TaskGenX: A Hardware-Software Proposal for Accelerating Task Parallelism

As chip multi-processors (CMPs) are becoming more and more complex, software solutions such as parallel programming models are attracting a lot of attention. Task-based parallel programming models offer an appealing approach to utilize complex CMPs. However, the increasing number of cores on modern CMPs is pushing research towards the use of fine grained parallelism. Task-based programming models need to be able to handle such workloads and offer performance and scalability. Using specialized hardware for boosting performance of task-based programming models is a common practice in the research community. Our paper makes the observation that task creation becomes a bottleneck when we execute fine grained parallel applications with many task-based programming models. As the number of cores increases the time spent generating the tasks of the application is becoming more critical to the entire execution. To overcome this issue, we propose TaskGenX. TaskGenX offers a solution for minimizing task creation overheads and relies both on the runtime system and a dedicated hardware. On the runtime system side, TaskGenX decouples the task creation from the other runtime activities. It then transfers this part of the runtime to a specialized hardware. We draw the requirements for this hardware in order to boost execution of highly parallel applications. From our evaluation using 11 parallel workloads on both symmetric and asymmetric multicore systems, we obtain performance improvements up to 15×, averaging to 3.1× over the baseline.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 671697 and No. 779877. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Ramon y Cajal fellowship number RYC-2016-21104. Finally, the authors would like to thank Thomas Grass for his valuable help with the simulator.Peer ReviewedPostprint (author's final draft

The intensive care infection score - a novel marker for the prediction of infection and its severity

Background: The prediction of infection and its severity remains difficult in the critically ill. A novel, simple biomarker derived from five blood-cell derived parameters that characterize the innate immune response in routine blood samples, the intensive care infection score (ICIS), could be helpful in this respect. We therefore compared the predictive value of the ICIS with that of the white blood cell count (WBC), C-reactive protein (CRP) and procalcitonin (PCT) for infection and its severity in critically ill patients. Methods: We performed a multicenter, cluster-randomized, crossover study in critically ill patients between January 2013 and September 2014. Patients with a suspected infection for which blood cultures were taken by the attending intensivist were included. Blood was taken at the same time for WBC, ICIS, CRP and PCT measurements in the control study periods. Results of imaging and cultures were collected. Patients were divided into groups of increasing likelihood of infection and invasiveness: group 1 without infection or with possible infection irrespective of cultures, group 2 with probable or microbiologically proven local infection without blood stream infection (BSI) and group 3 with BSI irrespective of local infection. Septic shock was assessed. Results: In total, 301 patients were enrolled. CRP, PCT and ICIS were higher in groups 2 and 3 than group 1. The area under the receiver operating characteristic curve (AUROC) for the prediction of infection was 0.70 for CRP, 0.71 for PCT and 0.73 for ICIS (P < 0.001). For the prediction of septic shock the AUROC was 0.73 for CRP, 0.85 for PCT and 0.76 for ICIS. These AUROC did not differ fro

Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype

Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidia politula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These patterns are incongruous with the phenotypic variation that informed prior taxonomy, and most subspecies were not supported as distinct evolutionary lineages. One of the nominal subspecies was found to be a cryptic species; consequently, we elevate C. p. laetipennis (Horn, 1913) to a full species. Although nuclear and mtDNA datasets recovered broadly similar evolutionary units, mito-nuclear discordance was more common than expected, being observed between nearly all geographically overlapping taxonomic pairs. Additionally, a pattern of ‘mitochondrial displacement’ was observed, where mitochondria from one species unidirectionally displace others. Overall, we found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading

Development of a Transplantable GFP+ B-Cell Lymphoma Tumor Cell Line From MHC-Defined Miniature Swine: Potential for a Large Animal Tumor Model

The lack of a reliable and reproducible large animal tumor model for the study of hemolymphatic malignancies limits the ability to explore the underlying pathophysiology and testing of novel therapies. The goal of this study was to develop an aggressive, trackable swine tumor cell line in mice for adoptive transfer into MHC matched swine. Two tumor cell lines, post-transplant lymphoproliferative disease (PTLD) 13271 and chronic myelogenous leukemia (CML) 14736, were previously established from the Massachusetts General Hospital (MGH) miniature swine herd. PTLD 13271 is a swine B-cell lymphoma line originating from an animal that developed PTLD following hematopoietic cell transplantation (HCT), while CML 14736 was generated from a swine that spontaneously developed CML. In order to select for aggressive tumor variants, both lines were passage into NOD/SCID IL-2 receptor γ−/− (NSG) mice. Tumor induced mortality in mice injected with CML14736 was 68% while 100% of mice injected with PTLD 13271 succumbed to PTLD by day 70. Based on aggressiveness, PTLD 13271 was selected for further development and re-passage into NSG mice resulting in increased tumor burden and metastasis. Transduction of the PTLD 13271 cell line with a green fluorescent protein (GFP)-expressing lentivirus facilitated tumor tracking when re-passaged in mice. Utilizing a tolerance induction strategy, GFP+ tumors were injected into an MHC matched miniature swine and successfully followed via flow cytometry for 48 h in circulation, although tumor engraftment was not observed. In summary, we report the development of an aggressive GFP+B-cell lymphoma cell line which has the potential for facilitating development of a large animal tumor model

