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

Cisplatin-induced emesis: systematic review and meta-analysis of the ferret model and the effects of 5-HT3 receptor antagonists

PURPOSE: The ferret cisplatin emesis model has been used for ~30 years and enabled identification of clinically used anti-emetics. We provide an objective assessment of this model including efficacy of 5-HT(3) receptor antagonists to assess its translational validity. METHODS: A systematic review identified available evidence and was used to perform meta-analyses. RESULTS: Of 182 potentially relevant publications, 115 reported cisplatin-induced emesis in ferrets and 68 were included in the analysis. The majority (n = 53) used a 10 mg kg(−1) dose to induce acute emesis, which peaked after 2 h. More recent studies (n = 11) also used 5 mg kg(−1), which induced a biphasic response peaking at 12 h and 48 h. Overall, 5-HT(3) receptor antagonists reduced cisplatin (5 mg kg(−1)) emesis by 68% (45–91%) during the acute phase (day 1) and by 67% (48–86%) and 53% (38–68%, all P < 0.001), during the delayed phase (days 2, 3). In an analysis focused on the acute phase, the efficacy of ondansetron was dependent on the dosage and observation period but not on the dose of cisplatin. CONCLUSION: Our analysis enabled novel findings to be extracted from the literature including factors which may impact on the applicability of preclinical results to humans. It reveals that the efficacy of ondansetron is similar against low and high doses of cisplatin. Additionally, we showed that 5-HT(3) receptor antagonists have a similar efficacy during acute and delayed emesis, which provides a novel insight into the pharmacology of delayed emesis in the ferret

Intravesical Ty21a vaccine promotes dendritic cells and T cell-mediated tumor regression in the MB49 bladder cancer model

Preclinical data shows that intravesical instillation of Ty21a/Vivotif\uae, a commercial vaccine against typhoid fever, is an effective alternative option to standard Bacillus-Calmette-Gu\ue9rin (BCG) immunotherapy for nonmuscle-invasive bladder cancer (NMIBC). Here we characterized the inflammatory effects of Ty21a on the bladder and investigated the immune mechanisms underlying tumor-regression towards the use of this bacterial vaccine in NMIBC patients. MB49 bladder tumor-bearing mice had significantly improved survival after intravesical instillations of Ty21a doses of 106 to 108 colony-forming units. By immunohistochemistry and morphology, both BCG and Ty21a instillations were associated with bladder inflammation, which was decreased with the use of low, but effective, doses of Ty21a. Flow cytometry analysis showed a significant infiltration of T cells, natural killer (NK) cells, and myeloid cells, compared with controls, after a single dose of Ty21a, whereas this was only observed after multiple doses of BCG. The induced myeloid cells were predominantly neutrophils and Ly6C+CD103+ dendritic cells (DC), the latter being significantly more numerous after instillation of Ty21a than BCG. Ex vivo infection of human leukocytes with Ty21a, but not BCG, similarly significantly increased DC frequency. CD4+ and CD8+ T cells, but not NK cells nor neutrophils, were required for effective Ty21a bladder tumor responses. Thus, the generation of antitumor adaptive immunity was identified as a key process underlying Ty21a-mediated treatment efficacy. Altogether, these results demonstrate mechanisms of intravesical Ty21a therapy and suggest its potential as a safe and effective treatment for NMIBC patients

