Displaying publications 1 - 20 of 22 in total

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  1. Fulltext Design of High Impedance Electromagnetic Surfaces for Mutual Coupling Reduction in Patch Antenna Array
    Islam MT, Alam MS
    Materials (Basel), 2013 Jan 07;6(1):143-155.
    PMID: 28809299 DOI: 10.3390/ma6010143
    A compact planar meander-bridge high impedance electromagnetic structure (MBHIES) was designed and its bandgap characteristics, mutual coupling reduction abilities were studied and compared in detail. Several parametric analyses were performed to obtain optimized design values and the transmission responses were calculated through the suspended microstrip line and waveguide simulation methods. The achieved bandgap is 2.3 GHz (2.55-4.85 GHz) with -61 dB minimum transmission coefficient level at the center frequency of 3.6 GHz. To see the effectiveness, the proposed design was inserted between a microstrip patch antenna array which operates at 3.8 GHz and whose operating bandwidth falls within the MBHIES bandgap. The surface wave suppression phenomenon was analyzed and simulated results are verified by measuring the fabricated prototypes, both are in good agreement. The configuration reduced the mutual coupling by 20.69 dB in simulation and 19.18 dB in measurement, without affecting the radiation characteristics of the array but increasing the gain slightly.
  2. Fulltext Gain enhancement of a multiband resonator using defected ground surface on epoxy woven glass material
    Alam MS, Islam MT, Arshad H
    ScientificWorldJournal, 2014;2014:159468.
    PMID: 24883354 DOI: 10.1155/2014/159468
    A multiband microstrip resonator is proposed in this study which is realized through a rectangular radiator with embedded symmetrical rectangular slots in it and a defected ground surface. The study is presented with detailed parametric analyses to understand the effect of various design parameters. The design and analyses are performed using the FIT based full-wave electromagnetic simulator CST microwave studio suite. With selected parameter values, the resonator showed a peak gain of 5.85 dBi at 5.2 GHz, 6.2 dBi at 8.3 GHz, 3.9 dBi at 9.5 GHz, 5.9 dBi at 12.2 GHz, and 4.7 dBi at 14.6 GHz. Meanwhile, the main lobe magnitude and the 3 dB angular beam width are 6.2 dBi and 86°, 5.9 dBi and 53.7°, 8.5 dBi and 43.9°, 8.6 dBi and 42.1°, and 4.7 dBi and 30.1°, respectively, at the resonant frequencies. The overall resonator has a compact dimension of 0.52λ  × 0.52λ  × 0.027λ at the lower resonant frequency. For practical validation, a lab prototype was built on a 1.6 mm thick epoxide woven glass fabric dielectric material which is measured using a vector network analyzer and within an anechoic chamber. The comparison between the simulated and measured results showed a very good understanding, which implies the practical suitability of the proposed multiband resonator design.
  3. Fulltext A chemometric approach to evaluate the effects of probe-type ultrasonication on the enzyme inactivation and quality attributes of fresh amla juice
    Aslam R, Alam MS, Ali A, Tao Y, Manickam S
    Ultrason Sonochem, 2023 Jan;92:106268.
    PMID: 36543045 DOI: 10.1016/j.ultsonch.2022.106268
    The enzymatic browning induced in amla juice due to the high activity of polyphenol oxidase (PPO) and peroxidase (POD) is one of the critical issues faced by the industry. The present study assessed the suitability of non-thermal, high-intensity ultrasound (US) on the inactivation of PPO and POD in fresh Indian Gooseberry juice. Ultrasonic waves, using a 6 mm titanium alloy probe were irradiated in the juice at a maximum power of 455 W and frequency of 20 kHz. The subsequent effects on biochemical attributes were studied using response surface methodology. Inactivation rates of 90.72 % and 73.18 %, respectively, for PPO and POD enzymes, were observed at the highest US intensity and exposure time. Numerical optimisation using the three-factor, three-level Box-Behnken design suggested that an optimum process at 70 % (energy density: 1610 Wcm-2) pulsed at 5 s on and 5 s off for 7 min 30 s resulted in PPO and POD inactivation of the order of 76.42 % and 64.57 % respectively. At these experimental conditions, the optimized levels of biochemical attributes i.e., ascorbic acid (738.50 mg/100 mL), total phenols (17.10 mg/mL), DPPH antioxidant activity (58.47 %), tannins (7.11 µg/mL), colour change (ΔE = 9.04) and flavonoids (6.14 mg/mL) were achieved. The overall statistical models were significant for all the responses except for reducing sugars. Furthermore, the approximation equations for individual responses indicated that the goodness of fit was adequate (R2 > 0.90). The results suggested that ultrasound is a suitable processing technique for amla juice stabilisation compared to thermal treatments that result in the loss of quality.
