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  • 1
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    Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit (2017)
    Royal Society
    Details
    Publication Date: 2017-09-21
    Description: This paper focuses on designing and implementing parallel adaptive inverse distance weighting (AIDW) interpolation algorithms by using the graphics processing unit (GPU). The AIDW is an improved version of the standard IDW, which can adaptively determine the power parameter according to the data points’ spatial distribution pattern and achieve more accurate predictions than those predicted by IDW. In this paper, we first present two versions of the GPU-accelerated AIDW, i.e. the naive version without profiting from the shared memory and the tiled version taking advantage of the shared memory. We also implement the naive version and the tiled version using two data layouts, structure of arrays and array of aligned structures, on both single and double precision. We then evaluate the performance of parallel AIDW by comparing it with its corresponding serial algorithm on three different machines equipped with the GPUs GT730M, M5000 and K40c. The experimental results indicate that: (i) there is no significant difference in the computational efficiency when different data layouts are employed; (ii) the tiled version is always slightly faster than the naive version; and (iii) on single precision the achieved speed-up can be up to 763 (on the GPU M5000), while on double precision the obtained highest speed-up is 197 (on the GPU K40c). To benefit the community, all source code and testing data related to the presented parallel AIDW algorithm are publicly available.
    Keywords: computer modelling and simulation
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 2
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    Temporal scaling of aging as an adaptive strategy of Escherichia coli (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Natural selection is thought to shape the evolution of aging patterns, although how life-history trajectories orchestrate the inherently stochastic processes associated with aging is unclear. Tracking clonal growth-arrested 〈i〉Escherichia coli〈/i〉 cohorts in an homogeneous environment at single-cell resolution, we demonstrate that the Gompertz law of exponential mortality characterizes bacterial lifespan distributions. By disentangling the rate of aging from age-independent components of longevity, we find that increasing cellular maintenance through the general stress pathway reduces the aging rate and rescales the lifespan distribution at the expense of growth. This trade-off between aging and growth underpins the evolutionary tuning of the general stress response pathway in adaptation to the organism’s feast-or-famine lifestyle. It is thus necessary to involve both natural selection and stochastic physiology to explain aging patterns.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Dominant nonlocal superconducting proximity effect due to electron-electron interaction in a ballistic double nanowire (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Cooper pair splitting (CPS) can induce nonlocal correlation between two normal conductors that are coupled to a superconductor. CPS in a double one-dimensional electron gas is an appropriate platform for extracting a large number of entangled electron pairs and is one of the key ingredients for engineering Majorana fermions with no magnetic field. In this study, we investigated CPS by using a Josephson junction of a gate-tunable ballistic InAs double nanowire. The measured switching current into the two nanowires is significantly larger than the sum of the switching current into the respective nanowires, indicating that interwire superconductivity is dominant compared with intrawire superconductivity. From its dependence on the number of propagating channels in the nanowires, the observed CPS is assigned to one-dimensional electron-electron interaction. Our results will pave the way for the utilization of one-dimensional electron-electron interaction to reveal the physics of high-efficiency CPS and to engineer Majorana fermions in double nanowire systems via CPS.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Monsoonal control on a delayed response of sedimentation to the 2008 Wenchuan earthquake (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Infrequent extreme events such as large earthquakes pose hazards and have lasting impacts on landscapes and biogeochemical cycles. Sediments provide valuable records of past events, but unambiguously identifying event deposits is challenging because of nonlinear sediment transport processes and poor age control. Here, we have been able to directly track the propagation of a tectonic signal into stratigraphy using reservoir sediments from before and after the 2008 Wenchuan earthquake. Cycles in magnetic susceptibility allow us to define a precise annual chronology and identify the timing and nature of the earthquake’s sedimentary record. The grain size and Rb/Sr ratio of the sediments responded immediately to the earthquake. However, the changes were muted until 2 years after the event, when intense monsoonal runoff drove accumulation of coarser grains and lower Rb/Sr sediments. The delayed response provides insight into how climatic and tectonic agents interact to control sediment transfer and depositional processes.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Fabrication of the heterojunction catalyst BiVO4/P25 and its visible-light photocatalytic activities (2018)
    Royal Society
    Details
    Publication Date: 2018-08-16
    Description: A heterojunction catalyst, BiVO 4 /P25, was successfully fabricated using a one-step hydrothermal method. The prepared composite was characterized using XRD, XPS, Raman, FT-IR, UV–vis, SEM, HRTEM and PL. The HRTEM pictures revealed that the heterostructured composite was composed of BiVO 4 and P25, and from the pictures of SEM we could see the P25 nanoparticles assembling on the surface of flower-shaped BiVO 4 nanostructures. The XPS spectra showed that the prepared catalyst consisted of Bi, V, O, Ti and C. The photocatalytic activity of BiVO 4 /P25 was evaluated by degraded methyl blue (MB) and tetracycline under visible light illumination ( 〉 420 nm), and the results showed that BiVO 4 /P25 composite has a better photocatalytic performance compared with pure BiVO 4 and the most active c-BiVO 4 /P25 sample showed enough catalytic stability after three successive reuses for MB photodegradation. The enhanced photocatalytic performance could mainly be attributed to the better optical absorption ability and good absorption ability of organic contaminants.
