Displaying publications 1 - 20 of 93 in total

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  1. The clinical significance of immunoglobulin A deficiency
    Latiff AH, Kerr MA
    Ann. Clin. Biochem., 2007 Mar;44(Pt 2):131-9.
    PMID: 17362578 DOI: 10.1258/000456307780117993
    IgA deficiency is the most common primary immunoglobulin deficiency. The prevalence in Caucasians is around one in 500, whereas in some Asian populations it is very uncommon. Most individuals with IgA deficiency are clinically asymptomatic. Those with symptoms of immunodeficiency have predominantly sinopulmonary or gastrointestinal infections, which are more severe when associated with IgG2, IgG4 or specific antibody deficiency. IgA deficiency is believed to be one end of a spectrum of immunodeficiency with common variable immunodeficiency at the most severe end. Although primary IgA deficiency is the most commonly encountered form, secondary deficiencies due to drugs or viral infections are recognized. IgA deficiencies can be partial or transient. Primary IgA deficiency is caused by a defect of terminal lymphocyte differentiation, which leads to underproduction of serum and mucosal IgA; affected individuals have normal IgA genes. A number of non-immunoglobulin genes have been implicated in IgA deficiency. There have been many diseases reported in association with IgA deficiency, particularly autoimmune diseases. The most common association is with coeliac disease (CD), which has special significance since CD is usually diagnosed by detection of specific IgA antibodies that are obviously lacking in IgA deficiency. There is no specific treatment for patients with symptomatic IgA deficiency. Antibiotics are prescribed in those with acute infections. A significant proportion of IgA-deficient individuals are reported to have anti-IgA antibodies in their serum. Although blood or blood products given to IgA-deficient individuals can lead to severe, even fatal, transfusion reactions, such reactions are rare.
  2. Fulltext In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas
    Tran PN, Savka MA, Gan HM
    Front Microbiol, 2017;8:1296.
    PMID: 28747902 DOI: 10.3389/fmicb.2017.01296
    The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans-P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.
  3. A comprehensive literature search to identify existing measures assessing "concentration" as a core outcome domain for sound-based interventions for chronic subjective tinnitus in adults
    Shabbir M, Akeroyd MA, Hall DA
    Prog Brain Res, 2021;262:209-224.
    PMID: 33931180 DOI: 10.1016/bs.pbr.2021.01.027
    The Core Outcome Measures in Tinnitus (COMiT) initiative has recommended a minimum standard of five outcomes when designing a clinical trial to assess the efficacy of sound-based interventions. These are: ability to ignore, concentration, quality of sleep, sense of control and tinnitus intrusiveness. The next stage is to consider what measurement instruments might be appropriate for assessing these constructs. The current study aimed to systematically gather existing instruments used to assess concentration. A total of 6240 potentially relevant records were identified. Duplicates and non-published works were removed, leaving a total of 3599 records. A procedure was developed to sample a subset of records, in order to identify relevant instruments without exhaustively reading all 3599 texts. Initially 559 records were identified by screening 1000 articles; 500 of which were randomly selected, and 500 were the most recent publications identified from the PubMed database. Using predefined criteria for data saturation, information about measures of concentration was extracted from the 559 full texts. However, data saturation was reached by 240. Thirteen candidate instruments were identified. The next step will be to assess content validity and feasibility of administration for all these candidate instruments. Findings will inform future recommendations for how to measure concentration in clinical trials to ensure results of trials can be easily compared, contrasted, and synthesized.
  4. Epiploic Appendagitis: An uncommon surgical diagnosis
    Michael A, Zakry Y, Hanif H
    Med J Malaysia, 2017 04;72(2):128-129.
    PMID: 28473679 MyJurnal
    Epiploic appendagitis or appendices epiploicae, is a rare cause of abdominal pain in patients with mild signs of abdominal pathology. It mimics diverticulitis or appendicitis clinically as there are no pathognomonic features. It is a surgical diagnosis presenting with localised, sharp, acute abdominal pain, not associated with symptoms like nausea, vomiting, fever or suggestive laboratory values. With the availability of abdominal CT scans and ultrasound, it will frequently be a differential diagnosis preventing unnecessary surgery for patients. However, it may be erroneous and therefore clinical judgement is of paramount importance. This report highlights this rare presentation and identifies management guidelines.
