Enhancing Resource Management through Prediction-based Policies

Task-based programming models are emerging as a promising alternative to make the most of multi-/many-core systems. These programming models rely on runtime systems, and their goal is to improve application performance by properly scheduling application tasks to cores. Additionally, these runtime systems offer policies to cope with application phases that lack in parallelism to fill all cores. However, these policies are usually static and favor either performance or energy efficiency. In this paper, we have extended a task-based runtime system with a lightweight monitoring and prediction infrastructure that dynamically predicts the optimal number of cores required for each application phase, thus improving both performance and energy efficiency. Through the execution of several benchmarks in multi-/many-core systems, we show that our prediction-based policies have competitive performance while improving energy efficiency when compared to state of the art policies.Comment: Postprint submitted and published at Euro-Par2020: International European Conference on Parallel and Distributed Computing (Springer) (https://link.springer.com/chapter/10.1007%2F978-3-030-57675-2_31

Extent and structure of health insurance expenditures for complementary and alternative medicine in Swiss primary care

BACKGROUND: The study is part of a nationwide evaluation of complementary and alternative medicine (CAM) in primary care in Switzerland. The goal was to evaluate the extent and structure of basic health insurance expenditures for complementary and alternative medicine in Swiss primary care. METHODS: The study was designed as a cross-sectional evaluation of Swiss primary care providers and included 262 certified CAM physicians, 151 noncertified CAM physicians and 172 conventional physicians. The study was based on data from a mailed questionnaire and on reimbursement information obtained from health insurers. It was therefore purely observational, without interference into diagnostic and therapeutic procedures applied or prescribed by physicians. Main outcome measures included average reimbursed costs per patient, structured into consultation- and medication-related costs, and referred costs. RESULTS: Total average reimbursed cost per patient did not differ between CAM physicians and conventional practitioners, but considerable differences were observed in cost structure. The proportions of reimbursed costs for consultation time were 56% for certified CAM, 41% for noncertified CAM physicians and 40% for conventional physicians; medication costs – including expenditures for prescriptions and directly dispensed drugs – respectively accounted for 35%, 18%, and 51% of costs. CONCLUSION: The results indicate no significant difference for overall treatment cost per patient between CAM and COM primary care in Switzerland. However, CAM physicians treat lower numbers of patients and a more cost-favourable patient population than conventional physicians. Differences in cost structure reflect more patient-centred and individualized treatment modalities of CAM physicians

Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making

Cells must make reliable decisions under fluctuating extracellular conditions, but also be flexible enough to adapt to such changes. How cells reconcile these seemingly contradictory requirements through the dynamics of cellular decision-making is poorly understood. To study this issue we quantitatively measured gene expression and protein localization in single cells of the model organism Bacillus subtilis during the progression to spore formation. We found that sporulation proceeded through noisy and reversible steps towards an irreversible, all-or-none commitment point. Specifically, we observed cell-autonomous and spontaneous bursts of gene expression and transient protein localization events during sporulation. Based on these measurements we developed mathematical population models to investigate how the degree of reversibility affects cellular decision-making. In particular, we evaluated the effect of reversibility on the 1) reliability in the progression to sporulation, and 2) adaptability under changing extracellular stress conditions. Results show that reversible progression allows cells to remain responsive to long-term environmental fluctuations. In contrast, the irreversible commitment point supports reliable execution of cell fate choice that is robust against short-term reductions in stress. This combination of opposite dynamic behaviors (reversible and irreversible) thus maximizes both adaptable and reliable decision-making over a broad range of changes in environmental conditions. These results suggest that decision-making systems might employ a general hybrid strategy to cope with unpredictably fluctuating environmental conditions

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation

Dermacentor reticulatus: a vector on the rise

Dermacentor reticulatus is a hard tick species with extraordinary biological features. It has a high reproduction rate, a rapid developmental cycle, and is also able to overcome years of unfavourable conditions. Dermacentor reticulatus can survive under water for several months and is cold-hardy even compared to other tick species. It has a wide host range: over 60 different wild and domesticated hosts are known for the three active developmental stages. Its high adaptiveness gives an edge to this tick species as shown by new data on the emergence and establishment of D. reticulatus populations throughout Europe. The tick has been the research focus of a growing number of scientists, physicians and veterinarians. Within the Web of Science database, more than a fifth of the over 700 items published on this species between 1897 and 2015 appeared in the last three years (2013–2015). Here we attempt to synthesize current knowledge on the systematics, ecology, geographical distribution and recent spread of the species and to highlight the great spectrum of possible veterinary and public health threats it poses. Canine babesiosis caused by Babesia canis is a severe leading canine vector-borne disease in many endemic areas. Although less frequently than Ixodes ricinus, D. reticulatus adults bite humans and transmit several Rickettsia spp., Omsk haemorrhagic fever virus or Tick-borne encephalitis virus. We have not solely collected and reviewed the latest and fundamental scientific papers available in primary databases but also widened our scope to books, theses, conference papers and specialists colleagues’ experience where needed. Besides the dominant literature available in English, we also tried to access scientific literature in German, Russian and eastern European languages as well. We hope to inspire future research projects that are necessary to understand the basic life-cycle and ecology of this vector in order to understand and prevent disease threats. We conclude that although great strides have been made in our knowledge of the eco-epidemiology of this species, several gaps still need to be filled with basic research, targeting possible reservoir and vector roles and the key factors resulting in the observed geographical spread of D. reticulatus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1599-x) contains supplementary material, which is available to authorized users

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

Detecting Non-Sibling Dependencies in OpenMP Task-Based Applications

International audienceThe advent of the multicore era led to the duplication of functional units through an increasing number of cores. To exploit those processors, a shared-memory parallel programming model is one possible direction. Thus, OpenMP is a good candidate to enable different paradigms: data parallelism (including loop-based directives) and control parallelism, through the notion of tasks with dependencies. But this is the programmer responsibility to ensure that data dependencies are complete such as no data races may happen. It might be complex to guarantee that no issue will occur and that all dependencies have been correctly expressed in the context of nested tasks. This paper proposes an algorithm to detect the data dependencies that might be missing on the OpenMP task clauses between tasks that have been generated by different parents. This approach is implemented inside a tool relying on the OMPT interface

Enhancing resource management through prediction-based policies

Task-based programming models are emerging as a promising alternative to make the most of multi-/many-core systems. These programming models rely on runtime systems, and their goal is to improve application performance by properly scheduling application tasks to cores. Additionally, these runtime systems offer policies to cope with application phases that lack in parallelism to fill all cores. However, these policies are usually static and favor either performance or energy efficiency. In this paper, we have extended a task-based runtime system with a lightweight monitoring and prediction infrastructure that dynamically predicts the optimal number of cores required for each application phase, thus improving both performance and energy efficiency. Through the execution of several benchmarks in multi-/many-core systems, we show that our prediction-based policies have competitive performance while improving energy efficiency when compared to state of the art policies.This project is supported by the European Union’s Horizon 2021 research and innovation programme under the grant agreement No 754304 (DEEP-EST), the Ministry of Economy of Spain through the Severo Ochoa Center of Excellence Program (SEV-2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P) and by the Generalitat de Catalunya (2017-SGR1481). This work was also supported by Project HPC-EUROPA3 (INFRAIA2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme.Peer ReviewedPostprint (author's final draft