Effect of temperature anisotropy on various modes and instabilities for a magnetized non-relativistic bi-Maxwellian plasma

Using kinetic theory for homogeneous collisionless magnetized plasmas, we present an extended review of the plasma waves and instabilities and discuss the anisotropic response of generalized relativistic dielectric tensor and Onsager symmetry properties for arbitrary distribution functions. In general, we observe that for such plasmas only those electromagnetic modes whose magnetic field perturbations are perpendicular to the ambient magneticeld, i.e.,B1 \perp B0, are effected by the anisotropy. However, in oblique propagation all modes do show such anisotropic effects. Considering the non-relativistic bi-Maxwellian distribution and studying the relevant components of the general dielectric tensor under appropriate conditions, we derive the dispersion relations for various modes and instabilities. We show that only the electromagnetic R- and L- waves, those derived from them and the O-mode are affected by thermal anisotropies, since they satisfy the required condition B1\perpB0. By contrast, the perpendicularly propagating X-mode and the modes derived from it (the pure transverse X-mode and Bernstein mode) show no such effect. In general, we note that the thermal anisotropy modifies the parallel propagating modes via the parallel acoustic effect, while it modifies the perpendicular propagating modes via the Larmor-radius effect. In oblique propagation for kinetic Alfven waves, the thermal anisotropy affects the kinetic regime more than it affects the inertial regime. The generalized fast mode exhibits two distinct acoustic effects, one in the direction parallel to the ambient magnetic field and the other in the direction perpendicular to it. In the fast-mode instability, the magneto-sonic wave causes suppression of the firehose instability. We discuss all these propagation characteristics and present graphic illustrations

Feasibility of identifying families for genetic studies of birth defects using the National Health Interview Survey

BACKGROUND: The purpose of this study was to determine whether the National Health Interview Survey is a useful source to identify informative families for genetic studies of birth defects. METHODS: The 1994/1995 National Health Interview Survey (NHIS) was used to identify households where individuals with two or more birth defects reside. Four groups of households were identified: 1) single non-familial (one individual with one birth defect); 2) single familial (more than one individual with one birth defect); 3) multiple non-familial (one individual with more than one birth defect), and 4) multiple familial (more than one individual with more than one birth defect). The March 2000 U.S. Census on households was used to estimate the total number of households in which there are individuals with birth defects. RESULTS: Of a total of 28,094 households and surveyed about birth defects and impairments, 1,083 single non-familial, 55 multiple non-familial, 54 single familial, and 8 multiple familial households were identified. Based on the 2000 U.S. census, it is estimated that there are 4,472,385 households where at least one person has one birth defect in the United States and in 234,846 of them there are at least two affected individuals. Western states had the highest prevalence rates. CONCLUSIONS: Population-based methods, such as the NHIS, are modestly useful to identify the number and the regions where candidate families for genetic studies of birth defects reside. Clinic based studies and birth defects surveillance systems that collect family history offer better probability of ascertainment

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

Motivation: Copy Number Variants (CNVs) are important genetic factors for studying human diseases. While high-throughput whole genome re-sequencing provides multiple lines of evidence for detecting CNVs, computational algorithms need to be tailored for different type or size of CNVs under different experimental designs. Results: To achieve optimal power and resolution of detecting CNVs at low depth of coverage, we implemented a Hidden Markov Model that integrates both depth of coverage and mate-pair relationship. The novelty of our algorithm is that we infer the likelihood of carrying a deletion jointly from multiple mate pairs in a region without the requirement of a single mate pairs being obvious outliers. By integrating all useful information in a comprehensive model, our method is able to detect medium-size deletions (200-2000bp) at low depth (<10× per sample). We applied the method to simulated data and demonstrate the power of detecting medium-size deletions is close to theoretical values. Availability: A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel

Prevalence of the metabolic syndrome in patients with carotid disease according to NHLBI/AHA and IDF criteria: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Metabolic syndrome (MetS) has been related to type 2 diabetes and cardiovascular diseases. Different criteria for diagnosis of MetS have been recommended, but there is no agreement about which criteria are best to use. The aim of the present study was to investigate agreement between the National Heart, Lung, and Blood Institute, American Heart Association (NHLBI/AHA) and the International Diabetes Federation (IDF) definitions of MetS in patients with symptomatic carotid disease and to compare the frequency of cardiovascular risk factor in patients with MetS diagnosed by these two sets of criteria.</p> <p>Methods</p> <p>The study was a cross-sectional one involving 644 consecutive patients with verified carotid disease who referred to the Vascular Surgery Clinic Dedinje in Belgrade during the period April 2006 - November 2007. Anthropometric parameters blood pressure, fasting plasma glucose and lipoproteins were measured using standard procedures.</p> <p>Results</p> <p>MetS was present in 67.9% of participants, according to IDF criteria, and in 64.9% of participants, according to the NHLBI/AHA criteria. A total of 119 patients were categorized differently by the two definitions. Out of all participants 10.7% had MetS by IDF criteria only and 7.8% of patients had MetS by NHLBI/AHA criteria only. The overall agreement of IDF and NHLBI/AHA criteria was 81.5% (Kappa 0.59, <it>p </it>< 0.001). In comparison with patients who met only IDF criteria, patients who met only NHLBI/AHA criteria had significantly more frequently cardiovascular risk factors with the exception of obesity which was significantly more frequent in patients with MetS diagnosed by IDF criteria.</p> <p>Conclusion</p> <p>The MetS prevalence in patients with symptomatic carotid disease was high regardless of criteria used for its diagnosis. Since some patients with known cardiovascular risk factors were lost by the use of IDF criteria it seems that NHLBI/AHA definition is more suitable for diagnosis of MetS. Large follow-up studies are needed to test prognostic value of these definitions.</p

En bloc Extended Total Thymectomy and Extrapleural Pneumonectomy in Masaoka stage IVA Thymomas

<p>Abstract</p> <p>Background</p> <p>Surgical excision is the primary treatment for a thymoma. However, for advanced thymoma that extends to within the thoracic cavity and for recurrent cases with pleural dissemination (Masaoka stage IVA), the appropriate treatment is controversial. We evaluated the safety of surgery and outcomes of seven patients that underwent an en bloc extended total thymectomy and extrapleural pneumonectomy for stage IVA thymomas.</p> <p>Methods</p> <p>From 1994 to 2009, five patients initially diagnosed with pleural dissemination and two patients with recurrent tumors in the pleura and lungs after a total thymectomy, were identified. Seven patients had an extrapleural pneumonectomy performed. For the first operation, five patients underwent additional en bloc extended total thymectomy.</p> <p>Results</p> <p>Two recurrent cases were identified 55.2 and 12.3 months after first operation. Two patients had WHO type B1-B2 tumors, two had B2, two had B2-B3, and one had a B3 tumor. The mean hospital stay was 15.3 days (range: 7-29). There was no operative mortality. Four patients had neoadjuvant chemotherapy and five were treated with adjuvant chemotherapy. The median survival was 30.6 months and the Kaplan-Meier 2-year survival was 100% (95% confidence interval: 24.6-36.6 months). One patient, who did not receive induction chemotherapy, had distant metastases after surgery.</p> <p>Conclusions</p> <p>En bloc extended total thymectomy and extrapleural pneumonectomy can be safely performed on selected patients with stage IVA thymomas and is expected to achieve complete local control. Although the treatment strategy has yet to be standardized, complete resection with appropriate systemic therapy may improve survival in otherwise fatal disease.</p

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/

Alcohol use behaviors and risk of metabolic syndrome in South Korean middle-aged men

<p>Abstract</p> <p>Background</p> <p>It is thought that small volumes of alcohol may have positive effects on health. However, excessive drinking results in serious health problems. An accurate method to determine individual alcohol use behaviors are needed to assess objectively the extent to which drinking affects health. This study investigated the association between risk of metabolic syndrome (MetS) and alcohol use behaviors in middle-aged South Korean men using the Alcohol Use Disorders Identification Test.</p> <p>Methods</p> <p>This study used data from the South Korea National Health and Nutrition Examination (KNHANES) IV (2008), which extracted the standard survey household by using the proportional systematic sampling method. Data of 714 participants from KNHANES IV, 2008 were analyzed using Surveyfreq and Surveylogistic regression to investigate the association between MetS and alcohol use behaviors in middle-aged South Korean men.</p> <p>Results</p> <p>After adjustment for education, smoking, and physical activity, alcohol use behaviors were significantly associated with an increased risk of hypertension [odds ratio (OR) = 2.54, 95% confidence interval (CI) = 1.5-4.06 in the hazardous group; OR = 2.99, 95% CI = 1.84-4.92 in the problem group]; impaired fasting glucose (OR = 2.15, 95% CI = 1.16-3.99 in the hazardous group; OR = 2.48, 95% CI = 1.42-4.33 in the problem group); dyslipidemia (OR = 2.19, 95% CI = 1.38-3.47 in the problem group); abdominal obesity (OR = 1.93, 95% CI = 1.17-3.19 in the hazardous group; OR = 1.85, 95% CI = 1.17-2.92 in the problem group); and MetS (OR = 2.16, 95% CI = 1.24-3.77 in the hazardous group; OR = 2.54, 95% CI = 1.41-4.58 in problem group).</p> <p>Conclusions</p> <p>This study found that excessive alcohol use behaviors increased the risk of hypertension, diabetes, dyslipidemia, abdominal obesity, and MetS. Considering the rising rate of alcohol consumption and heavy drinking at single sittings, a culture of less risky alcohol consumption must be established to promote health among middle-aged men.</p