Interaction of a Turbulent Wind with Ocean Surface Waves - Numerical Modeling

Wave-modeling can be categorized in terms of different scales and theoretical frameworks. This dissertation focuses on the numerical modeling of wind-wave generation and its effects on wave growth and propagations. As categorized by scales and methodologies, wind-wave modeling in this dissertation covers two main topics: 1) Large-scale modeling: wind-wave development in real seas. As a phase-average model, SWAN is employed to study the wind-wave environment in the Persian Gulf and Qatar. The wind-wave generation is parameterized as source terms in a spectral model. The special wind condition, called shamal, is particularly investigated. An experimental tower is installed around Doha Port, and by using video imagery, the in situ wave features are extracted and compared. 2) Small-scale modeling: de-tailed wave development using CFD (Computational Fluid Dynamics). A curvilinear surface-fitted moving grid model for three-dimensional Navier-Stokes equations is developed and used to simulate linear and non-linear waves with fully nonlinear surface conditions. Also, by simplifying it to a fixed rectilinear grid based on Cartesian formulations, a DNS (Direct Numerical Simulation) model is developed with an air-water fully-coupled domain and improved coupled interface conditions. By using this DNS model, the detail of wind-wave generation is investigated from still water and the applied top shear wind. For the second topic, the CFD problems are solved by an in-house numerical tool, SPX. SPX is a general PDE (Partial Differential Equations) framework, developed by using C++1y (shortened form of C++11/14/17), currently aiming at the structural domain. It is designed by modern software methodologies, such as generic programming, meta-programming and object-oriented programming. In addition, concept-based generic programming, an ongoing advanced software technology, is first introduced into the PDE numerical tool design. By using these modern design methodologies, all significant components used for solving PDE, particularly for fluid and wave problems, are all implemented in SPX. These components include high-performance numerical array, implicit solvers, grids, differential basis and operators, time integrators, and system infrastructures such as serializations and timer. On structured domain, a general PDE can be expressed by the arbitrary combination of any general differential operator and any arithmetic operator, which is the most challenging part of SPX design. This research proposes a general stencil operator design that integrates with the concept-based expression template. It is successfully demonstrated that the proposed design can automatically deduce the resulting stencils to represent the resulting field operator by giving an arbitrary PDE expression at any given grid point. With the deduced stencils, the user-defined PDE expression is therefore, numerically-solvable by using any solver. In consequence, SPX can be easily applied to any user-defined PDE problem on structural grids with arbitrary user-specified numerical components. Its design shows high flexibility and re-usability without sacrificing efficiency. The development of SPX, therefore, justifies the success of C++-Concept applications on the large-scale numerical framework design

MetaSquare: An integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

MOTIVATION: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource. RESULTS: MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods. AVAILABILITY AND IMPLEMENTATION: Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Prevalence of intestinal parasitic infections among school children in capital areas of the Democratic Republic of São Tomé and Príncipe, West Africa

Background: Although the Democratic Republic of Sao Tome and Principe (DRSTP) has undertaken school children-based deworming programs against intestinal parasitic infections (IPIs) using a single dose of mebendazole annually since 2005, it remains unclear as to the outcome to date. The present study intends to  investigate the recent IPIs status among school children living in capital areas of the DRSTP.Methods: A total of 252 school children (121 boys and 131 girls) of grades 4 and 5 from 4 primary schools located in the capital areas participated in the present study and their fresh fecal specimens were examined for the presence of any parasites using the merthiolate- iodine-formaldehyde concentration method as conducted.Results: The overall prevalence of IPIs was 64.7% (163/ 252). No significant gender difference in prevalence between boys (67.8%) and girls (61.8%) was found (p = 0.3). The majority of school children were infected with a single species of parasite (55.8%). Altogether, 12 different intestinal parasite species were identified in DRSTP school children, of which 9 species were pathogenic and the remaining 3 were non-pathogenic.Conclusion: Improving the detection method, sanitation facilities and personal hygiene as well as utilizing combined drugs are all important measures to greatly reduce IPIs in DRSTP school children.Keywords: Democratic Republic of Sao Tome and Principe, school children, intestinal parasitic infection

Gait performance and prefrontal cortex activation during single and dual task walking in older adults with different cognitive levels

BackgroundGrowing evidence shows the cognitive function influences the motor performance. The prefrontal cortex (PFC) as a part of the executive locomotor pathway is also important for cognitive function. This study investigated the differences in motor function and brain activity among older adults with different cognitive levels, and examined the significance of cognition on motor functions.MethodsNormal control (NC), individuals with mild cognitive impairment (MCI) or mild dementia (MD) were enrolled in this study. All participants received a comprehensive assessment including cognitive function, motor function, PFC activity during walking, and fear of fall. The assessment of cognitive function included general cognition, attention, executive function, memory, and visuo-spatial. The assessment of motor function included timed up and go (TUG) test, single walking (SW), and cognitive dual task walking (CDW).ResultsIndividuals with MD had worse SW, CDW and TUG performance as compared to individuals with MCI and NC. These gait and balance performance did not differ significantly between MCI and NC. Motor functions all correlated with general cognition, attention, executive function, memory, and visuo-spatial ability. Attention ability measured by trail making test A (TMT-A) was the best predictor for TUG and gait velocity. There were no significant differences in PFC activity among three groups. Nevertheless, the PFC activated more during CDW as compared with SW in individuals with MCI (p = 0.000), which was not demonstrated in the other two groups.ConclusionMD demonstrated worse motor function as compared to NC and MCI. The greater PFC activity during CDW in MCI may be considered as a compensatory strategy for maintaining the gait performance. Motor function was related to the cognitive function, and the TMT A was the best predictor for the gait related performance in present study among older adults

Crystallinity Improvement of ZnO Thin Film on Different Buffer Layers Grown by MBE

The material and optical properties of ZnO thin film samples grown on different buffer layers on sapphire substrates through a two-step temperature variation growth by molecular beam epitaxy were investigated. The thin buffer layer between the ZnO layer and the sapphire substrate decreased the lattice mismatch to achieve higher quality ZnO thin film growth. A GaN buffer layer slightly increased the quality of the ZnO thin film, but the threading dislocations still stretched along the c-axis of the GaN layer. The use of MgO as the buffer layer decreased the surface roughness of the ZnO thin film by 58.8% due to the suppression of surface cracks through strain transfer of the sample. From deep level emission and rocking curve measurements it was found that the threading dislocations play a more important role than oxygen vacancies for high-quality ZnO thin film growth

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Search for stop and higgsino production using diphoton Higgs boson decays

Results are presented of a search for a "natural" supersymmetry scenario with gauge mediated symmetry breaking. It is assumed that only the supersymmetric partners of the top-quark (stop) and the Higgs boson (higgsino) are accessible. Events are examined in which there are two photons forming a Higgs boson candidate, and at least two b-quark jets. In 19.7 inverse femtobarns of proton-proton collision data at sqrt(s) = 8 TeV, recorded in the CMS experiment, no evidence of a signal is found and lower limits at the 95% confidence level are set, excluding the stop mass below 360 to 410 GeV, depending on the higgsino mass