A First Survey on the Diversity of the R Community

The study presented here is a first attempt to capture the demographics and opinions of the R community, starting with the attendees of the useR! conference 2016. One aim of Forwards, the R Foundation taskforce on women and other under-represented groups, is to identify groups that are under-represented in the R community and to further stimulate ideas and take initiatives for widening their participation. Since R is an open-source software with various platforms for exchange, however, it is difficult to obtain information about its community – let alone define this community in the first place. As a starting point, a survey was conducted with the attendees of the useR! conference 2016 to document their sociodemographic and computational backgrounds, experiences and opinions. The present paper gives an overview of the results of this first survey. Most of the analysis focuses on women participants, that are generally under-represented in STEM (Science, Technology, Engineering, Mathematics) disciplines, but the results also show a severe underrepresentation of minorities. A surprising finding concerns a gender difference with regard to the experience with R and the publication of R packages. We investigated possible reasons for this difference by the means of a logistic regression analysis. The self-evident limitations of this first survey are discussed and directions for future research as well as potential means for improvement are outlined

Composition and physicochemical properties of dried berry pomace

[EN] BACKGROUND Berry pomace is a valuable but little used by-product of juice manufacturing. When processed to a stable fruit powder, the composition differs from that of the whole fruit. To facilitate application in foods, a detailed knowledge of its composition and physicochemical properties is essential. RESULTS Blackcurrant, redcurrant, chokeberry, rowanberry and gooseberry were selected for analysis. All pomace powders had a high fibre content (> 550 g kg(-1)) and a fat content of up to 200 g kg(-1). Despite identical milling conditions, the particle sizes of the pomace powders varied. This can be traced back to seed content and brittleness, which also becomes apparent with respect to surface characteristics. Blackcurrant pomace powder differed from other varieties in terms of its low water-binding capacity (3.2 g g(-1)) and a moderate moisture uptake, whereas chokeberry pomace powder showed the highest polyphenol content and rowanberry pomace powder was rich in flavonols. CONCLUSION The results obtained in the present study provide a comprehensive overview of the properties of berry pomace powder and allow conclusions to be made regarding their applicability for use in complex food systems. (c) 2018 Society of Chemical IndustryThe research project was approved during the second SUSFOOD ERA-Net call (www.susfood-era.net).The funding of the project, assured through the national partner organizations, is gratefully acknowledged: Federal Ministry of Education and Research via PTJ in Germany (grant 031B0004), INIA in Spain and FORMAS in Sweden.Reibner, AM.; Al Hamimi, S.; Quiles Chuliá, MD.; Schmidt, C.; Struck, S.; Hernando Hernando, MI.; Turner, C.... (2018). Composition and physicochemical properties of dried berry pomace. Journal of the Science of Food and Agriculture. 99(3):1284-1293. https://doi.org/10.1002/jsfa.930212841293993Elleuch, M., Bedigian, D., Roiseux, O., Besbes, S., Blecker, C., & Attia, H. (2011). 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The acute angiogenic signalling response to low-load resistance exercise with blood flow restriction

This study investigated protein kinase activation and gene expression of angiogenic factors in response to low-load resistance exercise with or without blood flow restriction (BFR). In a repeated measures cross-over design, six males performed four sets of bilateral knee extension exercise at 20% 1RM (reps per set = 30:15:15:continued to fatigue) with BFR (110 mmHg) and without (CON). Muscle biopsies were obtained from the vastus lateralis before, 2 and 4 h post-exercise. mRNA expression was determined using real-time RT-PCR. Protein phosphorylation/expression was determined using Western blot. p38MAPK phosphorylation was greater (p = 0.05) at 2 h following BFR (1.3 ± 0.8) compared to CON (0.4 ± 0.3). AMPK phosphorylation remained unchanged. PGC-1α mRNA expression increased at 2 h (5.9 ± 1.3 vs. 2.1 ± 0.8; p = 0.03) and 4 h (3.2 ± 0.8 vs. 1.5 ± 0.4; p = 0.03) following BFR exercise with no change in CON. PGC-1α protein expression did not change following either exercise. BFR exercise enhanced mRNA expression of vascular endothelial growth factor (VEGF) at 2 h (5.2 ± 2.8 vs 1.7 ± 1.1; p = .02) and 4 h (6.8 ± 4.9 vs. 2.5 ± 2.7; p = .01) compared to CON. mRNA expression of VEGF-R2 and hypoxia-inducible factor 1α increased following BFR exercise but only eNOS were enhanced relative to CON. Matrix metalloproteinase-9 mRNA expression was not altered in response to either exercise. Acute low-load resistance exercise with BFR provides a targeted angiogenic response potentially mediated through enhanced ischaemic and shear stress stimuli

Genetic inhibition of hepatic acetyl-CoA carboxylase activity increases liver fat and alters global protein acetylationa

Lipid deposition in the liver is associated with metabolic disorders including fatty liver disease, type II diabetes, and hepatocellular cancer. The enzymes acetyl-CoA carboxylase 1 (ACC1) and ACC2 are powerful regulators of hepatic fat storage; therefore, their inhibition is expected to prevent the development of fatty liver. In this study we generated liver-specific ACC1 and ACC2 double knockout (LDKO) mice to determine how the loss of ACC activity affects liver fat metabolism and whole-body physiology. Characterization of LDKO mice revealed unexpected phenotypes of increased hepatic triglyceride and decreased fat oxidation. We also observed that chronic ACC inhibition led to hyper-acetylation of proteins in the extra-mitochondrial space. In sum, these data reveal the existence of a compensatory pathway that protects hepatic fat stores when ACC enzymes are inhibited. Furthermore, we identified an important role for ACC enzymes in the regulation of protein acetylation in the extra-mitochondrial space