  5. Mesenteric bones: Intra-abdominal heterotopic ossification
    Michael A, Narasimman S, Jasjit Singh N
    Med J Malaysia, 2018 04;73(2):110-111.
    PMID: 29703875 MyJurnal
    Intra-abdominal heterotopic ossification usually develops after abdominal surgery and can cause complications such as bowel obstruction and even intestinal perforation. Bisphosphonates, NSAIDs and even local radiation is used as prophylaxis or treatment. Surgeons must consider heterotopic ossification and its complications as a differential when managing complex polytrauma patients with suspicious radiographic densities.
  6. Fulltext Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13, Isolated from Vitis vinifera L. Xylem Sap
    Lai WX, Gan HM, Hudson AO, Savka MA
    Genome Announc, 2016;4(1).
    PMID: 26847900 DOI: 10.1128/genomeA.01695-15
    The whole-genome sequence of a new genospecies of Methylobacterium sp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.
  7. Developmental changes in the endocrine stress response in orangutans (Pongo pygmaeus)
    Takeshita RSC, Mendonça RS, Bercovitch FB, Huffman MA
    J. Comp. Physiol. B, Biochem. Syst. Environ. Physiol., 2019 12;189(6):659-672.
    PMID: 31549180 DOI: 10.1007/s00360-019-01235-7
    Non-invasive measures of stress are crucial for captive and conservation management programs. The adrenal hormone dehydroepiandrosterone-sulfate (DHEAS) has recently been adopted as a stress marker, but there is little investigation of its relationship to glucocorticoids (GC), well-known indicators of stress. This study examined the influence of age, reproductive state and environment on GC and DHEAS levels in orangutans, to test whether the GC/DHEAS ratio can provide an index of stress response in primates. We measured fecal GC (fGC) and fecal DHEAS (fDHEAS) concentrations in 7 captive orangutans from zoological parks in Japan and 22 wild orangutans from Danum Valley Conservation Area, Malaysia. We found that in a stressful condition (transportation), fDHEAS levels increased 2 days after the fGC response, which occurred 1 day after the stressor. One pregnant female had elevated levels of both hormones, and a higher fGC/fDHEAS ratio than baseline. Females in the first year of lactation had fGC levels and the fGC/fDHEAS ratio significantly higher than both baseline and females in the second and subsequent years of lactation. There was no effect of age on fGC levels, but the fGC/fDHEAS ratio was higher in infants than adults and adolescents. fDHEAS concentrations were lower in infants than juveniles, adolescents and adults, a phenomenon known as adrenarche, shared with humans and other great apes. We suggest that changes in DHEAS during orangutan life history are associated with changes in the dynamics of maintaining homeostasis that vary with age and reproductive state. The GC/DHEAS ratio index is useful to evaluate age-related abilities of responding to stressful challenges.
  8. Fulltext Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4
    Gan HM, Lee MVL, Savka MA
    PeerJ, 2019;7:e6366.
    PMID: 30775173 DOI: 10.7717/peerj.6366
    The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
  9. Fulltext Genome sequence of Methylobacterium sp. strain GXF4, a xylem-associated bacterium isolated from Vitis vinifera L. grapevine
    Gan HM, Chew TH, Hudson AO, Savka MA
    J Bacteriol, 2012 Sep;194(18):5157-8.
    PMID: 22933776 DOI: 10.1128/JB.01201-12
    Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.
  10. Fulltext Genome sequence of Novosphingobium sp. strain Rr 2-17, a nopaline crown gall-associated bacterium isolated from Vitis vinifera L. grapevine
    Gan HM, Chew TH, Hudson AO, Savka MA
    J Bacteriol, 2012 Sep;194(18):5137-8.
    PMID: 22933764 DOI: 10.1128/JB.01159-12
    Novosphingobium sp. strain Rr 2-17 is an N-acyl homoserine lactone (AHL)-producing bacterium isolated from the crown gall tumor of a grapevine. To our knowledge, this is the first draft genome announcement of a plant-associated strain from the genus Novosphingobium.
  11. Fulltext Divergent Solutions to Visual Problem Solving across Mammalian Species
    Mustafar F, Harvey MA, Khani A, Arató J, Rainer G
    eNeuro, 2018 07 11;5(4).
