Structural alignment of RNA with triple helix structure

Structural alignment is useful in identifying members of ncRNAs. Existing tools are all based on the secondary structures of the molecules. There is evidence showing that tertiary interactions (the interaction between a single-stranded nucleotide and a base-pair) in triple helix structures are critical in some functions of ncRNAs. In this article, we address the problem of structural alignment of RNAs with the triple helix. We provide a formal definition to capture a simplified model of a triple helix structure, then develop an algorithm of O(mn(3)) time to align a query sequence (of length m) with known triple helix structure with a target sequence (of length n) with an unknown structure. The resulting algorithm is shown to be useful in identifying ncRNA members in a simulated genome. © Copyright 2012, Mary Ann Liebert, Inc. 2012.published_or_final_versio

2(Phenylmethylthio)benzaldehyde

In the title compound, C14H12OS, the two planar benzaldehyde and benzyl groups are inclined at 77.7 (1) °. The torsion angle about the central C--S bond is 174.9 (2) °. The molecules are held together in the crystal by van der Waals interactions.published_or_final_versio

Patient-specific instrument can achieve same accuracy with less resection time than navigation assistance in periacetabular pelvic tumor surgery: A cadaveric study

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Three Extensions of Tong and Richardson’s Algorithm for Finding the Optimal Path in Schedule-Based Railway Networks

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The pattern of cervical cancer screening in Hong Kong

Health Services Research Fund & Health Care and Promotion Fund: Research Dissemination Reports (Series 2)published_or_final_versio

Opioid-sparing effects of perioperative paracetamol and nonsteroidal anti-inflammatory drugs (NSAIDs) in children.

Perioperative pain in children can be effectively managed with systemic opioids, but addition of paracetamol or nonsteroidal anti-inflammatory drugs (NSAIDs) may reduce opioid requirements and potentially improve analgesia and/or reduce adverse effects

Risks for heart disease and lung cancer from passive smoking by workers in the catering industry

Workers in the catering industry are at greater risk of exposure to secondhand smoke (SHS) when smoke-free workplace policies are not in force. We determined the exposure of catering workers to SHS in Hong Kong and their risk of death from heart disease and lung cancer. Nonsmoking catering workers were provided with screening at their workplaces and at a central clinic. Participants reported workplace, home, and leisure time exposure to SHS. Urinary cotinine was estimated by enzyme immunoassay. Catering facilities were classified into three types: nonsmoking, partially restricted smoking (with nonsmoking areas), and unrestricted smoking. Mean urinary cotinine levels ranged from 3.3 ng/ml in a control group of 16 university staff through 6.4 ng/ml (nonsmoking), 6.1 ng/ml (partially restricted), and 15.9 ng/ml (unrestricted smoking) in 104 workers who had no exposures outside of work. Workers in nonsmoking facilities had exposures to other smoking staff. We modeled workers' mortality risks using average cotinine levels, estimates of workplace respirable particulates, risk data for cancer and heart disease from cohort studies, and national (US) and regional (Hong Kong) mortality for heart disease and lung cancer. We estimated that deaths in the Hong Kong catering workforce of 200,000 occur at the rate of 150 per year for a 40-year working-lifetime exposure to SHS. When compared with the current outdoor air quality standards for particulates in Hong Kong, 30% of workers exceeded the 24-h and 98% exceeded the annual air quality objectives due to workplace SHS exposures. © 2006 Oxford University Press.postprin

The health benefits of reduced air pollution: value and trade-offs

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Risk factors of developmental defects of enamel - A prospective cohort study

BACKGROUND AND OBJECTIVE: Current studies on the aetiology of developmental defects of enamel (DDE) are subject to recall bias because of the retrospective collection of information. Our objective was to investigate potential risk factors associated with the occurrence of DDE through a prospective cohort study. METHODS: Using a random community sample of Hong Kong children born in 1997, we performed a cohort study in which the subjects' background information, medical and dental records were prospectively collected. A clinical examination to identify DDE was conducted in 2010 when the subjects were 12 years old. The central incisor, lateral incisor and first molar in each quadrant were chosen as the index teeth and were examined 'wet' by two trained and calibrated examiners using the modified FDI (DDE) Index. RESULTS: With a response rate of 74.9%, the 514 examined subjects had matched data for background information. Diffuse opacites were the most common type of DDE. Of the various possible aetiological factors considered, only experience of severe diseases during the period 0-3 years was associated with the occurrence of 'any defect' (p = 0.017) and diffuse opacities (p = 0.044). The children with experience of severe diseases before 3 years of age were 7.89 times more likely to be affected by 'any defect' compared with those who did not have the experience (OR 7.89; 95% CI 1.07, 58.14; p = 0.043). However, after adjusting for confounding factors, the association no longer existed. CONCLUSION: No variables could be identified as risk factors of DDE in this Hong Kong birth cohort.published_or_final_versio

An efficient algorithm for optimizing whole genome alignment with noise

Motivation: This paper is concerned with algorithms for aligning two whole genomes so as to identify regions that possibly contain conserved genes. Motivated by existing heuristic-based software tools, we initiate the study of an optimization problem that attempts to uncover conserved genes with a global concern. Another interesting feature in our formulation is the tolerance of noise, which also complicates the optimization problem. A brute-force approach takes time exponential in the noise level. Results: We show how an insight into the optimization structure can lead to a drastic improvement in the time and space requirement [precisely, to O(k2n2) and O(k2n), respectively, where n is the size of the input and k is the noise level]. The reduced space requirement allows us to implement the new algorithm, called MaxMinCluster, on a PC. It is exciting to see that when tested with different real data sets, MaxMinCluster consistently uncovers a high percentage of conserved genes that have been published by GenBank. Its performance is indeed favorably compared to MUMmer (perhaps the most popular software tool for uncovering conserved genes in a whole-genome scale). © Oxford University Press 2004; all rights reserved.published_or_final_versio