  4. Genetic differentiation of the Fejervarya limnocharis complex from Bangladesh and other Asian countries elucidated by allozyme analyses
    Islam MM, Khan MM, Tjong DH, Alam MS, Sumida M
    Zoolog Sci, 2008 Mar;25(3):261-72.
    PMID: 18393563 DOI: 10.2108/zsj.25.261
    The present study was conducted to elucidate the genetic divergence and the phylogenetic relationships in the F. limnocharis complex from Bangladesh and other Asian countries such as Sri Lanka, Thailand, Malaysia, Taiwan and Japan by allozyme analyses. We used a total of 95 frogs of the F. limnocharis complex from these countries and F. cancrivora from the Philippines as an outgroup. Based on body size, the F. limnocharis complex from Bangladesh was divided into three distinct groups: large, medium and small types. Allozyme analyses were carried out with 28 loci encoding 20 enzymes and two blood proteins by horizontal starch-gel electrophoresis. When genetic distance was calculated, distinct divergence was found among the three types: mean genetic distance was 0.782 between the small and medium types, 1.458 between the large and medium types, and 1.520 between the large and small types. Phylogenetic trees based on genetic distance showed that all populations of Bangladesh small type strongly formed a cluster and were found to be most closely related to the Sri Lanka population; that all populations of Bangladesh large type formed a very strong cluster and were grouped with several populations from Thailand, Malaysia, Japan, and Taiwan; and that the medium type was segregated from all other groups. This may imply that each of the three types is a different species, and that the medium type is possibly an undescribed taxon.
  5. Computational algorithmic and molecular dynamics study of functional and structural impacts of non-synonymous single nucleotide polymorphisms in human DHFR gene
    Alam MS, Saleh MA, Mozibullah M, Riham AT, Solayman M, Gan SH
    Comput Biol Chem, 2021 Dec;95:107587.
    PMID: 34710812 DOI: 10.1016/j.compbiolchem.2021.107587
    Human dihydrofolate reductase (DHFR) is a conserved enzyme that is central to folate metabolism and is widely targeted in pathogenic diseases as well as cancers. Although studies have reported the fact that genetic mutations in DHFR leads to a rare autosomal recessive inborn error of folate metabolism and drug resistance, there is a lack of an extensive study on how the deleterious non-synonymous SNPs (nsSNPs) disrupt its phenotypic effects. In this study, we aim at discovering the structural and functional consequences of nsSNPs in DHFR by employing a combined computational approach consisting of ten recently developed in silico tools for identification of damaging nsSNPs and molecular dynamics (MD) simulation for getting deeper insights into the magnitudes of damaging effects. Our study revealed the presence of 12 most deleterious nsSNPs affecting the native phenotypic effects, with three (R71T, G118D, Y122D) identified in the co-factor and ligand binding active sites. MD simulations also suggested that these three SNPs particularly Y122D, alter the overall structural flexibility and dynamics of the native DHFR protein which can provide more understandings into the crucial roles of these mutants in influencing the loss of DHFR function.
  6. Vertical distributions of radionuclides along the tourist-attractive Marayon Tong Hill in the Bandarban district of Bangladesh
    Siraz MMM, Roy D, Dewan MJ, Alam MS, A M J, Rashid MB, et al.
    Environ Monit Assess, 2023 Feb 10;195(3):382.
