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Search Results: 1 - 10 of 53083 matches for " David Lye "
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Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics  [PDF]
Hailan Piao, Lye Meng Markillie, David E. Culley, Roderick I. Mackie, Matthias Hess
Advances in Microbiology (AiM) , 2013, DOI: 10.4236/aim.2013.31016

Metatranscriptomics—gene express profiling via DNA sequencing—is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of several phenotypes) of a microbial community. Furthermore, metatranscriptome studies can result in extensive catalogues of genes that encode for enzymes of industrial relevance. In both cases, a major challenge for generating a high quality metatranscriptome is the extreme lability of RNA and its susceptibility to ubiquitous RNAses. The microbial community (the microbiome) of the cow rumen efficiently degrades lignocelullosic biomass, generates significant amounts of methane, a greenhouse gas twenty times more potent than carbon dioxide, and is of general importance for the physiological wellbeing of the host animal. Metatranscriptomes of the rumen microbiome from animals kept under different conditions and from various types of rumen-incubated biomass can be expected to provide new insights into these highly interesting phenotypes and subsequently provide the framework for an enhanced understanding of this socioeconomically important ecosystem. The ability to isolate large amounts of intact RNA will significantly facilitate accurate transcript annotation and expression profiling. Here we report a method that combines mechanical disruption with chemical homogenization of the sample material and consistently yields 1 mg of intact RNA from 1 g of rumen-incubated biofuel feedstock. The yield of total RNA obtained with our method exceeds the RNA yield achieved with previously reported isolation techniques, which renders RNA isolated with the method presented here as an ideal starting material for metatranscriptomic analyses and other molecular biology applications that require significant amounts of starting material.

Combination strategies for pandemic influenza response - a systematic review of mathematical modeling studies
Vernon J Lee, David C Lye, Annelies Wilder-Smith
BMC Medicine , 2009, DOI: 10.1186/1741-7015-7-76
Abstract: We searched modeling publications through PubMed and associated references from 1990 to 30 September 2009. Inclusion criteria were modeling papers quantifying the effectiveness of combination strategies, both pharmaceutical and non-pharmaceutical.Nineteen modeling papers on combination strategies were selected. Four studies examined combination strategies on a global scale, 14 on single countries, and one on a small community. Stochastic individual-based modeling was used in nine studies, stochastic meta-population modeling in five, and deterministic compartmental modeling in another five. As part of combination strategies, vaccination was explored in eight studies, antiviral prophylaxis and/or treatment in 16, area or household quarantine in eight, case isolation in six, social distancing measures in 10 and air travel restriction in six studies. Two studies suggested a high probability of successful influenza epicenter containment with combination strategies under favorable conditions. During a pandemic, combination strategies delayed spread, reduced overall number of cases, and delayed and reduced peak attack rate more than individual strategies. Combination strategies remained effective at high reproductive numbers compared with single strategy. Global cooperative strategies, including redistribution of antiviral drugs, were effective in reducing the global impact and attack rates of pandemic influenza.Combination strategies increase the effectiveness of individual strategies. They include pharmaceutical (antiviral agents, antibiotics and vaccines) and non-pharmaceutical interventions (case isolation, quarantine, personal hygiene measures, social distancing and travel restriction). Local epidemiological and modeling studies are needed to validate efficacy and feasibility.Many countries have developed pandemic preparedness plans in response to the threat from pandemic influenza [1], to attempt containment of the virus or to reduce the pandemic's impact. The influe
Assessment of Microbial Communities and Their Relationship with Enzymatic Activity during Composting  [PDF]
Khoshrooz Kazemi, Baiyu Zhang, Leonard M. Lye
World Journal of Engineering and Technology (WJET) , 2017, DOI: 10.4236/wjet.2017.53B011
Microbial communities and enzyme activities are the main players during municipal solid waste (MSW) composting, but the relationship between microbial communities (i.e., mesophilic and thermophilic ones) and enzyme activities (i.e., dehydrogenase, β-glucosidase, phosphatase and urea) has not been well studied. Therefore, the objective of this work is to determine the enzymes profiles during municipal solid waste (MSW) composting and study the relationship between the mesophilic and thermophilic microbial profiles and enzyme activities. MSW was composted in a bench-scale composting reactor. Parameters including temperature, oxygen uptake rate, numbers of microbial populations (mesophilic and thermophilic bacteria and fungi) and enzyme activities were measured. Results showed higher dehydrogenase activities are related to higher numbers of mesophilic bacteria, while higher phosphatase and urea activities are associated with higher numbers of thermophilic fungi and mesophilic bacteria at the later stage of composting. In addition, results of the correlation analysis indicated significant correlations among enzyme activities and microbial population.