    PMID: 30073190 DOI: 10.1523/ENEURO.0167-18.2018
    Our understanding of the neurobiological underpinnings of learning and behavior relies on the use of invasive techniques, which necessitate the use of animal models. However, when different species learn the same task, to what degree are they actually producing the same behavior and engaging homologous neural circuitry? This question has received virtually no recent attention, even as the most powerful new methodologies for measuring and perturbing the nervous system have become increasingly dependent on the use of murine species. Here, we test humans, rats, monkeys, and an evolutionarily intermediate species, tree shrews, on a three alternative, forced choice, visual contrast discrimination task. As anticipated, learning rate, peak performance, and transfer across contrasts was lower in the rat compared to the other species. More interestingly, rats exhibited two major behavioral peculiarities: while monkeys and tree shrews based their choices largely on visual information, rats tended to base their choices on past reward history. Furthermore, as the task became more difficult, rats largely disengaged from the visual stimulus, reverting to innate spatial predispositions in order to collect rewards near chance probability. Our findings highlight the limitation of muridae as models for translational research, at least in the area of visually based decision making.
  12. Standardized questions in English for estimating tinnitus prevalence and severity, hearing difficulty and usage of healthcare resources, and their translation into 11 European languages
    Biswas R, Lugo A, Gallus S, Akeroyd MA, Hall DA
    Hear Res, 2019 06;377:330-338.
    PMID: 30853349 DOI: 10.1016/j.heares.2019.02.008
    INTRODUCTION: Prevalence estimates depend largely on the nature of the question asked to define the presence of the health condition, and the literature on the population burden of tinnitus and hearing difficulties is no different in this respect. The lack of standardized questions for data collection limits comparison across studies and across countries. The purpose of this short Technical Note is to report the first attempt to establish a set of standard questions developed for use in population-based surveys, and their adaptation and translation from English into 11 European languages.

    METHODS: Four questions and their corresponding response options were adapted from existing population-based surveys to assess tinnitus prevalence, tinnitus symptom severity, use of healthcare resources for tinnitus and hearing difficulty. The translated versions (Bulgarian, French, German, Greek, Italian, Latvian, Polish, Portuguese, Romanian, Russian, and Spanish) were generated using recognized methods to achieve a "world-for-world" translation.

    RESULTS: Translated versions were produced with acceptable functional equivalence to the original English-language version, as judged by a small panel of bilingual speakers who participated in the online field testing.

    CONCLUSION: This work is the first of its kind to promote multi-national standardization by creating a set of tools that can readily be used across countries. These are currently being used in a European-wide study of tinnitus prevalence, and have wider application across English- and Spanish speaking countries including the Americas and Oceania.

  13. An integrative look at frugivory and seed dispersal studies
    Campos-Arceiz A, Steele MA, Carlo TA, Xiong W
    Integr Zool, 2011 Jun;6(2):71-73.
    PMID: 21645272 DOI: 10.1111/j.1749-4877.2011.00241.x
  14. The status of natural radioactivity in Nigerian environments
    Olatunji MA, Khandaker MU, Nwankwo VUJ, Idris AM
    Radiat Environ Biophys, 2022 Nov;61(4):597-608.
    PMID: 36175773 DOI: 10.1007/s00411-022-00993-3
    Proper documentation of baseline radiation data of different environments is an important step toward adequate environmental monitoring, and it provides quick means to quantitatively check and determine possible radionuclide contamination by anthropogenic sources. Besides, such documentation is useful for decision making processes, assessment of dose rates to the public, epidemiological studies, and environmental regulations. This review summarizes the results of studies conducted on radioactivity in Nigerian environments. For most soil samples, the levels of radioactivity are well within the world averages of 33, 45, and 420 Bq kg-1 for 226Ra, 232Th and 40K, respectively. Other soil samples from regions such as Abeokuta in the southwest, and Jos in the northcentral have been described as high background radiation areas with radioactivity values comparable with those obtained from known high background radiation areas such as the Odisha (formerly Orissa) coast in India (with values reported as 350, 2,825, and 180 Bq kg-1 for 238U/226Ra, 232Th, and 40K, respectively). In some parts of Nigeria, surface and underground water sources used for drinking and other purposes also present elevated levels of 226Ra above the world range of 0.01 to 0.1 Bq l-1 and the tolerable levels recommended by the World Health Organization and U.S. Environmental Protection Agency. Corresponding radiation doses due to measured radioactivities from different environments were estimated and compared with those reported in similar studies around the world. More so, the human and environmental health hazards that might be associated with the reported radioactivity in different environmental settings are discussed. The present report is expected to support authorities in developing appropriate regulations to protect the public from radiation exposure arising from environmental radioactivity. The report also examines other areas of consideration for future studies to ensure adequate radiation monitoring in Nigeria.
