A logistic normal multinomial regression model for microbiome compositional data analysis.

Changes in human microbiome are associated with many human diseases. Next generation sequencing technologies make it possible to quantify the microbial composition without the need for laboratory cultivation. One important problem of microbiome data analysis is to identify the environmental/biological covariates that are associated with different bacterial taxa.

Developing an adaptive radiation therapy strategy for nasopharyngeal carcinoma.

Adaptive radiotherapy (ART) has recently been introduced to restore the planned dose distribution by accounting for the anatomic changes during treatment. By quantifying the anatomic changes in nasopharyngeal carcinoma (NPC) patients, this study aimed to establish an ART strategy for NPC cases. A total of 30 NPC patients treated with helical tomotherapy were recruited.

[Development and validation of the Informant Assessment of Geriatric Delirium Scale (I-AGeD). Recognition of delirium in geriatric patients].

Objectives: Delirium is common in older patients admitted to hospital. Information obtained from patient's relatives or caregivers may contribute to improved detection. Our aim was to develop a caregiver based questionnaire, the Informant Assessment of Geriatric Delirium (I-AGeD), to assist in better recognition of delirium in elderly patients.

Principal components methods for narrow-sense heritability in the analysis of multidimensional longitudinal cognitive phenotypes.

Background: Genetic association studies of longitudinal cognitive phenotypes are an alternate approach to discovering genetic risk factors for Alzheimer's disease (AD). However, the standard linear mixed model approach is limited in the face of multidimensional longitudinal data and multiple genotypes. In this setting, the principal components of heritability (PCH) approach may increase efficiency by deriving a linear combination of phenotypes to maximize the heritability attributable to a particular genetic locus.

Mutations in adenosine deaminase-like (ADAL) protein confer resistance to the antiproliferative agents N6-cyclopropyl-PMEDAP and GS-9219.

Background/aim: GS 9219 is a double prodrug of antiproliferative nucleotide analog 9-(2-Phosphonylmethoxyethyl)guanine (PMEG), with potent in vivo efficacy against various hematological malignancies. This study investigates the role of adenosine deaminase-like (ADAL) protein in the intracellular activation of GS-9219.

Materials And Methods: A cell line resistant to 9-(2-Phosphonylmethoxyethyl)-N(6)-cyclopropyl-2,6-diaminopurine (cPrPMEDAP), an intermediate metabolite of GS-9219, was generated and characterized.

Genetic susceptibility to refractive error: association of vasoactive intestinal peptide receptor 2 (VIPR2) with high myopia in Chinese.

Myopia is the most common ocular disease worldwide. We investigated the association of high myopia with the common single nucleotide polymorphisms (SNPs) of five candidate genes - early growth response 1 (EGR1), v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS), jun oncogene (JUN), vasoactive intestinal peptide (VIP), and vasoactive intestinal peptide receptor 2 (VIPR2). We recruited 1200 unrelated Chinese subjects with 600 cases (spherical equivalent ≤-8.

Powerful tests for association on quantitative trait loci incorporating imprinting effects.

Genomic imprinting is an important epigenetic factor in complex traits study, and there has recently been considerable interest in association study for quantitative traits by incorporating imprinting. However, these methods need the assumptions of Hardy-Weinberg equilibrium or only use information from families with one child. In this paper, by taking imprinting into account and making no assumption about the distribution of the quantitative traits, we propose two novel classes of Q-C-TDTI(c) and Q-C-MAX(c) family-based association tests for quantitative traits.

Evaluation of radiosurgery techniques--cone-based linac radiosurgery vs tomotherapy-based radiosurgery.

Performances of radiosurgery of intracranial lesions between cone-based Linac system and Tomotherapy-based system were compared in terms of dosimetry and time. Twelve patients with single intracranial lesion treated with cone-based Linac radiosurgery system from 2005 to 2009 were replanned for Tomotherapy-based radiosurgery treatment. The conformity index, homogeneity index (HI), and gradient score index (GSI) of each case was calculated.

A novel missense mutation in the NYX gene associated with high myopia.

Purpose: Myopia is a complex eye disorder. The X-linked form of complete congenital stationary night blindness (CSNB1A) is usually associated with moderate to high myopia, and is caused by mutations in the NYX gene. We explored if NYX mutations could be associated with high myopia, but not CSNB1A.

Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing.

Background: Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community.

Insertion/deletion polymorphisms in the ΔNp63 promoter are a risk factor for bladder exstrophy epispadias complex.

Bladder exstrophy epispadias complex (BEEC) is a severe congenital anomaly; however, the genetic and molecular mechanisms underlying the formation of BEEC remain unclear. TP63, a member of TP53 tumor suppressor gene family, is expressed in bladder urothelium and skin over the external genitalia during mammalian development. It plays a role in bladder development.

Copy number and expression alterations of miRNAs in the ovarian cancer cell line OVCAR-3: impact on kallikrein 6 protein expression.

Background: Kallikrein-related peptidase 6 (KLK6), a member of the serine protease family of kallikrein (KLK) genes, is dysregulated in ovarian carcinomas (OCa) and its overexpression is associated with poor prognosis. Regulation of its expression is poorly understood and is likely to be influenced by multiple mechanisms. The KLK locus is subject to copy number changes and heterogeneity in serous OCas.

Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case-control study in Chinese.

Background: The UMODL1 gene was found to be associated with high myopia in Japanese. This study aimed to investigate this gene for association with high myopia in Chinese.

