A GPU Implementation for Two-Dimensional Shallow Water Modeling

In this paper, we present a GPU implementation of a two-dimensional shallow water model. Water simulations are useful for modeling floods, river/reservoir behavior, and dam break scenarios. Our GPU implementation shows vast performance improvements over the original Fortran implementation. By taking advantage of the GPU, researchers and engineers will be able to study water systems more efficiently and in greater detail.Comment: 9 pages, 1 figur

Modeling Jar Test Results Using Gene Expression to Determine the Optimal Alum Dose in Drinking Water Treatment Plants

يعد التخثير من أهم العمليات في محطات تنقية مياه الشرب، ان استخدام مخثر الشبة يؤدي الى زيادة تركيز الألمنيوم المتبقي في المياه، والذي تم ربطه في العديد من الدراسات بمرض الزهايمر. لذلك فإنه من المهم استخدامه في الجرع الأمثل. في هذه الدراسة، تم إجراء أربع مراحل من التجارب لتحديد تأثير مواصفات المياه الخام، مثل: العكارة، pH، القلوية والحرارة على الجرعة الأمثل من مخثر الشبة  [   .14 O] للحصول على علاقة رياضية تمكن من الاستغناء عن الحاجة لتجارب الجرة. تم إجراء التجارب بظروف مختلفة وعلى مدى فصول السنة، وتم تحديد الجرعة الأمثل لكل دورة من التجارب لتشكيل نموذج يعتمد على التعابير الجينية.تم بناء النموذج عن طريق بيانات مواصفات المياه: العكارة، pH، الحرارة والقلوية للتنبؤ بقيمة جرعة الشبة الأمثل اللازمة، النموذج الذي تم الحصول عليه أعطى نتائج جيدة بمعامل ارتباط 0.91   ومربع جذر الأخطاء 1.8.  تمت مقارنة النتائج مع نموذج انحدار خطي والذي لم يكن كافيا لإعطاء نتائج جيدة نظرا لطبيعة العلاقة الغير خطية المعقدة.  سلاسل أخرى من التجارب تم القيام بها لتحديد الجرعة الأمثل اللازمة أثناء حدوث الفيضانات والتي تصل فيها قيم عكارة الى قيم عالية مع دراسة استخدام النشاء كمادة مساعدة للتخثير، تم الحصول على نموذج جيد للتنبؤ، بقيمة معامل 0.92 وجذر مربعات أخطاء   5.1.Coagulation is the most important process in drinking water treatment. Alum coagulant increases the aluminum residuals, which have been linked in many studies to Alzheimer's disease. Therefore, it is very important to use it with the very optimal dose. In this paper, four sets of experiments were done to determine the relationship between raw water characteristics: turbidity, pH, alkalinity, temperature, and optimum doses of alum [   .14 O] to form a mathematical equation that could replace the need for jar test experiments. The experiments were performed under different conditions and under different seasonal circumstances. The optimal dose in every set was determined, and used to build a gene expression model (GEP). The models were constructed using data of the jar test experiments: turbidity, pH, alkalinity, and temperature, to predict the coagulant dose. The best GEP model gave very good results with a correlation coefficient (0.91) and a root mean square error of 1.8. Multi linear regression was used to be compared with the GEP results; it could not give good results due to the complex nonlinear relation of the process. Another round of experiments was done with high initial turbidity like the values that comes to the plant during floods and heavy rain. To give an equation for these extreme values, with studying the use of starch as a coagulant aid, the best GEP gave good results with a correlation coefficient of 0.92 and RMSE 5.

Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics.

Microtubule dynamics and polarity stem from the polymerization of αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones and the Arl2 GTPase regulate α- and β-tubulin assembly into heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like structure for regulating αβ-tubulin. Biochemical assays and electron microscopy structures of multiple intermediates show the sequential binding of αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone, forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits ternary complex dissociation in vitro and causes severe defects in microtubule dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and Arl2 functions as a catalytic chaperone that regulates soluble αβ-tubulin assembly and maintenance to support microtubule dynamics

Isolation and characterization of microsatellite loci from two inbreeding bark beetle species (Coccotrypes)

We developed 14 microsatellite markers in Coccotrypes carpophagus and 14 in C. dactyliperda. These loci will be used for studying genetic structure and the level of inbreeding in populations in the Canary Islands and Madeira. As a result of long-term inbreeding, genetic variability is relatively low in these bark beetle species. We found one to five alleles per locus in 29 C. carpophagus and 41 C. dactyliperda from various localities. Eleven of the markers developed for C. carpophagus amplified in C. dactyliperda and seven of the markers developed for C. dactyliperda amplified in C. carpophagus

Cloned defective interfering influenza virus protects ferrets from pandemic 2009 influenza A virus and allows protective immunity to be established