  15. Can we safely deform a plate to fit every bone? Population-based fit assessment and finite element deformation of a distal tibial plate
    Harith H, Schmutz B, Malekani J, Schuetz MA, Yarlagadda PK
    Med Eng Phys, 2016 Mar;38(3):280-5.
    PMID: 26739124 DOI: 10.1016/j.medengphy.2015.11.012
    Anatomically precontoured plates are commonly used to treat periarticular fractures. A well-fitting plate can be used as a tool for anatomical reduction of the fractured bone. Recent studies highlighted that some plates fit poorly for many patients due to considerable shape variations between bones of the same anatomical site. While it is impossible to design one shape that fits all, it is also burdensome for the manufacturers and hospitals to produce, store and manage multiple plate shapes without the certainty of utilization by a patient population. In this study, we investigated the number of shapes required for maximum fit within a given dataset, and if they could be obtained by manually deforming the original plate. A distal medial tibial plate was automatically positioned on 45 individual tibiae, and the optimal deformation was determined iteratively using finite element analysis simulation. Within the studied dataset, we found that: (i) 89% fit could be achieved with four shapes, (ii) 100% fit was impossible through mechanical deformation, and (iii) the deformations required to obtain the four plate shapes were safe for the stainless steel plate for further clinical use. The proposed framework is easily transferable to other orthopaedic plates.
  16. Fulltext High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall
    Gan HM, Lee MVJ, Savka MA
    Microbiol Resour Announc, 2018 Sep;7(9).
    PMID: 30533933 DOI: 10.1128/MRA.01045-18
    Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of Allorhizobium vitis K309T (= ATCC 49767T, = NCPPB 3554T), a phytopathogenic strain isolated from a grapevine in Australia. The hybrid approach generated 50% fewer contigs and a 3-fold increase in the N 50 value compared with the previous Illumina-only assembly.
  17. Fulltext Fulminant necrotising amoebic colitis: A diagnostic conundrum
    Michael A, Jasjit SN, Prabhu R
    Med J Malaysia, 2015 Dec;70(6):365-6.
    PMID: 26988213 MyJurnal
    Fulminant necrotising amoebic colitis is a complication of untreated amoebiasis. This is seen in mainly low-income countries. It has a high mortality rate and is difficult to diagnose. We present an extremely rare case of fulminant necrotising amoebic colitis that caused diagnostic confusion in mimicking an acute abdomen, presumably caused by a perforated duodenal ulcer.
  18. Computed tomography of the thorax with 3D reconstruction in penetrating chest injury
    Michael A, Yahya ZO, Mdrazali I, Hanif H
    Med J Malaysia, 2017 02;72(1):75-76.
    PMID: 28255150 MyJurnal
    Penetrating chest wounds is less common but more deadly then blunt trauma. Majority of penetrating chest trauma can be managed conservatively with observation and simple thoracotomy. This case report highlights a bizarre occupational hazard causing a penetrating chest injury and the option of non-invasive management with the aid of computed tomography with 3D reconstruction.
  19. Fulltext Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family
    Gan HM, Gan HY, Ahmad NH, Aziz NA, Hudson AO, Savka MA
    Front Cell Infect Microbiol, 2014;4:188.
    PMID: 25621282 DOI: 10.3389/fcimb.2014.00188
    Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.
  20. Fulltext Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico
    Gan HY, Gan HM, Tarasco AM, Busairi NI, Barton HA, Hudson AO, et al.
    Genome Announc, 2014;2(6).
    PMID: 25377711 DOI: 10.1128/genomeA.01133-14
    Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (luxI) that is involved in cell-to-cell communication via quorum sensing.
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