Browse publications by year: 2016

  1. Yoon KB, Kim JY, Park YC
    PMID: 25418628 DOI: 10.3109/19401736.2014.982571
    We describe the characteristics of complete mitogenome of C. brachyotis in this article. The complete mitogenome of C. brachyotis is 16,701 bp long with a total base composition of 32.4% A, 25.7% T, 27.7% C and 14.2% G. The mitogenome consists of 13 protein-coding genes (11,408 bp), (KM659865) two rRNA (12S rRNA and 16S rRNA) genes (2,539 bp), 22 tRNA genes (1518 bp) and one control region (1239 bp).
    MeSH terms: Animals; Base Composition/genetics; Chiroptera/genetics*; Malaysia; RNA, Transfer/genetics; Base Pairing/genetics; Genes, Mitochondrial; Genome, Mitochondrial*
  2. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423510 DOI: 10.3109/19401736.2014.982585
    The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
    MeSH terms: Animals; Base Composition/genetics; Brachyura/genetics*; RNA, Transfer/genetics; Base Pairing/genetics; Genes, Mitochondrial; Genome, Mitochondrial*; Molecular Sequence Annotation
  3. Tan MH, Gan HM, Lee YP, Austin CM
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
    MeSH terms: Animals; Brachyura/genetics*; DNA, Mitochondrial/genetics; RNA, Transfer/genetics; Base Pairing/genetics; Genes, Mitochondrial; Genome, Mitochondrial*
  4. Chee SY, Mohd Nor SA
    PMID: 25471442 DOI: 10.3109/19401736.2014.987237
    This is the first study to identify and determine the phylogenetics of neritids found in Malaysia. In total, twelve species from the family Neritidae were recorded. Ten species were from the genus Nerita and two species were from the genus Neritina. DNA barcodes were successfully assigned to each species. Although some of these species were previously reported in the region, three are only presently reported in this study. The dendrogram showed Nerita and Neritina strongly supported in their respective monophyletic clades. Phylogenetic positions of some species appeared unstable in the trees. This could be due to the differences in a small number of nucleotides, thus minimizing genetic variation between each specimen and species.
    MeSH terms: Animals; Electron Transport Complex IV/classification; Electron Transport Complex IV/genetics; Electron Transport Complex IV/metabolism; Malaysia; Mollusca/classification; Mollusca/genetics*; Phylogeny; Genetic Variation*; Genome, Mitochondrial*; DNA Barcoding, Taxonomic*
  5. Shaqinah NN, Mazlina M, Zamri-Saad M, Hazilawati H, Jasni S
    Cytotechnology, 2016 Aug;68(4):1655-9.
    PMID: 25511802 DOI: 10.1007/s10616-014-9836-7
    Monocytes are widely used for immunological research, especially in the study of innate immune system. Although methods for isolation of human monocytes have been established, the procedure for non-human monocyte has not been well developed. This paper describes an improved method for isolation of monocyte and the subsequent macrophage cultivation from caprine blood. Monocytes were isolated from 16 ml of heparinized caprine blood using double density methods; the Ficoll and Percoll. The number of monocytes obtained was 5.12 ± 0.89 × 10(7) cells/ml at 70 % purity. The isolated monocytes were maintained in 10 % fetal bovine serum-enriched Dulbecco's Modified Eagle Medium for maturation to form macrophage cell culture. At the end of the experiment, the harvested macrophage was 2.48 ± 0.33 × 10(6) cells/ml.
  6. Palaniappan R, Sundaraj K, Sundaraj S, Huliraj N, Revadi SS
    Clin Respir J, 2016 Jul;10(4):486-94.
    PMID: 25515741 DOI: 10.1111/crj.12250
    BACKGROUND: Monitoring respiration is important in several medical applications. One such application is respiratory rate monitoring in patients with sleep apnoea. The respiratory rate in patients with sleep apnoea disorder is irregular compared with the controls. Respiratory phase detection is required for a proper monitoring of respiration in patients with sleep apnoea.

    AIMS: To develop a model to detect the respiratory phases present in the pulmonary acoustic signals and to evaluate the performance of the model in detecting the respiratory phases.

    METHODS: Normalised averaged power spectral density for each frame and change in normalised averaged power spectral density between the adjacent frames were fuzzified and fuzzy rules were formulated. The fuzzy inference system (FIS) was developed with both Mamdani and Sugeno methods. To evaluate the performance of both Mamdani and Sugeno methods, correlation coefficient and root mean square error (RMSE) were calculated.

    RESULTS: In the correlation coefficient analysis in evaluating the fuzzy model using Mamdani and Sugeno method, the strength of the correlation was found to be r = 0.9892 and r = 0.9964, respectively. The RMSE for Mamdani and Sugeno methods are RMSE = 0.0853 and RMSE = 0.0817, respectively.

