Displaying publications 41 - 60 of 1459 in total

  1. Ibahim MJ, Crosbie JC, Yang Y, Zaitseva M, Stevenson AW, Rogers PA, et al.
    PLoS ONE, 2014;9(6):e100547.
    PMID: 24945301 DOI: 10.1371/journal.pone.0100547
    High-dose synchrotron microbeam radiation therapy (MRT) has shown the potential to deliver improved outcomes over conventional broadbeam (BB) radiation therapy. To implement synchrotron MRT clinically for cancer treatment, it is necessary to undertake dose equivalence studies to identify MRT doses that give similar outcomes to BB treatments.
  2. Chew M, Abdul Rahim A, bin Haji Ross O
    PLoS ONE, 2014;9(6):e99072.
    PMID: 24914642 DOI: 10.1371/journal.pone.0099072
    A new anthurid isopod from dead coral rubble and stones in the intertidal area of Pulau Tinggi, Johor, Malaysia, is described. It is placed in a new genus and species, Tinggianthura alba. Tinggianthura is characterized by: (1) subtriangular carpus shape of pereopods 4-7, (2) pereopod 1 propodus palm without prominent tooth or steps and (3) maxillipedal palp 2-articled.
  3. Jahangirzadeh A, Basser H, Akib S, Karami H, Naji S, Shamshirband S
    PLoS ONE, 2014;9(2):e98592.
    PMID: 24919065 DOI: 10.1371/journal.pone.0098592
    The scour phenomenon around bridge piers causes great quantities of damages annually all over the world. Collars are considered as one of the substantial methods for reducing the depth and volume of scour around bridge piers. In this study, the experimental and numerical methods are used to investigate two different shapes of collars, i.e, rectangular and circular, in terms of reducing scour around a single bridge pier. The experiments were conducted in hydraulic laboratory at university of Malaya. The scour around the bridge pier and collars was simulated numerically using a three-dimensional, CFD model namely SSIIM 2.0, to verify the application of the model. The results indicated that although, both types of collars provides a considerable decrease in the depth of the scour, the rectangular collar, decreases scour depth around the pier by 79 percent, and has better performance compared to the circular collar. Furthermore, it was observed that using collars under the stream's bed, resulted in the most reduction in the scour depth around the pier. The results also show the SSIIM 2.0 model could simulate the scour phenomenon around a single bridge pier and collars with sufficient accuracy. Using the experimental and numerical results, two new equations were developed to predict the scour depth around a bridge pier exposed to circular and rectangular collars.
  4. Abram NK, Xofis P, Tzanopoulos J, MacMillan DC, Ancrenaz M, Chung R, et al.
    PLoS ONE, 2014;9(6):e95388.
    PMID: 24887555 DOI: 10.1371/journal.pone.0095388
    Lowland tropical forests are increasingly threatened with conversion to oil palm as global demand and high profit drives crop expansion throughout the world's tropical regions. Yet, landscapes are not homogeneous and regional constraints dictate land suitability for this crop. We conducted a regional study to investigate spatial and economic components of forest conversion to oil palm within a tropical floodplain in the Lower Kinabatangan, Sabah, Malaysian Borneo. The Kinabatangan ecosystem harbours significant biodiversity with globally threatened species but has suffered forest loss and fragmentation. We mapped the oil palm and forested landscapes (using object-based-image analysis, classification and regression tree analysis and on-screen digitising of high-resolution imagery) and undertook economic modelling. Within the study region (520,269 ha), 250,617 ha is cultivated with oil palm with 77% having high Net-Present-Value (NPV) estimates ($413/ha-yr-$637/ha-yr); but 20.5% is under-producing. In fact 6.3% (15,810 ha) of oil palm is commercially redundant (with negative NPV of $-299/ha-yr-$-65/ha-yr) due to palm mortality from flood inundation. These areas would have been important riparian or flooded forest types. Moreover, 30,173 ha of unprotected forest remain and despite its value for connectivity and biodiversity 64% is allocated for future oil palm. However, we estimate that at minimum 54% of these forests are unsuitable for this crop due to inundation events. If conversion to oil palm occurs, we predict a further 16,207 ha will become commercially redundant. This means that over 32,000 ha of forest within the floodplain would have been converted for little or no financial gain yet with significant cost to the ecosystem. Our findings have globally relevant implications for similar floodplain landscapes undergoing forest transformation to agriculture such as oil palm. Understanding landscape level constraints to this crop, and transferring these into policy and practice, may provide conservation and economic opportunities within these seemingly high opportunity cost landscapes.