Influenza A viruses are a major cause of morbidity and mortality in the human population, causing epidemics in the winter, and occasional worldwide pandemics. In addition there are periodic outbreaks in domestic poultry, horses, pigs, dogs, and cats. Infections of domestic birds can be fatal for the birds and their human contacts. Control in man operates through vaccines and antivirals, but both have their limitations. In the search for an alternative treatment we have focussed on defective interfering (DI) influenza A virus. Such a DI virus is superficially indistinguishable from a normal virus but has a large deletion in one of the eight RNAs that make up the viral genome. Antiviral activity resides in the deleted RNA. We have cloned one such highly active DI RNA derived from segment 1 (244 DI virus) and shown earlier that intranasal administration protects mice from lethal disease caused by a number of different influenza A viruses. A more cogent model of human influenza is the ferret. Here we found that intranasal treatment with a single dose of 2 or 0.2 µg 244 RNA delivered as A/PR/8/34 virus particles protected ferrets from disease caused by pandemic virus A/California/04/09 (A/Cal; H1N1). Specifically, 244 DI virus significantly reduced fever, weight loss, respiratory symptoms, and infectious load. 244 DI RNA, the active principle, was amplified in nasal washes following infection with A/Cal, consistent with its amelioration of clinical disease. Animals that were treated with 244 DI RNA cleared infectious and DI viruses without delay. Despite the attenuation of infection and disease by DI virus, ferrets formed high levels of A/Cal-specific serum haemagglutination-inhibiting antibodies and were solidly immune to rechallenge with A/Cal. Together with earlier data from mouse studies, we conclude that 244 DI virus is a highly effective antiviral with activity potentially against all influenza A subtypes

Suprasubduction-zone origin of the podiform chromitites of the Bir Tuluhah ophiolite, Saudi Arabia, during Neoproterozoic assembly of the Arabian Shield

The ultramafic section of a dismembered ophiolite is exposed at Bir Tuluhah, in the north-central part of the Arabian Shield. It is penetratively serpentinized and locally carbonate-altered to talc‑carbonate and quartz‑carbonate rocks (listvenite) along shear zones and fault planes. Despite the high degree of mineral replacement, preserved mesh and bastite textures and fresh relics of primary Cr-spinel and olivine show that the protoliths were mainly harzburgite with minor dunite, with sparse massive chromitite bodies of various forms and sizes. Olivine inclusions in the chromitite lenses have higher forsterite content and NiO concentrations than fresh olivine relics in the host harzburgites and dunites, due to subsolidus re-equilibration. Cr-spinels in the chromitites have higher Cr# (0.74–0.82) than those hosted in dunite (0.72–0.76) or harzburgite (0.55–0.66). The scarce Cr-spinel crystals in harzburgite that have Cr# < 0.6 are interpreted to represent the population least affected by melt-rock interaction. The chromitite bodies are interpreted to have formed just below the contact between the oceanic crust and mantle sections (i.e., the petrologic Moho). The primary olivine (high Fo and Ni content) and Cr-spinel core compositions (high Cr# and low TiO2 content) of the Bir Tuluhah serpentinized peridotite are typical of modern supra-subduction zone (SSZ) fore-arc peridotites and consistent with crystallization from boninitic magma. The multistage petrogenesis leading to the chromitite bodies begins with moderate to high degrees of melt extraction from the protoliths of the serpentinized harzburgites, followed by reaction with melt compositions that evolved from tholeiite to boninite and left dunite residues. The massive Cr-rich chromitites in the Bir Tuluhah ophiolite are most probably the residues of such interaction between depleted harzburgite and ascending melts; mixtures of the reacted melts formed boninites, which became saturated with chrome-rich spinel and crystallized chromite pods before ascending past the Moho. We offer a novel thermodynamic model of this mixing and reaction process that quantifies the yield of Cr-spinel

Petrogenesis of the post-collisional rare-metal-bearing Ad-Dayheen granite intrusion, Central Arabian Shield

At Hadhb't Ad-Dayheen, in the central Arabian Shield, a post-collisional igneous complex called the Ad-Dayheen intrusion is exposed. It was emplaced in the Early Ediacaran (613–625 Ma), during the final tectono-magmatic stage of Arabian Shield development. Despite limited and discontinuous ring-shaped outcrops due to alluvial cover and later faulting, three pulses of intrusion can be recognized in the field: an early pulse of monzogranite; a second pulse of syenogranite and alkali feldspar granite; and a final pulse of alkaline and peralkaline granite, mineralized microgranite, and pegmatite. Samples show distinctively low contents of CaO, MgO, and Sr in contrast to elevated concentrations of alkalis, Rb, Nb, Y, Ta, Hf, Ga, Zr and rare-earth elements (REE); these are common characteristics of post-collisional rare-metal-bearing A-type granites. The suite displays positive Nb–Ta anomalies and pronounced negative Eu anomalies (Eu/Eu* = 0.11–0.35). The alkaline/peralkaline granites and microgranite of the Ad-Dayheen intrusion feature disseminated mineralization, whereas mineralization is localized in the pegmatite. The primary magma feeding the Ad-Dayheen intrusion was mostly generated by partial melting of the juvenile crust of the Arabian Shield, with a minor mantle contribution. We argue that an episode of lithospheric delamination led to crustal uplift, erosional decompression, and generation of mantle melts that supplied heat to drive crustal melting. The anatectic deep crustal melts assimilated a F-bearing component that also added rare metals to the magma. Each pulse can be described by a fractional crystallization model, but the parental liquid of each subsequent pulse was first modified by further addition of fluorine and rare metals and loss of CaO, Sr, Ba, and Eu due to fluorite fractionation. Texture and morphology of the ore minerals indicate that mineralization (U, Th, Zr, Nb, Ta, Y, Hf and REE) took place in two stages: a magmatic stage coinciding with emplacement of the intrusion, followed by a hydrothermal stage. The magmatic process enriched the residual melt in high field strength elements (HFSE) and REE. The later hydrothermal stage further localized these elements and increased their concentrations to economic grades. The pegmatite is highly mineralized and contains high concentrations of U (81–179 μg/g), Th (244–600 μg/g), Zr (2397–14,927 μg/g), Nb (1352–2047 μg/g), Ta (96–156 μg/g), Y (828–2238 μg/g), Hf (131–377 μg/g) and ∑REE (1969–4761 μg/g)