KIM-1 and NGAL: new markers of obstructive nephropathy

Congenital obstructive nephropathy is the primary cause of chronic renal failure in children. Rapid diagnosis and initiation of the treatment are vital to preserve function and/or to slow down renal injury. The aim of our study was to determine whether urinary (u) kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) may be useful non-invasive biomarkers in children with congenital hydronephrosis (HN) caused by ureteropelvic junction obstruction. The study cohort consisted of 20 children with severe HN who required surgery (median age 2.16 years) and two control groups (control group 1: 20 patients with mild, non-obstructive HN; control group 2: 25 healthy children). All of the children had normal renal function. Immunoenzymatic ELISA commercial kits were used to measure uKIM-1 and uNGAL concentrations. The preoperative median uKIM-1/creatinine (cr.) and uNGAL levels were significantly greater in the children with severe HN than in both control groups. Three months after surgery, uNGAL had decreased significantly (p < 0.05) in the children with severe HN, but was still higher than that in control group 2 children (p < 0.05). Receiver operator characteristic analyses revealed a good diagnostic profile for uKIM-1 and uNGAL in terms of identifying a differential renal function of <40% in HN patients (area under the curve (AUC) 0.8 and 0.814, respectively) and <45% in all examined children (AUC 0.779 and 0.868, respectively). Based on these results, we suggest that increasing uNGAL and uKIM-1 levels are associated with worsening obstruction. Further studies are required to confirm a potential application of uKIM-1 and uNGAL as useful biomarkers for the diagnosis and progression of chronic kidney disease

The Rift Valley fever accessory proteins NSm and P78/NSm-GN are distinct determinants of virus propagation in vertebrate and invertebrate hosts.: Role of NSm-related proteins in RVFV infection

International audienceRift Valley fever virus (RVFV) is an enzootic virus circulating in Africa that is transmitted to its vertebrate host by a mosquito vector and causes severe clinical manifestations in humans and ruminants. RVFV has a tripartite genome of negative or ambisense polarity. The M segment contains five in-frame AUG codons that are alternatively used for the synthesis of two major structural glycoproteins, GN and GC, and at least two accessory proteins, NSm, a 14-kDa cytosolic protein, and P78/NSm-GN, a 78-kDa glycoprotein. To determine the relative contribution of P78 and NSm to RVFV infectivity, AUG codons were knocked out to generate mutant viruses expressing various sets of the M-encoded proteins. We found that, in the absence of the second AUG codon used to express NSm, a 13-kDa protein corresponding to an N-terminally truncated form of NSm, named NSm', was synthesized from AUG 3. None of the individual accessory proteins had any significant impact on RVFV virulence in mice. However, a mutant virus lacking both NSm and NSm' was strongly attenuated in mice and grew to reduced titers in murine macrophages, a major target cell type of RVFV. In contrast, P78 was not associated with reduced viral virulence in mice, yet it appeared as a major determinant of virus dissemination in mosquitoes. This study demonstrates how related accessory proteins differentially contribute to RVFV propagation in mammalian and arthropod hosts

Impacts of traditional food consumption advisories: Compliance, changes in diet and loss of confidence in traditional foods

<p>Abstract</p> <p>Background</p> <p>Food consumption advisories are often posted when industrial activities are expected to affect the quality and availability of traditional foods used by First Nations. We were recently involved in a project and asked to summarize details regarding the impacts of traditional food consumption advisories with respect to compliance, broader changes in diet and loss of confidence in traditional foods by people.</p> <p>Methods</p> <p>Our review was not conducted as a formal systematic comprehensive review; rather, we focused on primary and grey literature presenting academic, health practitioner and First Nations viewpoints on the topic available from literature databases (i.e., PubMed, Web of Knowledge^SM) as well as the internet search engine Google. Some information came from personal communications.</p> <p>Results</p> <p>Our overview suggests that when communicated effectively and clearly, and when community members are involved in the process, consumption advisories can result in a decrease in contaminant load in people. On the other hand, consumption advisories can lead to cultural loss and have been linked to a certain amount of social, psychological, nutritional, economic and lifestyle disruption. In some cases, communities have decided to ignore consumption advisories opting to continue with traditional lifestyles believing that the benefits of doing so outweigh the risk of following advisories.</p> <p>Conclusions</p> <p>We identified that there are both positive and negative aspects to the issuance of traditional food consumption advisories. A number of variables need to be recognized during the development and implementation of advisories in order to ensure a balance between human health, maintenance of cultures and industrial activity.</p

Galactic and Extragalactic Samples of Supernova Remnants: How They Are Identified and What They Tell Us

