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  1. Abdul-Mutalib, N.A., Syafinaz, A.N., Sakai, K., Shirai, Y.
    MyJurnal
    Foodborne disease has been associated with microorganisms like bacteria, fungi, viruses and parasites. Most commonly, the outbreaks take place due to the ingestion of pathogenic bacteria like Salmonella Typhi, Escherichia coli, Staphylococcus aureus, Vibrio cholera, Campylobacter jejuni, and Listeria monocytogenes. The disease usually happens as a result of toxin secretion of the microorganisms in the intestinal tract of the infected person. Usually, the level of hygiene in the food premises reflect the quality of the food item, hence restaurant or stall with poor sanitary condition is said to be the contributor to food poisoning outbreak. In Malaysia, food poisoning cases are not rare because the hot and humid climate of this country is very suitable for the growth of the foodborne bacteria. The government is also implementing strict rules to ensure workers and owners of food premises prioritize the cleanliness of their working area. Training programme for food handlers can also help them to implement hygiene as a routine in a daily basis. A lot of studies have been done to reduce foodborne diseases. The results can give information about the types of microorganisms, and other components that affect their growth. The result is crucial to determine how the spread of foodborne bacteria can be controlled safely and the outbreak can be reduced.
  2. Sakai K, Hassan MA, Vairappan CS, Shirai Y
    J Biosci Bioeng, 2022 Feb 09.
    PMID: 35151536 DOI: 10.1016/j.jbiosc.2022.01.001
    Palm oil is a representative and important biomass, not only as the most edible vegetable oil consumed worldwide, but also as a material for chemicals and biofuels. Despite the potential sustainability of the palm oil industry, it has conventionally emitted excess greenhouse gases, waste materials, and wastewater, brought land use change, thus affecting the natural environment. Therefore, the successful development of a sustainable palm oil industry is a touchstone for promoting the bioeconomy. Here, we first review the concept of the bioeconomy and the positive and negative aspects of the palm oil industry. Then, we consider solutions for introducing a green economy into the palm oil industry, such that it may coexist with biodiversity and environmental conservation toward the Sustainable Development Goals.
  3. Zainudin MHM, Ramli N, Hassan MA, Shirai Y, Tashiro K, Sakai K, et al.
    J Ind Microbiol Biotechnol, 2017 06;44(6):869-877.
    PMID: 28197796 DOI: 10.1007/s10295-017-1916-1
    A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from the palm oil industry in managing the disposal of these wastes. However, a deeper understanding of microbial diversity is required for the sustainable practice of the co-compositing process. In this study, an in-depth assessment of bacterial community succession at different stages of the pilot scale co-composting of OPEFB-POME anaerobic sludge was performed using 454-pyrosequencing, which was then correlated with the changes of physicochemical properties including temperature, oxygen level and moisture content. Approximately 58,122 of 16S rRNA gene amplicons with more than 500 operational taxonomy units (OTUs) were obtained. Alpha diversity and principal component analysis (PCoA) indicated that bacterial diversity and distributions were most influenced by the physicochemical properties of the co-composting stages, which showed remarkable shifts of dominant species throughout the process. Species related to Devosia yakushimensis and Desemzia incerta are shown to emerge as dominant bacteria in the thermophilic stage, while Planococcus rifietoensis correlated best with the later stage of co-composting. This study proved the bacterial community shifts in the co-composting stages corresponded with the changes of the physicochemical properties, and may, therefore, be useful in monitoring the progress of co-composting and compost maturity.
  4. Tin HS, Palaniveloo K, Anilik J, Vickneswaran M, Tashiro Y, Vairappan CS, et al.
    Microb Ecol, 2018 Feb;75(2):459-467.
    PMID: 28779295 DOI: 10.1007/s00248-017-1043-6
    Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing. A total of 30 soil samples yielded 893,752-OTU reads at ≥97% similarity from 5,446,512 good quality sequences. Soil from BWOP plantation showed highest unshared OTUs for organic (49.2%) and organic-mineral (50.9%) soil. MBOG soil showed a drop in unshared OTUs between organic (48.6%) and organic-mineral (33.9%). At phylum level, Proteobacteria dominated MBOG but shifted to Actinobacteria in logged and plantation soil. Present findings also indicated that only FELF exhibited change in bacterial communities along the soil depth, moving from the organic to the organic-mineral layer. Both layers of BWOP plantation soils deviated from other forests' soil in β-diversity analysis. To our knowledge, this is the first report on transitions of bacterial community structures with different soil horizons in the tropical rainforest including Borneo, Sabah. Borneo tropical soils form a large reservoir for soil bacteria and future exploration is needed for fully understanding the diversity structure and their bacterial functional properties.
