Dynamic Adaptable Asynchronous Progress Model for MPI RMA Multiphase Applications

Casper is a process-based asynchronous progress model for MPI one-sided communication on multi- and many-core architectures. The one-sided communication is not truly one-sided in most MPI implementations: the target process still relies on software progress to complete incoming operations. Casper allows the user to specify an arbitrary number of cores dedicated to background ghost processes and transparently redirects the RMA operations to ghost processes by utilizing the PMPI redirection and MPI-3 shared-memory technologies. Although Casper benefits applications that suffer from lack of asynchronous progress, the operation redirection design might not support complex multiphase applications effectively, which often involve dynamically changing communication density and computing workloads. In this paper, we present an adaptive mechanism in Casper to address the limitation of static asynchronous progress in multiphase applications. We exploit two adaptive strategies, a user-guided strategy and a fully transparent and automatic strategy based on self-profiling and prediction, to dynamically reconfigure the asynchronous progress in Casper according to real-time performance characteristics during multiphase execution. We evaluate the adaptive approaches in both microbenchmarks and a real quantum chemistry application suite, NWChem, on the Cray XC30 supercomputer and an Intel Omni-Path cluster.This material was based upon work supported by the U.S. Dept. of Energy, Office of Science, Advanced Scientific Computing Research (SC-21), under contract DE-AC02- 06CH11357. The experimental resources for this paper were provided by the National Energy Research Scientific Computing Center (NERSC) on the Edison Cray XC30 supercomputer and by the Laboratory Computing Resource Center on the Bebop cluster at Argonne National Laboratory. Antonio J. Peña is co-financed by the Spanish Ministry of Economy and Competitiveness under Juan de la Cierva fellowship number IJCI-2015-23266.Peer ReviewedPostprint (author's final draft

Ki67 Antigen as a Predictive Factor for Prognosis of Sinonasal Mucosal Melanoma

ObjectivesSinonasal mucosal melanoma is a rare and aggressive disease. The aim of this study was to analyze the clinical features of patients with sinonasal mucosal melanoma and to determine the role of Ki67 antigen as a predictor of prognosis in sinonasal mucosal melanoma.MethodsThis was a retrospective case-series study at a single institution, an academic tertiary referral center. From 1995 to 2007, 27 patients with sinonasal mucosal melanoma were reviewed retrospectively, and the expression of Ki67 antigen was assessed by immunohistochemistry.ResultsThe overall 5-yr survival rate was 33.9%. No significant differences were observed in 5-yr survival according to age, sex, stage, or the presence of melanin. The rates of local failure, regional failure, and distant failure were 37.0%, 14.8%, and 11.1%, respectively. Patients with spindle or mixed cell types had better prognoses than those with other cell types. At a cut-off value of 35%, patients with lower Ki67 scores showed better survival than those with higher Ki67 scores.ConclusionThe presence of spindle or mixed cell types may indicate a better prognosis than other cell types. Ki67 immunostaining may be a useful predictor of prognosis in patients with mucosal malignant melanoma of the sinonasal tract

Neutron Scattering Study of Spin Density Wave Order in the Superconducting State of Excess-Oxygen-Doped La2CuO4+y

We report neutron scattering measurements of spin density wave order within the superconducting state of a single crystal of predominately stage-4 La2CuO4+y with a Tc(onset) of 42 K. The low temperature elastic magnetic scattering is incommensurate with the lattice and is characterized by long-range order in the copper-oxide plane with the spin direction identical to that in the insulator. Between neighboring planes, the spins exhibit short-range correlations with a stacking arrangement reminiscent of that in the undoped antiferromagnetic insulator. The elastic magnetic peak intensity appears at the same temperature within the errors as the superconductivity, suggesting that the two phenomena are strongly correlated. These observations directly reveal the persistent influence of the antiferromagnetic order as the doping level increases from the insulator to the superconductor. In addition, our results confirm that spin density wave order for incommensurabilities near 1/8 is a robust feature of the La2CuO4-based superconductors.Comment: 14 pages, LaTeX, includes 8 figure

Malaria mosquito control using edible fish in western Kenya: preliminary findings of a controlled study

<p>Abstract</p> <p>Background</p> <p>Biological control methods are once again being given much research focus for malaria vector control. This is largely due to the emerging threat of strong resistance to pesticides. Larvivorous fish have been used for over 100 years in mosquito control and many species have proved effective. In the western Kenyan highlands the larvivorous fish <it>Oreochromis niloticus </it>L. (Perciformes: Cichlidae) (formerly <it>Tilapia nilotica</it>) is commonly farmed and eaten but has not been previously tested in the field for malaria mosquito control.</p> <p>Methods</p> <p>This fish was introduced into abandoned fishponds at an altitude of 1,880 m and the effect measured over six months on the numbers of mosquito immatures. For comparison an untreated control pond was used. During this time, all ponds were regularly cleared of emergent vegetation and fish re-stocking was not needed. Significant autocorrelation was removed from the time series data, and t-tests were used to investigate within a pond and within a mosquito type any differences before and after the introduction of <it>O. niloticus</it>. Mulla's formula was also used on the raw data to calculate the percentage reduction of the mosquito larvae.</p> <p>Results</p> <p>After <it>O. niloticus </it>introduction, mosquito densities immediately dropped in the treated ponds but increased in the control pond. This increase was apparently due to climatic factors. Mulla's formula was applied which corrects for that natural tendency to increase. The results showed that after 15 weeks the fish caused a more than 94% reduction in both <it>Anopheles gambiae s.l</it>. and <it>Anopheles funestus </it>(Diptera: Culicidae) in the treated ponds, and more than 75% reduction in culicine mosquitoes. There was a highly significantly reduction in <it>A. gambiae s.l</it>. numbers when compared to pre-treatment levels.</p> <p>Conclusion</p> <p>This study reports the first field trial data on <it>O. niloticus </it>for malaria mosquito control and shows that this species, already a popular food fish in western Kenya, is an apparently sustainable mosquito control tool which also offers a source of protein and income to people in rural areas. There should be no problem with acceptance of this malaria control method since the local communities already farm this fish species.</p