Supernova remnants (SNRs) arise from the interaction between the ejecta of a supernova (SN) explosion and the surrounding circumstellar and interstellar medium. Some SNRs, mostly nearby SNRs, can be studied in great detail. However, to understand SNRs as a whole, large samples of SNRs must be assembled and studied. Here, we describe the radio, optical, and X-ray techniques which have been used to identify and characterize almost 300 Galactic SNRs and more than 1200 extragalactic SNRs. We then discuss which types of SNRs are being found and which are not. We examine the degree to which the luminosity functions, surface-brightness distributions and multi-wavelength comparisons of the samples can be interpreted to determine the class properties of SNRs and describe efforts to establish the type of SN explosion associated with a SNR. We conclude that in order to better understand the class properties of SNRs, it is more important to study (and obtain additional data on) the SNRs in galaxies with extant samples at multiple wavelength bands than it is to obtain samples of SNRs in other galaxiesComment: Final 2016 draft of a chapter in "Handbook of Supernovae" edited by Athem W. Alsabti and Paul Murdin. Final version available at https://doi.org/10.1007/978-3-319-20794-0_90-

Stem cells and other innovative intra-articular therapies for osteoarthritis: what does the future hold?

Osteoarthritis (OA), the most common type of arthritis in the world, is associated with suffering due to pain, productivity loss, decreased mobility and quality of life. Systemic therapies available for OA are mostly symptom modifying and have potential gastrointestinal, renal, hepatic, and cardiac side effects. BMC Musculoskeletal Disorders recently published a study showing evidence of reparative effects demonstrated by homing of intra-articularly injected autologous bone marrow stem cells in damaged cartilage in an animal model of OA, along with clinical and radiographic benefit. This finding adds to the growing literature showing the potential benefit of intra-articular (IA) bone marrow stem cells. Other emerging potential IA therapies include IL-1 receptor antagonists, conditioned autologous serum, botulinum toxin, and bone morphogenetic protein-7. For each of these therapies, trial data in humans have been published, but more studies are needed to establish that they are safe and effective. Several additional promising new OA treatments are on the horizon, but challenges remain to finding safe and effective local and systemic therapies for OA

Massive stars as thermonuclear reactors and their explosions following core collapse

Nuclear reactions transform atomic nuclei inside stars. This is the process of stellar nucleosynthesis. The basic concepts of determining nuclear reaction rates inside stars are reviewed. How stars manage to burn their fuel so slowly most of the time are also considered. Stellar thermonuclear reactions involving protons in hydrostatic burning are discussed first. Then I discuss triple alpha reactions in the helium burning stage. Carbon and oxygen survive in red giant stars because of the nuclear structure of oxygen and neon. Further nuclear burning of carbon, neon, oxygen and silicon in quiescent conditions are discussed next. In the subsequent core-collapse phase, neutronization due to electron capture from the top of the Fermi sea in a degenerate core takes place. The expected signal of neutrinos from a nearby supernova is calculated. The supernova often explodes inside a dense circumstellar medium, which is established due to the progenitor star losing its outermost envelope in a stellar wind or mass transfer in a binary system. The nature of the circumstellar medium and the ejecta of the supernova and their dynamics are revealed by observations in the optical, IR, radio, and X-ray bands, and I discuss some of these observations and their interpretations.Comment: To be published in " Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars; ed. by Aruna Goswami & Eswar Reddy, Springer Verlag, 2009. Contains 21 figure

Towards actionable knowledge: A systematic analysis of mobile patient portal use

As the aging population grows, chronic illness increases, and our healthcare costs sharply increase, patient portals are positioned as a central component of patient engagement through the potential to change the physician-patient relationship and enable chronic disease self-management. A patient’s engagement in their healthcare contributes to improving health outcomes, and information technologies can support health engagement. In this chapter, we extend the existing literature by discovering design gaps for patient portals from a systematic analysis of negative users’ feedback from the actual use of patient portals. Specifically, we adopt a topic modeling approach, latent Dirichlet allocation (LDA) algorithm, to discover design gaps from online low rating user reviews of a common mobile patient portal, EPIC’s mychart. To validate the extracted gaps, we compared the results of LDA analysis with that of human analysis. Overall, the results revealed opportunities to improve collaboration and to enhance the design of portals intended for patient-centered care. Incorporating these changes may enable the technologies to have stronger position to influence health improvement and wellness