Pericyte derived chemokines amplify neutrophil recruitment across the cerebrovascular endothelial barrier

Excessive neutrophil extravasation can drive immunopathology, exemplified in pyogenic meningitis caused by Streptococcus pneumoniae infection. Insufficient knowledge of the mechanisms that amplify neutrophil extravasation has limited innovation in therapeutic targeting of neutrophil mediated pathology. Attention has focussed on neutrophil interactions with endothelia, but data from mouse models also point to a role for the underlying pericyte layer, as well as perivascular macrophages, the only other cell type found within the perivascular space in the cerebral microvasculature. We tested the hypothesis that human brain vascular pericytes (HBVP) contribute to neutrophil extravasation in a transwell model of the cerebral post-capillary venule. We show that pericytes augment endothelial barrier formation. In response to inflammatory cues, they significantly enhance neutrophil transmigration across the endothelial barrier, without increasing the permeability to small molecules. In our model, neither pericytes nor endothelia responded directly to bacterial stimulation. Instead, we show that paracrine signalling by multiple cytokines from monocyte derived macrophages drives transcriptional upregulation of multiple neutrophil chemokines by pericytes. Pericyte mediated amplification of neutrophil transmigration was independent of transcriptional responses by endothelia, but could be mediated by direct chemokine translocation across the endothelial barrier. Our data support a model in which microbial sensing by perivascular macrophages generates an inflammatory cascade where pericytes serve to amplify production of neutrophil chemokines that are translocated across the endothelial barrier to act directly on circulating neutrophils. In view of the striking redundancy in inflammatory cytokines that stimulate pericytes and in the neutrophil chemokines they produce, we propose that the mechanism of chemokine translocation may offer the most effective therapeutic target to reduce neutrophil mediated pathology in pyogenic meningitis

Translating the Dutch walking stairs, walking ability and rising and sitting questionnaires into German and assessing their concurrent validity with VAS measures of pain and activities in daily living

<p>Abstract</p> <p>Background</p> <p>The Dutch Walking Stairs, Walking Ability and Rising and Sitting Questionnaires are three validated instruments to measure physical activity and limitations in daily living in patients with lower extremity disorders living at home of which no German equivalents are available. Our scope was to translate the Walking Stairs, Walking Ability and Rising and Sitting Questionnaires into German and to verify its concurrent validity in the two domains pain and activities in daily living by comparing them with the corresponding measures on the Visual Analogue Scale.</p> <p>Methods</p> <p>We translated the Walking Stairs, Walking Ability and Rising and Sitting Questionnaires according to published guidelines. Demographic data and validity were assessed in 52 consecutive patients with Complex Regional Pain Syndrome 1 of the lower extremity. Information on age, duration of symptoms, type of Complex Regional Pain Syndrome 1 and type of initiating event were obtained. We assessed the concurrent validity in the two domains pain and activities in daily living by comparing them with the corresponding measures on the Visual Analogue Scale.</p> <p>Results</p> <p>We found that variability in the German Walking Stairs, Walking Ability and Rising and Sitting Questionnaires was largely explained by measures of pain and activities in daily living on the Visual Analogue Scale.</p> <p>Conclusion</p> <p>Our study shows that the domains pain and activities in daily living are properly represented in the German versions of the Walking Stairs, Walking Ability and Raising and Sitting Questionnaires. We would like to propagate their use in clinical practice and research alike.</p

An Overview of Recent Application of Medical Infrared Thermography in Sports Medicine in Austria

Medical infrared thermography (MIT) is used for analyzing physiological functions related to skin temperature. Technological advances have made MIT a reliable medical measurement tool. This paper provides an overview of MIT’s technical requirements and usefulness in sports medicine, with a special focus on overuse and traumatic knee injuries. Case studies are used to illustrate the clinical applicability and limitations of MIT. It is concluded that MIT is a non-invasive, non-radiating, low cost detection tool which should be applied for pre-scanning athletes in sports medicine

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θWatterson, θπ, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data

Enhancement of cutaneous immunity during aging by blocking p38 mitogen-activated protein (MAP) kinase-induced inflammation

Background Immunity decreases with age, which leads to reactivation of varicella zoster virus (VZV). In human subjects age-associated immune changes are usually measured in blood leukocytes; however, this might not reflect alterations in tissue-specific immunity. Objectives We used a VZV antigen challenge system in the skin to investigate changes in tissue-specific mechanisms involved in the decreased response to this virus during aging. Methods We assessed cutaneous immunity based on the extent of erythema and induration after intradermal VZV antigen injection. We also performed immune histology and transcriptomic analyses on skin biopsy specimens taken from the challenge site in young (65 years) subjects. Results Old human subjects exhibited decreased erythema and induration, CD4+ and CD8+ T-cell infiltration, and attenuated global gene activation at the site of cutaneous VZV antigen challenge compared with young subjects. This was associated with increased sterile inflammation in the skin in the same subjects related to p38 mitogen-activated protein kinase–related proinflammatory cytokine production (P < .0007). We inhibited systemic inflammation in old subjects by means of pretreatment with an oral small-molecule p38 mitogen-activated protein kinase inhibitor (Losmapimod; GlaxoSmithKline, Brentford, United Kingdom), which reduced both serum C-reactive protein levels and peripheral blood monocyte secretion of IL-6 and TNF-α. In contrast, cutaneous responses to VZV antigen challenge were increased significantly in the same subjects (P < .0003). Conclusion Excessive inflammation in the skin early after antigen challenge retards antigen-specific immunity. However, this can be reversed by inhibition of inflammatory cytokine production that can be used to promote vaccine efficacy and the treatment of infections and malignancy during aging