  5. Chin CFS, Furuya Y, Zainudin MHM, Ramli N, Hassan MA, Tashiro Y, et al.
    J Biosci Bioeng, 2017 Nov;124(5):506-513.
    PMID: 28736147 DOI: 10.1016/j.jbiosc.2017.05.016
    Previously, a unique co-compost produced by composting empty fruit bunch with anaerobic sludge from palm oil mill effluent, which contributed to establishing a zero-emission industry in Malaysia. Little was known about the bacterial functions during the composting process and fertilization capacity of this co-compost. We isolated 100 strains from the co-compost on 7 types of enumeration media and screened 25 strains using in vitro tests for 12 traits, grouping them according to three functions: plant growth promoting (fixation of nitrogen; solubilization of phosphorus, potassium, and silicate; production of 3-indoleacetic acid, ammonia, and siderophore), biocontrolling (production of chitinase and anti-Ganoderma activity), and composting (degradation of lignin, xylan, and cellulose). Using 16S rRNA gene sequence analysis, 25 strains with strong or multi-functional traits were found belong to the genera Bacillus, Paenibacillus, Citrobacter, Enterobacter, and Kosakonia. Furthermore, several strains of Citrobacter sedlakii exhibited a plant growth-stimulation in vivo komatsuna plant cultivation test. In addition, we isolated several multifunctional strains; Bacillus tequilensis CE4 (biocontrolling and composting), Enterobacter cloacae subsp. dissolvens B3 (plant growth promoting and biocontrolling), and C. sedlakii CESi7 (plant growth promoting and composting). Some bacteria in the co-compost play significant roles during the composting process and plant cultivation after fertilization, and some multifunctional strains have potential for use in accelerating the biodegradation of lignocellulosic biomass, protecting against Ganoderma boninense infection, and increasing the yield of palm oil.
  6. Zainudin MH, Mustapha NA, Maeda T, Ramli N, Sakai K, Hassan M
    Waste Manag, 2020 Apr 01;106:240-249.
    PMID: 32240940 DOI: 10.1016/j.wasman.2020.03.029
    Biochar has proven to be a feasible additive for mitigating nitrogen loss during the composting process. This study aims to evaluate the influence of biochar addition on bacterial community and physicochemical properties changes, including ammonium (NH4+), nitrite (NO2-) and nitrate (NO3-) contents during the composting of poultry manure. The composting was carried out by adding 20% (w/w) of biochar into the mixture of poultry manure and rice straw with a ratio of 2:1, and the same treatment without biochar was prepared as a control. The finished product of control compost recorded the high contents of NO2- and NO3- (366 mg/kg and 600 mg/kg) with reduced the total NH4+ content to 10 mg/kg. Meanwhile, biochar compost recorded a higher amount of total NH4+ content (110 mg/kg) with low NO2- and NO3- (161 mg/kg and 137 mg/kg) content in the final composting material. The principal component analysis showed that the dynamics of dominant genera related to Halomonas, Pusillimonas, and Pseudofulvimonas, all of which were known as nitrifying and denitrifying bacteria, was significantly correlated with the dynamic of NO2- and NO3- content throughout the composting process. The genera related to Pusillimonas, and Pseudofulvimonas appeared as the dominant communities as the NO2- and NO3- increased. In contrast, as the NO2- and NO3- concentration decreased, the Halomonas genus were notably enriched in biochar compost. This study revealed the bacterial community shifts corresponded with the change of physicochemical properties, which provides essential information for a better understanding of monitoring and improving the composting process.
  7. Abdul-Mutalib NA, Amin Nordin S, Osman M, Ishida N, Tashiro K, Sakai K, et al.
    Int J Food Microbiol, 2015 May 4;200:57-65.
    PMID: 25679309 DOI: 10.1016/j.ijfoodmicro.2015.01.022
