2,472 research outputs found
Direct -body code on low-power embedded ARM GPUs
This work arises on the environment of the ExaNeSt project aiming at design
and development of an exascale ready supercomputer with low energy consumption
profile but able to support the most demanding scientific and technical
applications. The ExaNeSt compute unit consists of densely-packed low-power
64-bit ARM processors, embedded within Xilinx FPGA SoCs. SoC boards are
heterogeneous architecture where computing power is supplied both by CPUs and
GPUs, and are emerging as a possible low-power and low-cost alternative to
clusters based on traditional CPUs. A state-of-the-art direct -body code
suitable for astrophysical simulations has been re-engineered in order to
exploit SoC heterogeneous platforms based on ARM CPUs and embedded GPUs.
Performance tests show that embedded GPUs can be effectively used to accelerate
real-life scientific calculations, and that are promising also because of their
energy efficiency, which is a crucial design in future exascale platforms.Comment: 16 pages, 7 figures, 1 table, accepted for publication in the
Computing Conference 2019 proceeding
Correction to: Sol–Gel Synthesis of High-Density Zeolitic Imidazolate Framework Monoliths via Ligand Assisted Methods: Exceptional Porosity, Hydrophobicity, and Applications in Vapor Adsorption (Advanced Functional Materials, (2021), 31, 5, (2008357), 10.1002/adfm.202008357)
In the original published version of this article, the bulk densities of the powder ZIF-8 and ZIF-67 were quoted as 0.96 g/cm3 and 0.94 g/cm3 respectively. However, the values for the powder samples’ true density were quoted in error. The correct bulk densities, used for calculating volume-relative capacities and surface areas, were 0.39 g/cm3 and 0.38 g/cm3 for ZIF-8 and ZIF-67, respectively. As this affects the calculated ‘volume-relative’ quantities, corrected tables and graphs are included below. The authors apologise for any inconvenience or confusion this error may have caused. Corrected tables Corrected values will be written and underlined in red. 1 Table Physical characteristics of ZIF samples. Surface areas and porosities expressed in mass-relative and volume-relative terms. Tpycometry = 25 °C. Tgas adsorption = -196 °C (Table presented.) a) Volume-relative quantities calculated by multiplying bulk density by mass-relative quantity b) Due to lack of micropores within sample, micropore volume could not be determined. 3 Table Summary of low concentration dynamic adsorption experiments. All measurements carried out at a toluene partial pressure of 0.00026, and a temperature of 25 °C (Table presented.) a) Calculated by dividing capacity when toluene is first detected by the capacity when the inlet and outlet concentrations of toluene are equal. 4 Table Estimated mass-relative and volume-relative toluene vapour capture productivities for adsorbents. Calculated using gravimetric toluene adsorption data at a partial pressure of 0.1 and a temperature of 25 °C (Table presented.) a) Time taken to reach a mass gradient value of 0.00075% dry mass per minute. Corrected main text figures 6 Figure (Figure presented.) Co-sorption volume-relative toluene vapour capacities as a function of process humidity, for zinc (left) and cobalt (right) ZIF samples. Partial pressure of toluene in all measurements, P/P0 = 0.005, while water vapour partial pressure varied. All measurements carried out at 25 °C. Corrected supplementary information figures S4 Figure (Figure presented.) Volume-relative nitrogen adsorption isotherms for zinc (left) and cobalt (right) samples. Temperature in all experiments is -196 °C. S5 Figure (Figure presented.) Volume-relative adsorption isotherms for zinc (left) and cobalt (right) samples: water (top), toluene (middle), methanol (bottom). Temperature in all experiments is 25 °C
Lack of phenotypic and evolutionary cross-resistance against parasitoids and pathogens in Drosophila melanogaster
BackgroundWhen organisms are attacked by multiple natural enemies, the evolution of a resistance mechanism to one natural enemy will be influenced by the degree of cross-resistance to another natural enemy. Cross-resistance can be positive, when a resistance mechanism against one natural enemy also offers resistance to another; or negative, in the form of a trade-off, when an increase in resistance against one natural enemy results in a decrease in resistance against another. Using Drosophila melanogaster, an important model system for the evolution of invertebrate immunity, we test for the existence of cross-resistance against parasites and pathogens, at both a phenotypic and evolutionary level.MethodsWe used a field strain of D. melanogaster to test whether surviving parasitism by the parasitoid Asobara tabida has an effect on the resistance against Beauveria bassiana, an entomopathogenic fungus; and whether infection with the microsporidian Tubulinosema kingi has an effect on the resistance against A. tabida. We used lines selected