  5. Esmaeilpour M, Naderifar V, Shukur Z
    PLoS ONE, 2014;9(9):e106313.
    PMID: 25243670 DOI: 10.1371/journal.pone.0106313
    Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem.
  6. Ghodsinejad Kalahroudi V, Kamalidehghan B, Arasteh Kani A, Aryani O, Tondar M, Ahmadipour F, et al.
    PLoS ONE, 2014;9(9):e106656.
    PMID: 25216246 DOI: 10.1371/journal.pone.0106656
    Oculocutaneous albinism (OCA) is a heterogeneous group of autosomal recessive disorders resulting from mutations of the tyrosinase (TYR) gene and presents with either complete or partial absence of pigment in the skin, hair and eyes due to a defect in an enzyme involved in the production of melanin. In this study, mutations in the TYR gene of 30 unrelated Iranian OCA1 patients and 100 healthy individuals were examined using PCR-sequencing. Additionally, in order to predict the possible effects of new mutations on the structure and function of tyrosinase, these mutations were analyzed by SIFT, PolyPhen and I-Mutant 2 software. Here, two new pathogenic p.C89S and p.H180R mutations were detected in two OCA1 patients. Moreover, the R402Q and S192Y variants, which are common non-pathogenic polymorphisms, were detected in 17.5% and 35% of the patients, respectively. The outcome of this study has extended the genotypic spectrum of OCA1 patients, which paves the way for more efficient carrier detection and genetic counseling.
  7. Burg NA, Pradhan A, Gonzalez RM, Morban EZ, Zhen EW, Sakchoowong W, et al.
    PLoS ONE, 2014;9(8):e104076.
    PMID: 25119899 DOI: 10.1371/journal.pone.0104076
    The Neotropical butterfly Dryas iulia has been collected from several locations in Thailand and Malaysia since 2007, and has been observed breeding in the wild, using introduced Passiflora foetida as a larval host plant. The butterfly is bred by a butterfly house in Phuket, Thailand, for release at weddings and Buddhist ceremonies, and we hypothesized that this butterfly house was the source of wild, Thai individuals. We compared wing patterns and COI barcodes from two, wild Thai populations with individuals obtained from this butterfly house. All Thai individuals resemble the subspecies D. iulia modesta, and barcodes from wild and captive Thai specimens were identical. This unique, Thai barcode was not found in any of the 30 specimens sampled from the wild in the species' native range, but is most similar to specimens from Costa Rica, where many exporting butterfly farms are located. These data implicate the butterfly house as the source of Thailand's wild D. iulia populations, which are currently so widespread that eradication efforts are unlikely to be successful.
  8. Loh SW, Ng WL, Yeo KS, Lim YY, Ea CK
    PLoS ONE, 2014;9(7):e103915.
    PMID: 25079219 DOI: 10.1371/journal.pone.0103915
    H3K9 methylation is one of the essential histone post-translational modifications for heterochromatin formation and transcriptional repression. Recently, several studies have demonstrated that H3K9 methylation negatively regulates the type I interferon response.
  9. Lee JH, Pooley NJ, Mohd-Adnan A, Martin SA
    PLoS ONE, 2014;9(7):e103729.