Diabetes with Hypertension as Risk Factors for Adult Dengue Hemorrhagic Fever in a Predominantly Dengue Serotype 2 Epidemic: A Case Control Study
Junxiong Pang ,Agus Salim,Vernon J. Lee,Martin L. Hibberd,Kee Seng Chia,Yee Sin Leo,David C. Lye
PLOS Neglected Tropical Diseases , 2012, DOI: 10.1371/journal.pntd.0001641
Abstract: Background Dengue hemorrhagic fever (DHF) is a severe form of dengue, characterized by bleeding and plasma leakage. A number of DHF risk factors had been suggested. However, these risk factors may not be generalized to all populations and epidemics for screening and clinical management of patients at risk of developing DHF. This study explored demographic and comorbidity risk factors for DHF in adult dengue epidemics in Singapore in year 2006 (predominantly serotype 1) and in year 2007–2008 (predominantly serotype 2). Methods A retrospective case-control study was conducted with 149 DHF and 326 dengue fever (DF) patients from year 2006, and 669 DHF and 1,141 DF patients from year 2007–2008. Demographic and reported comorbidity data were collected from patients previously. We performed multivariate logistic regression to assess the association between DHF and demographic and co-morbidities for year 2006 and year 2007–2008, respectively. Results Only Chinese (adjusted odds ratio [AOR] = 1.90; 95% confidence interval [CI]: 1.01–3.56) was independently associated with DHF in year 2006. In contrast, age groups of 30–39 years (AOR = 1.41; 95% CI:1.09–1.81), 40–49 years (AOR = 1.34; 95% CI:1.09–1.81), female (AOR = 1.57; 95% CI:1.28–1.94), Chinese (AOR = 1.67; 95% CI:1.24–2.24), diabetes (AOR = 1.78; 95% CI:1.06–2.97), and diabetes with hypertension (AOR = 2.16; 95%CI:1.18–3.96) were independently associated with DHF in year 2007–2008. Hypertension was proposed to have effect modification on the risk of DHF outcome in dengue patients with diabetes. Chinese who had diabetes with hypertension had 2.1 (95% CI:1.07–4.12) times higher risk of DHF compared with Chinese who had no diabetes and no hypertension. Conclusions Adult dengue patients in Singapore who were 30–49 years, Chinese, female, had diabetes or diabetes with hypertension were at greater risk of developing DHF during epidemic of predominantly serotype 2. These risk factors can be used to guide triaging of patients who require closer clinical monitoring and early hospitalization in Singapore, when confirmed in more studies.
Clinical Relevance and Discriminatory Value of Elevated Liver Aminotransferase Levels for Dengue Severity
Linda K. Lee ,Victor C. Gan,Vernon J. Lee,Adriana S. Tan,Yee Sin Leo,David C. Lye
PLOS Neglected Tropical Diseases , 2012, DOI: 10.1371/journal.pntd.0001676
Abstract: Background Elevation of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) is prominent in acute dengue illness. The World Health Organization (WHO) 2009 dengue guidelines defined AST or ALT≥1000 units/liter (U/L) as a criterion for severe dengue. We aimed to assess the clinical relevance and discriminatory value of AST or ALT for dengue hemorrhagic fever (DHF) and severe dengue. Methodology/Principal Findings We retrospectively studied and classified polymerase chain reaction positive dengue patients from 2006 to 2008 treated at Tan Tock Seng Hospital, Singapore according to WHO 1997 and 2009 criteria for dengue severity. Of 690 dengue patients, 31% had DHF and 24% severe dengue. Elevated AST and ALT occurred in 86% and 46%, respectively. Seven had AST or ALT≥1000 U/L. None had acute liver failure but one patient died. Median AST and ALT values were significantly higher with increasing dengue severity by both WHO 1997 and 2009 criteria. However, they were poorly discriminatory between non-severe and severe dengue (e.g., AST area under the receiver operating characteristic [ROC] curve = 0.62; 95% confidence interval [CI]: 0.57–0.67) and between dengue fever (DF) and DHF (AST area under the ROC curve = 0.56; 95% CI: 0.52–0.61). There was significant overlap in AST and ALT values among patients with dengue with or without warning signs and severe dengue, and between those with DF and DHF. Conclusions Although aminotransferase levels increased in conjunction with dengue severity, AST or ALT values did not discriminate between DF and DHF or non-severe and severe dengue.