Winter Movements of Louisiana Pine Snakes (Pituophis ruthveni) in Texas and Louisiana

Despite concerns that the Louisiana Pine Snake (Pituophis ruthveni) has been extirpated from large portions of its historic range, only a limited number of studies on their movement patterns have been published. Winter movement patterns are of particular interest since it has been hypothesized that impacts of management practices would be reduced during the winter. Using radiotelemetry, we determined winter movement patterns of Louisiana Pine Snakes (11 males, 8 females) in 5 study areas (2 in Louisiana and 3 in Texas). Movements during winter (November–February) were greatly curtailed compared to the remainder of the year; however, snakes occasionally undertook substantial movements. Relocations were typically within the snake’s previous active-season home range, and movements were more frequent in the early portion of winter. All hibernation sites were within Baird’s Pocket Gopher (Geomys breviceps) burrow systems at depths ranging from 13–25 cm. Louisiana Pine Snakes did not use communal hibernacula, nor did individual snakes return to previously used sites in successive years

Metabolic effects of bezafibrate in mitochondrial disease.

Funder: Medical Research Council (MRC): Confidence in Concept award to Newcastle UniversityMitochondrial disorders affect 1/5,000 and have no cure. Inducing mitochondrial biogenesis with bezafibrate improves mitochondrial function in animal models, but there are no comparable human studies. We performed an open-label observational experimental medicine study of six patients with mitochondrial myopathy caused by the m.3243A>G MTTL1 mutation. Our primary aim was to determine the effects of bezafibrate on mitochondrial metabolism, whilst providing preliminary evidence of safety and efficacy using biomarkers. The participants received 600-1,200 mg bezafibrate daily for 12 weeks. There were no clinically significant adverse events, and liver function was not affected. We detected a reduction in the number of complex IV-immunodeficient muscle fibres and improved cardiac function. However, this was accompanied by an increase in serum biomarkers of mitochondrial disease, including fibroblast growth factor 21 (FGF-21), growth and differentiation factor 15 (GDF-15), plus dysregulation of fatty acid and amino acid metabolism. Thus, although potentially beneficial in short term, inducing mitochondrial biogenesis with bezafibrate altered the metabolomic signature of mitochondrial disease, raising concerns about long-term sequelae

Experimental Demonstration of a Cognitive Optical Network for Reduction of Restoration Time

This paper presents the implementation and performance evaluation of a cognitive heterogeneous optical network testbed. The testbed integrates the CMP, the data plane and the cognitive system and reduces by 48% the link restoration time. This paper presents the implementation and performance evaluation of a cognitive heterogeneous optical network testbed. The testbed integrates the CMP, the data plane and the cognitive system and reduces by 48% the link restoration time

European guidelines on chronic mesenteric ischaemia - joint United European Gastroenterology, European Association for Gastroenterology, Endoscopy and Nutrition, European Society of Gastrointestinal and Abdominal Radiology, Netherlands Association of Hepatogastroenterologists, Hellenic Society of Gastroenterology, Cardiovascular and Interventional Radiological Society of Europe, and Dutch Mesenteric Ischemia Study group clinical guidelines on the diagnosis and treatment of patients with chronic mesenteric ischaemia

Chronic mesenteric ischaemia is a severe and incapacitating disease, causing complaints of post-prandial pain, fear of eating and weight loss. Even though chronic mesenteric ischaemia may progress to acute mesenteric ischaemia, chronic mesenteric ischaemia remains an underappreciated and undertreated disease entity. Probable explanations are the lack of knowledge and awareness among physicians and the lack of a gold standard diagnostic test. The underappreciation of this disease results in diagnostic delays, underdiagnosis and undertreating of patients with chronic mesenteric ischaemia, potentially resulting in fatal acute mesenteric ischaemia. This guideline provides a comprehensive overview and repository of the current evidence and multidisciplinary expert agreement on pertinent issues regarding diagnosis and treatment, and provides guidance in the multidisciplinary field of chronic mesenteric ischaemia