    PMID: 36759352 DOI: 10.1007/s10661-023-10921-7
    This is the first attempt in the world to depict the vertical distribution of radionuclides in the soil samples along several heights (900 feet, 1550 feet, and 1650 feet) of Marayon Tong hill in the Chittagong Hill Tracts, Bandarban by HPGe gamma-ray spectrometry. The average activity concentrations of 232Th, 226Ra, and 40K were found to be 37.15 ± 3.76 Bqkg-1, 19.69 ± 2.15 Bqkg-1, and 347.82 ± 24.50 Bqkg-1, respectively, where in most cases, 232Th exceeded the world average value of 30 Bqkg-1. According to soil characterization, soils ranged from slightly acidic to moderately acidic, with low soluble salts. The radium equivalent activity, outdoor and indoor absorbed dose rate, external and internal hazard indices, external and internal effective dose rates, gamma level index, and excess lifetime cancer risk were evaluated and found to be below the recommended or world average values; but a measurable activity of 137Cs was found at soils collected from ground level and at an altitude of 1550 feet, which possibly arises from the nuclear fallout. The evaluation of cumulative radiation doses to the inhabitants via periodic measurement is recommended due to the elevated levels of 232Th.This pioneering work in mapping the vertical distribution of naturally occurring radioactive materials (NORMs) can be an essential factual baseline data for the scientific community that may be used to evaluate the variation in NORMs in the future, especially after the commissioning of the Rooppur Nuclear Power Plant in Bangladesh in 2024.
  7. Evaluation of radioactivity in soil and rock samples from an undiscovered sea beach in the southeastern coastline of Bangladesh and associated health risk
    Siraz MMM, Kamal MH, Khan ZH, Alam MS, Al Mahmud J, Rashid MB, et al.
    Environ Monit Assess, 2023 Aug 10;195(9):1028.
    PMID: 37558890 DOI: 10.1007/s10661-023-11636-5
    This study marks the first-ever assessment of radiological hazards linked to the sands and rocks of Patuartek Sea Beach, situated along one of the world's longest sea beaches in Cox' Bazar of Bangladesh. Through the utilization of an HPGe detector, a comprehensive analysis of the activity concentrations of 226Ra, 232Th, and 40 K was conducted, and their activity ranged from 7 to 23 Bq/kg, 9-58 Bq/kg, and 172-340 Bq/kg, respectively, in soils, and 19-24 Bq/kg, 27-39 Bq/kg, and 340-410 Bq/kg, respectively, in rocks. Some sand samples exhibited elevated levels of 232Th, while the rock samples displayed higher levels of 40 K compared to the global average. The radiological hazard parameters were assessed, and no values surpassed the recommended limits set by several international organizations. Hence, the sands and rocks of Patuartek sea beach pose no significant radiological risk to the residents or tourists. The findings of this study provide crucial insights for the development of a radiological baseline map in the country, which is important due to the commissioning of the country's first nuclear power plant Rooppur Nuclear Power Plant. The data may also stimulate interest in the rare-earth minerals present in the area, which is important for the electronics industry, thorium-based nuclear fuel cycles.
  8. Fulltext A study on measuring the 222Rn in the Buriganga River and tap water of the megacity Dhaka
    Alam MS, Siraz MMM, A M J, Das SC, Bradley DA, Khandaker MU, et al.
    PLoS One, 2023;18(5):e0286267.
    PMID: 37220107 DOI: 10.1371/journal.pone.0286267
    Radon (222Rn), an inert gas, is considered a silent killer due to its carcinogenic characteristics. Dhaka city is situated on the banks of the Buriganga River, which is regarded as the lifeline of Dhaka city because it serves as a significant source of the city's water supply for domestic and industrial purposes. Thirty water samples (10 tap water from Dhaka city and 20 surface samples from the Buriganga River) were collected and analyzed using a RAD H2O accessory for 222Rn concentration. The average 222Rn concentration in tap and river water was 1.54 ± 0.38 Bq/L and 0.68 ± 0.29 Bq/L, respectively. All the values were found below the maximum contamination limit (MCL) of 11.1 Bq/L set by the USEPA, the WHO-recommended safe limit of 100 Bq/L, and the UNSCEAR suggested range of 4-40 Bq/L. The mean values of the total annual effective doses due to inhalation and ingestion were calculated to be 9.77 μSv/y and 4.29 μSv/y for tap water and river water, respectively. Although all these values were well below the permissible limit of 100 μSv/y proposed by WHO, they cannot be neglected because of the hazardous nature of 222Rn, especially considering their entry to the human body via inhalation and ingestion pathways. The obtained data may serve as a reference for future 222Rn-related works.
