Low W.Y.,Perdana University
AIP Conference Proceedings | Year: 2017
The Shannon entropy equation provides a way to estimate variability of amino acids sequences in a multiple sequence alignment of proteins. Knowledge of protein variability is useful in many areas such as vaccine design, identification of antibody binding sites, and exploration of protein 3D structural properties. In cases where the population entropies of a protein are of interest but only a small sample size can be obtained, a method based on linear regression and random subsampling can be used to estimate the population entropy. This method is useful for comparisons of entropies where the actual sequence counts differ and thus, correction for alignment size bias is needed. In the current work, an R based package named EntropyCorrect that enables estimation of population entropy is presented and an empirical study on how well this new algorithm performs on simulated dataset of various combinations of population and sample sizes is discussed. The package is available at https://github.com/lloydlow/EntropyCorrect. © 2017 Author(s).
Liu S.-H.,Johns Hopkins University |
Liu S.-H.,Chang Gung Memorial Hospital |
Cummings D.A.T.,Johns Hopkins University |
Zenilman J.M.,Johns Hopkins University |
And 3 more authors.
Cancer Epidemiology Biomarkers and Prevention | Year: 2014
Background: Variable detection of human papillomavirus (HPV) DNA can result in misclassification of infection status, but the extent of misclassification has not been quantitatively evaluated. Methods: In 2005-2007, 33 women of ages 22 to 53 years self-collected vaginal swabs twice per week for 16 consecutive weeks. Each of the 955 swabs collected was tested for 37 HPV types/subtypes. Assuming that a woman's underlying infection status did not change over the short study period, biases in prevalence estimates obtained from single versus multiple swabs were calculated. Using event history analysis methods, time to recurrent gain and loss of at least one HPV type was determined, separately. Baseline any-type and high risk- type HPV prevalence was 60.6% and 24.2%, respectively. Cumulative any-HPV and high-risk HPV prevalence over the 16-week period was 84.8% and 60.6%, separately. Results: Overall, there were 319 events of detection and 313 events of loss of detection. Median times to a recurrent detection and loss of detection were 11 and seven days, respectively. Neither vaginal sex nor condom use during follow-up was associated with recurrent viral detection or loss of detection. Assuming the cumulative 16-week prevalence reflects the true prevalence of infection, the baseline any-HPV prevalence underestimated infection status by 24.2%, with a bootstrapped mean of 20.2% [95% confidence interval (CI), 8.9%-29.6%]. Conclusions: These findings suggest that a substantial proportion of HPV-infected women are misclassified as being uninfected when using a single-time DNA measurement. Impact: Short-term variation in detectable HPV DNA needs to be considered while interpreting the natural history of infections using single samples collected at long intervals. Cancer Epidemiol Biomarkers Prev; 23(1); 200-8. © 2013 AACR.
Rositch A.F.,University of Maryland, Baltimore |
Nowak R.G.,University of Maryland, Baltimore |
Gravitt P.E.,Perdana University
Cancer | Year: 2014
BACKGROUND Invasive cervical cancer is thought to decline in women over 65 years old, the age at which cessation of routine cervical cancer screening is recommended. However, national cervical cancer incidence rates do not account for the high prevalence of hysterectomy in the United States. METHODS Using estimates of hysterectomy prevalence from the Behavioral Risk Factor Surveillance System (BRFSS), hysterectomy-corrected age-standardized and age-specific incidence rates of cervical cancer were calculated from the Surveillance, Epidemiology, and End Results (SEER) 18 registry in the United States from 2000 to 2009. Trends in corrected cervical cancer incidence across age were analyzed using Joinpoint regression. RESULTS Unlike the relative decline in uncorrected rates, corrected rates continue to increase after age 35-39 (APCCORRECTED=10.43) but at a slower rate than in 20-34 years (APCCORRECTED=161.29). The highest corrected incidence was among 65- to 69-year-old women, with a rate of 27.4 cases per 100,000 women as opposed to the highest uncorrected rate of 15.6 cases per 100,000 aged 40 to 44 years. Correction for hysterectomy had the largest impact on older, black women given their high prevalence of hysterectomy. CONCLUSIONS Correction for hysterectomy resulted in higher age-specific cervical cancer incidence rates, a shift in the peak incidence to older women, and an increase in the disparity in cervical cancer incidence between black and white women. Given the high and nondeclining rate of cervical cancer in women over the age of 60 to 65 years, when women are eligible to exit screening, risk and screening guidelines for cervical cancer in older women may need to be reconsidered. Cancer 2014;120:2032-2038. © 2014 American Cancer Society.
