Horizontal circulation and jumps in Hamiltonian wave models

We are interested in the numerical modeling of wave-current interactions around surf zones at beaches. Any model that aims to predict the onset of wave breaking at the breaker line needs to capture both the nonlinearity of the wave and its dispersion. We have therefore formulated the Hamiltonian dynamics of a new water wave model, incorporating both the shallow water and pure potential flow water wave models as limiting systems. It is based on a Hamiltonian reformulation of the variational principle derived by Cotter and Bokhove (2010) by using more convenient variables. Our new model has a three-dimensional velocity field consisting of the full three-dimensional potential velocity field plus extra horizontal velocity components. This implies that only the vertical vorticity component is nonzero. Boussinesq-type simplifications of the vertical flow profile follow directly from the new Hamiltonian formulation, such as extensions of variational Boussinesq models and Green-Naghdi equations. Since the full water wave dispersion is retained in the new model, waves can break. We therefore explore a variational approach to derive jump conditions for the new model and its Boussinesq simplifications

The StarScan plate measuring machine: overview and calibrations

The StarScan machine at the U.S. Naval Observatory (USNO) completed measuring photographic astrograph plates to allow determination of proper motions for the USNO CCD Astrograph Catalog (UCAC) program. All applicable 1940 AGK2 plates, about 2200 Hamburg Zone Astrograph plates, 900 Black Birch (USNO Twin Astrograph) plates, and 300 Lick Astrograph plates have been measured. StarScan comprises of a CCD camera, telecentric lens, air-bearing granite table, stepper motor screws, and Heidenhain scales to operate in a step-stare mode. The repeatability of StarScan measures is about 0.2 micrometer. The CCD mapping as well as the global table coordinate system has been calibrated using a special dot calibration plate and the overall accuracy of StarScan x,y data is derived to be 0.5 micrometer. Application to real photographic plate data shows that position information of at least 0.65 micrometer accuracy can be extracted from course grain 103a-type emulsion astrometric plates. Transformations between "direct" and "reverse" measures of fine grain emulsion plate measures are obtained on the 0.3 micrometer level per well exposed stellar image and coordinate, which is at the limit of the StarScan machine.Comment: 24 pages, 8 figures, accepted for PAS

RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation biomarkers might improve lymph node metastases detection. To identify epigenetically regulated genes associated with lymph node metastases, genome-wide methylation analysis was performed on 6 OOSCC with (pN+) and 6 OOSCC without (pN0) lymph node metastases and combined with a gene expression signature predictive for pN+ status in OOSCC. Selected genes were validated using an independent OOSCC cohort by immunohistochemistry and pyrosequencing, and on data retrieved from The Cancer Genome Atlas. A two-step statistical selection of differentially methylated sequences revealed 14 genes with increased methylation status and mRNA downregulation in pN+ OOSCC. RAB25, a known tumor suppressor gene, was the highest-ranking gene in the discovery set. In the validation sets, both RAB25 mRNA (P = 0.015) and protein levels (P = 0.012) were lower in pN+ OOSCC. RAB25 mRNA levels were negatively correlated with RAB25 methylation levels (P < 0.001) but RAB25 protein expression was not. Our data revealed that promoter methylation is a mechanism resulting in downregulation of RAB25 expression in pN+ OOSCC and decreased expression is associated with lymph node metastasis. Detection of RAB25 methylation might contribute to lymph node metastasis diagnosis and serve as a potential new therapeutic target in OOSCC

Relation of impaired fasting and postload glucose with incident type 2 diabetes in a Dutch population - The Hoorn study