  9. Evaluation of transfer factors of 226Ra, 232Th, and 40K radionuclides from soil to grass and mango in the northern region of Bangladesh
    Siraz MMM, Das SK, Mondol MS, Alam MS, Al Mahmud J, Rashid MB, et al.
    Environ Monit Assess, 2023 Apr 17;195(5):579.
    PMID: 37067680 DOI: 10.1007/s10661-023-11223-8
    Bangladesh is a rapidly developing country, which is vulnerable to various types of pollution due to the large-scale industrial and associated human activities that might potentially affect the locally harvested foodstuffs. Therefore, the transfer factor is an essential tool to assess the safety of foodstuffs due to the presence of natural radioactivity in environmental matrix and/or strata. This is a first study of its kind conducted in a well-known region for mango farming in Bangladesh, measuring the uptake of naturally occurring radioactive materials (NORMs) by grass and mango from soil to assess the ingestion doses to humans. The HPGe gamma-ray detector was used to determine the concentrations of NORMs in samples of soil (20), grass (10), and mango (10), which were then used to calculate the transfer factors of soil to grass and soil to mango. Average activity concentrations of 226Ra, 232Th, and 40K in associated soil samples (47.27 ± 4.10, 64.49 ± 4.32, 421.60 ± 28.85) of mango and 226Ra and 232Th in associated soil samples (45.07 ± 3.93, 52.17 ± 3.95) of grass were found to exceed the world average values. The average transfer factors (TFs) for mango were obtained in the order of 40K(0.80) > 226Ra (0.61) > 232Th (0.31), and for grass, it shows the order of 40K (0.78) > 232Th (0.64) > 226Ra (0.56). However, a few values (3 mango samples and 3 grass samples) of the estimated TFs exceeded the recommended limits. Moreover, Bangladesh lacks the transfer factors for most of the food crops; therefore, calculation of TFs in the major agricultural products is required all over Bangladesh, especially the foodstuffs produced near the Rooppur Nuclear Power Plant, which is scheduled to be commissioned in 2023.
  10. Fulltext Measurement of radioactivity in soils of Karamjal and Harbaria mangrove forest of Sundarbans for establishment of radiological database
    Siraz MMM, A M J, Alam MS, Rashid MB, Hossain Z, Khandaker MU, et al.
    PLoS One, 2023;18(10):e0289113.
    PMID: 37856554 DOI: 10.1371/journal.pone.0289113
    This work presents the first in-depth study of soil radioactivity in the mangrove forest of Bangladesh part of the Sundarbans. It used HPGe gamma-ray spectrometry to measure the amount of natural radioactivity in soil samples from Karamjal and Harbaria sites of the world's largest mangrove forest. The activity concentrations of most of the 226Ra (14±2 Bqkg-1 to 35±4 Bqkg-1) and 232Th (30±5 Bqkg-1 to 50±9 Bqkg-1) lie within the world average values, but the 40K concentration (370± 44 Bqkg-1 to 660±72 Bqkg-1) was found to have exceeded the world average value. The evaluation of radiological hazard parameters revealed that the outdoor absorbed dose rate (maximum 73.25 nGyh-1) and outdoor annual effective dose (maximum 0.09 mSvy-1) for most samples exceeded the corresponding world average values. The elevated concentration of 40K is mainly due to the salinity intrusion, usage of fertilizers and agricultural runoff, and migration of waste effluents along the riverbanks. Being the pioneering comprehensive research on the Bangladesh side of the Sundarbans, this study forms a baseline radioactivity for the Sundarbans before the commissioning of the Rooppur Nuclear Power Plant in Bangladesh.
