Displaying publications 1 - 20 of 36 in total

Abstract:
Sort:
  1. Marrero G, Schneider KL, Jenkins DM, Alvarez AM
    Int J Syst Evol Microbiol, 2013 Sep;63(Pt 9):3524-3539.
    PMID: 24003072 DOI: 10.1099/ijs.0.046490-0
    Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.
  2. Agha R, Abdall-Razak A, Crossley E, Dowlut N, Iosifidis C, Mathew G, et al.
    Int J Surg, 2019 Nov 06;72:156-165.
    PMID: 31704426 DOI: 10.1016/j.ijsu.2019.11.002
    INTRODUCTION: The STROCSS guideline was developed in 2017 to improve the reporting quality of observational studies in surgery. Building on its impact and usefulness, we sought to update the guidelines two years after its publication.

    METHODS: A steering group was formed to review the existing guideline and propose amendments to the 17-item checklist. A Delphi consensus exercise was utilised to determine agreement across a list of proposed modifications to the STROCSS 2017 guideline. An expert panel of 46 surgeons were invited to assess the proposed updates via Google Forms.

    RESULTS: The response rate was 91% (n = 42/46). High agreement was reached across all the items and the guideline was finalised in the first round. The checklist maintained 17-items, with modifications primarily considered to improve content and readability.

    CONCLUSIONS: The STROCSS 2019 guideline is hereby presented as a considered update to improve reporting of cohort, cross-sectional and case-control studies in surgery.

  3. Zhou J, Azizan EAB, Cabrera CP, Fernandes-Rosa FL, Boulkroun S, Argentesi G, et al.
    Nat Genet, 2021 Sep;53(9):1360-1372.
    PMID: 34385710 DOI: 10.1038/s41588-021-00906-y
    Most aldosterone-producing adenomas (APAs) have gain-of-function somatic mutations of ion channels or transporters. However, their frequency in aldosterone-producing cell clusters of normal adrenal gland suggests a requirement for codriver mutations in APAs. Here we identified gain-of-function mutations in both CTNNB1 and GNA11 by whole-exome sequencing of 3/41 APAs. Further sequencing of known CTNNB1-mutant APAs led to a total of 16 of 27 (59%) with a somatic p.Gln209His, p.Gln209Pro or p.Gln209Leu mutation of GNA11 or GNAQ. Solitary GNA11 mutations were found in hyperplastic zona glomerulosa adjacent to double-mutant APAs. Nine of ten patients in our UK/Irish cohort presented in puberty, pregnancy or menopause. Among multiple transcripts upregulated more than tenfold in double-mutant APAs was LHCGR, the receptor for luteinizing or pregnancy hormone (human chorionic gonadotropin). Transfections of adrenocortical cells demonstrated additive effects of GNA11 and CTNNB1 mutations on aldosterone secretion and expression of genes upregulated in double-mutant APAs. In adrenal cortex, GNA11/Q mutations appear clinically silent without a codriver mutation of CTNNB1.
  4. Al-Atabi M, Espino DM, Hukins DW, Buchan KG
    Proc Inst Mech Eng H, 2012 Apr;226(4):275-87.
    PMID: 22611868
    Repair of the mitral valve is defined (loosely) as a procedure that alters the valve structure, without replacement, enabling the natural valve itself to continue to perform under the physical conditions to which it is exposed. As the mitral valve is driven by flow and pressure, it should be feasible to analyse and assess its function, failure and repair as a mechanical system. This article reviews the current state of mechanical evaluation of surgical repairs of the failed mitral valve of the heart. This review describes the anatomy and physiology of the mitral valve, followed by the failure of the mitral valve from a mechanical point of view. The surgical methods used to repair failed valves are introduced, while the use of engineering analysis to aid understanding of mitral valve repair is also reviewed. Finally, a section on recommendations for development and future uses of engineering techniques to surgical repair are presented.
  5. De Simone B, Abu-Zidan FM, Chouillard E, Di Saverio S, Sartelli M, Podda M, et al.
    World J Emerg Surg, 2022 Dec 16;17(1):61.
    PMID: 36527038 DOI: 10.1186/s13017-022-00466-4
    BACKGROUND: The incidence of the highly morbid and potentially lethal gangrenous cholecystitis was reportedly increased during the COVID-19 pandemic. The aim of the ChoCO-W study was to compare the clinical findings and outcomes of acute cholecystitis in patients who had COVID-19 disease with those who did not.

