One-to-one direct modeling of experiments and astrophysical scenarios: pushing the envelope on kinetic plasma simulations

There are many astrophysical and laboratory scenarios where kinetic effects play an important role. These range from astrophysical shocks and plasma shell collisions, to high intensity laser-plasma interactions, with applications to fast ignition and particle acceleration. Further understanding of these scenarios requires detailed numerical modelling, but fully relativistic kinetic codes are computationally intensive, and the goal of one-to-one direct modelling of such scenarios and direct comparison with experimental results is still difficult to achieve. In this paper we discuss the issues involved in performing kinetic plasma simulations of experiments and astrophysical scenarios, focusing on what needs to be achieved for one-to-one direct modeling, and the computational requirements involved. We focus on code efficiency and new algorithms, specifically on parallel scalability issues, namely on dynamic load balancing, and on high-order interpolation and boosted frame simulations to optimize simulation performance. We also discuss the new visualization and data mining tools required for these numerical experiments and recent simulation work illustrating these techniques is also presented.Comment: 10 pages, 5 figure

Evaluation of random forest and ensemble methods at predicting complications following cardiac surgery

Cardiac patients undergoing surgery face increased risk of postoperative complications, due to a combination of factors, including higher risk surgery, their age at time of surgery and the presence of co-morbid conditions. They will therefore require high levels of care and clinical resources throughout their perioperative journey (i.e. before, during and after surgery). Although surgical mortality rates in the UK have remained low, postoperative complications on the other hand are common and can have a significant impact on patients’ quality of life, increase hospital length of stay and healthcare costs. In this study we used and compared several machine learning methods – random forest, AdaBoost, gradient boosting model and stacking – to predict severe postoperative complications after cardiac surgery based on preoperative variables obtained from a surgical database of a large acute care hospital in Scotland. Our results show that AdaBoost has the best overall performance (AUC = 0.731), and also outperforms EuroSCORE and EuroSCORE II in other studies predicting postoperative complications. Random forest (Sensitivity = 0.852, negative predictive value = 0.923), however, and gradient boosting model (Sensitivity = 0.875 and negative predictive value = 0.920) have the best performance at predicting severe postoperative complications based on sensitivity and negative predictive value

Killing Hypoxic Cell Populations in a 3D Tumor Model with EtNBS-PDT

An outstanding problem in cancer therapy is the battle against treatment-resistant disease. This is especially true for ovarian cancer, where the majority of patients eventually succumb to treatment-resistant metastatic carcinomatosis. Limited perfusion and diffusion, acidosis, and hypoxia play major roles in the development of resistance to the majority of front-line therapeutic regimens. To overcome these limitations and eliminate otherwise spared cancer cells, we utilized the cationic photosensitizer EtNBS to treat hypoxic regions deep inside in vitro 3D models of metastatic ovarian cancer. Unlike standard regimens that fail to penetrate beyond ∼150 µm, EtNBS was found to not only penetrate throughout the entirety of large (>200 µm) avascular nodules, but also concentrate into the nodules' acidic and hypoxic cores. Photodynamic therapy with EtNBS was observed to be highly effective against these hypoxic regions even at low therapeutic doses, and was capable of destroying both normoxic and hypoxic regions at higher treatment levels. Imaging studies utilizing multiphoton and confocal microscopies, as well as time-lapse optical coherence tomography (TL-OCT), revealed an inside-out pattern of cell death, with apoptosis being the primary mechanism of cell killing. Critically, EtNBS-based photodynamic therapy was found to be effective against the model tumor nodules even under severe hypoxia. The inherent ability of EtNBS photodynamic therapy to impart cytotoxicity across a wide range of tumoral oxygenation levels indicates its potential to eliminate treatment-resistant cell populations

Metastability in pressure-induced structural transformations of CdSe/ZnS core/shell nanocrystals