for increased resistance to A. tabida to test whether increased parasitoid resistance has an effect on resistance against B. bassiana and T. kingi. We used lines selected for increased tolerance against B. bassiana to test whether increased fungal resistance has an effect on resistance against A. tabida.Results/ConclusionsWe found no positive cross-resistance or trade-offs in the resistance to parasites and pathogens. This is an important finding, given the use of D. melanogaster as a model system for the evolution of invertebrate immunity. The lack of any cross-resistance to parasites and pathogens, at both the phenotypic and the evolutionary level, suggests that evolution of resistance against one class of natural enemies is largely independent of evolution of resistance against the other
Colour break in reverse bicolour daffodils is associated with the presence of Narcissus mosaic virus
<p>Abstract</p> <p>Background</p> <p>Daffodils (<it>Narcissus pseudonarcissus</it>) are one of the world's most popular ornamentals. They also provide a scientific model for studying the carotenoid pigments responsible for their yellow and orange flower colours. In reverse bicolour daffodils, the yellow flower trumpet fades to white with age. The flowers of this type of daffodil are particularly prone to colour break whereby, upon opening, the yellow colour of the perianth is observed to be 'broken' into patches of white. This colour break symptom is characteristic of potyviral infections in other ornamentals such as tulips whose colour break is due to alterations in the presence of anthocyanins. However, reverse bicolour flowers displaying colour break show no other virus-like symptoms such as leaf mottling or plant stunting, leading some to argue that the carotenoid-based colour breaking in reverse bicolour flowers may not be caused by virus infection.</p> <p>Results</p> <p>Although potyviruses have been reported to cause colour break in other flower species, enzyme-linked-immunoassays with an antibody specific to the potyviral family showed that potyviruses were not responsible for the occurrence of colour break in reverse bicolour daffodils. Colour break in this type of daffodil was clearly associated with the presence of large quantities of rod-shaped viral particles of lengths 502-580 nm in tepals. Sap from flowers displaying colour break caused red necrotic lesions on <it>Gomphrena globosa</it>, suggesting the presence of potexvirus. Red necrotic lesions were not observed in this indicator plant when sap from reverse bicolour flowers not showing colour break was used. The reverse transcriptase polymerase reactions using degenerate primers to carla-, potex- and poty-viruses linked viral RNA with colour break and sequencing of the amplified products indicated that the potexvirus <it>Narcissisus mosaic virus </it>was the predominant virus associated with the occurrence of the colour break.</p> <p>Conclusions</p> <p>High viral counts were associated with the reverse bicolour daffodil flowers that were displaying colour break but otherwise showed no other symptoms of infection. <it>Narcissus mosaic virus </it>was the virus that was clearly linked to the carotenoid-based colour break.</p
Entangled-State Cycles of Atomic Collective-Spin States
We study quantum trajectories of collective atomic spin states of
effective two-level atoms driven with laser and cavity fields. We show that
interesting ``entangled-state cycles'' arise probabilistically when the (Raman)
transition rates between the two atomic levels are set equal. For odd (even)
, there are () possible cycles. During each cycle the
-qubit state switches, with each cavity photon emission, between the states
, where is a Dicke state in a rotated
collective basis. The quantum number (), which distinguishes the
particular cycle, is determined by the photon counting record and varies
randomly from one trajectory to the next. For even it is also possible,
under the same conditions, to prepare probabilistically (but in steady state)
the Dicke state , i.e., an -qubit state with excitations,
which is of particular interest in the context of multipartite entanglement.Comment: 10 pages, 9 figure
Verified and potential pathogens of predatory mites (Acari: Phytoseiidae)
Several species of phytoseiid mites (Acari: Phytoseiidae), including species of the genera Amblyseius, Galendromus, Metaseiulus, Neoseiulus, Phytoseiulus and Typhlodromus, are currently reared for biological control of various crop pests and/or as model organisms for the study of predator¿prey interactions. Pathogen-free phytoseiid mites are important to obtain high efficacy in biological pest control and to get reliable data in mite research, as pathogens may affect the performance of their host or alter their reproduction and behaviour. Potential and verified pathogens have been reported for phytoseiid mites during the past 25 years. The present review provides an overview, including potential pathogens with unknown host effects (17 reports), endosymbiotic