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Fulltext Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context

Nazri A, Lio P

PLoS One, 2012;7(1):e28713.
PMID: 22253694 DOI: 10.1371/journal.pone.0028713

The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data. Typically, different datasets do not give single consistent network predictions but rather an ensemble of inconsistent networks inferred under the same reverse-engineering method that are only consistent with the specific experimentally measured data. Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate the reliability of these predictions. We review two existing meta-analysis approaches; the Fisher transformation combined coefficient test (FTCCT) and Fisher's inverse combined probability test (FICPT); and compare their performance with five well-known methods, ARACNe, Context Likelihood or Relatedness network (CLR), Maximum Relevance Minimum Redundancy (MRNET), Relevance Network (RN) and Bayesian Network (BN). We conducted in-depth numerical ensemble simulations and demonstrated for biological expression data that the meta-analysis approaches consistently outperformed the best gene regulatory network inference (GRNI) methods in the literature. Furthermore, the meta-analysis approaches have a low computational complexity. We conclude that the meta-analysis approaches are a powerful tool for integrating different datasets to give more accurate and reliable predictions for biological networks.
Fulltext SLC22A1-ABCB1 haplotype profiles predict imatinib pharmacokinetics in Asian patients with chronic myeloid leukemia

Singh O, Chan JY, Lin K, Heng CC, Chowbay B

PLoS One, 2012;7(12):e51771.
PMID: 23272163 DOI: 10.1371/journal.pone.0051771

This study aimed to explore the influence of SLC22A1, PXR, ABCG2, ABCB1 and CYP3A5 3 genetic polymorphisms on imatinib mesylate (IM) pharmacokinetics in Asian patients with chronic myeloid leukemia (CML).
Fulltext Qualitative inquiry into premarital sexual behaviours and contraceptive use among multiethnic young women: implications for education and future research

Wong LP

PLoS One, 2012;7(12):e51745.
PMID: 23272156 DOI: 10.1371/journal.pone.0051745

BACKGROUND: This study was a qualitative investigation into sexual attitudes and behaviours, and contraceptive use among Malaysian youth, based on constructs from the health belief model, theory of reasoned action, and problem behaviour theory.
METHODS: A total of 34 focus group discussions with 185 participants were conducted among the Malay (35%), Chinese (34%), and Indian (31%) young females between November, 2010 and April, 2011. The participants were secondary school students and university undergraduates from Selangor and the Federal Territory of Kuala Lumpur.
RESULTS: The study found a lack of knowledge about sexual issues and contraception among the participants. Many engaged in unprotected sexual intercourse and relied on periodic abstinence, natural methods, and traditional folk pregnancy preventive practices. The findings also revealed numerous categories of factors influencing sexual attitudes and behaviours: ethnic group and religion, level of religiosity, peer pressure and norms, and parental monitoring. With regard to condom use, factors such as embarrassment about condom acquisition, low perceived susceptibility to sexually transmitted infections (STIs), and perceived efficacy of traditional and folk methods of contraception, were uncovered from the discussions.
CONCLUSION: This study underscores the importance of development of culturally specific interventions that address the identified promoting factors of premarital sex. Behavioral interventions to promote condom use should increase awareness about condom effectiveness against not only unwanted pregnancies but also STIs.
Fulltext Investigating cultural evolution using phylogenetic analysis: the origins and descent of the southeast Asian tradition of warp ikat weaving

Buckley CD

PLoS One, 2012;7(12):e52064.
PMID: 23272211 DOI: 10.1371/journal.pone.0052064

The warp ikat method of making decorated textiles is one of the most geographically widespread in southeast Asia, being used by Austronesian peoples in Indonesia, Malaysia and the Philippines, and Daic peoples on the Asian mainland. In this study a dataset consisting of the decorative characters of 36 of these warp ikat weaving traditions is investigated using Bayesian and Neighbornet techniques, and the results are used to construct a phylogenetic tree and taxonomy for warp ikat weaving in southeast Asia. The results and analysis show that these diverse traditions have a common ancestor amongst neolithic cultures the Asian mainland, and parallels exist between the patterns of textile weaving descent and linguistic phylogeny for the Austronesian group. Ancestral state analysis is used to reconstruct some of the features of the ancestral weaving tradition. The widely held theory that weaving motifs originated in the late Bronze Age Dong-Son culture is shown to be inconsistent with the data.
Fulltext Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium

Ong SS, Wickneswari R

PLoS One, 2012;7(11):e49662.
PMID: 23251324 DOI: 10.1371/journal.pone.0049662

MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.
Fulltext The effects of comprehensive warm-up programs on proprioception, static and dynamic balance on male soccer players

Daneshjoo A, Mokhtar AH, Rahnama N, Yusof A

PLoS One, 2012;7(12):e51568.
PMID: 23251579 DOI: 10.1371/journal.pone.0051568

The study investigated the effects of FIFA 11+ and HarmoKnee, both being popular warm-up programs, on proprioception, and on the static and dynamic balance of professional male soccer players.
Fulltext Cost-effectiveness of buprenorphine and naltrexone treatments for heroin dependence in Malaysia

Ruger JP, Chawarski M, Mazlan M, Ng N, Schottenfeld R

PLoS One, 2012;7(12):e50673.
PMID: 23226534 DOI: 10.1371/journal.pone.0050673

AIMS: To aid public health policymaking, we studied the cost-effectiveness of buprenorphine, naltrexone, and placebo interventions for heroin dependence in Malaysia.
DESIGN: We estimated the cost-effectiveness ratios of three treatments for heroin dependence. We used a microcosting methodology to determine fixed, variable, and societal costs of each intervention. Cost data were collected from investigators, staff, and project records on the number and type of resources used and unit costs; societal costs for participants' time were estimated using Malaysia's minimum wage. Costs were estimated from a provider and societal perspective and reported in 2004 US dollars.
SETTING: Muar, Malaysia.
PARTICIPANTS: 126 patients enrolled in a randomized, double-blind, placebo-controlled clinical trial in Malaysia (2003-2005) receiving counseling and buprenorphine, naltrexone, or placebo for treatment of heroin dependence.
MEASUREMENTS: Primary outcome measures included days in treatment, maximum consecutive days of heroin abstinence, days to first heroin use, and days to heroin relapse. Secondary outcome measures included treatment retention, injection drug use, illicit opiate use, AIDS Risk Inventory total score, and drug risk and sex risk subscores.
FINDINGS: Buprenorphine was more effective and more costly than naltrexone for all primary and most secondary outcomes. Incremental cost-effectiveness ratios were below $50 for primary outcomes, mostly below $350 for secondary outcomes. Naltrexone was dominated by placebo for all secondary outcomes at almost all endpoints. Incremental treatment costs were driven mainly by medication costs, especially the price of buprenorphine.
CONCLUSIONS: Buprenorphine appears to be a cost-effective alternative to naltrexone that might enhance economic productivity and reduce drug use over a longer term.
Fulltext Can people guess what happened to others from their reactions?

Pillai D, Sheppard E, Mitchell P

PLoS One, 2012;7(11):e49859.
PMID: 23226227 DOI: 10.1371/journal.pone.0049859

Are we able to infer what happened to a person from a brief sample of his/her behaviour? It has been proposed that mentalising skills can be used to retrodict as well as predict behaviour, that is, to determine what mental states of a target have already occurred. The current study aimed to develop a paradigm to explore these processes, which takes into account the intricacies of real-life situations in which reasoning about mental states, as embodied in behaviour, may be utilised. A novel task was devised which involved observing subtle and naturalistic reactions of others in order to determine the event that had previously taken place. Thirty-five participants viewed videos of real individuals reacting to the researcher behaving in one of four possible ways, and were asked to judge which of the four 'scenarios' they thought the individual was responding to. Their eye movements were recorded to establish the visual strategies used. Participants were able to deduce successfully from a small sample of behaviour which scenario had previously occurred. Surprisingly, looking at the eye region was associated with poorer identification of the scenarios, and eye movement strategy varied depending on the event experienced by the person in the video. This suggests people flexibly deploy their attention using a retrodictive mindreading process to infer events.
Fulltext Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia

Sam IC, Loong SK, Michael JC, Chua CL, Wan Sulaiman WY, Vythilingam I, et al.

