Penalized item response theory models: application to epigenetic alterations in bladder cancer

Increasingly used in health-related applications, latent variable models provide an appealing framework for handling high-dimensional exposure and response data. Item response theory (IRT) models, which have gained widespread popularity, were originally developed for use in the context of educational testing, where extremely large sample sizes permitted the estimation of a moderate-to-large number of parameters. In the context of public health applications, smaller sample sizes preclude large parameter spaces. Therefore, we propose a penalized likelihood approach to reduce mean square error and improve numerical stability. We present a continuous family of models, indexed by a tuning parameter, that range between the Rasch model and the IRT model. The tuning parameter is selected by cross validation or approximations such as Akaike Information Criterion. While our approach can be placed easily in a Bayesian context, we find that our frequentist approach is more computationally efficient. We demonstrate our methodology on a study of methylation silencing of gene expression in bladder tumors. We obtain similar results using both frequentist and Bayesian approaches, although the frequentist approach is less computationally demanding. In particular, we find high correlation of methylation silencing among 16 loci in bladder tumors, that methylation is associated with smoking and also with patient survival.     

Characterization of UVC Light Sensitivity of Vaccinia Virus

Interest in airborne smallpox transmission has been renewed because of concerns regarding the potential use of smallpox virus as a biothreat agent. Air disinfection via upper-room 254-nm germicidal UV (UVC) light in public buildings may reduce the impact of primary agent releases, prevent secondary airborne transmission, and be effective prior to the time when public health authorities are aware of a smallpox outbreak. We characterized the susceptibility of vaccinia virus aerosols, as a surrogate for smallpox, to UVC light by using a benchtop, one-pass aerosol chamber. We evaluated virus susceptibility to UVC doses ranging from 0.1 to 3.2 J/m², three relative humidity (RH) levels (20%, 60%, and 80%), and suspensions of virus in either water or synthetic respiratory fluid. Dose-response plots show that vaccinia virus susceptibility increased with decreasing RH. These plots also show a significant nonlinear component and a poor fit when using a first-order decay model but show a reasonable fit when we assume that virus susceptibility follows a log-normal distribution. The overall effects of RH (P < 0.0001) and the suspending medium (P = 0.014) were statistically significant. When controlling for the suspending medium, the RH remained a significant factor (P < 0.0001) and the effect of the suspending medium was significant overall (P < 0.0001) after controlling for RH. Virus susceptibility did not appear to be a function of virus particle size. This work provides an essential scientific basis for the design of effective upper-room UVC installations for the prevention of airborne infection transmission of smallpox virus by characterizing the susceptibility of an important orthopoxvirus to UVC exposure.     

牛脾转移因子的提取工艺研究

目的：比较从牛脾中提取活性ＴＦ的不同方法。方法：分别利用Ｌａｗｒｅｎｃｅ－－透析法、Ｌａｗｒｅｎｃｅ－超滤法、超离心－超滤法提取,再以蛋白反应、红外及紫外扫描予以鉴定比较。结果：Ｌａｗｒｅｎｃｅ－超滤法和超离心－超滤法效果较好。结论：工业化生产中应采用Ｌａｗｒｅｎｃｅ－超滤法。     

A penalized latent class model for ordinal data

Latent class models provide a useful framework for clustering observations based on several features. Application of latent class methodology to correlated, high-dimensional ordinal data poses many challenges. Unconstrained analyses may not result in an estimable model. Thus, information contained in ordinal variables may not be fully exploited by researchers. We develop a penalized latent class model to facilitate analysis of high-dimensional ordinal data. By stabilizing maximum likelihood estimation, we are able to fit an ordinal latent class model that would otherwise not be identifiable without application of strict constraints. We illustrate our methodology in a study of schwannoma, a peripheral nerve sheath tumor, that included 3 clinical subtypes and 23 ordinal histological measures.     

Genetic determinants of UV-susceptibility in non-melanoma skin cancer

A milieu of cytokines and signaling molecules are involved in the induction of UV-induced immune suppression and thus the etiology of non-melanoma skin cancer (NMSC). Targeting the UV-induced immunosuppression pathway, and using a large population based study of NMSC, we have investigated the risk associated with functional variants in 10 genes (IL10, IL4, IL4R, TNF, TNFR2, HTR2A, HRH2, IL12B, PTGS2, and HAL). The most prominent single genetic effect was observed for IL10. There was increasing risk for both basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) with increasing number of variant IL10 haplotypes (BCC: p_trend = 0.0048; SCC: p_trend = 0.031). Having two IL10 GC haplotypes was associated with increased odds ratios of BCC and SCC (OR_BCC = 1.5, 95% CI 1.1–1.9; OR_SCC = 1.4, 95% CI 1.0–1.9), and these associations were largely confined to women (OR_BCC = 2.2, 95% CI 1.4–3.4; SCC: OR_SCC = 1.8, 95% CI 1.1–3.0). To examine how combinations of these variants contribute to risk of BCC and SCC, we used multifactor dimensionality reduction (MDR) and classification and regression trees (CART). Results from both of these methods found that in men, a combination of skin type, burns, IL10, IL4R, and possibly TNFR2 were important in both BCC and SCC. In women, skin type, burns, and IL10 were the most critical risk factors in SCC, with risk of BCC involving these same factors plus genetic variants in HTR2A, IL12B and IL4R. These data suggest differential genetic susceptibility to UV-induced immune suppression and skin cancer risk by gender.     

Functional diversity of reef molluscs along a tropical-to-temperate gradient

Coral Reefs - Global warming is leading to range shifts of marine species, threatening the structure and functioning of ecological communities and human populations that rely on them. The largest...     

Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas

The placenta acts not only as a conduit of nutrient and waste exchange between mother and developing fetus, but also functions as a regulator of the intrauterine environment. Recent work has identified changes in the expression of candidate genes, often through epigenetic alteration, which alter the placenta''s function and impact fetal growth. In this study, we used the Illumina Infinium HumanMethylation27 BeadChip array to examine genome-wide DNA methylation patterns in 206 term human placentas. Semi-supervised recursively partitioned mixture modeling was implemented to identify specific patterns of placental DNA methylation that could differentially classify intrauterine growth restriction (IUGR) and small for gestational age (SGA) placentas from appropriate for gestational age (AGA) placentas, and these associations were validated in a masked testing series of samples. Our work demonstrates that patterns of DNA methylation in human placenta are reliably and significantly associated with infant growth and serve as a proof of principle that methylation status in the human term placenta can function as a marker for the intrauterine environment, and could potentially play a critical functional role in fetal development.Key words: epigenetics, DNA methylation, placenta, intrauterine growth restriction, small for gestational age, development, human     

Vice-anvil use in nut processing by two Corvus species

Woodpeckers and certain passerine species secure encased food in the environment in various ways to facilitate the extraction of the contents with their bills. They do this by securing the food items in locations such as crevices and holes, newly defined in this paper as ‘vice-anvils’. Here I report that free-living New Caledonian crows (Corvus moneduloides) and rooks (Corvus frugilegus, in New Zealand) also use vice-anvils to process candlenuts and walnuts, respectively. New Caledonian crows placed candlenut sections in vice-anvils to aid kernel extraction, after the candlenuts had been dropped onto an anvil to break them open. In contrast, rooks used vice-anvils to secure walnuts while they broke the shell with their bills. Long-term use by rooks of a vice-anvil in a tree had produced a ‘purpose-made’ nut-cracking site. My findings extend the persistent use of specific vice-anvils to Corvus species and further demonstrate their innovative and flexible foraging behaviour.