  11. Assessment of radioactivity level and associated radiological hazard in fertilizer from Dhaka
    Siraz MMM, Al Mahmud J, Alam MS, Rashid MB, Hossain Z, Osman H, et al.
    Environ Monit Assess, 2024 Jan 23;196(2):192.
    PMID: 38263472 DOI: 10.1007/s10661-024-12328-4
    Miners, factory workers, traders, end-users, and foodstuff consumers all run the risk of encountering health hazards derived from the presence of elevated levels of radiation in fertilizers, as these groups often come into direct or indirect contact with fertilizers as well as raw materials throughout various linked processes such as mineral extractions, fertilizer production, agricultural practices. A total of 30 samples of various kinds of fertilizer produced in different factories in Dhaka megacity were analyzed to quantify the concentrations of primordial radionuclides using HPGe detector. Among the analyzed samples, average (range) concentration of 40K was found to be 9920 ± 1091 (8700 ± 957-11,500 ± 1265), 9100 ± 1001 (8600 ± 946-9600 ± 1056), 2565 ± 282 (2540 ± 279-2590 ± 285), and 3560 ± 392 (2620 ± 288-4500 ± 495) Bq/kg in the samples of Muriate of Potash Fertilizer, Sulphate of Potash Fertilizer, Humic Acid Fertilizer, and NPKS Fertilizer, respectively. Elevated concentration of 226Ra was found in Triple Super Phosphate Fertilizer with a mean (range) of 335 ± 37 (290 ± 32-380 ± 42) Bq/kg. The higher activity of 40K can be linked to the greater levels of elemental potassium in phosphate fertilizer. Elevated concentrations of radionuclides may also result from variations in chemical processes as well as the local geology of the mining areas where the raw materials were extracted for fertilizer production. Numerous fertilizer brands surpass prescribed limits for various hazardous parameters, presenting significant health risks to factory workers, farmers, and consumers of agricultural products. This study provides baseline information on the radioactivity of fertilizers, which could be used to develop mitigation methods, establish national fertilizer usage limits, justify regulatory frameworks, and raise public awareness of fertilizer overuse. The findings of the study could potentially help to explore the impact of fertilizer on the food chain.
  12. A pioneering study of the radiological mapping in the world's largest mangrove forest (the Sundarbans) and implications for the public and environment
    Al Mahmud J, Siraz MMM, Alam MS, Dewan MJ, Rashid MB, Khandaker MU, et al.
    Mar Pollut Bull, 2024 May;202:116349.
    PMID: 38604081 DOI: 10.1016/j.marpolbul.2024.116349
    Coastal Mangroves are facing growing threats due to the harmful consequences of human activities. This first-ever detailed study of natural radioactivity in soil samples collected from seven tourist destinations within the Sundarbans, the world's largest mangrove forest, was conducted using HPGe gamma-ray spectrometry. Although the activity levels of 226Ra (11 ± 1-44 ± 4 Bq/kg) and 232Th (13 ± 1-68 ± 6 Bq/kg) generally align with global averages, the concentration of 40K (250 ± 20-630 ± 55 Bq/kg) was observed to surpass the worldwide average primarily due to factors like salinity intrusion, fertilizer application, agricultural runoff, which suggests the potential existence of potassium-rich mineral resources near the study sites. The assessment of the hazard parameters indicates that the majority of these parameters are within the recommended limits. The soil samples do not pose a significant radiological risk to the nearby population. The results of this study can establish important radiological baseline data before the Rooppur Nuclear Power Plant begins operating in Bangladesh.
  13. Fulltext Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae
    Urmi UL, Nahar S, Rana M, Sultana F, Jahan N, Hossain B, et al.
    Infect Drug Resist, 2020;13:2863-2875.
    PMID: 32903880 DOI: 10.2147/IDR.S262493
    Introduction: Klebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs.

    Methods: This research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing.

    Results: Fifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination.

    Conclusion: The discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.

