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Fulltext Modified Unipolar Hemiarthroplasty for the Treatment of Metastatic Lesions of Proximal Femur with Pathological Fractures: Case Series of Six Patients

Lim CY, Mat-Hassan S, Awang M, Md-Ariff MF, Hau-Abdullah MA

Malays Orthop J, 2019 Nov;13(3):21-27.
PMID: 31890106 DOI: 10.5704/MOJ.1911.004

Introduction: Proximal femur resection and endoprosthetic reconstruction is the preferred treatment for extensive bony destruction and pathological fractures. Due to the relatively high cost of endoprosthesis, we adopted the modified unipolar hemiarthroplasty (MUH) for reconstruction when the mode of treatment was for palliation. Materials and Methods: This is a retrospective case study of six patients, who had bone and multi-organs metastases with extensive proximal femur involvement with pathologic fractures who underwent resection and MUH reconstruction during the period 2013 to 2017. All patients were classified as Group B / C based on Scandinavian Sarcoma Group survival scoring, with estimated survival of maximum six months. The basic MUH construct consisted of Austin-Moore prosthesis which was secured to a Küntscher nail using cerclage wire and cemented into the femoral canal. Subsequently, the whole length of the prosthesis which remained outside the canal was coated with cement. Results: The mean age was 61.8 years. The mean survival was 3.9 months, post-operation. There was no implant failure during patients' life span; however, a third of the patients developed infection. Wheel chair ambulation was started immediately post-operation for all patients, and two patients progressed to walking frame ambulation. The total cost of each construct was below US$490 in comparison to long-stem hemiarthroplasty (roughly US$ 1700). Conclusion: Our aim was to alleviate pain, facilitate rehabilitation, ease nursing care and improve quality of life for metastatic bone disease patients until end of life. MUH for the treatment of pathological fracture in proximal femoral metastases is a feasible palliative surgical modality in resource-limited settings.
Autophagy and senescence: A new insight in selected human diseases

Rajendran P, Alzahrani AM, Hanieh HN, Kumar SA, Ben Ammar R, Rengarajan T, et al.

J Cell Physiol, 2019 12;234(12):21485-21492.
PMID: 31144309 DOI: 10.1002/jcp.28895

Senescence and autophagy play important roles in homeostasis. Cellular senescence and autophagy commonly cause several degenerative processes, including oxidative stress, DNA damage, telomere shortening, and oncogenic stress; hence, both events are known to be interrelated. Autophagy is well known for its disruptive effect on human diseases, and it is currently proposed to have a direct effect on triggering senescence and quiescence. However, it is yet to be proven whether autophagy has a positive or negative impact on senescence. It is known that elevated levels of autophagy induce cell death, whereas inadequate autophagy can trigger cellular senescence. Both have important roles in human diseases such as aging, renal degeneration, neurodegenerative disorders, and cancer. Therefore, this review aims to highlight the relevance of senescence and autophagy in selected human ailments through a summary of recent findings on the connection and effects of autophagy and senescence in these diseases.
Raised levels of Il-6, Il-17a, and Il-22 in fatal leptospirosis

Wan Yusoff WSY, Abdullah M, Sekawi Z, Amran F, Yuhana MY, Mohd Taib N, et al.

Eur J Clin Microbiol Infect Dis, 2019 Dec;38(12):2349-2353.
PMID: 31529307 DOI: 10.1007/s10096-019-03699-5