    METHODS: Data were prospectively collected over 6 months (October 1, 2020, to April 30, 2021) with 1-month follow-up. In October 2020, Delta variant of SARS CoV-2 was isolated for the first time. Demographic and clinical data were analyzed and reported according to the STROBE guidelines. Baseline characteristics and clinical outcomes of patients who had COVID-19 were compared with those who did not.

    RESULTS: A total of 2893 patients, from 42 countries, 218 centers, involved, with a median age of 61.3 (SD: 17.39) years were prospectively enrolled in this study; 1481 (51%) patients were males. One hundred and eighty (6.9%) patients were COVID-19 positive, while 2412 (93.1%) were negative. Concomitant preexisting diseases including cardiovascular diseases (p 

  6. Perrone G, Giuffrida M, Abu-Zidan F, Kruger VF, Livrini M, Petracca GL, et al.
    World J Emerg Surg, 2024 Apr 16;19(1):14.
    PMID: 38627831 DOI: 10.1186/s13017-024-00543-w
    BACKGROUND: Literature suggests colonic resection and primary anastomosis (RPA) instead of Hartmann's procedure (HP) for the treatment of left-sided colonic emergencies. We aim to evaluate the surgical options globally used to treat patients with acute left-sided colonic emergencies and the factors that leading to the choice of treatment, comparing HP and RPA.

    METHODS: This is a prospective, international, multicenter, observational study registered on ClinicalTrials.gov. A total 1215 patients with left-sided colonic emergencies who required surgery were included from 204 centers during the period of March 1, 2020, to May 31, 2020. with a 1-year follow-up.

    RESULTS: 564 patients (43.1%) were females. The mean age was 65.9 ± 15.6 years. HP was performed in 697 (57.3%) patients and RPA in 384 (31.6%) cases. Complicated acute diverticulitis was the most common cause of left-sided colonic emergencies (40.2%), followed by colorectal malignancy (36.6%). Severe complications (Clavien-Dindo ≥ 3b) were higher in the HP group (P 