  14. Detection of mobile colistin-resistance gene variants (mcr-1 and mcr-2) in urinary tract pathogens in Bangladesh: the last resort of infectious disease management colistin efficacy is under threat
    Ara B, Urmi UL, Haque TA, Nahar S, Rumnaz A, Ali T, et al.
    Expert Rev Clin Pharmacol, 2021 Apr;14(4):513-522.
    PMID: 33691556 DOI: 10.1080/17512433.2021.1901577
    Background: Currently, colistin-resistant pathogens emerged has become a global health concern. This study assessed the distribution of mcr-1 to mcr-5 variants with the phenotypic colistin-resistance in bacterial isolates from urinary tract infection (UTI) patients in Bangladesh.Methods: A cross-sectional study was conducted between April 2017 and March 2018 to enroll uncomplicated UTI patients, and 142 urine samples were analyzed. Uropathogens were identified using the API-20E biochemical panel and 16s rRNA gene sequencing. Polymerase chain reactions detected the mcr gene variants in the UTI isolates. The phenotypic colistin-susceptibility was determined by the Kirby-Bauer disc-diffusion method and the minimal inhibitory concentration (MIC) measurement.Results: The combined carriage of mcr-1 and mcr-2 genes in 11.4% (14/123) of urinary tract pathogens. The mcr-positive pathogens include five Escherichia coli, three Klebsiella pneumoniae, three Pseudomonas putida, two Enterobacter cloacae, and one Enterobacter hormaechei. The mcr-positive variant showed significantly higher phenotypic colistin resistance with MIC between >16 µg/mL and >128 µg/mL (p
  15. Fulltext Barriers to routine G6PD testing prior to treatment with primaquine
    Ley B, Thriemer K, Jaswal J, Poirot E, Alam MS, Phru CS, et al.
    Malar J, 2017 08 10;16(1):329.
    PMID: 28797255 DOI: 10.1186/s12936-017-1981-y
    BACKGROUND: Primaquine is essential for the radical cure of vivax malaria, however its broad application is hindered by the risk of drug-induced haemolysis in individuals with glucose-6-phosphate-dehydrogenase (G6PD) deficiency. Rapid diagnostic tests capable of diagnosing G6PD deficiency are now available, but these are not used widely.

    METHODS: A series of qualitative interviews were conducted with policy makers and healthcare providers in four vivax-endemic countries. Routine G6PD testing is not part of current policy in Bangladesh, Cambodia or China, but it is in Malaysia. The interviews were analysed with regard to respondents perceptions of vivax malaria, -primaquine based treatment for malaria and the complexities of G6PD deficiency.

    RESULTS: Three barriers to the roll-out of routine G6PD testing were identified in all sites: (a) a perceived low risk of drug-induced haemolysis; (b) the perception that vivax malaria was benign and accordingly treatment with primaquine was not regarded as a priority; and, (c) the additional costs of introducing routine testing. In Malaysia, respondents considered the current test and treat algorithm suitable and the need for an alternative approach was only considered relevant in highly mobile and hard to reach populations.

    CONCLUSIONS: Greater efforts are needed to increase awareness of the benefits of the radical cure of Plasmodium vivax and this should be supported by economic analyses exploring the cost effectiveness of routine G6PD testing.

  16. Fulltext A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination
    Arick MA, Grover CE, Hsu CY, Magbanua Z, Pechanova O, Miller ER, et al.
    G3 (Bethesda), 2023 Mar 09;13(3).
    PMID: 36639248 DOI: 10.1093/g3journal/jkad009
    Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.
  17. Impact of metabolic risk factors on the severity and outcome of patients with alcohol-associated acute-on-chronic liver failure
    Duseja A, De A, Taneja S, Choudhury AK, Devarbhavi H, Hu J, et al.
    Liver Int, 2021 01;41(1):150-157.
    PMID: 32970356 DOI: 10.1111/liv.14671
    BACKGROUND: Metabolic risk factors may impact the severity and outcome of alcoholic liver disease. The present study evaluated this effect in patients with alcohol-associated acute-on-chronic liver failure (ACLF).

