Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5

We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5) and demonstrate that meso-scale molecular dynamics with more than $10^8$ particles is now possible on massively parallel MIMD computers. Typical runs show single particle update-times of $0.15 \mu s$ in 2 dimensions (2D) and approximately $1 \mu s$ in 3 dimensions (3D) on a 1024 node CM-5 without vector units, corresponding to more than 1.8 GFlops overall performance. We also present a scaling equation which agrees well with actually observed timings.Comment: 17 pages, Uuencoded compressed PostScript fil

User interfaces for computational science: a domain specific language for OOMMF embedded in Python

Computer simulations are used widely across the engineering and science disciplines, including in the research and development of magnetic devices using computational micromagnetics. In this work, we identify and review different approaches to configuring simulation runs: (i) the re-compilation of source code, (ii) the use of configuration files, (iii) the graphical user interface, and (iv) embedding the simulation specification in an existing programming language to express the computational problem. We identify the advantages and disadvantages of different approaches and discuss their implications on effectiveness and reproducibility of computational studies and results. Following on from this, we design and describe a domain specific language for micromagnetics that is embedded in the Python language, and allows users to define the micromagnetic simulations they want to carry out in a flexible way. We have implemented this micromagnetic simulation description language together with a computational backend that executes the simulation task using the Object Oriented MicroMagnetic Framework (OOMMF). We illustrate the use of this Python interface for OOMMF by solving the micromagnetic standard problem 4. All the code is publicly available and is open source

A Development Environment for Visual Physics Analysis

The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The project provides an extendable plug-in mechanism and includes plug-ins for designing the analysis flow, for running the analysis on batch systems, and for browsing the data content. The corresponding plug-ins are based on an object-oriented toolkit for modular data analysis. We introduce the main concepts of the project, describe the technical realization and demonstrate the functionality in example applications

A variational method based on weighted graph states

In a recent article [Phys. Rev. Lett. 97 (2006), 107206], we have presented a class of states which is suitable as a variational set to find ground states in spin systems of arbitrary spatial dimension and with long-range entanglement. Here, we continue the exposition of our technique, extend from spin 1/2 to higher spins and use the boson Hubbard model as a non-trivial example to demonstrate our scheme.Comment: 36 pages, 13 figure

Haptoglobin Phenotype, Preeclampsia Risk and the Efficacy of Vitamin C and E Supplementation to Prevent Preeclampsia in a Racially Diverse Population

Haptoglobin's (Hp) antioxidant and pro-angiogenic properties differ between the 1-1, 2-1, and 2-2 phenotypes. Hp phenotype affects cardiovascular disease risk and treatment response to antioxidant vitamins in some non-pregnant populations. We previously demonstrated that preeclampsia risk was doubled in white Hp 2-1 women, compared to Hp 1-1 women. Our objectives were to determine whether we could reproduce this finding in a larger cohort, and to determine whether Hp phenotype influences lack of efficacy of antioxidant vitamins in preventing preeclampsia and serious complications of pregnancy-associated hypertension (PAH). This is a secondary analysis of a randomized controlled trial in which 10,154 low-risk women received daily vitamin C and E, or placebo, from 9-16 weeks gestation until delivery. Hp phenotype was determined in the study prediction cohort (n = 2,393) and a case-control cohort (703 cases, 1,406 controls). The primary outcome was severe PAH, or mild or severe PAH with elevated liver enzymes, elevated serum creatinine, thrombocytopenia, eclampsia, fetal growth restriction, medically indicated preterm birth or perinatal death. Preeclampsia was a secondary outcome. Odds ratios were estimated by logistic regression. Sampling weights were used to reduce bias from an overrepresentation of women with preeclampsia or the primary outcome. There was no relationship between Hp phenotype and the primary outcome or preeclampsia in Hispanic, white/other or black women. Vitamin supplementation did not reduce the risk of the primary outcome or preeclampsia in women of any phenotype. Supplementation increased preeclampsia risk (odds ratio 3.30; 95% confidence interval 1.61-6.82, p<0.01) in Hispanic Hp 2-2 women. Hp phenotype does not influence preeclampsia risk, or identify a subset of women who may benefit from vitamin C and E supplementation to prevent preeclampsia

Understanding Face and Shame: A Servant-Leadership and Face Management Model

Clergy can have a negative impact on churches and other individuals when they knowingly or unknowingly attempt to save face, that is, try to protect their standing or reputation. The desire to gain face and the fear of losing face and feeling ashamed will likely permeate clergy’s decision-making processes without even being noticed. This study explores the essence of face and face management and the relationship between face management and two characteristics of servant-leadership—awareness and healing—in both Chinese and American churches through the methodology of hermeneutic phenomenology. Prior to this study, to my knowledge, no hermeneutic phenomenological research of face management has been conducted in a church setting. Through a review of the literature, four areas are explored: face and shame, face management, servant-leadership, and face, shame, and face management within the church. This study obtained approval from the Institutional Review Board and informed consent from the participants. Three Chinese and three American Christian ministers were chosen to complete a question sheet and participate in two semi-structured interview sessions. A first cycle of open coding and second cycle of pattern coding were used during data analysis. Face experiences are discussed in light of eight major themes: body, triggers, becoming, face concepts, strategies, emotions, servant-leadership, and the church. Findings from the study help build a servant-leadership and face management model, which can offer an anchored approach for clergy and pastoral counselors to address face and shame and to develop therapeutic interventions