  7. Gan HY, Noor ME, Saari NA, Musa N, Mustapha B, Usup G, et al.
    Genome Announc, 2015;3(2).
    PMID: 25814609 DOI: 10.1128/genomeA.00210-15
    Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The genome of this strain comprises 5,652,224 bp with 5,014 open reading frames, 9 rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and bacteriocin were also identified.
  8. Cheng TH, Ismail N, Kamaruding N, Saidin J, Danish-Daniel M
    Biotechnol Rep (Amst), 2020 Sep;27:e00482.
    PMID: 32514406 DOI: 10.1016/j.btre.2020.e00482
    Industrial enzymes are important for various biotechnological applications. Currently, the diversity of industrial enzymes-producing marine bacteria from Malaysia remains mostly unknown. This study investigated the diversity of industrial enzyme-producing marine bacteria from culture collections at the Institute of Marine Biotechnology, Universiti Malaysia Terengganu. Out of 200 bacterial isolates revived, 163 bacteria isolate were successfully growth. Marine bacteria produced enzymes with total scoring higher than four were selected for molecular identification using 16S rDNA. About 161 bacteria isolate secreted amylase (68.7 %), lipase (88.3 %) and protease (68.7 %). The phylogenetic analysis led to the identification of three major phyla, namely Proteobacteria, Firmicutes and Bacteroidetes. These phyla were differentiated into nine genera consisted of Bacillus, Chryseomicrobium, Photobacterium, Pseudoalteromonas, Ruegeria, Shewanella, Solibacillus, Tenacibaculum and Vibrio. Genetic variation was more likely to occur within similar marine bacteria species. The microbial community was found to affect the production of industrial enzymes and the diversity of marine bacteria.
  9. Tan MP, Amornsakun T, Siti Azizah MN, Habib A, Sung YY, Danish-Daniel M
    Mitochondrial DNA B Resour, 2019 Sep 12;4(2):2966-2969.
    PMID: 33365813 DOI: 10.1080/23802359.2019.1662741
    Eighty-four specimens collected from 13 populations from Malaysia, Thailand, and Vietnam were analysed, revealing 21 putative haplotypes with overall estimated haplotype and nucleotide diversities of 0.79 and 0.0079, respectively. High levels of diversity and an absence of founder effects were observed among populations in peninsular Malaysia. In contrast, populations from Sarawak exhibited low genetic diversity, which is a typical sign of colonies introduced from a single source. Historical translocation of Trichopodus pectoralis from Thailand to Malaysia, as well as to the Philippines, Indonesia, and Myanmar was apparent. Historical introduction of T. pectoralis from Vietnam was also detected in peninsular Malaysia.
  10. Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SA, Sung YY, et al.
    Evol Bioinform Online, 2019;15:1176934319892284.
    PMID: 31839703 DOI: 10.1177/1176934319892284
    Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.
  11. Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, et al.
    Mol Phylogenet Evol, 2020 05;146:106756.
    PMID: 32028032 DOI: 10.1016/j.ympev.2020.106756
    Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.
  12. Cheng TH, Saidin J, Danish-Daniel M, Gan HM, Mat Isa MN, Abu Bakar MF, et al.
    Genome Announc, 2018 Feb 08;6(6).
    PMID: 29439033 DOI: 10.1128/genomeA.00022-18
    Serratia marcescens
    subsp.sakuensisstrain K27 was isolated from sponge (Haliclona amboinensis). The genome of this strain consists of 5,325,727 bp, with 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for the production of amylases, lipases, and proteases. Gene clusters for the biosynthesis of nonribosomal peptides and thiopeptide were also identified.
  13. Hall DA, Ray J, Watson J, Sharman A, Hutchison J, Harris P, et al.
    Hear Res, 2019 06;377:153-166.
    PMID: 30939361 DOI: 10.1016/j.heares.2019.03.018
    AUT00063 is an experimental new medicine that has been demonstrated to suppress spontaneous hyperactivity by modulating the action of voltage-gated potassium-channels in central auditory cortical neurons of a rodent model. This neurobiological property makes it a good candidate for treating the central component of subjective tinnitus but this has not yet been tested in humans. The main purpose of the QUIET-1 (QUest In Eliminating Tinnitus) trial was to examine the effect of AUT00063 on the severity of tinnitus symptoms in people with subjective tinnitus. The trial was a randomised, placebo-controlled, observer, physician and participant blinded multi-centre superiority trial with two parallel groups and a primary endpoint of functional impact on