    METHODOLOGY: One thousand two hundred and sixteen prospectively enrolled patients with ACLF (males 98%, mean age 42.5 ± 9.4 years, mean CTP, MELD and AARC scores of 12 ± 1.4, 29.7 ± 7 and 9.8 ± 2 respectively) from the Asian Pacific Association for the Study of the Liver (APASL) ACLF Research Consortium (AARC) database were analysed retrospectively. Patients with or without metabolic risk factors were compared for severity (CTP, MELD, AARC scores) and day 30 and 90 mortality. Information on overweight/obesity, type 2 diabetes mellitus (T2DM), hypertension and dyslipidaemia were available in 1028 (85%), 1019 (84%), 1017 (84%) and 965 (79%) patients respectively.

    RESULTS: Overall, 392 (32%) patients died at day 30 and 528 (43%) at day 90. Overweight/obesity, T2DM, hypertension and dyslipidaemia were present in 154 (15%), 142 (14%), 66 (7%) and 141 (15%) patients, respectively, with no risk factors in 809 (67%) patients. Patients with overweight/obesity had higher MELD scores (30.6 ± 7.1 vs 29.2 ± 6.9, P = .007) and those with dyslipidaemia had higher AARC scores (10.4 ± 1.2 vs 9.8 ± 2, P = .014). Overweight/obesity was associated with increased day 30 mortality (HR 1.54, 95% CI 1.06-2.24, P = .023). None of other metabolic risk factors, alone or in combination, had any impact on disease severity or mortality. On multivariate analysis, overweight or obesity was significantly associated with 30-day mortality (aHR 1.91, 95% CI 1.41-2.59, P 

  18. Fulltext Challenges for achieving safe and effective radical cure of Plasmodium vivax: a round table discussion of the APMEN Vivax Working Group
    Thriemer K, Ley B, Bobogare A, Dysoley L, Alam MS, Pasaribu AP, et al.
    Malar J, 2017 04 05;16(1):141.
    PMID: 28381261 DOI: 10.1186/s12936-017-1784-1
    The delivery of safe and effective radical cure for Plasmodium vivax is one of the greatest challenges for achieving malaria elimination from the Asia-Pacific by 2030. During the annual meeting of the Asia Pacific Malaria Elimination Network Vivax Working Group in October 2016, a round table discussion was held to discuss the programmatic issues hindering the widespread use of primaquine (PQ) radical cure. Participants included 73 representatives from 16 partner countries and 33 institutional partners and other research institutes. In this meeting report, the key discussion points are presented and grouped into five themes: (i) current barriers for glucose-6-phosphate deficiency (G6PD) testing prior to PQ radical cure, (ii) necessary properties of G6PD tests for wide scale deployment, (iii) the promotion of G6PD testing, (iv) improving adherence to PQ regimens and (v) the challenges for future tafenoquine (TQ) roll out. Robust point of care (PoC) G6PD tests are needed, which are suitable and cost-effective for clinical settings with limited infrastructure. An affordable and competitive test price is needed, accompanied by sustainable funding for the product with appropriate training of healthcare staff, and robust quality control and assurance processes. In the absence of quantitative PoC G6PD tests, G6PD status can be gauged with qualitative diagnostics, however none of the available tests is currently sensitive enough to guide TQ treatment. TQ introduction will require overcoming additional challenges including the management of severely and intermediately G6PD deficient individuals. Robust strategies are needed to ensure that effective treatment practices can be deployed widely, and these should ensure that the caveats are outweighed by  the benefits of radical cure for both the patients and the community. Widespread access to quality controlled G6PD testing will be critical.
  19. Fulltext An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
    MalariaGEN, Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, et al.
    Wellcome Open Res, 2022;7:136.
    PMID: 35651694 DOI: 10.12688/wellcomeopenres.17795.1
    This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
  20. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
    Trimarsanto H, Amato R, Pearson RD, Sutanto E, Noviyanti R, Trianty L, et al.
    Commun Biol, 2022 Dec 23;5(1):1411.
    PMID: 36564617 DOI: 10.1038/s42003-022-04352-2
    Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.
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