Parthiban N.,University of Adelaide |
Parthiban N.,Perdana University |
Esterman A.,University of South Australia |
Mahajan R.,University of Adelaide |
And 7 more authors.
Journal of the American College of Cardiology | Year: 2015
Abstract Background Remote monitoring (RM) of implantable cardioverter-defibrillators (ICD) is an established technology integrated into clinical practice. One recent randomized controlled trial (RCT) and several large device database studies have demonstrated a powerful survival advantage for ICD patients undergoing RM compared with those receiving conventional in-office (IO) follow-up. Objectives This study sought to conduct a systematic published data review and meta-analysis of RCTs comparing RM with IO follow-up. Methods Electronic databases and reference lists were searched for RCTs reporting clinical outcomes in ICD patients who did or did not undergo RM. Data were extracted from 9 RCTs, including 6,469 patients, 3,496 of whom were randomized to RM and 2,973 to IO follow-up. Results In the RCT setting, RM demonstrated clinical outcomes comparable with office follow-up in terms of all-cause mortality (odds ratio [OR]: 0.83; p = 0.285), cardiovascular mortality (OR: 0.66; p = 0.103), and hospitalization (OR: 0.83; p = 0.196). However, a reduction in all-cause mortality was noted in the 3 trials using home monitoring (OR: 0.65; p = 0.021) with daily verification of transmission. Although the odds of receiving any ICD shock were similar in RM and IO patients (OR: 1.05; p = 0.86), the odds of inappropriate shock were reduced in RM patients (OR: 0.55; p = 0.002). Conclusions Meta-analysis of RCTs demonstrates that RM and IO follow-up showed comparable overall outcomes related to patient safety and survival, with a potential survival benefit in RCTs using daily transmission verification. RM benefits include more rapid clinical event detection and a reduction in inappropriate shocks. © 2015 American College of Cardiology Foundation.
Gravitt P.E.,Perdana University
Journal of Clinical Investigation | Year: 2011
The discovery that certain high-risk strains of human papillomavirus (HR-HPV) cause nearly 100% of invasive cervical cancer has spurred a revolution in cervical cancer prevention by promoting the development of viral vaccines. Although the efficacy of these vaccines has already been demonstrated, a complete understanding of viral latency and natural immunity is lacking, and solving these mysteries could help guide policies of cervical cancer screening and vaccine use. Here, we examine the epidemiological and biological understanding of the natural history of HPV infection, with an eye toward using these studies to guide the implementation of cervical cancer prevention strategies.
Burke A.E.,Family and Reproductive Health |
Gravitt P.E.,Perdana University
Cancer Research | Year: 2012
Understanding the fraction of newly detected human papillomavirus (HPV) infections due to acquisition and reactivation has important implications on screening strategies and prevention of HPV-associated neoplasia. Information on sexual activity and cervical samples for HPV DNA detection using Roche Linear Array were collected semiannually for two years from 700 women ages 35 to 60 years. Incidence and potential fraction of HPV associated with new and lifetime sexual partnerships were estimated using Poisson regression. Cox frailty models were used to estimate hazard ratios (HR) for potential risk factors of incident HPV detection. Recent and lifetime numbers of sexual partners were both strongly associated with incident HPV detection. However, only 13% of incident detections were attributed to new sexual partners, whereas 72% were attributed to 5 or more lifetime sexual partners. Furthermore, 155 of 183 (85%) incident HPV detections occurred during periods of sexual abstinence or monogamy, and were strongly associated with cumulative lifetime sexual exposure [HR: 4.1, 95% confidence interval (CI): 2.0-8.4). This association increased with increasing age. These data challenge the paradigm that incident HPV detection is driven by current sexual behavior and new viral acquisition in older women. Our observation that most incident HPV infection was attributable to past, not current, sexual behavior at older ages supports a natural history model of viral latency and reactivation. As the more highly exposed babyboomer generation of women with sexual debut after the sexual revolution transition to menopause, the implications of HPV reactivation at older ages on cervical cancer risk and screening recommendations should be carefully evaluated. ©2012 AACR.