PLoS One, 2012;7(11):e50476.
PMID: 23209750 DOI: 10.1371/journal.pone.0050476

Mosquito-borne Chikungunya virus (CHIKV) has recently re-emerged globally. The epidemic East/Central/South African (ECSA) strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia.
Fulltext Solution structures, dynamics, and ice growth inhibitory activity of peptide fragments derived from an antarctic yeast protein

Shah SH, Kar RK, Asmawi AA, Rahman MB, Murad AM, Mahadi NM, et al.

PLoS One, 2012;7(11):e49788.
PMID: 23209600 DOI: 10.1371/journal.pone.0049788

Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.
Fulltext DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes)

Mat Jaafar TN, Taylor MI, Mohd Nor SA, de Bruyn M, Carvalho GR

PLoS One, 2012;7(11):e49623.
PMID: 23209586 DOI: 10.1371/journal.pone.0049623

DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.
Fulltext Structural and morphology of ZnO nanorods synthesized using ZnO seeded growth hydrothermal method and its properties as UV sensing

Ridhuan NS, Razak KA, Lockman Z, Abdul Aziz A

PLoS One, 2012;7(11):e50405.
PMID: 23189199 DOI: 10.1371/journal.pone.0050405

In this study, zinc oxide (ZnO) nanorod arrays were synthesized using a simple hydrothermal reaction on ZnO seeds/n-silicon substrate. Several parameters were studied, including the heat-treatment temperature to produce ZnO seeds, zinc nitrate concentration, pH of hydrothermal reaction solution, and hydrothermal reaction time. The optimum heat-treatment temperature to produce uniform nanosized ZnO seeds was 400°C. The nanorod dimensions depended on the hydrothermal reaction parameters. The optimum hydrothermal reaction parameters to produce blunt tip-like nanorods (770 nm long and 80 nm in top diameter) were 0.1 M zinc nitrate, pH 7, and 4 h of growth duration. Phase analysis studies showed that all ZnO nanorods exhibited a strong (002) peak. Thus, the ZnO nanorods grew in a c-axis preferred orientation. A strong ultraviolet (UV) emission peak was observed for ZnO nanorods grown under optimized parameters with a low, deep-level emission peak, which indicated high optical property and crystallinity of the nanorods. The produced ZnO nanorods were also tested for their UV-sensing properties. All samples responded to UV light but with different sensing characteristics. Such different responses could be attributed to the high surface-to-volume ratio of the nanorods that correlated with the final ZnO nanorods morphology formed at different synthesis parameters. The sample grown using optimum synthesis parameters showed the highest responsivity of 0.024 A/W for UV light at 375 nm under a 3 V bias.
Fulltext Establishment of an in vitro system representing the chicken gut-associated lymphoid tissue

Alitheen NB, McClure SJ, Yeap SK, Kristeen-Teo YW, Tan SW, McCullagh P

PLoS One, 2012;7(11):e49188.
PMID: 23185307 DOI: 10.1371/journal.pone.0049188

The bursa of Fabricius is critical for B cell development and differentiation in chick embryos. This study describes the production in vitro, from dissociated cell suspensions, of cellular agglomerates with functional similarities to the chicken bursa. Co-cultivation of epithelial and lymphoid cells obtained from embryos at the appropriate developmental stage regularly led to agglomerate formation within 48 hours. These agglomerates resembled bursal tissue in having lymphoid clusters overlaid by well organized epithelium. Whereas lymphocytes within agglomerates were predominantly Bu-1a(+), a majority of those emigrating onto the supporting membrane were Bu-1a(-) and IgM(+). Both agglomerates and emigrant cells expressed activation-induced deaminase with levels increasing after 24 hours. Emigrating cells were actively proliferating at a rate in excess of both the starting cell population and the population of cells remaining in agglomerates. The potential usefulness of this system for investigating the response of bursal tissue to avian Newcastle disease virus (strain AF2240) was examined.
Fulltext MHD free convective boundary layer flow of a nanofluid past a flat vertical plate with Newtonian heating boundary condition