    This study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around Seri Kembangan, a city in Malaysia. Pyrosequencing generated 452,401 of total reads of OTUs with an average of 1.4×10(7) bacterial cells/cm(2). Proteobacteria, Firmicutes and Bacteroides were identified as the most abundant phyla in the samples. Taxonomic richness was generally high with >1000 operational taxonomic units (OTUs) observed across all samples. The highest appearance frequencies (100%) were OTUs closely related to Enterobacter sp., Enterobacter aerogenes, Pseudomonas sp. and Pseudomonas putida. Several OTUs were identified most closely related to known food-borne pathogens, including Bacillus cereus, Cronobacter sakazaki, Cronobacter turisensis, Escherichia coli, E. coli O157:H7, Hafnia alvei, Kurthia gibsonii, Salmonella bongori, Salmonella enterica, Salmonella paratyphi, Salmonella tyhpi, Salmonella typhimurium and Yersinia enterocolitica ranging from 0.005% to 0.68% relative abundance. The condition and grade of the food premises on a three point cleanliness scale did not correlate with the bacterial abundance and type. Regardless of the status and grades, all food premises have the same likelihood to introduce food-borne bacteria from cutting boards to their foods and must always prioritize the correct food handling procedure in order to avoid unwanted outbreak of food-borne illnesses.
  8. Yusof N, Hassan MA, Yee PL, Tabatabaei M, Othman MR, Mori M, et al.
    Waste Manag Res, 2011 Jun;29(6):602-11.
    PMID: 21447612 DOI: 10.1177/0734242X10397581
    Nitrification of mature sanitary landfill leachate with high-strength of N-NH(4) + (1080-2350 mg L(-1)) was performed in a 10 L continuous nitrification activated sludge reactor. The nitrification system was acclimatized with synthetic leachate during feed batch operation to avoid substrate inhibition before being fed with actual mature leachate. Successful nitrification was achieved with an approximately complete ammonium removal (99%) and 96% of N-NH(4) + conversion to N-NO(-) (3) . The maximum volumetric and specific nitrification rates obtained were 2.56 kg N-NH(4) (+) m(-3) day(-1) and 0.23 g N-NH(4) ( +) g(-1) volatile suspended solid (VSS) day(-1), respectively, at hydraulic retention time (HRT) of 12.7 h and solid retention time of 50 days. Incomplete nitrification was encountered when operating at a higher nitrogen loading rate of 3.14 kg N-NH(4) (+) m(-3) day(-1). The substrate overloading and nitrifiers competition with heterotrophs were believed to trigger the incomplete nitrification. Fluorescence in situ hybridization (FISH) results supported the syntrophic association between the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria. FISH results also revealed the heterotrophs as the dominant and disintegration of some AOB cell aggregates into single cells which further supported the incomplete nitrification phenomenon.
  9. Mohd-Nor D, Ramli N, Sharuddin SS, Hassan MA, Mustapha NA, Ariffin H, et al.
    Microbes Environ, 2019 Jun 27;34(2):121-128.
    PMID: 30905894 DOI: 10.1264/jsme2.ME18104
    Despite efforts to address the composition of the microbial community during the anaerobic treatment of palm oil mill effluent (POME), its composition in relation to biodegradation in the full-scale treatment system has not yet been extensively examined. Therefore, a thorough analysis of bacterial and archaeal communities was performed in the present study using MiSeq sequencing at the different stages of the POME treatment, which comprised anaerobic as well as facultative anaerobic and aerobic processes, including the mixed raw effluent (MRE), mixing pond, holding tank, and final discharge phases. Based on the results obtained, the following biodegradation processes were suggested to occur at the different treatment stages: (1) Lactobacillaceae (35.9%) dominated the first stage, which contributed to high lactic acid production; (2) the higher population of Clostridiaceae in the mixing pond (47.7%) and Prevotellaceae in the holding tank (49.7%) promoted acetic acid production; (3) the aceticlastic methanogen Methanosaetaceae (0.6-0.8%) played a role in acetic acid degradation in the open digester and closed reactor for methane generation; (4) Syntrophomonas (21.5-29.2%) appeared to be involved in the degradation of fatty acids and acetic acid by syntrophic cooperation with the hydrogenotrophic methanogen, Methanobacteriaceae (0.6-1.3%); and (5) the phenols and alcohols detected in the early phases, but not in the final discharge phase, indicated the successful degradation of lignocellulosic materials. The present results contribute to a better understanding of the biodegradation mechanisms involved in the different stages of the full-scale treatment of POME.
  10. Sakai K, Storozhenko T, Mizukami T, Ohashi H, Bouisset F, Tajima A, et al.
    PMID: 38566527 DOI: 10.1002/ccd.31020
    BACKGROUND: Two invasive methods are available to estimate microvascular resistance: bolus and continuous thermodilution. Comparative studies have revealed a lack of concordance between measurements of microvascular resistance obtained through these techniques.