Clinical manifestations of leptospirosis range from mild, common cold-like illness, to a life-threatening condition. The host immune response has been hypothesized to play a major role in leptospirosis outcome. Increased levels of inflammatory mediators, such as cytokines, may promote tissue damage that lead to increased disease severity. The question is whether cytokines levels may predict the outcome of leptospirosis and guide patient management. This study aimed to assess the association between Th1-, Th2-, and Th17-related cytokines with the clinical outcome of patients with leptospirosis. Different cytokine levels were measured in fifty-two plasma samples of hospitalized patients diagnosed with leptospirosis in Malaysia (January 2016-December 2017). Patients were divided into two separate categories: survived (n = 40) and fatal outcome (n = 12). Nineteen plasma samples from healthy individuals were obtained as controls. Cytokine quantification was performed using Simple Plex™ assays from ProteinSimple (San Jose, CA, USA). Measurements were done in triplicate and statistical analysis was performed using GraphPad software and SPSS v20. IL-6 (p = 0.033), IL-17A (p = 0.022), and IL-22 (p = 0.046) were significantly elevated in fatal cases. IL-17A concentration (OR 1.115; 95% CI 1.010-1.231) appeared to be an independent predictor of fatality of leptospirosis. Significantly higher levels of TNF-α (p ≤ 0.0001), IL-6 (p ≤ 0.0001), IL-10 (p ≤ 0.0001), IL-12 (p ≤ 0.0001), IL17A (p ≤ 0.0001), and IL-18 (p ≤ 0.0001) were observed among leptospirosis patients in comparison with healthy controls. Our study shows that certain cytokine levels may serve as possible prognostic biomarkers in leptospirosis patients.
Selection of reference genes for quantitative studies in acute myeloid leukaemia

Lee C, Yiau KXS, Lee LJ, Chong PP, Chang KM, Abdullah M

Malays J Pathol, 2019 Dec;41(3):313-326.
PMID: 31901916

INTRODUCTION: Quantitative polymerase chain reaction (qPCR) is commonly used in the investigation of acute myeloid leukaemias (AML). Stable reference genes (RG) are essential for accurate and reliable reporting but no standard method for selection has been endorsed.
MATERIALS AND METHODS: We evaluated simple statistics and published model-based approaches. Multiplex-qPCR was conducted to determine the expression of 24 candidate RG in AMLs (N=9). Singleplex-qPCR was carried out on selected RG (SRP14, B2M and ATP5B) and genes of interest in AML (N=15) and healthy controls, HC (N=12).
RESULTS: RG expression levels in AML samples were highly variable and coefficient of variance (CV) ranged from 0.37% to 10.17%. Analysis using GeNorm and Normfinder listed different orders of most stable genes but the top seven (ACTB, UBE2D2, B2M, NF45, RPL37A, GK, QARS) were the same. In singleplex-qPCR, SRP14 maintained the lowest CV in AML samples. B2M, one of most stable reference genes in AML, was expressed near significantly different in AML and HC. GeNorm selected ATP5B+SRP14 while Normfinder chose SRP14+B2M as the best two RG in combination. The median expressions of combined RG genes in AML compared to HC were less significantly different than individually implying smaller expression variation after combination. Genes of interest normalised with RG in combination or individually, displayed significantly different expression patterns.
CONCLUSIONS: The selection of best reference gene in qPCR must consider all sample sets. Model-based approaches are important in large candidate gene analysis. This study showed combination of RG SRP14+B2M was the most suitable normalisation factor for qPCR analysis of AML and healthy individuals.
Fulltext Graphene-based hybrid nanoparticle of doxorubicin for cancer chemotherapy

SreeHarsha N, Maheshwari R, Al-Dhubiab BE, Tekade M, Sharma MC, Venugopala KN, et al.

Int J Nanomedicine, 2019;14:7419-7429.
PMID: 31686814 DOI: 10.2147/IJN.S211224

Background: Prostate cancer (PC) has the highest prevalence in men and accounts for a high rate of neoplasia-related death. Doxorubicin (DOX) is one of the most widely used anti-neoplastic drugs for prostate cancer among others. However, it has low specificity and many side effects and affects normal cells. More recently, there have been newly developed drug delivery tools which are graphene or graphene-based, used to increase the specificity of the delivered drug molecules. The graphene derivatives possess both π-π stacking and increased hydrophobicity, factors that increase the likelihood of drug delivery. Despite this, the hydrophilicity of graphene remains problematic, as it induced problems with stability. For this reason, the use of a chitosan coating remains one way to modify the surface features of graphene.
Method: In this investigation, a hybrid nanoparticle that consisted of a DOX-loaded reduced graphene oxide that is stabilized with chitosan (rGOD-HNP) was developed.
Result: The newly developed rGOD-HNP demonstrated high biocompatibility and efficiency in entrapping DOX (~65%) and releasing it in a controlled manner (~50% release in 48 h). Furthermore, it was also demonstrated that rGOD-HNP can intracellularly deliver DOX and more specifically in PC-3 prostate cancer cells.
Conclusion: This delivery tool offers a feasible and viable method to deliver DOX photo-thermally in the treatment of prostate cancer.
Fulltext Elevated interleukin-25 and its association to Th2 cytokines in systemic lupus erythematosus with lupus nephritis