Detection of Genetically Altered Copper Levels in Drosophila Tissues by Synchrotron X-Ray Fluorescence Microscopy
Jessica C. Lye, Joab E. C. Hwang, David Paterson, Martin D. de Jonge, Daryl L. Howard, Richard Burke
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026867
Abstract: Tissue-specific manipulation of known copper transport genes in Drosophila tissues results in phenotypes that are presumably due to an alteration in copper levels in the targeted cells. However direct confirmation of this has to date been technically challenging. Measures of cellular copper content such as expression levels of copper-responsive genes or cuproenzyme activity levels, while useful, are indirect. First-generation copper-sensitive fluorophores show promise but currently lack the sensitivity required to detect subtle changes in copper levels. Moreover such techniques do not provide information regarding other relevant biometals such as zinc or iron. Traditional techniques for measuring elemental composition such as inductively coupled plasma mass spectroscopy are not sensitive enough for use with the small tissue amounts available in Drosophila research. Here we present synchrotron x-ray fluorescence microscopy analysis of two different Drosophila tissues, the larval wing imaginal disc, and sectioned adult fly heads and show that this technique can be used to detect changes in tissue copper levels caused by targeted manipulation of known copper homeostasis genes.
Formative evaluation of the telecare fall prevention project for older veterans
Isomi M Miake-Lye, Angel Amulis, Debra Saliba, Paul G Shekelle, Linda K Volkman, David A Ganz
BMC Health Services Research , 2011, DOI: 10.1186/1472-6963-11-119
Abstract: To evaluate the intervention we: 1) interviewed patient and employee stakeholders, 2) reviewed participating patients' electronic health record data and 3) abstracted information from meeting minutes. We describe the implementation process, including whether the project was implemented according to plan; identify barriers and facilitators to implementation; and assess the incremental benefit to the quality of health care for fall prevention received by patients in the project. We also estimate the cost of developing the pilot project.The project underwent multiple changes over its life span, including the addition of an option to mail patients educational materials about falls. During the project's lifespan, 113 patients were considered for inclusion and 35 participated. Patient and employee interviews suggested support for the project, but revealed that transportation to medical care was a major barrier in following up on fall risks identified by nurse telephone triage. Medical record review showed that the project enhanced usual medical care with respect to home safety counseling. We discontinued the program after 18 months due to staffing limitations and competing priorities. We estimated a cost of $9194 for meeting time to develop the project.The project appeared feasible at its outset but could not be sustained past the first cycle of evaluation due to insufficient resources and a waning of local leadership support due to competing national priorities. Future projects will need both front-level staff commitment and prolonged high-level leadership involvement to thrive.One quarter to one third of people aged 65 years and older experience at least one fall annually[1]. The effects of falls can impact daily life for community-dwelling older adults (those living independently outside of nursing homes or facilities that provide similar levels of care) [2,3]. Falls, or even the fear of falling, can cause older people to limit their activities, reducing their independ
Implications of Discordance in World Health Organization 1997 and 2009 Dengue Classifications in Adult Dengue
Victor C. Gan, David C. Lye, Tun L. Thein, Frederico Dimatatac, Adriana S. Tan, Yee-Sin Leo
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060946