    CONCLUSION: The correlation coefficient and the RMSE of the proposed fuzzy models in detecting the respiratory phases reveals that Sugeno method performs better compared with the Mamdani method.

    MeSH terms: Algorithms; Humans; Models, Theoretical; Monitoring, Physiologic/methods; Sleep Apnea Syndromes/physiopathology*; Fuzzy Logic; Respiratory Rate
  7. Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3983-3984.
    PMID: 25541305
    The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.
    MeSH terms: Animals; Base Composition; Sequence Analysis, DNA; Codon, Initiator; Codon, Terminator; Evolution, Molecular; Gene Order*; Anomura/genetics*; Genes, Mitochondrial*; Genome, Mitochondrial*; Genome Size
  8. Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3981-3982.
    PMID: 25541307
    The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
    MeSH terms: Animals; Base Composition; Brachyura/genetics*; Sequence Analysis, DNA; Codon, Initiator; Codon, Terminator; Evolution, Molecular; Gene Order*; Genes, Mitochondrial*; Genome, Mitochondrial*; Genome Size
  9. Gan HY, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3985-3986.
    PMID: 25543913
    The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
    MeSH terms: Animals; Base Composition; Sequence Analysis, DNA; Evolution, Molecular; Gene Order*; Decapoda (Crustacea)/genetics*; Genes, Mitochondrial*; Genome Size
  10. Bhabha FK, Magee J, Ng SY, Grills CE, Su J, Orchard D
    Australas J Dermatol, 2016 Feb;57(1):e20-2.
    PMID: 25557526 DOI: 10.1111/ajd.12257
    Multiple dermatofibromas is a rare entity consisting of more than fifteen lesions. Multiple clustered dermatofibroma is a distinct variant of multiple dermatofibromas and is defined as a well-demarcated plaque composed of individual dermatofibromas. We report a 16-year-old boy with multiple clustered dermatofibroma in a segmental distribution, which has previously not been reported in the literature.
    MeSH terms: Adolescent; Humans; Male; Neoplasms, Multiple Primary/diagnosis; Neoplasms, Multiple Primary/pathology*; Skin Neoplasms/diagnosis; Skin Neoplasms/pathology*; Histiocytoma, Benign Fibrous/diagnosis; Histiocytoma, Benign Fibrous/pathology*
  11. Siriwardena BS, Rasnayaka RM, Masood Y, Masood M, Kumarasiri PV, Tilakaratne WM
    J Investig Clin Dent, 2016 May;7(2):127-31.
    PMID: 25573428 DOI: 10.1111/jicd.12145
    AIM: The high incidence rates for oral cancer (excluding lip) are especially found in the South and South-East Asia. Therefore, the aim of the present study was to investigate the relationship between sex, age, site, and metastasis of a large sample with oral squamous cell carcinoma (OSCC).

    METHODS: A total of 989 OSCC treated with neck dissection were selected. All the relevant data were recorded from biopsy request forms. The patients were divided into seven groups, and there were nine different oral sites.

    RESULTS: The male-to-female ratio of the sample was 4:1. Most of the patients were aged between 30 and 60 years. Of the 989 patients, approximately 40% patients had metastasis. Age <30 years showed a higher probability of metastasis compared to higher age groups, but it was not statistically significant. Palate cancers had more than 14 times higher chance of metastasis, followed by maxilla (4.6 times) and tongue (2.8 times).

    CONCLUSION: The present study provides important information on the metastatic potential of OSCC in different oral sites, and identifies high-risk age groups for metastasis. This will be helpful in planning neck treatment for OSCC.