The Apostasia genome and the evolution of orchids

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth(1-3). Here we report the draft genome sequence of Apostasia shenzhenica(4), a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms

Evolutionary, multi-scale analysis of river bank line retreat using continuous wavelet transforms: Jamuna River, Bangladesh

In this study continuous wavelet transforms are used to explore spatio-temporal patterns of multi-scale bank line retreat along a 204 km reach of the Jamuna River, Bangladesh. A sequence of eight bank line retreat series, derived from remotely-sensed imagery for the period 1987-1999, is transformed using the Morlet mother wavelet. Bank erosion is shown to operate at several characteristic spatial and temporal scales. Local erosion and bank line retreat are shown to occur in short, well defined reaches characterised by temporal persistence at the same location, and separated by relatively stable reaches. In contrast, evidence of downstream propagation of bank line retreat patterns is evident at larger spatial scales. The intensity of localised bank line retreat (i.e. at scales of 0 - 20 km) is strongly related to the magnitude of monsoonal peak discharge, but this relationship weakens as the spatial scale of erosion increases. The potential of continuous wavelet analysis to enhancing our understanding of morphological evolution in complex fluvial systems with multi-channel planforms is discussed

Calcium Sulfate and Platelet-Rich Plasma make a novel osteoinductive biomaterial for bone regeneration

BACKGROUND: With the present study we introduce a novel and simple biomaterial able to induce regeneration of bone. We theorized that nourishing a bone defect with calcium and with a large amount of activated platelets may initiate a series of biological processes that culminate in bone regeneration. Thus, we engineered CS-Platelet, a biomaterial based on the combination of Calcium Sulfate and Platelet-Rich Plasma in which Calcium Sulfate also acts as an activator of the platelets, therefore avoiding the need to activate the platelets with an agonist. METHODS: First, we tested CS-Platelet in heterotopic (muscle) and orthotopic (bone) bone regeneration bioassays. We then utilized CS-Platelet in a variety of dental and craniofacial clinical cases, where regeneration of bone was needed. RESULTS: The heterotopic bioassay showed formation of bone within the muscular tissue at the site of the implantation of CS-Platelet. Results of a quantitative orthotopic bioassay based on the rat calvaria critical size defect showed that only CS-Platelet and recombinant human BMP2 were able to induce a significant regeneration of bone. A non-human primate orthotopic bioassay also showed that CS-Platelet is completely resorbable. In all human clinical cases where CS-Platelet was used, a complete bone repair was achieved. CONCLUSION: This study showed that CS-Platelet is a novel biomaterial able to induce formation of bone in heterotopic and orthotopic sites, in orthotopic critical size bone defects, and in various clinical situations. The discovery of CS-Platelet may represent a cost-effective breakthrough in bone regenerative therapy and an alternative or an adjuvant to the current treatments

The 'Harmonizing Optimal Strategy for Treatment of coronary artery stenosis - sAfety & effectiveneSS of drug-elUting stents & antiplatelet REgimen' (HOST-ASSURE) trial: study protocol for a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Second-generation drug-eluting stents (DES) have raised the bar of clinical performance. These stents are mostly made from cobalt chromium alloy. A newer generation DES has been developed from platinum chromium alloy, but clinical data regarding the efficacy and safety of the platinum chromium-based everolimus-eluting stent (PtCr-EES) is limited, with no comparison data against the cobalt chromium-based zotarolimus-eluting stent (CoCr-ZES). In addition, an antiplatelet regimen is an integral component of medical therapy after percutaneous coronary intervention (PCI). A 1-week duration of doubling the dose of clopidogrel (double-dose antiplatelet therapy (DDAT)) was shown to improve outcome at 1 month compared with conventional dose in acute coronary syndrome (ACS) patients undergoing PCI. However in Asia, including Korea, the addition of cilostazol (triplet antiplatelet therapy (TAT)) is used more commonly than doubling the dose of clopidogrel in high-risk patients.</p> <p>Methods</p> <p>In the 'Harmonizing Optimal Strategy for Treatment of coronary artery stenosis - sAfety & effectiveneSS of drug-elUting stents & antiplatelet REgimen' (HOST-ASSURE) trial, approximately 3,750 patients are being prospectively and randomly assigned in a 2 × 2 factorial design according to the type of stent (PtCr-EES vs CoCr-ZES) and antiplatelet regimen (TAT vs DDAT). The first primary endpoint is target lesion failure at 1 year for the stent comparison, and the second primary endpoint is net clinical outcome at 1 month for comparison of antiplatelet therapy regimen.</p> <p>Discussion</p> <p>The HOST-ASSURE trial is the largest study yet performed to directly compare the efficacy and safety of the PtCr-EES versus CoCr-ZES in an 'all-comers' population. In addition, this study will also compare the clinical outcome of TAT versus DDAT for 1-month post PCI.</p> <p>Trial registration</p> <p>ClincalTrials.gov number <a href="http://www.clinicaltrials.gov/ct2/show/NCT01267734">NCT01267734</a>.</p