Wolbachia (seven reports), other bacteria (including Cardinium and Spiroplasma) (four reports), cases of unidentified diseases (three reports) and cases of verified pathogens (six reports). From the latter group four reports refer to Microsporidia, one to a fungus and one to a bacterium. Only five entities have been studied in detail, including Wolbachia infecting seven predatory mite species, other endosymbiotic bacteria infecting Metaseiulus (Galendromus, Typhlodromus) occidentalis (Nesbitt), the bacterium Acaricomes phytoseiuli infecting Phytoseiulus persimilis Athias-Henriot, the microsporidium Microsporidium phytoseiuli infecting P. persimilis and the microsporidium Oligosproridium occidentalis infecting M. occidentalis. In four cases (Wolbachia, A. phytoseiuli, M. phytoseiuli and O. occidentalis) an infection may be connected with fitness costs of the host. Moreover, infection is not always readily visible as no obvious gross symptoms are present. Monitoring of these entities on a routine and continuous basis should therefore get more attention, especially in commercial mass-production. Special attention should be paid to field-collected mites before introduction into the laboratory or mass rearing, and to mites that are exchanged among rearing facilities. However, at present general pathogen monitoring is not yet practical as effects of many entities are unknown. More research effort is needed concerning verified and potential pathogens of commercially reared arthropods and those used as model organisms in research
Effective connectivity reveals strategy differences in an expert calculator
Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of “cortical hubs” supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material
Yukawa potentials in systems with partial periodic boundary conditions I : Ewald sums for quasi-two dimensional systems
Yukawa potentials are often used as effective potentials for systems as
colloids, plasmas, etc. When the Debye screening length is large, the Yukawa
potential tends to the non-screened Coulomb potential ; in this small screening
limit, or Coulomb limit, the potential is long ranged. As it is well known in
computer simulation, a simple truncation of the long ranged potential and the
minimum image convention are insufficient to obtain accurate numerical data on
systems. The Ewald method for bulk systems, i.e. with periodic boundary
conditions in all three directions of the space, has already been derived for
Yukawa potential [cf. Y., Rosenfeld, {\it Mol. Phys.}, \bm{88}, 1357, (1996)
and G., Salin and J.-M., Caillol, {\it J. Chem. Phys.}, \bm{113}, 10459,
(2000)], but for systems with partial periodic boundary conditions, the Ewald
sums have only recently been obtained [M., Mazars, {\it J. Chem. Phys.}, {\bf
126}, 056101 (2007)]. In this paper, we provide a closed derivation of the
Ewald sums for Yukawa potentials in systems with periodic boundary conditions
in only two directions and for any value of the Debye length. A special
attention is paid to the Coulomb limit and its relation with the
electroneutrality of systems.Comment: 40 pages, 5 figures and 4 table
Recombination rate and selection strength in HIV intra-patient evolution
The evolutionary dynamics of HIV during the chronic phase of infection is
driven by the host immune response and by selective pressures exerted through
drug treatment. To understand and model the evolution of HIV quantitatively,
the parameters governing genetic diversification and the strength of selection
need to be known. While mutation rates can be measured in single replication
cycles, the relevant effective recombination rate depends on the probability of
coinfection of a cell with more than one virus and can only be inferred from
population data. However, most population genetic estimators for recombination
rates assume absence of selection and are hence of limited applicability to
HIV, since positive and purifying selection are important in HIV evolution.
Here, we estimate the rate of recombination and the distribution of selection
coefficients from time-resolved sequence data tracking the evolution of HIV
within single patients. By examining temporal changes in the genetic
composition of the population, we estimate the effective recombination to be
r=1.4e-5 recombinations per site and generation. Furthermore, we provide
evidence that selection coefficients of at least 15% of the observed
non-synonymous polymorphisms exceed 0.8% per generation. These results provide
a basis for a more detailed understanding of the evolution of HIV. A
particularly interesting case is evolution in response to drug treatment, where
recombination can facilitate the rapid acquisition of multiple resistance
mutations. With the methods developed here, more precise and more detailed
studies will be possible, as soon as data with higher time resolution and
greater sample sizes is available.Comment: to appear in PLoS Computational Biolog
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