Selvaraja M, Abdullah M, Arip M, Chin VK, Shah A, Amin Nordin S

PLoS One, 2019;14(11):e0224707.
PMID: 31697750 DOI: 10.1371/journal.pone.0224707

Systemic lupus erythematosus (SLE) is an autoimmune disorder that is associated with lupus nephritis, initiated by the deposition of immune complexes in the kidney; subsequently, this induces the overexpression of cytokines. Lupus nephritis is known as one of the major clinical manifestations that affect the disease severity in SLE patients. An increased number of resident periglomerular and immune cells in the kidney has the potential to affect the equilibrium of different immune cell subsets, such as Th1, Th2, Th17, and Tregs, which may be central to the induction of tissue damage in kidney by exerting either proinflammatory or anti-inflammatory effects, or both. This equilibrium has yet to be confirmed, as new players such as IL-25 remain undiscovered. IL-25 is a cytokine of the IL-17 family, which stimulates Th2-mediated immune response when overly expressed. Thus, the aim of this research is to determine the plasma levels of IL-25 and Th2-associated cytokines (IL-4, IL-5, IL-6, IL-9, IL-10, IL-13) in SLE patients with (SLE-LN) and without lupus nephritis. Sixty-four (n = 64) SLE patients and fifteen (n = 15) healthy individuals were recruited. This study demonstrated that the IL-9, IL-10 and IL-25 had significantly increased expressions in SLE-LN, followed by SLE without LN, compared to healthy controls. Meanwhile, IL-5 and IL-6 had significantly reduced. No significant difference was observed with IL-13, while the level of IL-4 was undetectable. Furthermore, IL-9 and IL-10 were significantly correlated with the IL-25, and IL-25, IL-9 and IL-10 were positively correlated with the disease severity score, SLEDAI. In conclusion, IL-25 and its associated Th2 cytokines (IL-9 and IL-10) may be involved in SLE pathogenesis. These cytokines could be potential biomarkers in monitoring and predicting the disease severity during SLE pathogenesis.
Lignocellulosic biomass supported metal nanoparticles for the catalytic reduction of organic pollutants

Akhtar K, Ali F, Sohni S, Kamal T, Asiri AM, Bakhsh EM, et al.

Environ Sci Pollut Res Int, 2020 Jan;27(1):823-836.
PMID: 31811610 DOI: 10.1007/s11356-019-06908-y

Lignocellulosic biomass waste is a cheap, eco-friendly, and sustainable raw material for a wide array of applications. In the present study, an easy, fast, and economically feasible route has been proposed for the preparation of different zero-valent metal nanoparticles (ZV-MNPs) based on Cu, Co, Ag, and Ni NPs using empty fruit bunch (EFB) biomass residue as support material. The catalytic efficiency of ZV-MNPs/EFB catalyst was investigated against five model pollutants, such as methyl orange (MO), congo red (CR), methylene blue (MB), acridine orange (AO), and 4-nitrophenol (4-NP) using NaBH4 as a source of hydrogen and electron. Comparative study revealed that among as-prepared ZV-MNPs/EFB catalysts, Cu-NPs immobilized onto EFB (Cu/EFB) exhibited maximum catalytic efficiency towards pollutant abasement. Degradation reactions were highly efficient, and were completed within a short time (4 min) in case of MO, CR, and MB, whilst AO and 4-NP were reduced in less than 15 min. Kinetic investigation revealed that the degradation rate of model pollutants accorded with pseudo-first order model. Furthermore, supported catalysts were easily recovered after the completion of experiment by simply pulling the catalyst from reaction system. Recyclability tests performed on Cu/EFB revealed that more than 97% of the reduction was achieved in case of MO dye for four successive cycles of reuse. The as-prepared heterostructure showed multifunctional properties, such as enhanced uptake of contaminants, high catalytic efficiency, and easy recovery, hence, offers great prospects in wastewater purification.
Fulltext Structural changes and band gap tunability with incorporation of n-butylammonium iodide in perovskite thin film