    MeSH terms: Adult; Biopsy; Carcinoma, Squamous Cell/secondary*; Female; Humans; Lip Neoplasms/secondary*; Male; Mouth Neoplasms/pathology*; Neoplasm Metastasis; Retrospective Studies; Neck Dissection
  12. Jahn Kassim PN, Alias F
    J Relig Health, 2016 Feb;55(1):119-34.
    PMID: 25576401 DOI: 10.1007/s10943-014-9995-z
    Religion and spirituality have always played a major and intervening role in a person's life and health matters. With the influential development of patient autonomy and the right to self-determination, a patient's religious affiliation constitutes a key component in medical decision making. This is particularly pertinent in issues involving end-of-life decisions such as withdrawing and withholding treatment, medical futility, nutritional feeding and do-not-resuscitate orders. These issues affect not only the patient's values and beliefs, but also the family unit and members of the medical profession. The law also plays an intervening role in resolving conflicts between the sanctity of life and quality of life that are very much pronounced in this aspect of healthcare. Thus, the medical profession in dealing with the inherent ethical and legal dilemmas needs to be sensitive not only to patients' varying religious beliefs and cultural values, but also to the developing legal and ethical standards as well. There is a need for the medical profession to be guided on the ethical obligations, legal demands and religious expectations prior to handling difficult end-of-life decisions. The development of comprehensive ethical codes in congruence with developing legal standards may offer clear guidance to the medical profession in making sound medical decisions.
    MeSH terms: Clinical Decision-Making/ethics*; Humans; Religion and Medicine*; Terminal Care/legislation & jurisprudence*; Terminal Care/ethics*; Withholding Treatment/legislation & jurisprudence*; Withholding Treatment/ethics*
  13. Zaman SA, Sarbini SR
    Crit Rev Biotechnol, 2016 Jun;36(3):578-84.
    PMID: 25582732 DOI: 10.3109/07388551.2014.993590
    Resistant starch is defined as the total amount of starch and the products of starch degradation that resists digestion in the small intestine. Starches that were able to resist the digestion will arrive at the colon where they will be fermented by the gut microbiota, producing a variety of products which include short chain fatty acids that can provide a range of physiological benefits. There are several factors that could affect the resistant starch content of a carbohydrate which includes the starch granule morphology, the amylose-amylopectin ratio and its association with other food component. One of the current interests on resistant starch is their potential to be used as a prebiotic, which is a non-digestible food ingredient that benefits the host by stimulating the growth or activity of one or a limited number of beneficial bacteria in the colon. A resistant starch must fulfill three criterions to be classified as a prebiotic; resistance to the upper gastrointestinal environment, fermentation by the intestinal microbiota and selective stimulation of the growth and/or activity of the beneficial bacteria. The market of prebiotic is expected to reach USD 198 million in 2014 led by the export of oligosaccharides. Realizing this, novel carbohydrates such as resistant starch from various starch sources can contribute to the advancement of the prebiotic industry.
    MeSH terms: Gastrointestinal Microbiome; Amylopectin; Amylose; Bacteria; Colon; Fatty Acids, Volatile; Fermentation; Intestine, Small; Oligosaccharides; Starch; Bioreactors; Prebiotics
  14. Gholizadeh H, Abu Osman NA, Eshraghi A, Arifin N, Chung TY
    Prosthet Orthot Int, 2016 Aug;40(4):509-16.
    PMID: 25583929 DOI: 10.1177/0309364614564022
    BACKGROUND: This article describes a total surface bearing prosthetic socket for a patient (25-year-old female) with a bulbous stump.

    CASE DESCRIPTION AND METHODS: The subject had unstable excessive soft tissue at the distal end of the residuum. After 2 years of prosthetic use, she experienced several problems, including pain in the residual limb and knee joint. Pressure distribution was evaluated during ambulation. We also designed a total surface bearing socket with Velcro as suspension system to distribute the load evenly on the residual limb, and to facilitate donning procedure.

    FINDINGS AND OUTCOMES: The main site of weight bearing in the old prosthesis (patellar tendon bearing) was anterior proximal region of the residual limb, especially the patellar tendon. The pressure was almost 10 times higher than the distal region during level walking. Pressures were distributed more evenly with the total surface bearing socket design, and the donning was much easier.

    CONCLUSION: Pressure distribution within the socket could be affected by socket design and suspension system. Using the total surface bearing socket and Velcro as suspension system might facilitate donning of prosthesis and reduce traction at the end of residual limb during the swing phase of gait.

    CLINICAL RELEVANCE: Proper socket design and suspension system based on the amputees' need can facilitate rehabilitation process and lead to the amputee's satisfaction. The pressure is distributed more uniformly over the residual limb by the total surface bearing socket compared to the patellar tendon bearing socket for lower limb amputees with unusual stump shape.

