Runtime Coordinated Heterogeneous Tasks in Charm++

Effective utilization of the increasingly heterogeneous hardware in modern supercomputers is a significant challenge. Many applications have seen performance gains by using GPUs, but many implementations leave CPUs sitting idle.In this paper, we describe a runtime managed system for coordinating heterogeneous execution. This system manages data transfers to and from GPU devices and schedules work across the computational resources of the system. The programmer need only tag methods and parameters to enable heterogeneous execution.Using this system, we observe improvements in programmer productivity and application performance. For selected benchmarks, when using heterogeneous execution we observe speedups of up to 3.09x relative to using only the host cores or only the device

Regulation of Signal Transducer and Activator of Transcription Signaling by the Tyrosine Phosphatase PTP-BL

SummarySignal Transducer and Activator of Transcription (STAT) proteins are a family of latent cytoplasmic transcription factors that are activated by tyrosine phosphorylation after cytokine stimulation. One mechanism by which STAT signaling is regulated is by dephosphorylation through the action of protein tyrosine phosphatases (PTP). We have identified PTP-Basophil like (PTP-BL) as a STAT PTP. PTP-BL dephosphorylates STAT proteins in vitro and in vivo, resulting in attenuation of STAT-mediated gene activation. In CD4+ T cells, PTP-BL deficiency leads to increased and prolonged activation of STAT4 and STAT6, and consequently enhanced T helper 1 (Th1) and Th2 cell differentiation. Taken together, our findings demonstrate that PTP-BL is a physiologically important negative regulator of the STAT signaling pathway

Great Canadian Lagerstätten 3. Late Ordovician Konservat-Lagerstätten in Manitoba

Konservat-Lagerstätten, deposits in which soft-bodied or lightly sclerotized fossils are preserved, are very rare in Ordovician strata. Three significant sites are known from Upper Ordovician rocks in Manitoba: at Cat Head – McBeth Point, William Lake, and Airport Cove. These sites are in two distinct sedimentary basins: the former two are in the Williston Basin, while the latter is in the Hudson Bay Basin. All three sites contain marine fossils, but each has a different assemblage that contributes a distinct piece of the diversity picture. Important groups represented at one or more of the sites include seaweeds (algae), sponges, cnidarian medusae (jellyfish), conulariids, trilobites, eurypterids, xiphosurids (horseshoe crabs), and pycnogonids (‘sea spiders’). The different biotas reflect depositional conditions at each site. Many of the fossils are unknown elsewhere in the Ordovician at the family level or higher. The province of Manitoba therefore makes a significant contribution to knowledge of Late Ordovician biodiversity.SOMMAIRELes lagerstätten de conservation, ces sédiments contenant des fossiles d’organismes à corps mou ou légèrement sclérotisés particulièrement bien conservés, sont très rares dans les strates ordoviciennes.  Trois sites d’importance sont connus dans des roches de l'Ordovicien supérieur à Cat Head, Manitoba, soit McBeth Point, William Lake et  Airport Cove.  Ces sites sont situés dans deux bassins sédimentaires distincts : les deux premiers sont situés dans le bassin de Williston, tandis que le second est situé dans le bassin de la baie d'Hudson.  Les trois sites contiennent des fossiles marins, mais chacun présente un assemblage différent, chacun montrant une composante distincte de la diversité biologique d’alors.  Les groupes les plus importants représentés, dans un ou plusieurs de ces sites, sont les algues, les éponges, les cnidarian medusae (méduses), les conularides, les trilobites, les euryptérides, xiphosurides (limules) et pycnogonides.  Les différents biotopes reflètent les conditions de dépôt de chaque site.  Nombre de ces fossiles sont inconnus ailleurs dans l'Ordovicien, au niveau de la famille ou du taxon supérieur de la classification.  Ainsi, la province du Manitoba offre-t-elle une contribution importante à la connaissance de la biodiversité de l'Ordovicien supérieur

An orally active formulation of angiotensin-(1-7) produces an antithrombotic effect