Uddin MJ, Khan WA, Ismail AI

PLoS One, 2012;7(11):e49499.
PMID: 23166688 DOI: 10.1371/journal.pone.0049499

Steady two dimensional MHD laminar free convective boundary layer flows of an electrically conducting Newtonian nanofluid over a solid stationary vertical plate in a quiescent fluid taking into account the Newtonian heating boundary condition is investigated numerically. A magnetic field can be used to control the motion of an electrically conducting fluid in micro/nano scale systems used for transportation of fluid. The transport equations along with the boundary conditions are first converted into dimensionless form and then using linear group of transformations, the similarity governing equations are developed. The transformed equations are solved numerically using the Runge-Kutta-Fehlberg fourth-fifth order method with shooting technique. The effects of different controlling parameters, namely, Lewis number, Prandtl number, buoyancy ratio, thermophoresis, Brownian motion, magnetic field and Newtonian heating on the flow and heat transfer are investigated. The numerical results for the dimensionless axial velocity, temperature and nanoparticle volume fraction as well as the reduced Nusselt and Sherwood number have been presented graphically and discussed. It is found that the rate of heat and mass transfer increase as Newtonian heating parameter increases. The dimensionless velocity and temperature distributions increase with the increase of Newtonian heating parameter. The results of the reduced heat transfer rate is compared for convective heating boundary condition and found an excellent agreement.
Fulltext Newtonian versus special-relativistic statistical predictions for low-speed scattering

Liang SN, Borondo F, Lan BL

PLoS One, 2012;7(11):e48447.
PMID: 23152774 DOI: 10.1371/journal.pone.0048447

The statistical predictions of Newtonian and special-relativistic mechanics, which are calculated from an initially Gaussian ensemble of trajectories, are compared for a low-speed scattering system. The comparisons are focused on the mean dwell time, transmission and reflection coefficients, and the position and momentum means and standard deviations. We find that the statistical predictions of the two theories do not always agree as conventionally expected. The predictions are close if the scattering is non-chaotic but they are radically different if the scattering is chaotic and the initial ensemble is well localized in phase space. Our result indicates that for low-speed chaotic scattering, special-relativistic mechanics must be used, instead of the standard practice of using Newtonian mechanics, to obtain empirically-correct statistical predictions from an initially well-localized Gaussian ensemble.
Fulltext Overexpressing 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) in the lactococcal mevalonate pathway for heterologous plant sesquiterpene production

Song AA, Abdullah JO, Abdullah MP, Shafee N, Othman R, Tan EF, et al.

PLoS One, 2012;7(12):e52444.
PMID: 23300671 DOI: 10.1371/journal.pone.0052444

Isoprenoids are a large and diverse group of metabolites with interesting properties such as flavour, fragrance and therapeutic properties. They are produced via two pathways, the mevalonate pathway or the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. While plants are the richest source of isoprenoids, they are not the most efficient producers. Escherichia coli and yeasts have been extensively studied as heterologous hosts for plant isoprenoids production. In the current study, we describe the usage of the food grade Lactococcus lactis as a potential heterologous host for the production of sesquiterpenes from a local herbaceous Malaysian plant, Persicaria minor (synonym Polygonum minus). A sesquiterpene synthase gene from P. minor was successfully cloned and expressed in L. lactis. The expressed protein was identified to be a β-sesquiphellandrene synthase as it was demonstrated to be functional in producing β-sesquiphellandrene at 85.4% of the total sesquiterpenes produced based on in vitro enzymatic assays. The recombinant L. lactis strain developed in this study was also capable of producing β-sesquiphellandrene in vivo without exogenous substrates supplementation. In addition, overexpression of the strain's endogenous 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR), an established rate-limiting enzyme in the eukaryotic mevalonate pathway, increased the production level of β-sesquiphellandrene by 1.25-1.60 fold. The highest amount achieved was 33 nM at 2 h post-induction.
Fulltext Medical students' attitudes toward abortion education: Malaysian perspective

Tey NP, Yew SY, Low WY, Su'ut L, Renjhen P, Huang MS, et al.