Rebecca LWX, Burhanudin ZA, Abdullah M, Saheed MSM

Heliyon, 2020 Feb;6(2):e03364.
PMID: 32072054 DOI: 10.1016/j.heliyon.2020.e03364

The current work presents structural change and band gap tunability using hybrid organic-inorganic perovskite with the incorporation of long chain ammonium halide. Thin films of MAPbI3 with different ratio of n-butylammonium iodide (BAI) have been successfully deposited on the substrate using a single step coating technique. X-ray diffraction scans revealed the transition of the 3D structure of MAPbI3 to quasi-2D perovskite structure when BAI loading increase with a crystallite size range approximately 16 nm. This structural changeis reflected in the band gap as it increased from 1.59 eV for bulk crystal MAPbI3 to 2.13 eV for BAI and MAPbI3 ratio of 1:1. Correspondingly, photoluminescence measurement showed a blue shift in perovskite emission due to the transition of 3D to 2D layered structure perovskite. Raman spectra confirm that all fabricated films are of pristine quality and no corresponding degradation peaks of PbI2 is observed. These characteristics are important to address the single step deposition method of hybrid perovskite for perovskite solar cells application.
Fulltext Elevated levels of IL-8 in fatal leptospirosis

Wan Yusoff WSY, Abdullah M, Sekawi Z, Amran F, Yuhana MY, Mohd Taib N, et al.

Pathog Glob Health, 2020 03;114(2):99-103.
PMID: 32024441 DOI: 10.1080/20477724.2020.1724356

Leptospirosis causes a wide range of clinical outcomes, including organ failure and death. Early treatment significantly increases the chances of cure. Interleukin-8 (IL-8) is a chemoattractant cytokine for neutrophil and is associated with multiple organ failure. Research has indicated IL-8 to be raised in severe and fatal cases of leptospirosis, but its suitability as a prognostic biomarker has yet to be confirmed. This study aimed to evaluate the significance of IL-8 with the clinical outcomes of leptospirosis patients. Plasma IL-8 was measured in fifty-two samples from hospitalized patients and nineteen healthy controls. The comparisons were made between mild, severe-survived and fatal groups identified by clinical or laboratory findings. IL-8 was significantly higher in fatal (p = 0.01) compared to mild cases. IL-8 was also significantly higher in fatal (p = 0.02) when compared to survived cases of leptospirosis. IL-8 levels in the plasma of fatal leptospirosis cases were significantly elevated compared to survived cases and may serve as a potential prognostic biomarker in determining the possible outcome of leptospirosis patients.
Significant Clinical Presentation of Leptospirosis in Relation to Sociodemographic and Risk Factors in a Tertiary Hospital, Malaysia

Mohd Taib N, Ahmad H, Soh KL, Md Shah A, Amin Nordin S, Than Thian Lung L, et al.

Vector Borne Zoonotic Dis, 2020 04;20(4):268-274.
PMID: 32013800 DOI: 10.1089/vbz.2018.2417

Introduction:
Incidence of leptospirosis has increased within the past few years in many countries. Its clinical presentations were generally nonspecific, making it difficult to assist in the diagnosis. Besides the determination of the common clinical features, the sociodemographic background is essential to identify high-risk populations to assist in prevention.
Methods:
Data for this study were obtained from electronic medical records among patients clinically diagnosed with leptospirosis at a tertiary hospital in Malaysia from the years 2011 to 2015 and were recorded using standard pro forma. Associations between clinical features and sociodemographics were performed using bivariate analysis and logistic regression.
Results:
Data were collected from 283 patients. Their mean age was 30.71 years old. Out of 283 patients, 206 (72.8%) were male. Involvement in outdoor events and water activities was the highest risk factor of acquiring leptospirosis in 64 (22.7%) patients followed by 59 (20.8%) patients who were staying in crowded housing areas with poor sanitation. Although fever was the main clinical presentation in 274 (96.8%) patients with leptospirosis, gastrointestinal (GIT) symptoms were the second most frequent in 159 (56.2%) patients followed by pulmonary symptoms, myalgia, headache, and jaundice. From the total number of 283 patients, only 21 (92.6%) presented with severe leptospirosis. GIT symptoms were a significant predictor for leptospirosis severity, while the age group was the significant sociodemographic factor toward GIT presentation in leptospirosis. The relationship between GIT symptoms and crowded housing areas with poor sanitation was also significant. Multivariable logistic regression showed that crowded housing areas with poor sanitation (odds ratio [OR] = 3.570, p
Fulltext Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

Singh R, Low EL, Ooi LC, Ong-Abdullah M, Ting NC, Nookiah R, et al.