    AIMS: This study aimed to examine the influence of vessel volume on bolus thermodilution measurements.

    METHODS: We prospectively included patients with angina with non-obstructive coronary arteries (ANOCA) undergoing bolus and continuous thermodilution assessments. All patients underwent coronary CT angiography to extract vessel volume. Coronary microvascular dysfunction was defined as coronary flow reserve (CFR) 

  11. Yamanaka A, Iwakiri A, Yoshikawa T, Sakai K, Singh H, Himeji D, et al.
    PLoS One, 2014;9(3):e92777.
    PMID: 24667794 DOI: 10.1371/journal.pone.0092777
    A Japanese man suffered from acute respiratory tract infection after returning to Japan from Bali, Indonesia in 2007. Miyazaki-Bali/2007, a strain of the species of Nelson Bay orthoreovirus, was isolated from the patient's throat swab using Vero cells, in which syncytium formation was observed. This is the sixth report describing a patient with respiratory tract infection caused by an orthoreovirus classified to the species of Nelson Bay orthoreovirus. Given the possibility that all of the patients were infected in Malaysia and Indonesia, prospective surveillance on orthoreovirus infections should be carried out in Southeast Asia. Furthermore, contact surveillance study suggests that the risk of human-to-human infection of the species of Nelson Bay orthoreovirus would seem to be low.
  12. Munhoz D, Collet C, Mizukami T, Yong A, Leone AM, Eftekhari A, et al.
    Am Heart J, 2023 Nov;265:170-179.
    PMID: 37611857 DOI: 10.1016/j.ahj.2023.07.016
    INTRODUCTION: Diffuse disease has been identified as one of the main reasons leading to low post-PCI fractional flow reserve (FFR) and residual angina after PCI. Coronary pressure pullbacks allow for the evaluation of hemodynamic coronary artery disease (CAD) patterns. The pullback pressure gradient (PPG) is a novel metric that quantifies the distribution and magnitude of pressure losses along the coronary artery in a focal-to-diffuse continuum.

    AIM: The primary objective is to determine the predictive capacity of the PPG for post-PCI FFR.

    METHODS: This prospective, large-scale, controlled, investigator-initiated, multicenter study is enrolling patients with at least 1 lesion in a major epicardial vessel with a distal FFR ≤ 0.80 intended to be treated by PCI. The study will include 982 subjects. A standardized physiological assessment will be performed pre-PCI, including the online calculation of PPG from FFR pullbacks performed manually. PPG quantifies the CAD pattern by combining several parameters from the FFR pullback curve. Post-PCI physiology will be recorded using a standardized protocol with FFR pullbacks. We hypothesize that PPG will predict optimal PCI results (post-PCI FFR ≥ 0.88) with an area under the ROC curve (AUC) ≥ 0.80. Secondary objectives include patient-reported and clinical outcomes in patients with focal vs. diffuse CAD defined by the PPG. Clinical follow-up will be collected for up to 36 months, and an independent clinical event committee will adjudicate events.

