Effect of Ni content in CuNi alloys on the repassivation behavior of passive films by Pseudomonas aeruginosa and Desulfovibrio vulgaris.

A study employed surface morphology observation, corrosion product composition analysis, and electrochemical measurements to investigate differences in passive film breakdown and repassivation processes between pre-passivated B10 and B30 CuNi alloys under synergistic corrosion by Pseudomonas aeruginosa (P. aeruginosa) and Desulfovibrio vulgaris (D. vulgaris) in seawater, attributable to their differing Ni content.

Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins.

In most vertebrates, teeth are continuously shed and replaced throughout life, while mammals and several lineages of reptiles have reduced replacement to only one or two generations. In contrast to the vast majority of their living relatives, members of the lizard families Chamaeleonidae and Agamidae have dispensed with lifelong tooth replacement, instead developing acrodont dentition that fuses to the jawbone to be used for the lifetime of the animal. Though, the loss of tooth replacement has not come without a cost.

Sex-specific and cell-specific regulation of ER stress and neuroinflammation after traumatic brain injury in juvenile mice.

Endoplasmic reticulum (ER) stress and neuroinflammation play an important role in secondary brain damage after traumatic brain injury (TBI). Due to the complex brain cytoarchitecture, multiple cell types are affected by TBI. However, cell type-specific and sex-specific responses to ER stress and neuroinflammation remain unclear.

New Empirical Bayes Models to Jointly Analyze Multiple RNA-Sequencing Data in a Hypophosphatasia Disease Study.

Hypophosphatasia is a rare inherited metabolic disorder caused by the deficiency of tissue-nonspecific alkaline phosphatase. More severe and early onset cases present symptoms of muscle weakness, diminished motor coordination, and epileptic seizures. These neurological manifestations are poorly characterized.

A weighted empirical Bayes risk prediction model using multiple traits.

With rapid advances in high-throughput sequencing technology, millions of single-nucleotide variants (SNVs) can be simultaneously genotyped in a sequencing study. These SNVs residing in functional genomic regions such as exons may play a crucial role in biological process of the body. In particular, non-synonymous SNVs are closely related to the protein sequence and its function, which are important in understanding the biological mechanism of sequence evolution.

Penalized Variable Selection for Lipid-Environment Interactions in a Longitudinal Lipidomics Study.

Lipid species are critical components of eukaryotic membranes. They play key roles in many biological processes such as signal transduction, cell homeostasis, and energy storage. Investigations of lipid-environment interactions, in addition to the lipid and environment main effects, have important implications in understanding the lipid metabolism and related changes in phenotype.

Differences in Perceptions of Incivility Among Disciplines in Higher Education.

Background: Incivility occurs in various forms in higher education and negatively affects teaching and learning outcomes. It has not been determined if incivility is more prevalent in one discipline than another.

Purpose: The purpose of this study was to compare faculty and student perceptions of incivility across disciplines at a large public university.

Enhanced Platelet-Activating Factor Synthesis Facilitates Acute and Delayed Effects of Ethanol-Intoxicated Thermal Burn Injury.

Thermal burn injuries in patients who are alcohol-intoxicated result in greater morbidity and mortality. Murine models combining ethanol and localized thermal burn injury reproduce the systemic toxicity seen in human subjects, which consists of both acute systemic cytokine production with multiple organ dysfunction, as well as a delayed systemic immunosuppression. However, the exact mechanisms for these acute and delayed effects are unclear.

Increased urinary angiotensin converting enzyme 2 and neprilysin in patients with type 2 diabetes.

Angiotensin converting enzyme 2 (ACE2) and neprilysin (NEP) are metalloproteases that are highly expressed in the renal proximal tubules. ACE2 and NEP generate renoprotective angiotensin (1-7) from angiotensin II and angiotensin I, respectively, and therefore could have a major role in chronic kidney disease (CKD). Recent data demonstrated increased urinary ACE2 in patients with diabetes with CKD and kidney transplants.

