incidence of anaphylaxis to other foods was also higher in group III than in group I (<i>p</i> = 0.04), as was CM-induced anaphylaxis (<i>p</i> = 0.03). Furthermore, milk and casein-specific immunoglobulin E (IgE) levels were significantly higher in group III than in group II after birth and remained high thereafter (<i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> The history of anaphylaxis and high milk-specific IgE levels were associated with persistent CM allergy.