INTRODUCTION AND OBJECTIVE: The heptapeptide angiotensin-(1-7) is a component of the renin-angiotensin system, which promotes many beneficial cardiovascular effects, including antithrombotic activity. We have recently shown that the antithrombotic effect of angiotensin-(1-7) involves receptor Mas-mediated NO-release from platelets. Here, we describe an orally active formulation based on angiotensin-(1-7) inclusion in cyclodextrin [Ang-(1-7)- CyD] as an antithrombotic agent. Cyclodextrins are pharmaceutical tools that are used to enhance drug stability, absorption across biological barriers and gastric protection. METHOD: To test the antithrombotic effect of Ang-(1-7)-CyD, thrombus formation was induced in the abdominal vena cava of spontaneously hypertensive rats that were pretreated either acutely or chronically with Ang-(1-7)-CyD. Male Mas-knockout and wild-type mice were used to verify the role of the Mas receptor on the effect of Ang-(1-7)-CyD. RESULTS: Acute or chronic oral treatment with Ang-(1-7)-CyD promoted an antithrombotic effect (measured by thrombus weight; all values are, respectively, untreated vs. treated animals) in spontaneously hypertensive rats (acute: 2.86 + 0.43 mg vs. 1.14 + 0.40 mg; chronic: 4.27 + 1.03 mg vs. 1.39 + 0.68 mg). This effect was abolished in Mas-knockout mice (thrombus weight in Mas wild-type: 0.76 + 0.10 mg vs. 0.37 + 0.02 mg; thrombus weight in Mas-knockout: 0.96 + 0.11 mg vs. 0.87 + 0.14 mg). Furthermore, the antithrombotic effect of Ang-(1-7)-CyD was associated with an increase in the plasma level of Angiotensin-(1-7). CONCLUSION: These results show for the first time that the oral formulation Ang-(1-7)-CyD has biological activity and produces a Mas-dependent antithrombotic effect

An Open-Publishing Response to the COVID-19 Infodemic

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript\u27s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis

Low leakage-current InAsSb nanowire photodetectors on silicon

Axially doped p–i–n InAs0.93Sb0.07 nanowire arrays have been grown on Si substrates and fabricated into photodetectors for shortwave infrared detection. The devices exhibit a leakage current density around 2 mA/cm2 and a 20% cutoff of 2.3 μm at 300 K. This record low leakage current density for InAsSb based devices demonstrates the suitability of nanowires for the integration of III–V semiconductors with silicon technology

WHO Global Survey on Maternal and Perinatal Health in Latin America: classifying caesarean sections

<p>Abstract</p> <p>Background</p> <p>Caesarean section rates continue to increase worldwide with uncertain medical consequences. Auditing and analysing caesarean section rates and other perinatal outcomes in a reliable and continuous manner is critical for understanding reasons caesarean section changes over time.</p> <p>Methods</p> <p>We analyzed data on 97,095 women delivering in 120 facilities in 8 countries, collected as part of the 2004-2005 Global Survey on Maternal and Perinatal Health in Latin America. The objective of this analysis was to test if the "10-group" or "Robson" classification could help identify which groups of women are contributing most to the high caesarean section rates in Latin America, and if it could provide information useful for health care providers in monitoring and planning effective actions to reduce these rates.</p> <p>Results</p> <p>The overall rate of caesarean section was 35.4%. Women with single cephalic pregnancy at term without previous caesarean section who entered into labour spontaneously (groups 1 and 3) represented 60% of the total obstetric population. Although women with a term singleton cephalic pregnancy with a previous caesarean section (group 5) represented only 11.4% of the obstetric population, this group was the largest contributor to the overall caesarean section rate (26.7% of all the caesarean sections). The second and third largest contributors to the overall caesarean section rate were nulliparous women with single cephalic pregnancy at term either in spontaneous labour (group 1) or induced or delivered by caesarean section before labour (group 2), which were responsible for 18.3% and 15.3% of all caesarean deliveries, respectively.</p> <p>Conclusion</p> <p>The 10-group classification could be easily applied to a multicountry dataset without problems of inconsistencies or misclassification. Specific groups of women were clearly identified as the main contributors to the overall caesarean section rate. This classification could help health care providers to plan practical and effective actions targeting specific groups of women to improve maternal and perinatal care.</p

Alterations in the steroid hormone receptor co-chaperone FKBPL are associated with male infertility: a case-control study

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Male infertility is a common cause of reproductive failure in humans. In mice, targeted deletions of the genes coding for FKBP6 or FKBP52, members of the FK506 binding protein family, can result in male infertility. In the case of FKBP52, this reflects an important role in potentiating Androgen Receptor (AR) signalling in the prostate and accessory glands, but not the testis. In infertile men, no mutations of FKBP52 or FKBP6 have been found so far, but the gene for FKBP-like (FKBPL) maps to chromosome 6p21.3, an area linked to azoospermia in a group of Japanese patients. Methods To determine whether mutations in FKBPL could contribute to the azoospermic phenotype, we examined expression in mouse and human tissues by RNA array blot, RT-PCR and immunohistochemistry and sequenced the complete gene from two azoospermic patient cohorts and matching control groups. FKBPL-AR interaction was assayed using reporter constructs in vitro. Results FKBPL is strongly expressed in mouse testis, with expression upregulated at puberty. The protein is expressed in human testis in a pattern similar to FKBP52 and also enhanced AR transcriptional activity in reporter assays. We examined sixty patients from the Japanese patient group and found one inactivating mutation and one coding change, as well as a number of non-coding changes, all absent in fifty-six controls. A second, Irish patient cohort of thirty showed another two coding changes not present in thirty proven fertile controls. Conclusions Our results describe the first alterations in the gene for FKBPL in azoospermic patients and indicate a potential role in AR-mediated signalling in the testis.Published versio

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids