nSharma: Numerical Simulation Heterogeneity Aware Runtime Manager for OpenFOAM

CFD simulations are a fundamental engineering application,implying huge workloads, often with dynamic behaviour due to run-time mesh refinement. Parallel processing over heterogeneous distributedmemory clusters is often used to process such workloads. The executionof dynamic workloads over a set of heterogeneous resources leads to loadimbalances that severely impacts execution time, when static uniformload distribution is used. This paper proposes applying dynamic, het-erogeneity aware, load balancing techniques within CFD simulations.nSharma, a software package that fully integrates with OpenFOAM, ispresented and assessed. Performance gains are demonstrated, achievedby reducing busy times standard deviation among resources, i.e. hetero-geneous computing resources are kept busy with useful work due to aneffective workload distribution. To best of authors’ knowledge, nSharmais the first implementation and integration of heterogeneity aware loadbalancing in OpenFOAM and will be made publicly available in order tofoster its adoption by the large community of OpenFOAM users.The authors would like to thank the financial funding by FEDER through the COMPETE 2020 Program, the National Funds through FCT under the projects UID/CTM/50025/2013. The first author was partially funded by the PT-FLAD Chair on Smart Cities & Smart Governance and also by the School of Engineering, University of Minho within project Performance Portability on Scalable Heterogeneous Computing Systems. The authors also wish to thank Kyle Mooney for making available his code supporting migration of dynamically refined meshes, as well as acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources

Atypical Phenotype in Two Patients with LAMA2 Mutations

Congenital muscular dystrophy type 1A is caused by mutations in the LAMA2 gene, which encodes the a2-chain of laminin. We report two patients with partial laminin-a2 deficiency and atypical phenotypes, one with almost exclusive central nervous system involvement (cognitive impairment and refractory epilepsy) and the second with marked cardiac dysfunction, rigid spine syndrome and limb-girdle weakness. Patients underwent clinical, histopathological, imaging and genetic studies. Both cases have two heterozygous LAMA2 variants sharing a potentially pathogenic missense mutation c.2461A>C (p.Thr821Pro) located in exon 18. Brain MRI was instrumental for the diagnosis, since muscular examination and motor achievements were normal in the first patient and there was a severe cardiac involvement in the second. The clinical phenotype of the patients is markedly different which could in part be explained by the different combination of mutations types (two missense versus a missense and a truncating mutation)

Methodological considerations for kinematic analysis of upper limbs in healthy and poststroke adults Part II: a systematic review of motion capture systems and kinematic metrics

To review the methods used to analyze the kinematics of upper limbs (ULs) of healthy and poststroke adults, namely the motion capture systems and kinematic metrics. A database of articles published in the last decade was compiled using the following search terms combinations: (“upper extremity” OR “upper limb” OR arm) AND (kinematic OR motion OR movement) AND (analysis OR assessment OR measurement). The articles included in this review: (1) had the purpose to analyze objectively three-dimension kinematics of ULs, (2) studied functional movements or activities of daily living involving ULs, and (3) studied healthy and/or poststroke adults. Fourteen articles were included (four studied a healthy sample, three analyzed poststroke patients, and seven examined both poststroke and healthy participants). Most articles used optoelectronic systems with markers; however, the presentation of laboratory and task-specific errors is missing. Markerless systems, used in some studies, seem to be promising alternatives for implementation of kinematic analysis in hospitals and clinics, but the literature proving their validity is scarce. Most articles analyzed “joint kinematics” and “end-point kinematics,” mainly related with reaching. The different stroke locations of the samples were not considered in their analysis and only three articles described their psychometric properties. Future research should validate portable motion capture systems, document their specific error at the acquisition place and for the studied task, include grasping and manipulation analysis, and describe psychometric properties.info:eu-repo/semantics/publishedVersio

Future directions for the management of pain in osteoarthritis.