    MeSH terms: Adult; Amputation; Amputation Stumps; Artificial Limbs*; Female; Humans; Prosthesis Design*; Tibia; Walking/physiology*; Weight-Bearing/physiology*
  15. Liew KB, Odeniyi MA, Peh KK
    Pharm Dev Technol, 2016;21(3):346-53.
    PMID: 25597618 DOI: 10.3109/10837450.2014.1003657
    Freeze drying technology has not been maximized and reported in manufacturing orally disintegrating films. The aim of this study was to explore the freeze drying technology in the formulation of sildenafil orally disintegrating films and compare the physical properties with heat-dried orally disintegrating film. Central composite design was used to investigate the effects of three factors, namely concentration of carbopol, wheat starch and polyethylene glycol 400 on the tensile strength and disintegration time of the film. Heat-dried films had higher tensile strength than films prepared using freeze-dried method. For folding endurance, freeze-dried films showed improved endurance than heat-dried films. Moreover, films prepared using freeze-dried methods were thicker and had faster disintegration time. Formulations with higher amount of carbopol and starch showed higher tensile strength and thickness whereas formulations with higher PEG 400 content showed better flexibility. Scanning electron microscopy showed that the freeze-dried films had more porous structure compared to the heat-dried film as a result of the release of water molecule from the frozen structure when it was subjected to freeze drying process. The sildenafil film was palatable. The dissolution profiles of freeze-dried and heat-dried films were similar to Viagra® with f2 of 51.04 and 65.98, respectively.
    MeSH terms: Sildenafil Citrate; Acrylic Resins; Freeze Drying; Freezing; Hot Temperature; Microscopy, Electron, Scanning; Polyethylene Glycols; Solubility; Starch; Tensile Strength; Water; Triticum
  16. Gan HM, Tan MH, Lee YP, Hammer MP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4187-4188.
    PMID: 25600740
    The mitogenome of an Australian sample of the mudskipper, Periophthalmus minutus, was recovered from partial sequencing using the MiSeq sequencer. This mudskipper has a mitogenome of 16,506 base pairs (55% A + T content) made up of two ribosomal subunit genes, 13 protein-coding genes, 22 transfer RNAs, and a 838 bp non-coding AT-rich region. This is the first sequenced mitogenome for the genus Periophthalmus and the fifth for the subfamily Oxudercinae.
    MeSH terms: Animals; Perciformes/genetics*; RNA/genetics*; RNA, Transfer/genetics*; Mitochondrial Proteins/genetics*; Fish Proteins/genetics*; Genome, Mitochondrial*
  17. Gan HY, Gan HM, Tan MH, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4099-4100.
    PMID: 25629489
    The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
    MeSH terms: Animals; Base Composition/genetics; Crustacea/genetics*; RNA, Transfer/genetics; Gene Order/genetics*; Decapoda (Crustacea)/genetics*; Anomura/genetics*; Genome, Mitochondrial/genetics*
  18. Austin CM, Tan MH, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4176-4177.
    PMID: 25630729
    Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
    MeSH terms: Animals; Base Composition; Mitochondria/genetics*; RNA, Ribosomal/genetics; RNA, Transfer/genetics; Open Reading Frames; Sequence Analysis, DNA/methods*; Gene Order; Decapoda (Crustacea)/genetics*; Genome, Mitochondrial; Endangered Species; High-Throughput Nucleotide Sequencing/methods*; Genome Size
  19. Beng TS, Ahmad F, Loong LC, Chin LE, Zainal NZ, Guan NC, et al.
    Am J Hosp Palliat Care, 2016 Jul;33(6):555-60.
    PMID: 25632044 DOI: 10.1177/1049909115569048
    A pilot study was conducted to evaluate the efficacy of 5-minute mindful breathing in distress reduction. Twenty palliative care patients and family caregivers with a distress score ≥4 measured by the Distress Thermometer were recruited and randomly assigned to mindful breathing or "listening" (being listened to). Median distress reductions after 5 minutes were 2.5 for the mindful breathing group and 1.0 for the listening group. A significantly larger reduction in the distress score was observed in the mindful breathing group (Mann-Whitney U test: U = 8.0, n1 = n2 = 10, mean rank1 = 6.30, mean rank2 = 14.70, z = -3.208, P = .001). The 5-minute mindful breathing could be useful in distress reduction in palliative care.
    MeSH terms: Adaptation, Psychological; Adult; Aged; Female; Humans; Male; Middle Aged; Palliative Care/methods*; Palliative Care/psychology; Pilot Projects; Stress, Psychological/psychology; Stress, Psychological/therapy*; Caregivers/psychology*; Mind-Body Therapies/methods*; Mindfulness/methods*
  20. Haniff AN, Gam LH
    Biotechnol Appl Biochem, 2016 Mar;63(2):266-72.
    PMID: 25640279 DOI: 10.1002/bab.1357
    Smoking, passive smoking, and nonsmoking are conditions that give different degrees of stress to the body. In this study, a proteomic technique was used to analyze differentially urinary protein expression between these three groups of subjects. Urinary proteins were precipitated using ammonium sulfate followed by separation according to molecular weights using SDS-PAGE. The gel was stained by Coommassie blue, and the image of the gel was captured for the comparison study. The protein bands that were consistently detected but expressed at different intensity between the smokers and nonsmokers were targeted for further analysis. Three targeted protein bands were excised from the gel, consisting of a unique protein band of smokers and a pair of differentially expressed protein bands from smokers and nonsmokers. The proteins were digested in gel by trypsin. The tryptic peptides were analyzed with ultra performance liquid chromatography-tandem mass spectrometry. Protein identity was determined by the product ion spectrum in the MS/MS scan. Four unique proteins from the smokers, namely, pancreatic alpha amylase, proepidermal growth factor, protein 4.1, and prostatic acid phosphatase, were found to be potential urinary biomarkers to indicate smoking status of a person.
    MeSH terms: Smoking
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