Masica D.L.,Johns Hopkins University |
Sosnay P.R.,Johns Hopkins University |
Sosnay P.R.,Perdana University |
Cutting G.R.,Johns Hopkins University |
Karchin R.,Johns Hopkins University
Human Mutation | Year: 2012
Cystic fibrosis transmembrane conductance regulator (CFTR) mutation is associated with a phenotypic spectrum that includes cystic fibrosis (CF). The disease liability of some common CFTR mutations is known, but rare mutations are seen in too few patients to categorize unequivocally, making genetic diagnosis difficult. Computational methods can predict the impact of mutation, but prediction specificity is often below that required for clinical utility. Here, we present a novel supervised learning approach for predicting CF from CFTR missense mutation. The algorithm begins by constructing custom multiple sequence alignments called phenotype-optimized sequence ensembles (POSEs). POSEs are constructed iteratively, by selecting sequences that optimize predictive performance on a training set of CFTR mutations of known clinical significance. Next, we predict CF disease liability from a different set of CFTR mutations (test-set mutations). This approach achieves improved prediction performance relative to popular methods recently assessed using the same test-set mutations. Of clinical significance, our method achieves 94% prediction specificity. Because databases such as HGMD and locus-specific mutation databases are growing rapidly, methods that automatically tailor their predictions for a specific phenotype may be of immediate utility. If the performance achieved here generalizes to other systems, the approach could be an excellent tool to help establish genetic diagnoses. © 2012 Wiley Periodicals, Inc.
Abidin Z.L.Z.,Perdana University |
Ming W.T.,Sungai Buloh Hospital |
Loch A.,University of Malaya |
Hilmi I.,University of Malaya |
Hautmann O.,University of Malaya
Transplant International | Year: 2013
The rate of organ donations from deceased donors in Malaysia is among the lowest in the world. This may be because of the passivity among health professionals in approaching families of potential donors. A questionnaire-based study was conducted amongst health professionals in two tertiary hospitals in Kuala Lumpur, Malaysia. Four hundred and sixty-two questionnaires were completed. 93.3% of health professionals acknowledged a need for organ transplantation in Malaysia. 47.8% were willing to donate their organs (with ethnic and religious differences). Factors which may be influencing the shortage of organs from deceased donors include: nonrecognition of brainstem death (38.5%), no knowledge on how to contact the Organ Transplant Coordinator (82.3%), and never approaching families of a potential donor (63.9%). There was a general attitude of passivity in approaching families of potential donors and activating transplant teams among many of the health professionals. A misunderstanding of brainstem death and its definition hinder identification of a potential donor. Continuing medical education and highlighting the role of the Organ Transplant Coordinator, as well as increasing awareness of the public through religion and the media were identified as essential in improving the rate of organ donations from deceased donors in Malaysia. © 2012 The Authors Transplant International © 2012 European Society for Organ Transplantation. Published by Blackwell Publishing Ltd.
Niroumand H.,Perdana University
2nd International Conference on Sustainable Construction Materials and Technologies | Year: 2010
The earth brick are including of clay, water and different materials. The earth bricks can make an evolution for reduce of cost and increase of compressive strength compared to concrete blocks. The last experiments showed weakness in earth blocks without additional materials. Thus we had many testing in earth bricks with different additional materials. In this paper we had survey role of shred tires in earth brick strength compared to wood particles. This paper showed change of compressive strength in earth bricks with different additional material due to made different bricks with shred tires and wood particles by sizes 10cm×10cm×10cm in compressive tests 3,7,14 and 21 days and bricks had 20% moisture content. The tires are one of which environmental pollution and less is used after consumption in the automotive industry, thus we used a cheap material for survey of strength in earth brick.
Rafiza S.,Institute for Medical Research |
Rampal K.G.,Perdana University
International Journal of Tuberculosis and Lung Disease | Year: 2012
BACKGROUND: Serial testing for tuberculosis (TB) exposure has been advocated among health care workers (HCWs) at risk of nosocomial infection. OBJECTIVE: To determine the incidence and factors associated with TB infection among selected HCWs in Malaysia and to determine interferon-gamma response in serial testing. DESIGN: A cohort of 769 HCWs were retested after 1 year using QuantiFERON®-TB Gold In-Tube. Incidence of TB infection was determined among HCWs who previously tested negative. Conversion and reversion rates using several definitions were explored. RESULTS: Incidence of TB infection was 9.9 per 100 workers per year (95%CI 7.9-12.3). Working in the Emergency Department (ED; RR 2.18, 95%CI 1.07-4.43) was significantly associated with risk of TB infection. Reversion and conversion occurred frequently, with 46.7% reversion among HCWs with baseline interferon-gamma (IFN-γ) levels of 0.35-0.70 international units (IU)/ml, and 23.8% conversion among HCWs with baseline IFN-γ levels of 0.20-0.34 IU/ml. CONCLUSIONS: TB infection control measures need to be strengthened, particularly in the ED, as the incidence of TB was high. Conversion and reversion rates in serial testing were high, and further studies are needed to facilitate its interpretation. © 2012 The Union.