New Phytol, 2020 04;226(2):426-440.
PMID: 31863488 DOI: 10.1111/nph.16387

Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS-box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two-hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele-specific. Our findings reveal allele-specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single-gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.
Pathology and Host Immune Evasion During Human Leptospirosis: a Review

Chin VK, Basir R, Nordin SA, Abdullah M, Sekawi Z

Int Microbiol, 2020 May;23(2):127-136.
PMID: 30875033 DOI: 10.1007/s10123-019-00067-3

Human leptospirosis is considered as one of the most widespread and potentially fatal zoonotic diseases that causes high mortality and morbidity in the endemic regions of tropical and subtropical countries. The infection can arise from direct or indirect exposure of human through contaminated environment that contains leptospires or animal reservoirs that carry leptospires. The clinical manifestations during human leptospirosis ranges from asymptomatic, mild infections to severe and life-threatening complications involving multi-organ failures with kidneys, lungs and liver severely affected. Despite much efforts have been put in to unravel the pathogenesis during human leptospirosis, it remains obscure to which extent the host factors or the pathogen itself contribute towards the pathogenesis. Host innate immunity, especially, polymorphonuclear neutrophils and complement system are involved in the first line of defense during human leptospirosis. However, pathogenic Leptospira has acquired diverse evasion strategies to evade from host immunity and establish infection in infected hosts. Hence, in this review, we focus on organs pathology during human leptospiral infection and host evasion strategies employed by Leptospira. A profound understanding on leptospiral immunity and how Leptospira subvert the immune system may provide new insights on the development of therapeutic regimens against this species in future.
Fulltext Data for the subsurface characterization of Pahang River Basin with the application of Transient Electromagnetic geophysical surveys

Arifin H, Kayode J, Arifin K, Zahir Z, Abdullah M, Azmi A

Data Brief, 2020 Jun;30:105491.
PMID: 32373680 DOI: 10.1016/j.dib.2020.105491

The Transient Electro-Magnetic (TEM) geophysical technique was deployed to map and characterized the subsurface of Pahang River Basin along the East Coast Peninsula Malaysia. The data aimed at differentiating between the massive zones and the weak zones within the region, to also assess and differentiate the subsurface structures and comes up with recommendations for policy decision, formulation and plans on the flooding impact, surface water and groundwater managements, in addition to other environmental related issues ravaging the area. The data presented in this paper, showed the properties of the subsurface rocks underlain the region as beneficial to the Agriculturists; Climatologists; Engineers; Environmentalists; Geoscientists, Hydrologists and Policy formulation officers. The TEM data collection utilized a 100 m x 100 m single loop coil for both the Transmitter (Tx) loop and the Receiver (Rx) loop to produce a total surface area coverage of 10,000 m2 per survey line along a single profile. The total area covered in the data extended across an average area of 30 km x 40 km in parts of Maran, Temerloh and Jerantut districts, within the State of Pahang, East Coast, Peninsula Malaysia. The conductivity data recorded varied from -20 mS/m to about 440 mS/m at a maximum depth of about 375 m. On the other hand, the resistivity data recorded varied from 0 Oh-m to about 1000 Oh-m. The information derived from the data are intended for potential abstraction by the Malaysian Groundwater Management Board; the Department of Mineral and Geoscience; Department of Irrigation and Drainage; the Pahang State Water Board, and the Department of Agriculture.
Effect of cellulose nano fibers and nano clays on the mechanical, morphological, thermal and dynamic mechanical performance of kenaf/epoxy composites

Khan A, Asiri AM, Jawaid M, Saba N, Inamuddin

Carbohydr Polym, 2020 Jul 01;239:116248.
PMID: 32414444 DOI: 10.1016/j.carbpol.2020.116248

