ITG sideband coupling models for zonal flows

Four-wave interaction model between ITG mode and zonal flow was derived using fluid equations. In this model, the zonal flow is excited non-linearly by ITG turbulence via Reynolds stress. Numerical simulations show that the system allows for a small range above the ITG threshold where the zonal flow can stabilize an unstable ITG mode, effectively increasing eta(i) threshold, an effect which has been called the Dimits shift. However, the shift is smaller than in known cases such that in the Cyclone base

Laparoendoscopic single-site surgery adrenalectomy : own experience and matched case-control study with standard laparoscopic adrenalectomy

INTRODUCTION: At our institution, laparoendoscopic single-site surgery (LESS) has been established as a technique for laparoscopic nephrectomy since 2011, and since 2012 in selected cases for adrenalectomy (AE) as well. AIM: To compare LESS AE with standard laparoscopic AE (SLAE). MATERIAL AND METHODS: Between 3/2012 and 7/2014, 35 adrenalectomies were performed. In 18 (51.4%), a LESS approach was chosen. Indications were strictly non-complicated cases (body mass index (BMI) < 34 kg/m(2), tumour ≤ 7 cm, non-malignant aetiology, no previous surgery). All LESS procedures were done by one surgeon. Standard equipment was a 10 mm rigid 0° camera, Triport+, one pre-bent grasper, and a sealing instrument. The approach was pararectal in all cases except one (transumbilical in a slim man). Three patients with LESS were excluded (2 partial AEs only, one adrenal cancer converted to SLAE and then to open surgery). These 15 LESS AE procedures were compared to 15 SLAEs with similar characteristics chosen among 54 SLAEs performed in the period 1/2008–2/2012. RESULTS: In 8 cases (53.3%) of LESS AE, a 3 mm port was added to elevate the liver/spleen. Mean parameters of LESS AE vs. SLAE (Wilcoxon test): maximal tumour diameter 43.7 mm vs. 36.1 mm (p = 0.28), time of surgery 63.3 min vs. 55.3 min (p = 0.22), blood loss 38.0 ml vs. 38.0 ml (p = 0.38), BMI 26.9 kg/m(2) vs. 28.5 kg/m(2) (p = 0.13), discharge from hospital 5.4 days vs. 3.9 days (p = 0.038). There were no complications in either group. CONCLUSIONS: The LESS AE is feasible in selected cases, especially small left-sided tumours in thin patients with no history of previous abdominal operations, but requires an additional port in half of the cases

Identification of a Proliferation Gene Cluster Associated with HPV E6/E7 Expression Level and Viral DNA Load in Invasive Cervical Carcinoma

Specific HPV DNA sequences are associated with more than 90% of invasive carcinomas of the uterine cervix. Viral E6 and E7 oncogenes are key mediators in cell transformation by disrupting TP53 and RB pathways. To investigate molecular mechanisms involved in the progression of invasive cervical carcinoma, we performed a gene expression study on cases selected according to viral and clinical parameters. Using Coupled Two-Way Clustering and Sorting Points Into Neighbourhoods methods, we identified a Cervical Cancer Proliferation Cluster composed of 163 highly correlated transcripts, many of which corresponded to E2F pathway genes controlling cell proliferation, whereas no primary TP53 targets were present in this cluster. The average expression level of the genes of this cluster was higher in tumours with an early relapse than in tumours with a favourable course (P=0.026). Moreover, we found that E6/E7 mRNA expression level was positively correlated with the expression level of the cluster genes and with viral DNA load. These findings suggest that HPV E6/E7 expression level plays a key role in the progression of invasive carcinoma of the uterine cervix via the deregulation of cellular genes controlling tumour cell proliferation. HPV expression level may thus correspond to a biological marker useful for prognosis assessment and specific therapy of the disease

Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN

In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL

Tree-code based improvement of computational performance of the x-ray–matter-interaction simulation tool XMDYN

In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL

Kinetic Boltzmann approach adapted for modeling highly ionized matter created by x-ray irradiation of a solid

We report on the kinetic Boltzmann approach adapted for simulations of highly ionized matter created from a solid by its x-ray irradiation. X rays can excite inner-shell electrons, which leads to the creation of deeply lying core holes. Their relaxation, especially in heavier elements, can take complicated paths, leading to a large number of active configurations. Their number can be so large that solving the set of respective evolution equations becomes computationally inefficient and another modeling approach should be used instead. To circumvent this complexity, the commonly used continuum models employ a superconfiguration scheme. Here, we propose an alternative approach which still uses “true” atomic configurations but limits their number by restricting the sample relaxation to the predominant relaxation paths. We test its reliability, performing respective calculations for a bulk material consisting of light atoms and comparing the results with a full calculation including all relaxation paths. Prospective application for heavy elements is discussed

Tracing X-ray-induced formation of warm dense gold with Boltzmann kinetic equations

In this paper, we report on the Boltzmann kinetic equation approach adapted for simulations of warm dense matter created by irradiation of bulk gold with intense ultrashort X-ray pulses. X-rays can excite inner-shell electrons, which triggers creation of deep-lying core holes. Their relaxation, especially in heavier elements such as gold (atomic number Z=79) takes complicated pathways, involving collisional processes, and leading through a large number of active configurations. This number can be so high that solving a set of evolution equations for each configuration becomes computationally inefficient, and another modeling approach should be used instead. Here, we use the earlier introduced ’predominant excitation and relaxation path’ approach. It still uses true atomic configurations but limits their number by restricting material relaxation to a selected set of predominant pathways for material excitation and relaxation. With that, we obtain time-resolved predictions for excitation and relaxation in X-ray irradiated bulk of gold, including the respective change of gold optical properties. We compare the predictions with the available data from high-energy-density experiments. Their good agreement indicates ability of the Boltzmann kinetic equation approach to describe warm dense matter created from high-Z materials after their irradiation with X rays, which can be validated in future experiments