Item does not contain fulltextCONTEXT: Persons with impaired glucose tolerance (IGT) are known to have an elevated risk of developing diabetes mellitus. Less is known about diabetes risk among persons with impaired fasting glucose (IFG) or with normal glucose levels. OBJECTIVE: To determine the incidence of diabetes in relation to baseline fasting and postload glucose levels and other risk factors. DESIGN, SETTING, AND PARTICIPANTS: Population-based cohort study conducted from October 1989 to February 1992 among 1342 nondiabetic white residents of Hoorn, the Netherlands, aged 50 to 75 years at baseline, in whom fasting plasma glucose (FPG) levels and glucose levels 2 hours after a 75-g oral glucose tolerance test were measured at baseline and at follow-up in 1996-1998. MAIN OUTCOME MEASURES: Cumulative incidence of diabetes, defined according to the diagnostic criteria of the World Health Organization (WHO-1985 and WHO-1999) and the American Diabetes Association (ADA-1997), during a mean follow-up of 6.4 years, compared among participants with IFG, IGT, and normal glucose levels at baseline. RESULTS: The cumulative incidence of diabetes was 6.1%, 8.3%, and 9.9% according to the WHO-1985, ADA, and WHO-1999 criteria, respectively. The cumulative incidence of diabetes (WHO-1999 criteria) for participants with both IFG and IGT was 64.5% compared with 4.5% for those with normal glucose levels at baseline. The odds ratios for diabetes (WHO-1999 criteria), adjusted for age, sex, and follow-up duration, were 10.0 (95% confidence interval [CI], 6.1-16.5), 10.9 (95% CI, 6.0-19.9), and 39.5 (95% CI, 17.0-92.1), respectively, for those having isolated IFG, isolated IGT, and both IFG and IGT. In addition to FPG and 2-hour postload glucose levels (P<.001 for both), the waist-hip ratio also was an important risk factor for developing diabetes (P =.002). CONCLUSION: In this study, the cumulative incidence of diabetes was strongly related to both IFG and IGT at baseline and, in particular, to the combined presence of IFG and IGT

Strain Distribution During Growth of Ge/Si(001) and the Effect of Surfactant Layers

Grazing incidence X-ray diffraction has been employed to determine directly the distribution of strain in the plane of the interface during deposition of Ge onto Si(001). The corresponding strain distribution has also been deduced for a relaxed island whose atomic structure has been determined by molecular dynamics. The results illustrate the central role of elastic deformation of islands in the initial stage of strain relief. The results are also compared with those for growth with a Sb surfactant layer which suppresses island formation. An investigation of surfactant-like behaviour is also presented for homoepitaxial growth of Ag on Ag(111), where sub-monolayer coverages of Sb promote a layer-by-layer growth mode over a wide temperature range

Dissociative recombination and electron-impact de-excitation in CH photon emission under ITER divertor-relevant plasma conditions

For understanding carbon erosion and redeposition in nuclear fusion devices, it is important to understand the transport and chemical break-up of hydrocarbon molecules in edge plasmas, often diagnosed by emission of the CH A^2\Delta - X^2\Pi Ger\"o band around 430 nm. The CH A-level can be excited either by electron-impact or by dissociative recombination (D.R.) of hydrocarbon ions. These processes were included in the 3D Monte Carlo impurity transport code ERO. A series of methane injection experiments was performed in the high-density, low-temperature linear plasma generator Pilot-PSI, and simulated emission intensity profiles were benchmarked against these experiments. It was confirmed that excitation by D.R. dominates at T_e < 1.5 eV. The results indicate that the fraction of D.R. events that lead to a CH radical in the A-level and consequent photon emission is at least 10%. Additionally, quenching of the excited CH radicals by electron impact de-excitation was included in the modeling. This quenching is shown to be significant: depending on the electron density, it reduces the effective CH emission by a factor of 1.4 at n_e=1.3*10^20 m^-3, to 2.8 at n_e=9.3*10^20 m^-3. Its inclusion significantly improved agreement between experiment and modeling

Nothing moves a surface: vacancy mediated surface diffusion

We report scanning tunneling microscopy observations, which imply that all atoms in a close-packed copper surface move frequently, even at room temperature. Using a low density of embedded indium `tracer' atoms, we visualize the diffusive motion of surface atoms. Surprisingly, the indium atoms seem to make concerted, long jumps. Responsible for this motion is an ultra-low density of surface vacancies, diffusing rapidly within the surface. This interpretation is supported by a detailed analysis of the displacement distribution of the indium atoms, which reveals a shape characteristic for the vacancy mediated diffusion mechanism that we propose.Comment: 4 pages; for associated movie, see http://www-lion.leidenuniv.nl/sections/cm/groups/interface/projects/therm