A Comparison of Two Shallow Water Models with Non-Conforming Adaptive Grids: classical tests

In an effort to study the applicability of adaptive mesh refinement (AMR) techniques to atmospheric models an interpolation-based spectral element shallow water model on a cubed-sphere grid is compared to a block-structured finite volume method in latitude-longitude geometry. Both models utilize a non-conforming adaptation approach which doubles the resolution at fine-coarse mesh interfaces. The underlying AMR libraries are quad-tree based and ensure that neighboring regions can only differ by one refinement level. The models are compared via selected test cases from a standard test suite for the shallow water equations. They include the advection of a cosine bell, a steady-state geostrophic flow, a flow over an idealized mountain and a Rossby-Haurwitz wave. Both static and dynamics adaptations are evaluated which reveal the strengths and weaknesses of the AMR techniques. Overall, the AMR simulations show that both models successfully place static and dynamic adaptations in local regions without requiring a fine grid in the global domain. The adaptive grids reliably track features of interests without visible distortions or noise at mesh interfaces. Simple threshold adaptation criteria for the geopotential height and the relative vorticity are assessed.Comment: 25 pages, 11 figures, preprin

Optimization of the design of OMNIS, the observatory of multiflavor neutrinos from supernovae

A Monte Carlo code has been developed to simulate the operation of the planned detectors in OMNIS, a supernova neutrino observatory. OMNIS will detect neutrinos originating from a core collapse supernova by the detection of spalled neutrons from Pb- or Fe-nuclei. This might be accomplished using Gd-loaded liquid scintillator. Results for the optimum configuration for such modules with respect to both neutron detection efficiency and cost efficiency are presented. Careful consideration has been given to the expected levels of radioactive backgrounds and their effects. The results show that the amount of data to be processed by a software trigger can be reduced to the <10kHz region and a neutron, once produced in the detector, can be detected and identified with an efficiency of >30%.Comment: Elsevier preprint; 29 pages, 23 figure

Agreed Definitions and a Shared Vision for New Standards in Stroke Recovery Research: The Stroke Recovery and Rehabilitation Roundtable Taskforce

The first Stroke Recovery and Rehabilitation Roundtable established a game changing set of new standards for stroke recovery research. Common language and definitions were required to develop an agreed framework spanning the four working groups: translation of basic science, biomarkers of stroke recovery, measurement in clinical trials and intervention development and reporting. This paper outlines the working definitions established by our group and an agreed vision for accelerating progress in stroke recovery research

Dependence of magnetic field generation by thermal convection on the rotation rate: a case study

Dependence of magnetic field generation on the rotation rate is explored by direct numerical simulation of magnetohydrodynamic convective attractors in a plane layer of conducting fluid with square periodicity cells for the Taylor number varied from zero to 2000, for which the convective fluid motion halts (other parameters of the system are fixed). We observe 5 types of hydrodynamic (amagnetic) attractors: two families of two-dimensional (i.e. depending on two spatial variables) rolls parallel to sides of periodicity boxes of different widths and parallel to the diagonal, travelling waves and three-dimensional "wavy" rolls. All types of attractors, except for one family of rolls, are capable of kinematic magnetic field generation. We have found 21 distinct nonlinear convective MHD attractors (13 steady states and 8 periodic regimes) and identified bifurcations in which they emerge. In addition, we have observed a family of periodic, two-frequency quasiperiodic and chaotic regimes, as well as an incomplete Feigenbaum period doubling sequence of bifurcations of a torus followed by a chaotic regime and subsequently by a torus with 1/3 of the cascade frequency. The system is highly symmetric. We have found two novel global bifurcations reminiscent of the SNIC bifurcation, which are only possible in the presence of symmetries. The universally accepted paradigm, whereby an increase of the rotation rate below a certain level is beneficial for magnetic field generation, while a further increase inhibits it (and halts the motion of fluid on continuing the increase) remains unaltered, but we demonstrate that this "large-scale" picture lacks many significant details.Comment: 39 pp., 22 figures (some are low quality), 5 tables. Accepted in Physica

Making optical atomic clocks more stable with 10−1610^{-16} level laser stabilization

The superb precision of an atomic clock is derived from its stability. Atomic clocks based on optical (rather than microwave) frequencies are attractive because of their potential for high stability, which scales with operational frequency. Nevertheless, optical clocks have not yet realized this vast potential, due in large part to limitations of the laser used to excite the atomic resonance. To address this problem, we demonstrate a cavity-stabilized laser system with a reduced thermal noise floor, exhibiting a fractional frequency instability of $2 \times 10^{-16}$. We use this laser as a stable optical source in a Yb optical lattice clock to resolve an ultranarrow 1 Hz transition linewidth. With the stable laser source and the signal to noise ratio (S/N) afforded by the Yb optical clock, we dramatically reduce key stability limitations of the clock, and make measurements consistent with a clock instability of $5 \times 10^{-16} / \sqrt{\tau}$

Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1

<div><h3>Background</h3><p>The <em>Salmonella</em> genomic island 1 (SGI1) is a 42.4 kb integrative mobilizable element containing several antibiotic resistance determinants embedded in a complex integron segment In104. The numerous SGI1 variants identified so far, differ mainly in this segment and the explanations of their emergence were mostly based on comparative structure analyses. Here we provide experimental studies on the stability, entrapment and variant formation of this peculiar gene cluster originally found in <em>S</em>. Typhimurium.</p> <h3>Methodology/Principal Findings</h3><p>Segregation and conjugation tests and various molecular techniques were used to detect the emerging SGI1 variants in <em>Salmonella</em> populations of 17 <em>Salmonella enterica</em> serovar Typhimurium DT104 isolates from Hungary. The SGI1s in these isolates proved to be fully competent in excision, conjugal transfer by the IncA/C helper plasmid R55, and integration into the <em>E. coli</em> chromosome. A trap vector has been constructed and successfully applied to capture the island on a plasmid. Monitoring of segregation of SGI1 indicated high stability of the island. SGI1-free segregants did not accumulate during long-term propagation, but several SGI1 variants could be obtained. Most of them appeared to be identical to SGI1-B and SGI1-C, but two new variants caused by deletions via a short-homology-dependent recombination process have also been detected. We have also noticed that the presence of the conjugation helper plasmid increased the formation of these deletion variants considerably.</p> <h3>Conclusions/Significance</h3><p>Despite that excision of SGI1 from the chromosome was proven in SGI1⁺<em>Salmonella</em> populations, its complete loss could not be observed. On the other hand, we demonstrated that several variants, among them two newly identified ones, arose with detectable frequencies in these populations in a short timescale and their formation was promoted by the helper plasmid. This reflects that IncA/C helper plasmids are not only involved in the horizontal spreading of SGI1, but may also contribute to its evolution.</p> </div

Cancer incidence among capacitor manufacturing workers exposed to polychlorinated biphenyls

We evaluated cancer incidence in a cohort of polychlorinated biphenyl (PCB) exposed workers. Incident cancers, identified using state registries, were compared to those in a national population using standardized incidence ratios. Trends in prostate cancer incidence with cumulative PCB exposure were evaluated using standardized rate ratios and Cox regression models. For selected sites, cumulative PCB exposure was compared between aggressive (fatal/distant stage) and localized/regional cancers. We identified 3,371 invasive first primary cancer diagnoses among 21,317 eligible workers through 2007. Overall relative incidence was reduced. Elevations were only observed for respiratory cancers and among women, urinary organ cancers. Among men, prostate cancer incidence was reduced and not associated with cumulative PCB exposure although median exposures were significantly higher for aggressive compared to localized/regional prostate cancers. Previously observed associations between cumulative PCB exposure and prostate cancer mortality were not confirmed in this analysis; prostate cancer stage at diagnosis may explain the discrepancy. Am. J. Ind. Med. 60:198-207, 2017. Published 2016. This article is a U.S. Government work and is in the public domain in the USA

Benign breast disease, recent alcohol consumption, and risk of breast cancer: a nested case–control study

INTRODUCTION: Alcohol consumption is a well-established risk factor for breast cancer. Some studies have suggested that the risk of breast cancer associated with alcohol consumption is greater for women with a history of benign breast disease (BBD). We hypothesized that among women with biopsy-confirmed BBD, recent alcohol consumption would increase the risk of breast cancer in women with proliferative breast disease to a greater extent than in women with nonproliferative breast disease. METHODS: We conducted a nested case–control study in the Nurses' Health Study I and II. The cases (n = 282) were women diagnosed with incident breast cancer, with a prior biopsy-confirmed breast disease. The controls (n = 1,223) were participants with a previous BBD biopsy, but without a diagnosis of breast cancer. Pathologists reviewed benign breast biopsy slides in a blinded fashion and classified the BBD as nonproliferative, proliferative without atypia, or atypical hyperplasia, according to standard criteria. RESULTS: Women with nonproliferative breast disease consuming ≥ 15 g of alcohol per day had a nonsignificant 67% increased risk of breast cancer (odds ratio = 1.67; 95% confidence interval 0.65 to 4.34) compared with nondrinkers. There was no evidence that recent alcohol consumption increased the risk of breast cancer to a greater extent in women with proliferative BBD than among women with nonproliferative BBD (P for interactio n = 0.20). CONCLUSION: Contrary to our a priori hypothesis, there was no evidence that recent alcohol consumption increased the risk of breast cancer to a greater extent among women with proliferative BBD than among women with nonproliferative BBD

Cardiosphere-derived cells suppress allogeneic lymphocytes by production of PGE2 acting via the EP4 receptor

derived cells (CDCs) are a cardiac progenitor cell population, which have been shown to possess cardiac regenerative properties and can improve heart function in a variety of cardiac diseases. Studies in large animal models have predominantly focussed on using autologous cells for safety, however allogeneic cell banks would allow for a practical, cost-effective and efficient use in a clinical setting. The aim of this work was to determine the immunomodulatory status of these cells using CDCs and lymphocytes from 5 dogs. CDCs expressed MHC I but not MHC II molecules and in mixed lymphocyte reactions demonstrated a lack of lymphocyte proliferation in response to MHC-mismatched CDCs. Furthermore, MHC-mismatched CDCs suppressed lymphocyte proliferation and activation in response to Concanavalin A. Transwell experiments demonstrated that this was predominantly due to direct cell-cell contact in addition to soluble mediators whereby CDCs produced high levels of PGE2 under inflammatory conditions. This led to down-regulation of CD25 expression on lymphocytes via the EP4 receptor. Blocking prostaglandin synthesis restored both, proliferation and activation (measured via CD25 expression) of stimulated lymphocytes. We demonstrated for the first time in a large animal model that CDCs inhibit proliferation in allo-reactive lymphocytes and have potent immunosuppressive activity mediated via PGE2

Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components