Preconditioned iterative minimization for linear-scaling electronic structure calculations

Linear-scaling electronic structure methods are essential for calculations on large systems. Some of these approaches use a systematic basis set, the completeness of which may be tuned with an adjustable parameter similar to the energy cut-off of plane-wave techniques. The search for the electronic ground state in such methods suffers from an ill-conditioning which is related to the kinetic contribution to the total energy and which results in unacceptably slow convergence. We present a general preconditioning scheme to overcome this ill-conditioning and implement it within our own first-principles linear-scaling density functional theory method. The scheme may be applied in either real space or reciprocal space with equal success. The rate of convergence is improved by an order of magnitude and is found to be almost independent of the size of the basis

Years off Your Life? The Effects of Homicide on Life Expectancy by Neighborhood and Race/Ethnicity in Los Angeles County

Homicide is one of the leading causes of death in Los Angeles County and is known to be elevated in low-income urban neighborhoods and in black males. However, because homicide occurs primarily among young adults, mortality rate statistics may underrepresent its importance. We estimated the impact of homicide on life expectancy by demographic group and geographic area in Los Angeles County, 2001–2006. Life expectancy estimates were calculated using mortality records and population estimates for Los Angeles County. Cause elimination techniques were used to estimate the impact of homicide on life expectancy. Homicide was estimated to reduce life expectancy by 0.4 years for Los Angeles County residents and by 2.1 years for black males. The impact of homicide on life expectancy was higher in low-income neighborhoods. In some low-income urban neighborhoods, homicide was estimated to decrease life expectancy in black males by nearly 5 years. Homicide causes substantial reductions in life expectancy in Los Angeles County. Its impact is magnified among black males and in low-income urban areas, underscoring the need for homicide reduction in urban centers

How many is enough? Determining optimal count totals for ecological and palaeoecological studies of testate amoebae

Testate amoebae are increasingly used in ecological and palaeoecological studies of wetlands. To characterise the amoeba community a certain number of individuals need to be counted under the microscope. To date, most studies have aimed for 150 individuals, but that sample size is not based on adequate evidence. When testate amoeba concentrations are low, it can be difficult or impossible to reach this total. The impacts of lower count totals have never been seriously scrutinised. We investigated the impact of count size on number of taxa identified, quantitative inferences of environmental variables and the strength of the links between amoebae and environmental data in the context of predicting depth to water table. Low counts were simulated by random selection of individuals from four existing datasets. Results show progressively diminishing returns by all criteria as count size increases from low numbers to counts of 150. A higher count is required to identify all taxa than to adequately characterise the community for transfer function inference. We suggest that in most cases, it will be a more efficient use of time to count a greater number of samples to a lower count. While a count of 50 individuals may be sufficient for some samples from some sites we recommend that counts of 100 individuals should be sufficient for most samples. Counts need only be increased to 150 or more where the aim is to identify relatively minor, but still potentially ecologically relevant community changes. This approach will help reduce lack of replication and low resolution, which are common limitations in testate amoeba-based palaeoecological and ecological studies

Environmental differences between sites control the diet and nutrition of the carnivorous plant Drosera rotundifolia

Background and aims: Carnivorous plants are sensitive to small changes in resource availability, but few previous studies have examined how differences in nutrient and prey availability affect investment in and the benefit of carnivory. We studied the impact of site-level differences in resource availability on ecophysiological traits of carnivory for Drosera rotundifolia L. Methods: We measured prey availability, investment in carnivory (leaf stickiness), prey capture and diet of plants growing in two bogs with differences in N deposition and plant available N: Cors Fochno (0.62 g m−2 yr.−1, 353 μg l−1), Whixall Moss (1.37 g m−2 yr.−1, 1505 μg l−1). The total N amount per plant and the contributions of prey/root N to the plants’ N budget were calculated using a single isotope natural abundance method. Results: Plants at Whixall Moss invested less in carnivory, were less likely to capture prey, and were less reliant on prey-derived N (25.5% compared with 49.4%). Actual prey capture did not differ between sites. Diet composition differed – Cors Fochno plants captured 62% greater proportions of Diptera. Conclusions: Our results show site-level differences in plant diet and nutrition consistent with differences in resource availability. Similarity in actual prey capture may be explained by differences in leaf stickiness and prey abundance

Comparative risk judgements for oral health hazards among Norwegian adults: a cross sectional study

BACKGROUND: This study identified optimistic biases in health and oral health hazards, and explored whether comparative risk judgements for oral health hazards vary systematically with socio-economic characteristics and self-reported risk experience. METHODS: A simple random sample of 1,190 residents born in 1972 was drawn from the population resident in three counties of Norway. A total of 735 adults (51% women) completed postal questionnaires at home. RESULTS: Mean ratings of comparative risk judgements differed significantly (p < 0.001) from the mid point of the scales. T-values ranged from -13.1 and -12.1 for the perceived risk of being divorced and loosing all teeth to -8.2 and -7.8 (p < 0.001) for having gum disease and toothdecay. Multivariate analyses using General Linear Models, GLM, revealed gender differences in comparative risk judgements for gum disease, whereas social position varied systematically with risk judgements for tooth decay, gum disease and air pollution. The odds ratios for being comparatively optimistic with respect to having gum disease were 2.9, 1.9, 1.8 and 1.5 if being satisfied with dentition, having a favourable view of health situation, and having high and low involvement with health enhancing and health detrimental behaviour, respectively. CONCLUSION: Optimism in comparative judgements for health and oral health hazards was evident in young Norwegian adults. When judging their comparative susceptibility for oral health hazards, they consider personal health situation and risk behaviour experience

Fast network centrality analysis using GPUs

<p>Abstract</p> <p>Background</p> <p>With the exploding volume of data generated by continuously evolving high-throughput technologies, biological network analysis problems are growing larger in scale and craving for more computational power. General Purpose computation on Graphics Processing Units (GPGPU) provides a cost-effective technology for the study of large-scale biological networks. Designing algorithms that maximize data parallelism is the key in leveraging the power of GPUs.</p> <p>Results</p> <p>We proposed an efficient data parallel formulation of the All-Pairs Shortest Path problem, which is the key component for shortest path-based centrality computation. A betweenness centrality algorithm built upon this formulation was developed and benchmarked against the most recent GPU-based algorithm. Speedup between 11 to 19% was observed in various simulated scale-free networks. We further designed three algorithms based on this core component to compute closeness centrality, eccentricity centrality and stress centrality. To make all these algorithms available to the research community, we developed a software package <it>gpu</it>-<it>fan </it>(GPU-based Fast Analysis of Networks) for CUDA enabled GPUs. Speedup of 10-50× compared with CPU implementations was observed for simulated scale-free networks and real world biological networks.</p> <p>Conclusions</p> <p><it>gpu</it>-<it>fan </it>provides a significant performance improvement for centrality computation in large-scale networks. Source code is available under the GNU Public License (GPL) at <url>http://bioinfo.vanderbilt.edu/gpu-fan/</url>.</p

Accreditation Standard Guideline Initiative for Tai Chi and Qigong Instructors and Training Institutions.

Evidence of the health and wellbeing benefits of Tai Chi and Qigong (TQ) have emerged in the past two decades, but TQ is underutilized in modern health care in Western countries due to lack of promotion and the availability of professionally qualified TQ instructors. To date, there are no government regulations for TQ instructors or for training institutions in China and Western countries, even though TQ is considered to be a part of Traditional Chinese medicine that has the potential to manage many chronic diseases. Based on an integrative health care approach, the accreditation standard guideline initiative for TQ instructors and training institutions was developed in collaboration with health professionals, integrative medicine academics, Tai Chi and Qigong master instructors and consumers including public safety officers from several countries, such as Australia, Canada, China, Germany, Italy, Korea, Sweden and USA. In this paper, the rationale for organizing the Medical Tai Chi and Qigong Association (MTQA) is discussed and the accreditation standard guideline for TQ instructors and training institutions developed by the committee members of MTQA is presented. The MTQA acknowledges that the proposed guidelines are broad, so that the diversity of TQ instructors and training institutions can be integrated with recognition that these guidelines can be developed with further refinement. Additionally, these guidelines face challenges in understanding the complexity of TQ associated with different principles, philosophies and schools of thought. Nonetheless, these guidelines represent a necessary first step as primary resource to serve and guide health care professionals and consumers, as well as the TQ community

Smoking in cars in England: a study of school students in an English city

Background Exposure to secondhand smoke is associated with an increased risk of adverse health effects among children. Although smoking in the home is an established major source of exposure, less is known about rules on smoking in cars. Methods In a survey including a sample of secondary school students in Nottingham (UK) in 2012, participants were asked whether smoking was allowed in the family car, and how often the respondent travelled in a car in which smoking was allowed. Rules on smoking in cars were investigated in relation to socio-demographic variables and whether children had ever smoked themselves using logistic regression. Results Of 4,190 students aged 11–16 who provided data, approximately 12% reported that smoking was allowed in their family car and 35% that they travelled in a car where smoking was allowed at least sometimes. Absence of smoke free rules in the family car was more likely to be reported by children from more disadvantaged families, if parents and friends were smokers and if smoking was allowed in the main home. These factors, and having a sibling who smokes, were also independently associated with an increased risk of travelling in a car in which smoking was allowed at least sometimes. Respondents who were not protected from secondhand smoke in the car were also more likely to have ever smoked (adjusted odds ratio 1.59, 95% CI 1.18-2.14). Conclusions Absence of smoke free rules in a family car and travelling in a car where smoking was allowed was relatively common among secondary school students, was strongly related to social disadvantage and a higher risk of smoking experimentation. Measures to prevent such exposure are therefore indicated

Parenteral provision of micronutrients to pediatric patients: an international expert consensus paper

© 2020 The Authors. Published by Wiley. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1002/jpen.1990INTRODUCTION:Micronutrients (vitamins and trace elements) are essential to all nutrition. For children and neonates who are dependent upon nutrition support therapies for growth and development, the prescribed regimen must supply all essential components. This paper aims to facilitate interpretation of existing clinical guidelines into practical approaches for the provision of micronutrients in pediatric parenteral nutrition. METHODS:An international, interdisciplinary expert panel was convened to review recent evidence-based guidelines and published literature to develop consensus- based recommendation on practical micronutrient provision in pediatric parenteral nutrition. RESULTS:The guidelines and evidence have been interpreted as answers to 10 commonly asked questions around the practical principles for provision and monitoring of micronutrients in pediatric patients CONCLUSION: Micronutrients are an essential part of all parenteral nutrition and should be included in the pediatric nutrition therapy care plan.Published versio