Evacuation performance evaluation tool.

Objective: Hospitals conduct evacuation exercises to improve performance during emergency events. An essential aspect in this process is the creation of reliable and valid evaluation tools. The objective of this article is to describe the development and implications of a disaster evacuation performance tool that measures one portion of the very complex process of evacuation.

A new model calling procedure for Illumina BeadArray data.

Background: Accurate genotype calling for high throughput Illumina data is an important step to extract more genetic information for a large scale genome wide association studies. Many popular calling algorithms use mixture models to infer genotypes of a large number of single nucleotide polymorphisms in a fast and efficient way. In practice, mixture models are mostly restricted to infer genotypes for common SNPs where their minor allele frequencies are quite large.

Radiation therapy generates platelet-activating factor agonists.

Pro-oxidative stressors can suppress host immunity due to their ability to generate oxidized lipid agonists of the platelet-activating factor-receptor (PAF-R). As radiation therapy also induces reactive oxygen species, the present studies were designed to define whether ionizing radiation could generate PAF-R agonists and if these lipids could subvert host immunity. We demonstrate that radiation exposure of multiple tumor cell lines in-vitro, tumors in-vivo, and human subjects undergoing radiation therapy for skin tumors all generate PAF-R agonists.

An Empirical Bayes risk prediction model using multiple traits for sequencing data.

The rapidly developing sequencing technologies have led to improved disease risk prediction through identifying many novel genes. Many prediction methods have been proposed to use rich genomic information to predict binary disease outcomes. It is intuitive that these methods can be further improved by making efficient use of the rich information in measured quantitative traits that are correlated with binary outcomes.

M(3)-S: a genotype calling method incorporating information from samples with known genotypes.

Background: A key challenge in analyzing high throughput Single Nucleotide Polymorphism (SNP) arrays is the accurate inference of genotypes for SNPs with low minor allele frequencies. A number of calling algorithms have been developed to infer genotypes for common SNPs, but they are limited in their performance in calling rare SNPs. The existing algorithms can be broadly classified into three categories, including: population-based methods, SNP-based methods, and a hybrid of the two approaches.

A bivariate variance components model for mapping iQTLs underlying endosperm traits.

Genomic imprinting plays a pivotal role in early stage development in plants. Linkage analysis has been proven to be useful in mapping imprinted quantitative trait loci (iQTLs) underlying imprinting phenotypic traits in natural populations or experimental crosses. For correlated traits, studies have shown that multivariate genetic linkage analysis can improve QTL mapping power and precision, especially when a QTL has a pleiotropic effect on several traits.

Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data.

We consider the application of Efron's empirical Bayes classification method to risk prediction in a genome-wide association study using the Genetic Analysis Workshop 17 (GAW17) data. A major advantage of using this method is that the effect size distribution for the set of possible features is empirically estimated and that all subsequent parameter estimation and risk prediction is guided by this distribution. Here, we generalize Efron's method to allow for some of the peculiarities of the GAW17 data.

M(3): an improved SNP calling algorithm for Illumina BeadArray data.

Summary: Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype-genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform well.

Functional mapping of dynamic traits with robust t-distribution.

Functional mapping has been a powerful tool in mapping quantitative trait loci (QTL) underlying dynamic traits of agricultural or biomedical interest. In functional mapping, multivariate normality is often assumed for the underlying data distribution, partially due to the ease of parameter estimation. The normality assumption however could be easily violated in real applications due to various reasons such as heavy tails or extreme observations.

Designs for linkage analysis and association studies of complex diseases.

Genetic linkage analysis has been a traditional means for identifying regions of the genome with large genetic effects that contribute to a disease. Following linkage analysis, association studies are widely pursued to fine-tune regions with significant linkage signals. For complex diseases which often involve function of multi-genetic variants each with small or moderate effect, linkage analysis has little power compared to association studies.

Functional mapping imprinted quantitative trait loci underlying developmental characteristics.

Background: Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL) mapping focusing on single trait analysis.