Methods: Two groups of unrelated Han Chinese from Hong Kong were recruited using the same criteria: Sample Set 1 comprising 356 controls (spherical equivalent, SE, within ±1 diopter or D) and 356 cases (SE ≤ -8D), and Sample Set 2 comprising 394 controls and 526 cases.

Lipid-sensing high-throughput ApoA-I assays.

Apolipoprotein A-I (ApoA-I), a primary protein component of high-density lipoprotein (HDL), plays an important role in cholesterol metabolism mediating the formation of HDL and the efflux of cellular cholesterol from macrophage foam cells in arterial walls. Lipidation of ApoA-I is mediated by adenosine triphosphate (ATP) binding cassette A1 (ABCA1). Insufficient ABCA1 activity may lead to increased risk of atherosclerosis due to reduced HDL formation and cholesterol efflux.

Association of high myopia with crystallin beta A4 (CRYBA4) gene polymorphisms in the linkage-identified MYP6 locus.

Background: Myopia is the most common ocular disorder worldwide and imposes tremendous burden on the society. It is a complex disease. The MYP6 locus at 22 q12 is of particular interest because many studies have detected linkage signals at this interval.

The HCV non-nucleoside inhibitor Tegobuvir utilizes a novel mechanism of action to inhibit NS5B polymerase function.

Tegobuvir (TGV) is a novel non-nucleoside inhibitor (NNI) of HCV RNA replication with demonstrated antiviral activity in patients with genotype 1 chronic HCV infection. The mechanism of action of TGV has not been clearly defined despite the identification of resistance mutations mapping to the NS5B polymerase region. TGV does not inhibit NS5B enzymatic activity in biochemical assays in vitro, suggesting a more complex antiviral mechanism with cellular components.

A powerful parent-of-origin effects test for qualitative traits incorporating control children in nuclear families.

Genomic imprinting is an important epigenetic phenomenon in studying complex traits and has generally been examined by detecting parent-of-origin effects of alleles. The parental-asymmetry test (PAT) based on nuclear families with both parents and its extensions to deal with missing parental genotypes is simple and powerful for such a task. However, these methods only use case (affected) children in nuclear families and thus do not make full use of information on control (unaffected) children, if available, in these families.

N-glycosylation of colorectal cancer tissues: a liquid chromatography and mass spectrometry-based investigation.

Colorectal cancer is the third most common cancer worldwide with an annual incidence of ~1 million cases and an annual mortality rate of ~655,000 individuals. There is an urgent need for identifying novel targets to develop more sensitive, reliable, and specific tests for early stage detection of colon cancer. Post-translational modifications are known to play an important role in cancer progression and immune surveillance of tumors.

Assessment of extracts from red yeast rice for herb-drug interaction by in-vitro and in-vivo assays.

Red yeast rice (RYR) is made by fermenting the yeast Monascus purpureus over rice. It is a source of natural red food colorants, a food garnish and a traditional medication. Results of the current study demonstrated that polar fractions of the RYR preparations contained herbal-drug interaction activity, which if left unremoved, enhanced P-glycoprotein activity and inhibited the major drug metabolizing cytochromes P450, i,e, CYP 1A2, 2C9 and 3A4.

Association of IGF1 gene haplotypes with high myopia in Chinese adults.

Objective: To investigate the association of high myopia with common single-nucleotide polymorphisms (SNPs) in the IGF1, IGFBP3, and IGFBP4 genes in a Chinese population.

Methods: For our case-control study, we recruited 600 unrelated participants: 300 case participants with high myopia (-8.00 diopters or less) and 300 emmetropic controls (within ±1.

Identifying contributors of two-person DNA mixtures by familial database search.

The role of familial database search as a crime-solving tool has been increasingly recognized by forensic scientists. As an enhancement to the existing familial search approach on single source cases, this article presents our current progress in exploring the potential use of familial search to mixture cases. A novel method was established to predict the outcome of the search, from which a simple strategy for determining an appropriate scale of investigation by the police force is developed.

Attitudes and perceived barriers influencing incident reporting by nurses and their correlation with reported incidents: A systematic review.

Background: Clinical incident reporting is an integral feature of risk management system in the healthcare sector. By reporting clinical incidents, nurses allow for learning from errors, identification of error patterns and development of error preventive strategies. The need to understand attitudes to reporting, perceived barriers and incident reporting patterns by nurses are the core highlights of this review.

Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage.

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined.

Robust Mantel-Haenszel test under genetic model uncertainty allowing for covariates in case-control association studies.

The trend test under the additive model is commonly used when a case-control genetic association study is carried out. However, for many complex diseases, the underlying genetic models are unknown and a mis-specification of the genetic model may result in a substantial loss of power. MAX3 has been proposed as an efficiency robust test against genetic model uncertainty which takes the maximum absolute value of the trend test statistics under the recessive, additive, and dominant models.

Dosimetric evaluation of a three-phase adaptive radiotherapy for nasopharyngeal carcinoma using helical tomotherapy.

Adaptive radiotherapy (ART) has been introduced to correct the radiation-induced anatomic changes in head and neck cases during a treatment course. This study evaluated the potential dosimetric benefits of applying a 3-phase adaptive radiotherapy protocol in nasopharyngeal carcinoma (NPC) patients compared with the nonadaptive single-phase treatment protocol. Ten NPC patients previously treated with this 3-phase radiation protocol using Hi-Art Tomotherapy were recruited.