PLoS One, 2012;7(12):e52116.
PMID: 23300600 DOI: 10.1371/journal.pone.0052116

Abortion is a serious public health issue, and it poses high risks to the health and life of women. Yet safe abortion services are not readily available because few doctors are trained to provide such services. Many doctors are unaware of laws pertaining to abortion. This article reports survey findings on Malaysian medical students' attitudes toward abortion education and presents a case for including abortion education in medical schools.
Fulltext Phylogeographic pattern of the striped snakehead, Channa striata in Sundaland: ancient river connectivity, geographical and anthropogenic signatures [corrected]

Tan MP, Jamsari AF, Siti Azizah MN

PLoS One, 2012;7(12):e52089.
PMID: 23284881 DOI: 10.1371/journal.pone.0052089

A phylogeographic study of an economically important freshwater fish, the striped snakehead, Channa striata in Sundaland was carried out using data from mtDNA ND5 gene target to elucidate genetic patterning. Templates obtained from a total of 280 individuals representing 24 sampling sites revealed 27 putative haplotypes. Three distinct genetic lineages were apparent; 1)northwest Peninsular Malaysia, 2)southern Peninsular, east Peninsular, Sumatra and SW (western Sarawak) and 3) central west Peninsular and Malaysian Borneo (except SW). Genetic structuring between lineages showed a significant signature of natural geographical barriers that have been acting as effective dividers between these populations. However, genetic propinquity between the SW and southern Peninsular and east Peninsular Malaysia populations was taken as evidence of ancient river connectivity between these regions during the Pleistocene epoch. Alternatively, close genetic relationship between central west Peninsular Malaysia and Malaysian Borneo populations implied anthropogenic activities. Further, haplotype sharing between the east Peninsular Malaysia and Sumatra populations revealed extraordinary migration ability of C. striata (>500 km) through ancient connectivity. These results provide interesting insights into the historical and contemporary landscape arrangement in shaping genetic patterns of freshwater species in Sundaland.
Fulltext Influenza vaccination guidelines and vaccine sales in southeast Asia: 2008-2011

Gupta V, Dawood FS, Muangchana C, Lan PT, Xeuatvongsa A, Sovann L, et al.

PLoS One, 2012;7(12):e52842.
PMID: 23285200 DOI: 10.1371/journal.pone.0052842

Southeast Asia is a region with great potential for the emergence of a pandemic influenza virus. Global efforts to improve influenza surveillance in this region have documented the burden and seasonality of influenza viruses and have informed influenza prevention strategies, but little information exists about influenza vaccination guidelines and vaccine sales.
Fulltext Morphological phylogenetic analysis of seven varieties of Ficus deltoidea Jack from the Malay Peninsula of Malaysia

Fatihah HN, Mat N, Zaimah AR, Zuhailah MN, Norhaslinda H, Khairil M, et al.

PLoS One, 2012;7(12):e52441.
PMID: 23285045 DOI: 10.1371/journal.pone.0052441

This study is the first report to suggest a morphological phylogenetic framework for the seven varieties of Ficus deltoidea Jack (Ficus: Moraceae) from the Malay Peninsula of Malaysia. Several molecular-based classifications on the genus Ficus had been proposed, but neither had discussed the relationship between seven varieties of F. deltoidea to its allies nor within the varieties. The relationship between seven varieties of F. deltoidea is still debated due to the extreme morphological variabilities and ambiguous boundaries between taxa. Thus, the correct identification of these varieties is important as several morphological characters are variety-specific. To test the monophyly and further resolved the relationship in F. deltoidea, a morphological phylogenetic analysis was conducted based on herbarium specimens representing the seven varieties of F. deltoidea that were collected from the Malay Peninsula of Malaysia, by using related species of the genus Ficus; F. grossularioides, F. ischnopoda and F. oleifolia as the outgroups. Parsimony and neighbour-joining analyses indicated that F. deltoidea is monophyletic, in that the seven varieties of F. deltoidea nested into two clades; clade subspecies deltoidea (var. deltoidea, var. bilobata, var. angustifolia, var. kunstleri and var. trengganuensis) and clade subspecies motleyana (var. intermedia and var. motleyana).

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