SR-IOV in High Performance Computing

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MERRA/AS: The MERRA Analytic Services Project Interim Report

MERRA AS is a cyberinfrastructure resource that will combine iRODS-based Climate Data Server (CDS) capabilities with Coudera MapReduce to serve MERRA analytic products, store the MERRA reanalysis data collection in an HDFS to enable parallel, high-performance, storage-side data reductions, manage storage-side driver, mapper, reducer code sets and realized objects for users, and provide a library of commonly used spatiotemporal operations that can be composed to enable higher-order analyses

The effects of publishing emergency department wait time on patient utilization patterns in a community with two emergency department sites: a retrospective, quasi-experiment design

BACKGROUND: Providing emergency department (ED) wait time information to the public has been suggested as a mechanism to reduce lengthy ED wait times (by enabling patients to select the ED site with shorter wait time), but the effects of such a program have not been evaluated. We evaluated the effects of such a program in a community with two ED sites. METHODS: Descriptive statistics for wait times of the two sites before and after the publication of wait time information were used to evaluate the effects of the publication of wait time information on wait times. Multivariate logistical regression was used to test whether or not individual patients used published wait time to decide which site to visit. RESULTS: We found that the rates of wait times exceeding 4 h, and the 95th percentile of wait times in the two sites decreased after the publication of wait time information, even though the average wait times experienced a slight increase. We also found that after controlling for other factors, the site with shorter wait time had a higher likelihood of being selected after the publication of wait time information, but there was no such relationship before the publication. CONCLUSIONS: These findings were consistent with the hypothesis that the publication of wait time information leads to patients selecting the site with shorter wait time. While publishing ED wait time information did not improve average wait time, it reduced the rates of lengthy wait times

Can increased primary care access reduce demand for emergency care? Evidence from England's 7-day GP opening

Restricted access to primary care can lead to avoidable, excessive use of expensive emergency care. Since 2013, partly to alleviate overcrowding at the Accident & Emergency (A&E) units of hospitals, the UK has been piloting 7-day opening of General Practitioner (GP) practices to improve primary care access for patients. We evaluate the impact of these pilots on patient attendances at A&E. We estimate that 7-day GP opening has reduced A&E attendances by patients of pilot practices by 9.9% with most of the impact on weekends which see A&E attendances fall by 17.9%. The effect is non-monotonic in case severity with most of the fall occurring in cases of moderate severity. An additional finding is that there is also a 9.9% fall in weekend hospital admissions (from A&E) which is entirely driven by a fall in admissions of elderly patients. The impact on A&E attendances appears to be bigger among wealthier patients. We present evidence in support of a causal interpretation of our results and discuss policy implications

Taking the pulse of COVID-19: A spatiotemporal perspective

The sudden outbreak of the Coronavirus disease (COVID-19) swept across the world in early 2020, triggering the lockdowns of several billion people across many countries, including China, Spain, India, the U.K., Italy, France, Germany, and most states of the U.S. The transmission of the virus accelerated rapidly with the most confirmed cases in the U.S., and New York City became an epicenter of the pandemic by the end of March. In response to this national and global emergency, the NSF Spatiotemporal Innovation Center brought together a taskforce of international researchers and assembled implemented strategies to rapidly respond to this crisis, for supporting research, saving lives, and protecting the health of global citizens. This perspective paper presents our collective view on the global health emergency and our effort in collecting, analyzing, and sharing relevant data on global policy and government responses, geospatial indicators of the outbreak and evolving forecasts; in developing research capabilities and mitigation measures with global scientists, promoting collaborative research on outbreak dynamics, and reflecting on the dynamic responses from human societies.Comment: 27 pages, 18 figures. International Journal of Digital Earth (2020

Extreme Multiple Reticulate Origins of the Pteris cadieri Complex (Pteridaceae)

The Pteris cadieri complex displays extensive morphological variation and seems to have originated through hybridization. However, the members of this complex reproduce by apogamy, which usually limits genetic variation. To evaluate the hypotheses of hybrid origins, the pattern of evolution in this species complex is reconstructed. Multiple methodologies were used. Diploids, triploids, and tetraploids were identified by chromosome counts and flow cytometry. Nuclear DNA markers (cytosolic phosphoglucose isomerase gene, PgiC) were used, together with chloroplast DNA markers (atpB-rbcL spacer and rbcL gene) to infer the biparental and maternal lineages of the Pteris cadieri complex. The three cpDNA haplotype groups and five PgiC alleles found in this study indicate that the evolution of the Pteris cadieri complex has been extremely reticulate. Up to 11 taxa belonging to eight morphs were identified. By comparing genetic variation in the Pteris cadieri in two independent areas, Hainan and Taiwan, we inferred that hybridization has occurred independently in different areas. Furthermore, we found evidence for phenological divergence (evergreen and deciduous) within Taiwan. We propose that the Pteris cadieri complex originated from different genetic lineages through multiple hybridizations in different geographical areas, leading to its present morphological diversity

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)

<p>Abstract</p> <p>Background</p> <p>The genus <it>Cuscuta </it>L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context.</p> <p>Results</p> <p>Here we present a well-supported phylogeny of <it>Cuscuta </it>using sequences of the nuclear ribosomal internal transcribed spacer and plastid <it>rps2</it>, <it>rbcL </it>and <it>matK </it>from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus <it>Cuscuta </it>is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with <it>rbcL </it>exhibiting even higher levels of purifying selection in <it>Cuscuta </it>than photosynthetic relatives. Nuclear genome size is highly variable within <it>Cuscuta</it>, particularly within subgenus <it>Grammica</it>, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species.</p> <p>Conclusion</p> <p>Some morphological characters traditionally used to define major taxonomic splits within <it>Cuscuta </it>are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of <it>Cuscuta </it>retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.</p

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd