Novel Likelihood Ratio Tests for Screening Gene‐Gene and Gene‐Environment Interactions With Unbalanced Repeated‐Measures Data

There has been extensive literature on modeling gene‐gene interaction (GGI) and gene‐environment interaction (GEI) in case‐control studies with limited literature on statistical methods for GGI and GEI in longitudinal cohort studies. We borrow ideas from the classical two‐way analysis of variance literature to address the issue of robust modeling of interactions in repeated‐measures studies. While classical interaction models proposed by Tukey and Mandel have interaction structures as a function of main effects, a newer class of models, additive main effects and multiplicative interaction (AMMI) models, do not have similar restrictive assumptions on the interaction structure. AMMI entails a singular value decomposition of the cell residual matrix after fitting the additive main effects and has been shown to perform well across various interaction structures. We consider these models for testing GGI and GEI from two perspectives: likelihood ratio test based on cell means and a regression‐based approach using individual observations. Simulation results indicate that both approaches for AMMI models lead to valid tests in terms of maintaining the type I error rate, with the regression approach having better power properties. The performance of these models was evaluated across different interaction structures and 12 common epistasis patterns. In summary, AMMI model is robust with respect to misspecified interaction structure and is a useful screening tool for interaction even in the absence of main effects. We use the proposed methods to examine the interplay between the hemochromatosis gene and cumulative lead exposure on pulse pressure in the Normative Aging Study.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99643/1/gepi21744-sup-0001-si.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/99643/2/gepi21744.pd

Shear driven formation of nano-diamonds at sub-gigapascals and 300 K

The transformation pathways of carbon at high pressures are of broad interest for synthesis of novel materials and for revealing the Earth's geological history. We have applied large plastic shear on graphite in a rotational anvil cell to form hexagonal diamond and nanocrystalline cubic diamond at extremely low pressures of 0.4 and 0.7 GPa, which are 50 and 100 times lower than the transformation pressures under hydrostatic compression and well below the phase equilibrium. Large shearing accompanied with pressure elevation to 3 GPa also leads to formation of a new orthorhombic diamond phase. Our results demonstrate new mechanisms and new means for plastic shear-controlled material synthesis at drastically reduced pressures, enabling new technologies for material synthesis. The result also has significant geological implications

Shear driven formation of nano-diamonds at sub-gigapascals and 300 K

The transformation pathways of carbon at high pressures are of broad interest for synthesis of novel materials and for revealing the Earth's geological history. We have applied large plastic shear on graphite in rotational anvils to form hexagonal and nanocrystalline cubic diamond at extremely low pressures of 0.4 and 0.7 GPa, which are 50 and 100 times lower than the transformation pressures under hydrostatic compression and well below the phase equilibrium. Large shearing accompanied with pressure elevation to 3 GPa also leads to formation of a new orthorhombic diamond phase. Our results demonstrate new mechanisms and new means for plastic shear-controlled material synthesis at drastically reduced pressures, enabling new technologies for material synthesis. The results indicate that the micro-diamonds found in the low pressure-temperature crust could have formed during a large shear producing event, such as tectonic rifting and continued plate collision, without the need to postulate subduction to the mantle.Comment: 15 pages, 6 figures, 3 table

Charged particle elliptic flow in p+p collisions at LHC energies in a transport model PACIAE

The parton and hadron cascade model PACIAE based on PYTHIA was used to investigate the charged particle elliptic flow in minimum bias pp collisions at the LHC energies. The strings were distributed randomly in the transverse ellipsoid of the pp collision system with major axis of $R$ (proton radius) and minor axis of $R(1-\xi)$ before parton rescattering. The charged particle elliptic flow as a function of the random number $\xi$ and transverse momentum $p_T$ were investigated. The calculated $v_2/\epsilon$ as a function of reaction energy increases monotonously with increasing reaction energy up to $\sqrt{s}\sim$7 TeV and then turns to saturation. With the parton-parton cross section enlarges three times in parton rescattering, the rapidity integrated charged particle elliptic flow may reach 0.025 at $p_T \sim$2 GeV/c in the minimum bias pp collisions at $\sqrt{s}$=7 TeV.Comment: 7 pages, 4 figure

Shear driven formation of nano-diamonds at sub-gigapascals and 300 K

The transformation pathways of carbon at high pressures are of broad interest for synthesis of novel materials and for revealing the Earth's geological history. We have applied large plastic shear on graphite in a rotational anvil cell to form hexagonal diamond and nanocrystalline cubic diamond at extremely low pressures of 0.4 and 0.7 GPa, which are 50 and 100 times lower than the transformation pressures under hydrostatic compression and well below the phase equilibrium. Large shearing accompanied with pressure elevation to 3 GPa also leads to formation of a new orthorhombic diamond phase. Our results demonstrate new mechanisms and new means for plastic shear-controlled material synthesis at drastically reduced pressures, enabling new technologies for material synthesis. The result also has significant geological implications

Pathotyping the Zoonotic Pathogen Streptococcus suis: Novel Genetic Markers To Differentiate Invasive Disease-Associated Isolates from Non-Disease-Associated Isolates from England and Wales.

Streptococcus suis is one of the most important zoonotic bacterial pathogens of pigs, causing significant economic losses to the global swine industry. S. suis is also a very successful colonizer of mucosal surfaces, and commensal strains can be found in almost all pig populations worldwide, making detection of the S. suis species in asymptomatic carrier herds of little practical value in predicting the likelihood of future clinical relevance. The value of future molecular tools for surveillance and preventative health management lies in the detection of strains that genetically have increased potential to cause disease in presently healthy animals. Here we describe the use of genome-wide association studies to identify genetic markers associated with the observed clinical phenotypes (i) invasive disease and (ii) asymptomatic carriage on the palatine tonsils of pigs on UK farms. Subsequently, we designed a multiplex PCR to target three genetic markers that differentiated 115 S. suis isolates into disease-associated and non-disease-associated groups, that performed with a sensitivity of 0.91, a specificity of 0.79, a negative predictive value of 0.91, and a positive predictive value of 0.79 in comparison to observed clinical phenotypes. We describe evaluation of our pathotyping tool, using an out-of-sample collection of 50 previously uncharacterized S. suis isolates, in comparison to existing methods used to characterize and subtype S. suis isolates. In doing so, we show our pathotyping approach to be a competitive method to characterize S. suis isolates recovered from pigs on UK farms and one that can easily be updated to incorporate global strain collections.This work was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) Knowledge Transfer Network CASE studentship co-funded by Zoetis (previously Pfizer Animal Health UK) and with significant contribution from BQP Ltd (Award Reference: BB/L502479/1). Funding bodies provided scholarship support but had no part in study design, data collection, analysis and interpretation of data or in writing the manuscript. AWT is supported by a BBSRC Longer and Larger (LoLa) grant (Award Reference: BB/G019274/1). LAW is supported by a Dorothy Hodgkin Fellowship funded by the Royal Society (Grant Number: DH140195) and a Sir Henry Dale Fellowship co-funded by the Royal Society and Wellcome Trust (Grant Number: 109385/Z/15/Z)

Advances in estimation by the item sum technique using auxiliary information in complex surveys

To collect sensitive data, survey statisticians have designed many strategies to reduce nonresponse rates and social desirability response bias. In recent years, the item count technique (ICT) has gained considerable popularity and credibility as an alternative mode of indirect questioning survey, and several variants of this technique have been proposed as new needs and challenges arise. The item sum technique (IST), which was introduced by Chaudhuri and Christofides (2013) and Trappmann et al. (2014), is one such variant, used to estimate the mean of a sensitive quantitative variable. In this approach, sampled units are asked to respond to a two-list of items containing a sensitive question related to the study variable and various innocuous, nonsensitive, questions. To the best of our knowledge, very few theoretical and applied papers have addressed the IST. In this article, therefore, we present certain methodological advances as a contribution to appraising the use of the IST in real-world surveys. In particular, we employ a generic sampling design to examine the problem of how to improve the estimates of the sensitive mean when auxiliary information on the population under study is available and is used at the design and estimation stages. A Horvitz-Thompson type estimator and a calibration type estimator are proposed and their efficiency is evaluated by means of an extensive simulation study. Using simulation experiments, we show that estimates obtained by the IST are nearly equivalent to those obtained using “true data” and that in general they outperform the estimates provided by a competitive randomized response method. Moreover, the variance estimation may be considered satisfactory. These results open up new perspectives for academics, researchers and survey practitioners, and could justify the use of the IST as a valid alternative to traditional direct questioning survey modes.Ministerio de Economía y Competitividad of SpainMinisterio de Educacion, Cultura y Deporteproject PRIN-SURWE

The Mitochondrial Ca(2+) Uniporter: Structure, Function, and Pharmacology.

Mitochondrial Ca(2+) uptake is crucial for an array of cellular functions while an imbalance can elicit cell death. In this chapter, we briefly reviewed the various modes of mitochondrial Ca(2+) uptake and our current understanding of mitochondrial Ca(2+) homeostasis in regards to cell physiology and pathophysiology. Further, this chapter focuses on the molecular identities, intracellular regulators as well as the pharmacology of mitochondrial Ca(2+) uniporter complex

The Impact of Smoking on Clinical and Therapeutic Effects in Asthmatics

Smoking is associated with poor symptom control and impaired therapeutic responses in asthma. A total of 843 patients with asthma were recruited. The patients received treatment for 1 yr according to the severity of their asthma. We compared the forced expiratory volume in 1 sec (FEV1), the ratio of FEV1 to forced vital capaity (FVC), atopy, total IgE, emphysema on high-resolution computed tomography (HRCT), the number of near-fatal asthma attacks, and physiological fixed airway obstruction between the smoking and nonsmoking groups. The study population consisted of 159 (18.8%) current smokers, 157 (18.7%) ex-smokers, and 525 (62.5%) nonsmokers. Although the prevalence of atopy was not different between the smoking and nonsmoking groups, the total IgE was higher among the smokers than the nonsmokers. Compared with the nonsmoking group, the smokers had a lower FEV1 % predicted and forced expiratory flow between 25 and 75% of FVC. A greater prevalence of emphysema and a significantly higher number of asthmatic patients with fixed airway obstruction were detected in the smoking versus nonsmoking group. The 37.5% of asthmatic patients who were former or current smokers showed decreased pulmonary function and increased IgE, emphysema on HRCT, and fixed airway obstruction, indicating that smoking can modulate the clinical and therapeutic responses in asthma