tinnitus 28 days after the first drug dosing day. The trial design overcame the scale and logistical challenges of delivering a scientifically robust, statistically powered multi-centre study for subjective tinnitus within the National Health Service in England. The trial was terminated early for futility. Overall, 212 participants consented across 18 sites with 91 participants randomised to groups using age, gender, tinnitus symptom severity and hearing status as minimisation factors. While the pharmacokinetic markers confirm the uptake of AUT00063 in the body, within the expected therapeutic range, with respect to clinical benefit findings indicated that AUT00063 was not effective in alleviating tinnitus symptoms (1.56 point change in Tinnitus Functional Index). In terms of clinical harms, results indicated that a daily dose of 800 mg capsules of AUT00063 taken for 28 days was safe and well tolerated. These findings provide significant advances in the drug development field for hearing sciences, but raise questions about the predictive validity of certain rodent models of noise-induced hearing loss and tinnitus, as least for the mechanism evaluated in the present study. Trial Registration: (EudraCT) 2014-002179-27; NCT02315508.
  14. Yek C, Nam VS, Leang R, Parker DM, Heng S, Souv K, et al.
    PMID: 35373190 DOI: 10.3389/fitd.2021.788590
    Southeast Asia (SEA) emerged relatively unscathed from the first year of the global SARS-CoV-2 pandemic, but as of July 2021 the region is experiencing a surge in case numbers primarily driven by Alpha (B.1.1.7) and subsequently the more transmissible Delta (B.1.617.2) variants. While initial disease burden was mitigated by swift government responses, favorable cultural and societal factors, the more recent rise in cases suggests an under-appreciation of prior prevalence and over-appreciation of possible cross-protective immunity from exposure to endemic viruses, and highlights the effects of vaccine rollout at varying tempos and of variable efficacy. This burgeoning crisis is further complicated by co-existence of malaria and dengue in the region, with implications of serological cross-reactivity on interpretation of SARS-CoV-2 assays and competing resource demands impacting efforts to contain both endemic and pandemic disease.
  15. Pinto SL, Janiak MC, Dutyschaever G, Barros MAS, Chavarria AG, Martin MP, et al.
    R Soc Open Sci, 2023 Jul;10(7):230451.
    PMID: 37448478 DOI: 10.1098/rsos.230451
    Dietary variation within and across species drives the eco-evolutionary responsiveness of genes necessary to metabolize nutrients and other components. Recent evidence from humans and other mammals suggests that sugar-rich diets of floral nectar and ripe fruit have favoured mutations in, and functional preservation of, the ADH7 gene, which encodes the ADH class 4 enzyme responsible for metabolizing ethanol. Here we interrogate a large, comparative dataset of ADH7 gene sequence variation, including that underlying the amino acid residue located at the key site (294) that regulates the affinity of ADH7 for ethanol. Our analyses span 171 mammal species, including 59 newly sequenced. We report extensive variation, especially among frugivorous and nectarivorous bats, with potential for functional impact. We also report widespread variation in the retention and probable pseudogenization of ADH7. However, we find little statistical evidence of an overarching impact of dietary behaviour on putative ADH7 function or presence of derived alleles at site 294 across mammals, which suggests that the evolution of ADH7 is shaped by complex factors. Our study reports extensive new diversity in a gene of longstanding ecological interest, offers new sources of variation to be explored in functional assays in future study, and advances our understanding of the processes of molecular evolution.
  16. Matupang DM, Zulkifli HI, Arnold J, Lazim AM, Ghaffar MA, Musa SM
    Mar Pollut Bull, 2023 Apr;189:114762.
    PMID: 36870137 DOI: 10.1016/j.marpolbul.2023.114762
    Plastic can be degraded into microplastic (<5 mm) and has been polluting worldwide marine environment and negatively impact human health. Microplastics in marine organisms are still understudied in Malaysia, let alone from a subclass Elasmobranchii. Five tropical shark species (Carcharhinus dussumieri, Carcharhinus sorrah, Chiloscyllium hasseltii, Chiloscyllium punctatum, and Scoliodon laticaudus) were examined for the presence of microplastics. 74 sharks were sampled from the local wet market and 100 % of samples contained microplastics. A total of 2211 plastic particles were found in gastrointestinal tracts (GIT) and gills, where 29.88 ± 2.34 particles per shark (mean ± SEM). Black (40.07 %) and fiber (84.44 %) microplastics were the most dominant. Extracted microplastic sizes ranged from 0.007 mm to 4.992 mm. This study suggests that microplastic uptake is gender-related for some shark species. A subsample of microplastics (10 %) was used for polymer type identification, where polyester was recorded the highest (43.95 %).
