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

Initial Results from an In-Vacuum Undulator in the NSLS X-ray Ring

A short period, in vacuum undulator for the NSLS X-Ray Ring has been developed and has achieved its project design goals during commissioning studies. The device is called IVUN (In-Vacuum UNdulator) and employs magnet arrays (31 periods, with an 11 mm period) developed at SPring-8, while the requisite vacuum chamber and mechanical systems were developed at the NSLS. At a magnet gap of 3.3 mm, IVUN produces 4.6 keV radiation in the fundamental, with useful photon fluxes in both the 2nd and 3rd harmonics. The magnet gap is adjustable between 2 mm and 10 mm. A brief overview of IVUN is presented, together with initial commissioning results: the dependence of electron beam lifetime and bremsstrahlung on magnet gap, and the output radiation spectrum

Multiphoton excitation and photodynamic activity of macromolecular derivatizated mTHPC

Multiphoton excitation of photosensitizers in photodynamic therapy constitutes a promising approach, because of the increasing tissue penetration for longer wavelength of illumination. In this contribution the photodynamic activity of polyethylene glycol macromolecular derivatized mTHPC upon two-photon excitation is established. To test the photo- activity of the photosensitizer, human colon carcinoma cells, HCT-116, were incubated with 2 {mu} g/ml of mTHPC- CMPEG4 in the nutrition medium. Subsequent pulsed laser irradiation at 784 nm focused down on growing cell monolayers restricts cell vitality clearly within 24 hours after irradiation. To investigate whether an anoxic or euoxic energy transfer mechanism is involved, a uric acid assay was performed to test for the generation of singlet oxygen. Upon single-photon excitation mTHPC-CMPEG4 in TriPEG decomposed uric acid via the generation of singlet oxygen. Using femtosecond pulsed laser irradiation no decomposition of the uric acid was found, implying an anoxic energy transfer mechanism after tow-photon excitation. However, at present, we cannot exclude local hyperthermic effects in the cells containing the photosensitizer to contribute to the photodynamic activity upon two-photon excitation

Collaborative work during interventional radiological procedures based on a multicast satellite-terrestrial network

Collaboration is a key requirement in several contemporary interventional radiology procedures (IRPs). This work proposes a multicast hybrid satellite system capable of supporting advanced IRP collaboration, and evaluates its feasibility and applicability. Following a detailed IRP requirements study, we have developed a system which supports IRP collaboration through the employment of a hybrid satellite-terrestrial network, a prototype multicast version of wavelet based interactive communication system (WinVicos) application, and a partition aggregation and conditional coding (PACC) wavelet codec. A semistructured questionnaire was also used to receive evaluative feedback from collaborating participants. The departments of interventional radiology of University Hospital of Patras, Greece and of Charite Hospital of Berlin, Germany have been connected on the system. Eight interventional radiologists and a vascular surgeon participated periodically in three satellite-terrestrial "fully collaborative" IRPs (average time 90 min) of high complexity and in four terrestrial educational sessions with great success, evidenced by considerable improving the IRP outcomes (clinical and educational). In case of high complexity, where the simultaneous presence of remote interventional expert and/or surgeon is required, advanced collaboration among staff of geographically dispersed international centers is feasible via integration of existing networking and other technologies