Abstract: Background Revised dengue guidelines were published by the World Health Organization (WHO) in 2009 addressing severe dengue cases not classified by dengue hemorrhagic fever (DHF) and shock syndrome (DSS). Methods and Principal Findings We conducted a retrospective cohort study to compare WHO 2009 and 1997 classifications using 1278 adult dengue cases confirmed by polymerase chain reaction assay from Singapore epidemics in 2004 and 2007 (predominantly serotype 1 and 2 respectively).DHF occurred in 14.3%, DSS 2.7% and severe dengue 16.0%. The two WHO dengue classifications were discordant in defining severe disease (p<0.001). Five DSS patients (15%) were classified as non-severe dengue without warning signs. Of severe dengue patients, 107 did not fulfil DHF criteria. Of these, 14.9% had self-resolving isolated elevated aminotransferases, 18.7% gastrointestinal bleeding without hemodynamic compromise and 56.1% plasma leakage with isolated tachycardia. We compared both guidelines against requirement for intensive care including the single death in this series: all six had severe dengue; only four had DHF as two lacked bleeding manifestations but had plasma leakage. Increasing length of hospitalization was noted among severe cases with both classifications but the trend was only statistically significant for WHO 2009. Length of hospitalization was significantly longer for severe plasma leakage compared with severe bleeding or organ impairment. Requirement for hospitalization increased using WHO 2009 from 17.0% to 51.3%. Conclusions While the WHO 2009 dengue classification is clinically useful, we propose retaining criteria for plasma leakage and hemodynamic compromise from WHO 1997, and refining definitions of severe bleeding and organ impairment to improve clinical relevance having found that differences in these accounted for the discordance between classifications. Findings from our retrospective study may be limited by the study site - a tertiary referral center in a hyperendemic country - and should be evaluated in a wider range of geographic settings.
The Performance and Efficiency of Growth and Value Stocks: Evidence from Asia
Chun-Teck Lye
The International Journal of Applied Economics and Finance , 2012,
Abstract: This study uses Sortino ratio optimization approach to examine the risk-adjusted performance, returns and downside risks of growth and value stocks in Asian countries. Best, worst and equally-weighted country-level portfolios are constructed from the indices of the selected developed and emerging Asian countries. This study also uses price delay measures incorporated with rolling window method to scrutinize the market efficiency of growth and value stocks. The overall findings from sample period of 2 July 1997 to 28 September 2011 disclosed that the value stocks consistently outperformed the growth stocks in terms risk-adjusted performance, returns and downside risks. The results from rolling price delay measures revealed that the value stocks are relatively inefficient in comparison to growth stocks. Hence, the findings provide additional evidence in supporting the existence of value premium is attributable to the market inefficiency.
Enhanced Stutzer Index Optimization Using Hybrid Genetic Algorithm and Sequential Quadratic Programming
Chun-Teck Lye
Journal of Applied Sciences , 2011,
Abstract: This study presents a hybrid approach by associating the Genetic Algorithm (GA) and the Sequential Quadratic Programming (SQP) to improve the Stutzer Index optimization. The Stutzer Index is a well-recognized portfolio performance measure that provides unbiased estimates of risk-adjusted performance. However, the tasks in optimizing and determining a good starting point for the constrained optimization of Stutzer Index are challenging, especially with the additional constraint on the negative term θ. By integrating GA and SQP, this study anticipates the hybrid model to improve the efficiency and the performance of the optimization. The optimal indices obtained from both the SQP and the hybrid GA-SQP that used the initial guess recommended by Stutzer and the optimal index acquired via the hybrid GA-SQP with random starting point, for different period of data and number of assets respectively, are utilized for the comparative study. The results revealed that the hybrid model is superior in the Stutzer Index optimization, owing to the consistent capability of GA to locate the global optimum region and SQP to reach the optimal solution. The results also attested that the hybrid model enhanced the efficiency of the optimization as it does not required user-defined starting point and can sufficiently attained the optimal solution by utilizing a randomly generated starting point. In general, the hybrid model is competent in improving the efficiency and the performance of the Stutzer Index optimization, albeit the enhancement is not statistically significant in smaller number of observations.
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