Osteoarthritis (OA) is the predominant form of arthritis worldwide, resulting in a high degree of functional impairment and reduced quality of life owing to chronic pain. To date, there are no treatments that are known to modify disease progression of OA in the long term. Current treatments are largely based on the modulation of pain, including NSAIDs, opiates and, more recently, centrally acting pharmacotherapies to avert pain. This review will focus on the rationale for new avenues in pain modulation, including inhibition with anti-NGF antibodies and centrally acting analgesics. The authors also consider the potential for structure modification in cartilage/bone using growth factors and stem cell therapies. The possible mismatch between structural change and pain perception will also be discussed, introducing recent techniques that may assist in improved patient phenotyping of pain subsets in OA. Such developments could help further stratify subgroups and treatments for people with OA in future

Assessment of physical activity by accelerometer and IPAQ-short version in patients with chronic kidney disease undergoing hemodialysis

This is the peer-reviewed but unedited manuscript version of the following article: Blood Purification 2015;40:3, pp.250-255. The final, published version is available at http://www.karger.com/?doi=10.1159/000437040Aim: To compare the short version of International Physical Activity Questionnaire (IPAQ) and the accelerometer measurement of physical activity (PA) in patients undergoing hemodialysis. Methods: Sample consisted of 40 patients (19 men) aged 45 ± 16 years. Patients reported their PA using the IPAQ during a face-to-face interview, and wore an Actigraph GT3-X accelerometer for 1 week to obtain minutes per day of light PA, moderate-to-vigorous PA (MVPA) and total PA as well as raw counts per day (vector magnitude). Results: All PA-related variables were significantly correlated among instruments (r = 0.34-0.47) when analyzed as a group. However, when analyzed separately by gender, the relationships were present for women only (r = 0.46-0.62). IPAQ significantly underestimated light PA (IPAQ vs. accelerometer: 180.0 vs. 251.1 min/day, p = 0.019), but no differences were found between methods for MVPA and total PA. Conclusion: Modest correlations were found between self-reported PA time by IPAQ (short version) and accelerometer, but only in women. However, the IPAQ may underestimate light PA, which is the main form of PA in this population

Two Separate Effects Contribute to Regulatory T Cell Defect in Systemic Lupus Erythematosus Patients and Their Unaffected Relatives

Forkhead box P3 (FoxP3)+ regulatory T cells (Tregs ) are functionally deficient in systemic lupus erythematosus (SLE), characterized by reduced surface CD25 [the interleukin (IL)-2 receptor alpha chain]. Low-dose IL-2 therapy is a promising current approach to correct this defect. To elucidate the origins of the SLE Treg phenotype, we studied its role through developmentally defined regulatory T cell (Treg ) subsets in 45 SLE patients, 103 SLE-unaffected first-degree relatives and 61 unrelated healthy control subjects, and genetic association with the CD25-encoding IL2RA locus. We identified two separate, uncorrelated effects contributing to Treg CD25. (1) SLE patients and unaffected relatives remarkably shared CD25 reduction versus controls, particularly in the developmentally earliest CD4+ FoxP3+ CD45RO- CD31+ recent thymic emigrant Tregs . This first component effect influenced the proportions of circulating CD4+ FoxP3high CD45RO+ activated Tregs . (2) In contrast, patients and unaffected relatives differed sharply in their activated Treg CD25 state: while relatives as control subjects up-regulated CD25 strongly in these cells during differentiation from naive Tregs , SLE patients specifically failed to do so. This CD25 up-regulation depended upon IL2RA genetic variation and was related functionally to the proliferation of activated Tregs , but not to their circulating numbers. Both effects were found related to T cell IL-2 production. Our results point to (1) a heritable, intrathymic mechanism responsible for reduced CD25 on early Tregs and decreased activation capacity in an extended risk population, which can be compensated by (2) functionally independent CD25 up-regulation upon peripheral Treg activation that is selectively deficient in patients. We expect that Treg -directed therapies can be monitored more effectively when taking this distinction into account.info:eu-repo/semantics/publishedVersio