  17. Nurhafizah WWI, Lee KL, Laith A AR, Nadirah M, Danish-Daniel M, Zainathan SC, et al.
    J Invertebr Pathol, 2021 11;186:107594.
    PMID: 33878330 DOI: 10.1016/j.jip.2021.107594
    Global high demand for Pacific white shrimp Penaeus vannamei has led to intensified cultivation and a wide range of disease problems, including bacterial diseases due to vibrios. Three presumptive luminescent Vibrio harveyi strains (Vh5, Vh8 and Vh10) were isolated from the hepatopancreas (Vh5) and haemolymph (Vh8 and Vh10) of diseased growout Pacific white shrimp from a farm in Setiu, Terengganu, Malaysia, using Vibrio harveyi agar (VHA) differential medium. All three strains were identified as V. harveyi by biochemical characteristics. 16S rRNA gene-based phylogenetic analyses by neighbour-joining, maximum likelihood and maximum parsimony methods showed all three strains in the V. harveyi cluster. All three strains were β-haemolytic and positive for motility, biofilm formation and extracellular products (caseinase, gelatinase, lipase, DNase, amylase and chitinase). Vh10 was subjected to pathogenicity test in Pacific white shrimp by immersion challenge and determined to have a LC50 of 6.0 × 108 CFU mL-1 after 168 h of exposure. Antibiotic susceptibility tests showed that all strains were resistant to oxytetracycline (OXT30), oleandomycin (OL15), amoxicillin (AML25), ampicillin (AMP10) and colistin sulphate (CT25) but sensitive to doxycycline (DO30), flumequine (UB30), oxolinic acid (OA2), chloramphenicol (C30), florfenicol (FFC30), nitrofurantoin (F5) and fosfomycin (FOS50). Each strain was also resistant to a slightly different combination of eight other antibiotics, with an overall multiple antibiotic resistance (MAR) index of 0.40, suggesting prior history of heavy exposure to the antibiotics. Vh10 infection resulted in pale or discoloured hepatopancreas, empty guts, reddening, necrosis and luminescence of uropods, as well as melanised lesions in tail muscle. Histopathological examination showed necrosis of intertubular connective tissue and tubule, sloughing of epithelial cells in hepatopancreatic tubule, haemocytic infiltration, massive vacuolation and loss of hepatopancreatic tubule structure.
  18. Abouammo MD, Narayanan MS, Alsavaf MB, Alwabili M, Gosal JS, Bhuskute GS, et al.
    PMID: 38506519 DOI: 10.1227/ons.0000000000001119
    BACKGROUND AND OBJECTIVES: Expanded endonasal approaches (EEAs) have proven safe and effective in treating select petrous apex (PA) pathologies. Angled endoscopes and instruments have expanded indications for such approaches; however, the complex neurovascular anatomy surrounding the petrous region remains a significant challenge. This study evaluates the feasibility, anatomic aspects, and limitations of a contralateral nasofrontal trephination (CNT) route as a complementary corridor improving access to the PA.

    METHODS: Expanded endonasal and CNT approaches to the PA were carried out bilaterally in 15 cadaveric heads with endovascular latex injections. The distance to the PA, angle between instruments through the 2 approach portals, and surgical freedom were measured and compared.

    RESULTS: Three-dimensional DICOM-based modeling and visualization indicate that the CNT route reduces the distance to the target located within the contralateral PA by an average of 3.33 cm (19%) and affords a significant increase in the angle between instruments (15.60°; 54%). Furthermore, the vertical vector of approach is improved by 28.97° yielding a caudal reach advantage of 2 cm. The area of surgical freedom afforded by 3 different approaches (endonasal, endonasal with an endoscope in CNT portal, and endonasal with an instrument in CNT portal) was compared at 4 points: the dural exit point of the 6th cranial nerve, jugular foramen, foramen lacerum, and petroclival fissure. The mean area of surgical freedom provided by both approaches incorporating the CNT corridor was superior to EEA alone at each of the surgical targets (P =

Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links