    PMID: 25078784 DOI: 10.1371/journal.pone.0103729
    Ferritin is a highly-conserved iron-storage protein that has also been identified as an acute phase protein within the innate immune system. The iron-storage function is mediated through complementary roles played by heavy (H)-chain subunit as well as the light (L) in mammals or middle (M)-chain in teleosts, respectively. In this study, we report the identification of five ferritin subunits (H1, H2, M1, M2, M3) in the Atlantic salmon that were supported by the presence of iron-regulatory regions, gene structure, conserved domains and phylogenetic analysis. Tissue distribution analysis across eight different tissues showed that each of these isoforms is differentially expressed. We also examined the expression of the ferritin isoforms in the liver and kidney of juvenile Atlantic salmon that was challenged with Aeromonas salmonicida as well as in muscle cell culture stimulated with interleukin-1β. We found that each isoform displayed unique expression profiles, and in certain conditions the expressions between the isoforms were completely diametrical to each other. Our study is the first report of multiple ferritin isoforms from both the H- and M-chains in a vertebrate species, as well as ferritin isoforms that showed decreased expression in response to infection. Taken together, the results of our study suggest the possibility of functional differences between the H- and M-chain isoforms in terms of tissue localisation, transcriptional response to bacterial exposure and stimulation by specific immune factors.
  10. Mokhtar SS, Marshall CR, Phipps ME, Thiruvahindrapuram B, Lionel AC, Scherer SW, et al.
    PLoS ONE, 2014;9(6):e100371.
    PMID: 24956385 DOI: 10.1371/journal.pone.0100371
    Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.
  11. Abdul Razak F, Jensen HJ
    PLoS ONE, 2014;9(6):e99462.
    PMID: 24955766 DOI: 10.1371/journal.pone.0099462
    'Causal' direction is of great importance when dealing with complex systems. Often big volumes of data in the form of time series are available and it is important to develop methods that can inform about possible causal connections between the different observables. Here we investigate the ability of the Transfer Entropy measure to identify causal relations embedded in emergent coherent correlations. We do this by firstly applying Transfer Entropy to an amended Ising model. In addition we use a simple Random Transition model to test the reliability of Transfer Entropy as a measure of 'causal' direction in the presence of stochastic fluctuations. In particular we systematically study the effect of the finite size of data sets.
  12. Chan PL, Rose RJ, Abdul Murad AM, Zainal Z, Low ET, Ooi LC, et al.
    PLoS ONE, 2014;9(6):e99774.
    PMID: 24927412 DOI: 10.1371/journal.pone.0099774
    The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.
  13. Khezrian M, Jahan A, Kadir WM, Ibrahim S
    PLoS ONE, 2014;9(6):e97831.
    PMID: 24897426 DOI: 10.1371/journal.pone.0097831
    Web services today are among the most widely used groups for Service Oriented Architecture (SOA). Service selection is one of the most significant current discussions in SOA, which evaluates discovered services and chooses the best candidate from them. Although a majority of service selection techniques apply Quality of Service (QoS), the behaviour of QoS-based service selection leads to service selection problems in Multi-Criteria Decision Making (MCDM). In the existing works, the confidence level of decision makers is neglected and does not consider their expertise in assessing Web services. In this paper, we employ the VIKOR (VIšekriterijumskoKOmpromisnoRangiranje) method, which is absent in the literature for service selection, but is well-known in other research. We propose a QoS-based approach that deals with service selection by applying VIKOR with improvement of features. This research determines the weights of criteria based on user preference and accounts for the confidence level of decision makers. The proposed approach is illustrated by an example in order to demonstrate and validate the model. The results of this research may facilitate service consumers to attain a more efficient decision when selecting the appropriate service.
  14. Chen Y, Azman SN, Kerishnan JP, Zain RB, Chen YN, Wong YL, et al.
    PLoS ONE, 2014;9(10):e109012.