The EMBLA survey - metal-poor stars in the Galactic bulge

Cosmological models predict the oldest stars in the Galaxy should be found closest to the centre of the potential well, in the bulge. The Extremely Metal-poor BuLge stars with AAOmega survey (EMBLA) successfully searched for these old, metal-poor stars by making use of the distinctive SkyMapper photometric filters to discover candidate metal-poor stars in the bulge. Their metal-poor nature was then confirmed using the AAOmega spectrograph on the Anglo-Australian Telescope. Here we present an abundance analysis of 10 bulge stars with −2.8 < [Fe/H] < −1.7 from MIKE/Magellan observations, in total determining the abundances of 22 elements. Combining these results with our previous high-resolution data taken as part of the Gaia-ESO Survey, we have started to put together a picture of the chemical and kinematic nature of the most metal-poor stars in the bulge. The currently available kinematic data are consistent with the stars belonging to the bulge, although more accurate measurements are needed to constrain the stars’ orbits. The chemistry of these bulge stars deviates from that found in halo stars of the same metallicity. Two notable differences are the absence of carbon-enhanced metal-poor bulge stars, and the α element abundances exhibit a large intrinsic scatter and include stars which are underabundant in these typically enhanced elements.LMH and MA have been supported by the Australian Research Council (grant FL110100012). ARC acknowledges support from the European Union FP7 programme through ERC grant number 320360. DY is supported through an Australian Research Council Future Fellowship (FT140100554). Research on metal-poor stars with SkyMapper is supported through Australian Research Council Discovery Projects grants DP120101237 and DP150103294 (PI: Da Costa). This publication makes use of data products from the Two Micron All Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation. This paper includes data gathered with the 6.5 metre Magellan Telescopes located at Las Campanas Observatory, Chile.This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/mnras/stw100

Bird-spiders (Arachnida, Mygalomorphae) as perceived by the inhabitants of the village of Pedra Branca, Bahia State, Brazil

This paper deals with the conceptions, knowledge and attitudes of the inhabitants of the county of Pedra Branca, Bahia State, on mygalomorph spiders locally known as 'caranguejeiras' (bird-spiders). It is launched here a new filed within ethnozoology: ethnoarachnology, which is defined as the transdisciplinary study of the relationships between human beings and bird-spiders. Data were collected from February to June 2005 by means of open-ended interviews carried out with 30 individuals, which ages ranged from 13 to 86 years old. It was recorded some traditional knowledge regarding the following items: taxonomy, biology, habitat, ecology, seasonality, and behavior. Results show that bird-spiders are classified as "insects". The most commented aspect of the interaction between bird-spiders and inhabitants of Pedra Branca is related to their dangerousness, since they said these spiders are very venomous and can cause health problems. In general, the traditional zoological knowledge of Pedra Branca's inhabitants concerning these spiders is coherent with the academic knowledge

Bias in the prediction of genetic gain due to mass and half-sib selection in random mating populations

The prediction of gains from selection allows the comparison of breeding methods and selection strategies, although these estimates may be biased. The objective of this study was to investigate the extent of such bias in predicting genetic gain. For this, we simulated 10 cycles of a hypothetical breeding program that involved seven traits, three population classes, three experimental conditions and two breeding methods (mass and half-sib selection). Each combination of trait, population, heritability, method and cycle was repeated 10 times. The predicted gains were biased, even when the genetic parameters were estimated without error. Gain from selection in both genders is twice the gain from selection in a single gender only in the absence of dominance. The use of genotypic variance or broad sense heritability in the predictions represented an additional source of bias. Predictions based on additive variance and narrow sense heritability were equivalent, as were predictions based on genotypic variance and broad sense heritability. The predictions based on mass and family selection were suitable for comparing selection strategies, whereas those based on selection within progenies showed the largest bias and lower association with the realized gain