108 research outputs found
Design and Implementation of MPICH2 over InfiniBand with RDMA Support
For several years, MPI has been the de facto standard for writing parallel
applications. One of the most popular MPI implementations is MPICH. Its
successor, MPICH2, features a completely new design that provides more
performance and flexibility. To ensure portability, it has a hierarchical
structure based on which porting can be done at different levels. In this
paper, we present our experiences designing and implementing MPICH2 over
InfiniBand. Because of its high performance and open standard, InfiniBand is
gaining popularity in the area of high-performance computing. Our study focuses
on optimizing the performance of MPI-1 functions in MPICH2. One of our
objectives is to exploit Remote Direct Memory Access (RDMA) in Infiniband to
achieve high performance. We have based our design on the RDMA Channel
interface provided by MPICH2, which encapsulates architecture-dependent
communication functionalities into a very small set of functions. Starting with
a basic design, we apply different optimizations and also propose a
zero-copy-based design. We characterize the impact of our optimizations and
designs using microbenchmarks. We have also performed an application-level
evaluation using the NAS Parallel Benchmarks. Our optimized MPICH2
implementation achieves 7.6 s latency and 857 MB/s bandwidth, which are
close to the raw performance of the underlying InfiniBand layer. Our study
shows that the RDMA Channel interface in MPICH2 provides a simple, yet
powerful, abstraction that enables implementations with high performance by
exploiting RDMA operations in InfiniBand. To the best of our knowledge, this is
the first high-performance design and implementation of MPICH2 on InfiniBand
using RDMA support.Comment: 12 pages, 17 figure
Munc18-1 promotes larger dense-core vesicle docking.
AbstractSecretory vesicles dock at the plasma membrane before Ca2+ triggers their exocytosis. Exocytosis requires the assembly of SNARE complexes formed by the vesicle protein Synaptobrevin and the membrane proteins Syntaxin-1 and SNAP-25. We analyzed the role of Munc18-1, a cytosolic binding partner of Syntaxin-1, in large dense-core vesicle (LDCV) secretion. Calcium-dependent LDCV exocytosis was reduced 10-fold in mouse chromaffin cells lacking Munc18-1, but the kinetic properties of the remaining release, including single fusion events, were not different from controls. Concomitantly, mutant cells displayed a 10-fold reduction in morphologically docked LDCVs. Moreover, acute overexpression of Munc18-1 in bovine chromaffin cells increased the amount of releasable vesicles and accelerated vesicle supply. We conclude that Munc18-1 functions upstream of SNARE complex formation and promotes LDCV docking
Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species
The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions
Phylogeography Unplugged: Comparative Surveys in the Genomic Era
In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ( unplugged ) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches
Phylogeography Unplugged: Comparative Surveys in the Genomic Era
In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo- Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (“unplugged”) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches
Three Hypervelocity White Dwarfs in Gaia DR2: Evidence for Dynamically Driven Double-Degenerate Double-Detonation Type Ia Supernovae
Double detonations in double white dwarf (WD) binaries undergoing unstable
mass transfer have emerged in recent years as one of the most promising Type Ia
supernova (SN Ia) progenitor scenarios. One potential outcome of this
"dynamically driven double-degenerate double-detonation" (D^6) scenario is that
the companion WD survives the explosion and is flung away with a velocity equal
to its > 1000 km/s pre-SN orbital velocity. We perform a search for these
hypervelocity runaway WDs using Gaia's second data release. In this paper, we
discuss seven candidates followed up with ground-based instruments. Three
sources are likely to be some of the fastest known stars in the Milky Way, with
total Galactocentric velocities between 1000 and 3000 km/s, and are consistent
with having previously been companion WDs in pre-SN Ia systems. However,
although the radial velocity of one of the stars is > 1000 km/s, the radial
velocities of the other two stars are puzzlingly consistent with 0. The
combined five-parameter astrometric solutions from Gaia and radial velocities
from follow-up spectra yield tentative 6D confirmation of the D^6 scenario. The
past position of one of these stars places it within a faint, old SN remnant,
further strengthening the interpretation of these candidates as hypervelocity
runaways from binary systems that underwent SNe Ia.Comment: Accepted for publication in ApJ. Minor corrections for clarity. D6
spectra are available as ancillary data file
Genome-Wide Association Analysis Identifies a Mutation in the Thiamine Transporter 2 (SLC19A3) Gene Associated with Alaskan Husky Encephalopathy
Alaskan Husky Encephalopathy (AHE) has been previously proposed as a mitochondrial encephalopathy based on neuropathological similarities with human Leigh Syndrome (LS). We studied 11 Alaskan Husky dogs with AHE, but found no abnormalities in respiratory chain enzyme activities in muscle and liver, or mutations in mitochondrial or nuclear genes that cause LS in people. A genome wide association study was performed using eight of the affected dogs and 20 related but unaffected control AHs using the Illumina canine HD array. SLC19A3 was identified as a positional candidate gene. This gene controls the uptake of thiamine in the CNS via expression of the thiamine transporter protein THTR2. Dogs have two copies of this gene located within the candidate interval (SLC19A3.2 – 43.36–43.38 Mb and SLC19A3.1 – 43.411–43.419 Mb) on chromosome 25. Expression analysis in a normal dog revealed that one of the paralogs, SLC19A3.1, was expressed in the brain and spinal cord while the other was not. Subsequent exon sequencing of SLC19A3.1 revealed a 4bp insertion and SNP in the second exon that is predicted to result in a functional protein truncation of 279 amino acids (c.624 insTTGC, c.625 C>A). All dogs with AHE were homozygous for this mutation, 15/41 healthy AH control dogs were heterozygous carriers while 26/41 normal healthy AH dogs were wild type. Furthermore, this mutation was not detected in another 187 dogs of different breeds. These results suggest that this mutation in SLC19A3.1, encoding a thiamine transporter protein, plays a critical role in the pathogenesis of AHE.University of California, Davis. School of Veterinary Medicine. Center for Companion Animal Healt
Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago
Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions
Evidence for Extended Hydrogen-Poor CSM in the Three-Peaked Light Curve of Stripped Envelope Ib Supernova
We present multi-band ATLAS photometry for SN 2019tsf, a stripped-envelope
Type Ib supernova (SESN). The SN shows a triple-peaked light curve and a late
(re-)brightening, making it unique among stripped-envelope systems. The
re-brightening observations represent the latest photometric measurements of a
multi-peaked Type Ib SN to date. As late-time photometry and spectroscopy
suggest no hydrogen, the potential circumstellar material (CSM) must be H-poor.
Moreover, late (>150 days) spectra show no signs of narrow emission lines,
further disfavouring CSM interaction. On the contrary, an extended CSM
structure is seen through a follow-up radio campaign with Karl G. Jansky Very
Large Array (VLA), indicating a source of bright optically thick radio emission
at late times, which is highly unusual among H-poor SESNe. We attribute this
phenomenology to an interaction of the supernova ejecta with
spherically-asymmetric CSM, potentially disk-like, and we present several
models that can potentially explain the origin of this rare Type Ib supernova.
The warped disc model paints a novel picture, where the tertiary companion
perturbs the progenitors CSM, that can explain the multi-peaked light curves of
SNe, and here we apply it to SN 2019tsf. This SN 2019tsf is likely a member of
a new sub-class of Type Ib SNe and among the recently discovered class of SNe
that undergo mass transfer at the moment of explosionComment: 23 pages, Comments are welcome, Submitted to Ap
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