The aim of the present research work has focused on investigating the effect of cellulose nanofibers (CNFs) and nano clays (montmorillonite (MMT) & organoclay (OMMT)) at 0.75Wt % on the performance of kenaf/epoxy composites. Mechanical (tensile and flexural) and thermal properties of composites in terms of morphology, thermal stability, weight loss, and dynamic mechanical properties were analyzed. The obtained results revealed that the integration of stiff CNFs as filler enhanced the mechanical and thermal properties, storage and loss modulus while a considerable decrease in Tan δ was realized compared to kenaf/epoxy composites. Enhancement in the properties was observed for OMMT and CNFs composites compared to MMT/kenaf/epoxy composites, which is attributed to the uniform filler distribution and interfacial adhesion between CNFs, OMMT, kenaf and epoxy matrix. The obtained results revealed that OMMT and CNFs based kenaf/epoxy composites can be an efficient alternative for construction applications.
Fulltext Induction of apoptosis and role of paclitaxel-loaded hyaluronic acid-crosslinked nanoparticles in the regulation of AKT and RhoA

Chaudhry GE, Akim A, Zafar MN, Abdullah MA, Sung YY, Muhammad TST

J Adv Pharm Technol Res, 2020 07 14;11(3):101-106.
PMID: 33102192 DOI: 10.4103/japtr.JAPTR_26_20

Cancer is a complex multifactorial disease and leading causes of death worldwide. Despite the development of many anticancer drugs, there is a reduced survival rate due to severe side effects. The nontargeted approach of convention drugs is one of the leading players in context to toxicity. Hyaluronan is a versatile bio-polymer and ligand of the receptor (CD44) on cancer cells. The MCF-7 and HT-29 cancer cell lines treated with hyaluronic acid-paclitaxel (HA-PTX) showed the distinguishing morphological features of apoptosis. Flow cytometric analysis showed that HA-PTX induces apoptosis as a significant mode of cell death. The activation level of tumor suppressor protein (p53) increased after PTX treatment in MCF-7, but no changes observed in HT-29 might be due to hereditary mutations. The lack of suppression in AKT and Rho A protein suggest the use of possible inhibitors in future studies which might could play a role in increasing the sensitivity of drug towards mutated cells line and reducing the possibilities for cancer cell survival, migration, and metastasis.
Fulltext An integrated linkage map of interspecific backcross 2 (BC2) populations reveals QTLs associated with fatty acid composition and vegetative parameters influencing compactness in oil palm

Yaakub Z, Kamaruddin K, Singh R, Mustafa S, Marjuni M, Ting NC, et al.

BMC Plant Biol, 2020 Jul 29;20(1):356.
PMID: 32727448 DOI: 10.1186/s12870-020-02563-5

BACKGROUND: Molecular breeding has opened new avenues for crop improvement with the potential for faster progress. As oil palm is the major producer of vegetable oil in the world, its improvement, such as developing compact planting materials and altering its oils' fatty acid composition for wider application, is important.
RESULTS: This study sought to identify the QTLs associated with fatty acid composition and vegetative traits for compactness in the crop. It integrated two interspecific backcross two (BC2) mapping populations to improve the genetic resolution and evaluate the consistency of the QTLs identified. A total 1963 markers (1814 SNPs and 149 SSRs) spanning a total map length of 1793 cM were integrated into a consensus map. For the first time, some QTLs associated with vegetative parameters and carotene content were identified in interspecific hybrids, apart from those associated with fatty acid composition. The analysis identified 8, 3 and 8 genomic loci significantly associated with fatty acids, carotene content and compactness, respectively.
CONCLUSIONS: Major genomic region influencing the traits for compactness and fatty acid composition was identified in the same chromosomal region in the two populations using two methods for QTL detection. Several significant loci influencing compactness, carotene content and FAC were common to both populations, while others were specific to particular genetic backgrounds. It is hoped that the QTLs identified will be useful tools for marker-assisted selection and accelerate the identification of desirable genotypes for breeding.
Fulltext Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS

Abdullah M, Suraiya S, Mohamad S, Harun A

Data Brief, 2020 Aug;31:105949.
PMID: 32671154 DOI: 10.1016/j.dib.2020.105949

In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.
DNA methylation changes in clonally propagated oil palm

Sarpan N, Taranenko E, Ooi SE, Low EL, Espinoza A, Tatarinova TV, et al.