    PMID: 25272005 DOI: 10.1371/journal.pone.0109012
    One of the most common cancers worldwide is oral squamous cell carcinoma (OSCC), which is associated with a significant death rate and has been linked to several risk factors. Notably, failure to detect these neoplasms at an early stage represents a fundamental barrier to improving the survival and quality of life of OSCC patients. In the present study, serum samples from OSCC patients (n = 25) and healthy controls (n = 25) were subjected to two-dimensional gel electrophoresis (2-DE) and silver staining in order to identify biomarkers that might allow early diagnosis. In this regard, 2-DE spots corresponding to various up- and down-regulated proteins were sequenced via high-resolution MALDI-TOF mass spectrometry and analyzed using the MASCOT database. We identified the following differentially expressed host-specific proteins within sera from OSCC patients: leucine-rich α2-glycoprotein (LRG), alpha-1-B-glycoprotein (ABG), clusterin (CLU), PRO2044, haptoglobin (HAP), complement C3c (C3), proapolipoprotein A1 (proapo-A1), and retinol-binding protein 4 precursor (RBP4). Moreover, five non-host factors were detected, including bacterial antigens from Acinetobacter lwoffii, Burkholderia multivorans, Myxococcus xanthus, Laribacter hongkongensis, and Streptococcus salivarius. Subsequently, we analyzed the immunogenicity of these proteins using pooled sera from OSCC patients. In this regard, five of these candidate biomarkers were found to be immunoreactive: CLU, HAP, C3, proapo-A1 and RBP4. Taken together, our immunoproteomics approach has identified various serum biomarkers that could facilitate the development of early diagnostic tools for OSCC.
  15. De Silva JR, Lau YL, Fong MY
    PLoS ONE, 2014;9(9):e108951.
    PMID: 25268233 DOI: 10.1371/journal.pone.0108951
    The Duffy blood group is of major interest in clinical medicine as it plays an important role in Plasmodium knowlesi and Plasmodium vivax infection. In the present study, the distribution of Duffy blood group genotypes and allelic frequencies among P. knowlesi infected patients as well as healthy individuals in Peninsular Malaysia were determined. The blood group of 60 healthy blood donors and 51 P. knowlesi malaria patients were genotyped using allele specific polymerase chain reaction (ASP-PCR). The data was analyzed using Fisher's exact test in order to assess the significance of the variables. Our results show a high proportion of the FY*A/FY*A genotype (>85% for both groups) and a high frequency of the FY*A allele (>90% for both groups). The FY*A/FY*A genotype was the most predominant genotype in both infected and healthy blood samples. The genotype frequency did not differ significantly between the donor blood and the malaria patient groups. Also, there was no significant correlation between susceptibility to P. knowlesi infection with any Duffy blood genotype.
  16. Balaji Raghavendran HR, Puvaneswary S, Talebian S, Murali MR, Raman Murali M, Naveen SV, et al.
    PLoS ONE, 2014;9(8):e104389.
    PMID: 25140798 DOI: 10.1371/journal.pone.0104389
    A comparative study on the in vitro osteogenic potential of electrospun poly-L-lactide/hydroxyapatite/collagen (PLLA/HA/Col, PLLA/HA, and PLLA/Col) scaffolds was conducted. The morphology, chemical composition, and surface roughness of the fibrous scaffolds were examined. Furthermore, cell attachment, distribution, morphology, mineralization, extracellular matrix protein localization, and gene expression of human mesenchymal stromal cells (hMSCs) differentiated on the fibrous scaffolds PLLA/Col/HA, PLLA/Col, and PLLA/HA were also analyzed. The electrospun scaffolds with a diameter of 200-950 nm demonstrated well-formed interconnected fibrous network structure, which supported the growth of hMSCs. When compared with PLLA/H%A and PLLA/Col scaffolds, PLLA/Col/HA scaffolds presented a higher density of viable cells and significant upregulation of genes associated with osteogenic lineage, which were achieved without the use of specific medium or growth factors. These results were supported by the elevated levels of calcium, osteocalcin, and mineralization (P<0.05) observed at different time points (0, 7, 14, and 21 days). Furthermore, electron microscopic observations and fibronectin localization revealed that PLLA/Col/HA scaffolds exhibited superior osteoinductivity, when compared with PLLA/Col or PLLA/HA scaffolds. These findings indicated that the fibrous structure and synergistic action of Col and nano-HA with high-molecular-weight PLLA played a vital role in inducing osteogenic differentiation of hMSCs. The data obtained in this study demonstrated that the developed fibrous PLLA/Col/HA biocomposite scaffold may be supportive for stem cell based therapies for bone repair, when compared with the other two scaffolds.
