FESOM-C v.2: coastal dynamics on hybrid unstructured meshes

We describe FESOM-C, the coastal branch of the Finite-volumE Sea ice – Ocean Model (FESOM2), which shares with FESOM2 many numerical aspects, in particular its finite-volume cell-vertex discretization. Its dynamical core differs in the implementation of time stepping, the use of a terrain-following vertical coordinate, and the formulation for hybrid meshes composed of triangles and quads. The first two distinctions were critical for coding FESOM-C as an independent branch. The hybrid mesh capability improves numerical efficiency, since quadrilateral cells have fewer edges than triangular cells. They do not suffer from spurious inertial modes of the triangular cell-vertex discretization and need less dissipation. The hybrid mesh capability allows one to use quasi-quadrilateral unstructured meshes, with triangular cells included only to join quadrilateral patches of different resolution or instead of strongly deformed quadrilateral cells. The description of the model numerical part is complemented by test cases illustrating the model performance.</p

Prediction of outcome in locally advanced breast cancer by post-chemotherapy nodal status and baseline serum tumour markers

In spite of the apparent improvement in outcome in locally advanced breast cancer, the prognosis remains dismal in many patients. The aim of this study was to define prognostic subgroups within this heterogeneous entity. Between 1990 and 1999, 104 consecutive patients with locally advanced breast cancer were treated by a multimodality programme consisting of 4–6 courses of CAF induction chemotherapy followed by surgery, breast-conserving when feasible. In most cases, chemotherapy was then resumed, up to a total of eight courses, followed by locoregional radiation therapy. Patients with hormone receptor-positive tumours received tamoxifen (20 mg day−1) for 5 years. At a median follow-up of 57 months, the 5-year overall survival for the entire group and the disease-free survival for the 94 operated patients were 65% and 53%, respectively. Univariate analysis identified 10 prognostic factors of overall and disease-free survival, of which four retained significance on multivariate analysis: inflammatory breast cancer (P=0.0000, P=0.0004, respectively), baseline tumour markers (P=0.003 for both), post-chemotherapy number of involved nodes (P=0.003; P=0.017) and extracapsular spread (P=0.052; P=0.014). In conclusion, besides inflammatory features, baseline tumour markers and post-chemotherapy nodal status are strong predictors of outcome in locally advanced breast cancer

First Lasing of a High-Gain Harmonic Generation Free-Electron Laser Experiment.

We report on the first lasing of a high-gain harmonic generation (HGHG) free-electron laser (FEL). The experiment was conducted at the Accelerator Test Facility (ATF) at Brookhaven National Laboratory (BNL). This is a BNL experiment in collaboration with the Advanced Photon Source (APS) at Argonne National Laboratory. A preliminary measurement gives a high-gain harmonic generation (HGHG) pulse energy that is 2 x 10{sup 7} times larger than the spontaneous radiation, In a purely self-amplified spontaneous emission (SASE) mode of operation, the signal was measured as 10 times larger than the spontaneous radiation in the same distance ({approximately}2 m) through the same wiggler. This means the HGHG signal is 2 x 10{sup 6} times larger than the SASE signal. To obtain the same saturated output power by the SASE process, the radiator would have to be 3 times longer (6 m)

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

LOW-BARRIER ROTATION-PSEUDOROTATION HAMILTONIAN AND APPLICATION TO THE B STATE OF Na3Na_{3}

$^{1}$N. Ohashi, M. Tsuura and J. T. Hougen, J. Mol, Spectrosc. 173, 79-99 (1995). $^{2}$W. E. Ernst and S. Rakowsky, Can. J. Phys. 72, 1307-1314 (1994).Author Institution: Department of Phjysics, Faculty of Science, Kanazawa University; Molecular Physics Division, National Institute of Standards and Technology; Department of Physics, The Pennsylvania State University; Max-Planck-Institut f\""{u}r Str\""{o}mungsforschung, The Pennsylvania State UniversityA formalism has been developed for treating the rotation-pseudorotation problem in $Na_{3}$ molecules which has many analogies with, but is not identical to, the traditional principal axis formalism for methyl-top internal rotor molecules. The pseudorotational coordinate (angle) $X_{p}$ and $D_{3}h$ group theory are taken from our previously developed high barrier $formalism^{1}$, and lead to a molecular Hamiltonian containing the following terms (up to second order) $$H = FP_{X_{p}}^{2}+\frac{1}{2}V_{3}(1-\cos3x_{p})+BJ^{2}+(C-B)J_{z}^{2}+QP_{X_{p}}J_{z}+f_+J_+^{2}+f_-j_-^{2}$$ The first two terms ($F, V_{3}$) represent the three-indentical-well particle-on-a-ring pseudorotational problem. The next two terms (B,C) represent an oblate symmetric top rotational Hamiltonian (z axis perpendicular to the $Na_{3}$ plane). The fifth term (Q) represents the coriolis interaction between the pseudo-rotational and overall-rotational angular momentum. Up to this point the Hamiltonian can be mapped onto that for methyl-group internal rotation in an oblate symmetric top. The final two terms are peculiar to the present problem. They contain products of the rotational angular momentum ladder operators $J_{\pm} = J_{x}iiJ_{y}$ and coefficients f$_+$, which unlike the coefficients $F, v_{3}$, B, C, Q above cannot be constants, but must be expressed as a Fourier series in the pseudorotation functions $\exp(\pm imx_{p}$), where $m = +1$ mod 3. These final two terms allow for ""rotation"" of the asymmetric rotor A, B, C axes when pseudorotation occurs and each of the Na atoms in turn occupies the apex position in the distorted triangle equilibrium structure. As might be expected, they are responsible for a number of unusual features in the rotational energy level pattern. Various aspects of the energy levels arising from this Hamiltonian when the barrier $\nu_{3}$ = 0 will be discussed, as well as a relatively successful fit of $published^{2}$ and unpublished measurements from earlier B-X pump-probe experiments