‘Where we stayed was very bad …’: migrant children’s perspectives on life in informal rented accommodation in two southern African cities

Most research and initiatives relating to children's experiences of urban space have focused on the physical environment. Housing policies in Third World countries have also emphas- ised the provision of physical infrastructure and buildings, and urban aesthetics. In this paper the authors draw on the voices of young informants from Maseru (Lesotho), and Blantyre (Malawi), who, in discussions concerning moving house, chose to talk about social and economic aspects of life in the informal sector rented accommodation that is increasingly characteristic of these and many other African cities. The children offer insight into the peopling of urban space, mapping unruly environments characterised by disorder, gossip, and social contestation, far removed from the hard technocratic spaces imagined by planners. Their observations are important not only because children represent a very large and relatively neglected proportion of African urban dwellers but also because they offer a unique insight into the dynamic character of urban environments. As close observers of adult decisionmaking processes, children are informed commentators on motivations for moving house as well as the impacts of urban environments on their own lives. Not only do the children highlight the inadequacies of the informal private rental sector but they also offer a window onto why it is inadequate

Preliminary study of p53 and c-erbB-2 expression in gallbladder cancer in Indian patients manuscript id: 8962091628764582

BACKGROUND: The inactivation of the tumour suppressor gene and activation of the proto-oncogene are the key steps in the development of the human cancer. The p53 and c-erbB-2 are the best examples of it. In the present study, our aim was to determine the role of these genes in the carcinogenesis of gallbladder by immunohistochemistry. METHODS: In all 78 consecutive patients of gall bladder diseases were studied for p53 and c-erbB-2 expression immunohistochemically and their expression was correlated with the age, grades and stages of the disease and presence of stone. An informed consent was obtained in each case. Chi square and z test were applied to see the association of p53 and c-erbB-2 over expression with other clinicopathological factors. RESULTS: Eight (20%) patients of gall bladder cancer were positive for p53 expression and 10 (25%) patients for c-erbB-2. The p53 positivity increased with increasing grade while cerbB-2 positivity decreased with increasing grade of gall bladder cancer. Mean age in cerbB-2 positive cases were lesser as compared to negative cases while p53 did not show such association with age. CONCLUSION: Only one case of gall bladder cancer co-expressed the p53 and c-erbB-2, thereby suggesting that p53 and c-erbB-2 may have independent role in carcinogenesis of gall bladder cancer. c-erbB-2 over expression in adenoma and younger age group indicates its role as an early event in carcinogenesis of gallbladder. However study of larger sample is required to further validate the results

Using motivational techniques to reduce cardiometabolic risk factors in long term psychiatric inpatients: A naturalistic interventional study

Background People with severe mental illness have markedly reduced life expectancy; cardiometabolic disease is a major cause. Psychiatric hospital inpatients have elevated levels of cardiometabolic risk factors and are to a high degree dependent of the routines and facilities of the institutions. Studies of lifestyle interventions to reduce cardiometabolic risk in psychiatric inpatients are few. The current study aimed at assessing the feasibility and effects of a lifestyle intervention including Motivational Interviewing (MI) on physical activity levels, cardiometabolic risk status and mental health status in psychotic disorder inpatients. Methods Prospective naturalistic intervention study of 83 patients at long term inpatient psychosis treatment wards in South-Eastern Norway. Patients were assessed 3–6 months prior to, at start and 6 months after a life-style intervention program including training of staff in MI, simple changes in routines and improvements of facilities for physical exercise. Assessments were done by clinical staff and included level of physical activity, motivation, life satisfaction, symptom levels (MADRS, AES-C, PANSS, and GAF) as well as anthropometric and biochemical markers of cardiometabolic risk. A mixed model was applied to analyze change over time. Results A total of 88% of patients received MI interventions, with a mean of 2.5 MI interventions per week per patient. The physical activity level was not increased, but activity level was positively associated with motivation and negatively associated with positive symptoms. Triglyceride levels and number of smokers were significantly reduced and a significant decrease in symptom levels was observed. Conclusions The current results suggest that a simple, low cost life-style intervention program focusing on motivational change is feasible and may reduce symptoms and improve lifestyle habits in psychosis patients in long term treatment facilities. Similar programs may easily be implemented in other psychiatric hospitals.submittedVersio

Street-connectedness and education in Kenya: Experiences of formal schooling as rationale for inclusive pedagogies of practice

This paper contributes to the literature on street-connectedness and inclusive education, presenting original research findings from two Kenyan studies aiming to understand street-connected young people’s experiences of education. The first focused on transitioning from the street into education or training to explore the challenges of making that transition. The second, on young people who had lived on the street for extended periods of time and were still there at the time of data generation. From these studies, significant understandings emerged concerning: a) education as motivating initial migrations to the street; b) the role of fear, embarrassment and shame in preventing young people going (back) into formal education; and c) how acceptance and support are key to overcoming feelings of not belonging and challenges faced when transitioning from the street into schools. The paper provides empirical evidence that should be considered when planning inclusive education provision for street-connected young people globally