    Keywords: chemical engineering
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 7
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    Low-energy transmission electron diffraction and imaging of large-area graphene (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-09-02
    Description: Two-dimensional (2D) materials have attracted interest because of their excellent properties and potential applications. A key step in realizing industrial applications is to synthesize wafer-scale single-crystal samples. Until now, single-crystal samples, such as graphene domains up to the centimeter scale, have been synthesized. However, a new challenge is to efficiently characterize large-area samples. Currently, the crystalline characterization of these samples still relies on selected-area electron diffraction (SAED) or low-energy electron diffraction (LEED), which is more suitable for characterizing very small local regions. This paper presents a highly efficient characterization technique that adopts a low-energy electrostatically focused electron gun and a super-aligned carbon nanotube (SACNT) film sample support. It allows rapid crystalline characterization of large-area graphene through a single photograph of a transmission-diffracted image at a large beam size. Additionally, the low-energy electron beam enables the observation of a unique diffraction pattern of adsorbates on the suspended graphene at room temperature. This work presents a simple and convenient method for characterizing the macroscopic structures of 2D materials, and the instrument we constructed allows the study of the weak interaction with 2D materials.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Stretchable ultrasonic transducer arrays for three-dimensional imaging on complex surfaces (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-03-24
    Description: Ultrasonic imaging has been implemented as a powerful tool for noninvasive subsurface inspections of both structural and biological media. Current ultrasound probes are rigid and bulky and cannot readily image through nonplanar three-dimensional (3D) surfaces. However, imaging through these complicated surfaces is vital because stress concentrations at geometrical discontinuities render these surfaces highly prone to defects. This study reports a stretchable ultrasound probe that can conform to and detect nonplanar complex surfaces. The probe consists of a 10 x 10 array of piezoelectric transducers that exploit an "island-bridge" layout with multilayer electrodes, encapsulated by thin and compliant silicone elastomers. The stretchable probe shows excellent electromechanical coupling, minimal cross-talk, and more than 50% stretchability. Its performance is demonstrated by reconstructing defects in 3D space with high spatial resolution through flat, concave, and convex surfaces. The results hold great implications for applications of ultrasound that require imaging through complex surfaces.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉RNA binding proteins are key players in posttranscriptional regulation and have been implicated in neurodevelopmental and neuropsychiatric disorders. Here, we report a significant burden of heterozygous, likely gene-disrupting variants in 〈i〉CSDE1〈/i〉 (encoding a highly constrained RNA binding protein) among patients with autism and related neurodevelopmental disabilities. Analysis of 17 patients identifies common phenotypes including autism, intellectual disability, language and motor delay, seizures, macrocephaly, and variable ocular abnormalities. HITS-CLIP revealed that Csde1-binding targets are enriched in autism-associated gene sets, especially FMRP targets, and in neuronal development and synaptic plasticity–related pathways. Csde1 knockdown in primary mouse cortical neurons leads to an overgrowth of the neurites and abnormal dendritic spine morphology/synapse formation and impaired synaptic transmission, whereas mutant and knockdown experiments in 〈i〉Drosophila〈/i〉 result in defects in synapse growth and synaptic transmission. Our study defines a new autism-related syndrome and highlights the functional role of CSDE1 in synapse development and synaptic transmission.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Mechanism of Vps4 hexamer function revealed by cryo-EM (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-04-15
    Description: Vps4 is a member of AAA + ATPase (adenosine triphosphatase associated with diverse cellular activities) that operates as an oligomer to disassemble ESCRT-III (endosomal sorting complex required for transport III) filaments, thereby catalyzing the final step in multiple ESCRT-dependent membrane remodeling events. We used electron cryo-microscopy to visualize oligomers of a hydrolysis-deficient Vps4 (vacuolar protein sorting-associated protein 4) mutant in the presence of adenosine 5'-triphosphate (ATP). We show that Vps4 subunits assemble into an asymmetric hexameric ring following an approximate helical path that sequentially stacks substrate-binding loops along the central pore. The hexamer is observed to adopt an open or closed ring configuration facilitated by major conformational changes in a single subunit. The structural transition of the mobile Vps4 subunit results in the repositioning of its substrate-binding loop from the top to the bottom of the central pore, with an associated translation of 33 Å. These structures, along with mutant-doping experiments and functional assays, provide evidence for a sequential and processive ATP hydrolysis mechanism by which Vps4 hexamers disassemble ESCRT-III filaments.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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