    RESULTS: Recruitment is ongoing and is expected to be completed in the second half of 2023.

    CONCLUSION: This international, large-scale, prospective study with pre-specified powered hypotheses will determine the ability of the preprocedural PPG index to predict optimal revascularization assessed by post-PCI FFR. In addition, it will evaluate the impact of PPG on treatment decisions and the predictive performance of PPG for angina relief and clinical outcomes.

  13. Baird AH, Guest JR, Edwards AJ, Bauman AG, Bouwmeester J, Mera H, et al.
    Sci Data, 2021 01 29;8(1):35.
    PMID: 33514754 DOI: 10.1038/s41597-020-00793-8
    The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.
  14. Nguyen TN, Qureshi MM, Klein P, Yamagami H, Abdalkader M, Mikulik R, et al.
    J Stroke, 2022 May;24(2):256-265.
    PMID: 35677980 DOI: 10.5853/jos.2022.00752
    BACKGROUND AND PURPOSE: Recent studies suggested an increased incidence of cerebral venous thrombosis (CVT) during the coronavirus disease 2019 (COVID-19) pandemic. We evaluated the volume of CVT hospitalization and in-hospital mortality during the 1st year of the COVID-19 pandemic compared to the preceding year.

    METHODS: We conducted a cross-sectional retrospective study of 171 stroke centers from 49 countries. We recorded COVID-19 admission volumes, CVT hospitalization, and CVT in-hospital mortality from January 1, 2019, to May 31, 2021. CVT diagnoses were identified by International Classification of Disease-10 (ICD-10) codes or stroke databases. We additionally sought to compare the same metrics in the first 5 months of 2021 compared to the corresponding months in 2019 and 2020 (ClinicalTrials.gov Identifier: NCT04934020).

    RESULTS: There were 2,313 CVT admissions across the 1-year pre-pandemic (2019) and pandemic year (2020); no differences in CVT volume or CVT mortality were observed. During the first 5 months of 2021, there was an increase in CVT volumes compared to 2019 (27.5%; 95% confidence interval [CI], 24.2 to 32.0; P<0.0001) and 2020 (41.4%; 95% CI, 37.0 to 46.0; P<0.0001). A COVID-19 diagnosis was present in 7.6% (132/1,738) of CVT hospitalizations. CVT was present in 0.04% (103/292,080) of COVID-19 hospitalizations. During the first pandemic year, CVT mortality was higher in patients who were COVID positive compared to COVID negative patients (8/53 [15.0%] vs. 41/910 [4.5%], P=0.004). There was an increase in CVT mortality during the first 5 months of pandemic years 2020 and 2021 compared to the first 5 months of the pre-pandemic year 2019 (2019 vs. 2020: 2.26% vs. 4.74%, P=0.05; 2019 vs. 2021: 2.26% vs. 4.99%, P=0.03). In the first 5 months of 2021, there were 26 cases of vaccine-induced immune thrombotic thrombocytopenia (VITT), resulting in six deaths.

    CONCLUSIONS: During the 1st year of the COVID-19 pandemic, CVT hospitalization volume and CVT in-hospital mortality did not change compared to the prior year. COVID-19 diagnosis was associated with higher CVT in-hospital mortality. During the first 5 months of 2021, there was an increase in CVT hospitalization volume and increase in CVT-related mortality, partially attributable to VITT.

  15. Nguyen TN, Qureshi MM, Klein P, Yamagami H, Mikulik R, Czlonkowska A, et al.
    Neurology, 2023 Jan 24;100(4):e408-e421.
    PMID: 36257718 DOI: 10.1212/WNL.0000000000201426
    BACKGROUND AND OBJECTIVES: Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).

    METHODS: We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.

    RESULTS: There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.

    DISCUSSION: There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.

    TRIAL REGISTRATION INFORMATION: This study is registered under NCT04934020.

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