Plant Cell Rep, 2020 Sep;39(9):1219-1233.
PMID: 32591850 DOI: 10.1007/s00299-020-02561-9

KEY MESSAGE: Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling. One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the "mantled" phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3' region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5' UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.
Fulltext Venous thromboembolism prevention protocol for adapting prophylaxis recommendations to the potential risk post total knee replacement: a randomized controlled trial

Alameri MA, Syed Sulaiman SA, Ashour AM, Al-Saati MF

Pharm Pract (Granada), 2020 09 22;18(3):2025.
PMID: 33029262 DOI: 10.18549/PharmPract.2020.3.2025

Background: Total knee replacement (TKR) is a major orthopedic surgery that is considered high risk for the development of venous thromboembolism (VTE).
Objective: The aim of this study is to evaluate the clinical outcomes that resulted from the use of a new proposed VTE risk stratification protocol for selecting a suitable extended VTE prophylaxis for post TKR surgery patients administered in conjunction with patient education programs.
Method: A randomized controlled trial was conducted in two medical centers in Saudi Arabia. A total of 242 patients were enrolled in the study, 121 patients in each group. The experimental group (A) was assessed by using the proposed VTE risk stratification protocol and also took part in patient education programs about TKR and its complications. The control group (B) was assessed by using the 2005 Caprini risk assessment tool and no education programs were given to this group. Both groups were followed for 35 days post operation.
Results: The mean age of the participants was 65.86 (SD 8.67) and the majority of them were female 137 (56.6%). The mean body mass index of the study sample was 32.46 (SD 5.51). There were no significant differences between the two groups except for surgery type; the proportion of bilateral TKR in group A was higher than in group B (69/121 (28.5%) vs. 40/121(16.5%), p<0.05). There were no confirmed pulmonary embolism cases in the study sample and diagnosis of deep-vein thrombosis was confirmed in 12/242 (5.0%) of patients: 1/121 (0.8%) in group A and 11/121 (9.1%) in group B (p<0.05). The readmission rate for all patients was 2.5% (6/242), all of whom were in group B (p<0.05).
Conclusion: The proposed VTE risk stratification protocol that was applied in conjunction with patient education programs reduced VTE complications and readmission events, post TKR surgery. Trial Registration: ClinicalTrials.gov: Identifier: NCT04031859.
Mucosal responses of brown-marbled grouper Epinephelus fuscoguttatus (Forsskål, 1775) following intraperitoneal infection with Vibrio harveyi

Chieng CCY, Daud HM, Yusoff FM, Thompson KD, Abdullah M

J Fish Dis, 2020 Oct;43(10):1249-1258.
PMID: 32830331 DOI: 10.1111/jfd.13222

Groupers are popular aquaculture species in South-East Asia, but their cultivation is affected by infectious disease outbreaks. Mucosa-associated lymphoid tissues provide a first-line defence against pathogens; however, few studies are available relating to cellular or proteomic responses of mucosal immunity in grouper. Skin, gill and intestine were sampled from brown-marbled grouper Epinephelus fuscoguttatus (Forsskål, 1775) at 4 and 96 hr post-infection (hpi) and 7 days post-infection (dpi) following intraperitoneal infection with Vibrio harveyi, and stained with haematoxylin/eosin and Alcian Blue/periodic acid-Schiff. Skin mucus was analysed by 2D-gel electrophoresis, and proteins modulated by the bacterial infection identified. In the infected fish, significant increases in sacciform cells in skin and increased levels of nucleoside diphosphate kinase in mucus were detected at 4 hpi. At 96 hpi, goblet cells containing acidic mucins significantly increased in the intestine, while those containing mixed mucins increased in skin and gills of infected fish. Proteasome subunit alpha type-I and extracellular Cu/Zn superoxide dismutase levels also increased in mucus. Rodlet and mast cells did not appear to respond to the infection. Mucosal tissues of grouper appeared actively involved in response to Vibrio infection. This information may help future research on improving grouper health, production and vaccine development.

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