  17. Greenwood MP, Greenwood M, Paton JF, Murphy D
    PLoS ONE, 2014;9(8):e104802.
    PMID: 25111786 DOI: 10.1371/journal.pone.0104802
    Salt appetite, the primordial instinct to favorably ingest salty substances, represents a vital evolutionary important drive to successfully maintain body fluid and electrolyte homeostasis. This innate instinct was shown here in Sprague-Dawley rats by increased ingestion of isotonic saline (IS) over water in fluid intake tests. However, this appetitive stimulus was fundamentally transformed into a powerfully aversive one by increasing the salt content of drinking fluid from IS to hypertonic saline (2% w/v NaCl, HS) in intake tests. Rats ingested HS similar to IS when given no choice in one-bottle tests and previous studies have indicated that this may modify salt appetite. We thus investigated if a single 24 h experience of ingesting IS or HS, dehydration (DH) or 4% high salt food (HSD) altered salt preference. Here we show that 24 h of ingesting IS and HS solutions, but not DH or HSD, robustly transformed salt appetite in rats when tested 7 days and 35 days later. Using two-bottle tests rats previously exposed to IS preferred neither IS or water, whereas rats exposed to HS showed aversion to IS. Responses to sweet solutions (1% sucrose) were not different in two-bottle tests with water, suggesting that salt was the primary aversive taste pathway recruited in this model. Inducing thirst by subcutaneous administration of angiotensin II did not overcome this salt aversion. We hypothesised that this behavior results from altered gene expression in brain structures important in thirst and salt appetite. Thus we also report here lasting changes in mRNAs for markers of neuronal activity, peptide hormones and neuronal plasticity in supraoptic and paraventricular nuclei of the hypothalamus following rehydration after both DH and HS. These results indicate that a single experience of drinking HS is a memorable one, with long-term changes in gene expression accompanying this aversion to salty solutions.
  18. ManickamAchari V, Bryce RA, Hashim R
    PLoS ONE, 2014;9(6):e101110.
    PMID: 24978205 DOI: 10.1371/journal.pone.0101110
    The rational design of a glycolipid application (e.g. drug delivery) with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20%) in the hydrophobic region of the lamellar crystal (LC) phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.
  19. Shawish HB, Wong WY, Wong YL, Loh SW, Looi CY, Hassandarvish P, et al.
    PLoS ONE, 2014;9(6):e100933.
    PMID: 24977407 DOI: 10.1371/journal.pone.0100933
    The biological properties of thiosemicarbazone have been widely reported. The incorporation of some transition metals such as Fe, Ni and Cu to thiosemicarbazone complexes is known to enhance its biological effects. In this study, we incorporated nickel(II) ions into thiosemicarbazone with N4-substitution groups H3L (H; H3L1, CH3; H3L2, C6H5; H3L3 and C2H5; H3L4) and examined its potential anti-inflammatory activity.
  20. Gul T, Islam S, Shah RA, Khan I, Shafie S
    PLoS ONE, 2014;9(6):e97552.
    PMID: 24949988 DOI: 10.1371/journal.pone.0097552
    In this work, we have carried out the influence of temperature dependent viscosity on thin film flow of a magnetohydrodynamic (MHD) third grade fluid past a vertical belt. The governing coupled non-linear differential equations with appropriate boundary conditions are solved analytically by using Adomian Decomposition Method (ADM). In order to make comparison, the governing problem has also been solved by using Optimal Homotopy Asymptotic Method (OHAM). The physical characteristics of the problem have been well discussed in graphs for several parameter of interest.
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