The kinetics and thermodynamics of structural transformations under pressure depend strongly on particle size due to the influence of surface free energy. By suitable design of surface structure, composition, and passivation it is possible, in principle, to prepare nanocrystals in structures inaccessible to bulk materials. However, few realizations of such extreme size-dependent behavior exist. Here we show with molecular dynamics computer simulation that in a model of CdSe/ZnS core/shell nanocrystals the core high pressure structure can be made metastable under ambient conditions by tuning the thickness of the shell. In nanocrystals with thick shells, we furthermore observe a wurtzite to NiAs transformation, which does not occur in the pure bulk materials. These phenomena are linked to a fundamental change in the atomistic transformation mechanism from heterogenous nucleation at the surface to homogenous nucleation in the crystal core. Our results suggest a new route towards expanding the range of available nanoscale materials

Conclusions and recommendations of a who expert consultation meeting on iron supplementation for infants and young children in malaria endemic areas [Conclusions et recommandations à l\u27issue de la consultation de l\u27oms sur la lutte contre la carence martiale chez le nourrisson et le jeune enfant dans les pays d\u27endémie palustre]

This article presents the results of an expert consultation meeting aimed at evaluating the safety and public health implications of administering supplemental iron to infants and young children in malaria-endemic areas. Participants at this meeting that took place in Lyon, France on June 12-14, 2006 reached consensus on several important issues related to iron supplementation for infants and young children in malaria-endemic areas. The conclusions in this report apply specifically to regions where malaria is endemic

Engaging diverse communities participating in clinical trials: case examples from across Africa

<p>Abstract</p> <p>Background</p> <p>In the advent of increasing international collaborative research involving participants drawn from populations with diverse cultural backgrounds, community engagement becomes very critical for the smooth conduction of the research. The African Malaria Network Trust (AMANET) is a pan-African non-governmental organization that sponsors and technically supports malaria vaccine trials in various African countries.</p> <p>Case description</p> <p>AMANET sponsored phase Ib or IIb clinical trials of several malaria vaccine candidates in various Africa countries. In Burkina Faso, Mali and Tanzania trials of the merozoite surface protein 3 -- in its Long Synthetic Peptide configuration (MSP3 LSP) -- were conducted. In Mali, the apical membrane antigen 1 (AMA1) was tested, while a hybrid of glutamate rich protein (GLURP) and MSP3 (GMZ2) was tested in Gabon. AMANET recognizes the importance of engaging with the communities from which trial participants are drawn, hence community engagement was given priority in all project activities conducted in the various countries.</p> <p>Discussion and evaluation</p> <p>Existing local social systems were used to engage the communities from which clinical trial participants were drawn. This article focuses on community engagement activities employed at various AMANET-supported clinical trial sites in different countries, highlighting subtle differences in the approaches used. The paper also gives some general pros and cons of community engagement.</p> <p>Conclusions</p> <p>Community engagement enables two-way sharing of accurate information and ideas between researchers and researched communities, which helps to create an environment conducive to smooth research activities with enhanced sense of research ownership by the communities.</p

Aging Kit Mutant Mice Develop Cardiomyopathy

Both bone marrow (BM) and myocardium contain progenitor cells expressing the c-Kit tyrosine kinase. The aims of this study were to determine the effects of c-Kit mutations on: i. myocardial c-Kit+ cells counts and ii. the stability of left ventricular (LV) contractile function and structure during aging. LV structure and contractile function were evaluated (echocardiography) in two groups of Kit mutant (W/Wv and W41/W42) and in wild type (WT) mice at 4 and 12 months of age and the effects of the mutations on LV mass, vascular density and the numbers of proliferating cells were also determined. In 4 month old Kit mutant and WT mice, LV ejection fractions (EF) and LV fractional shortening rates (FS) were comparable. At 12 months of age EF and FS were significantly decreased and LV mass was significantly increased only in W41/W42 mice. Myocardial vascular densities and c-Kit+ cell numbers were significantly reduced in both mutant groups when compared to WT hearts. Replacement of mutant BM with WT BM at 4 months of age did not prevent these abnormalities in either mutant group although they were somewhat attenuated in the W/Wv group. Notably BM transplantation did not prevent the development of cardiomyopathy in 12 month W41/W42 mice. The data suggest that decreased numbers and functional capacities of c-Kit+ cardiac resident progenitor cells may be the basis of the cardiomyopathy in W41/W42 mice and although defects in mutant BM progenitor cells may prove to be contributory, they are not causal