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  1. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  2. Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
  3. Adiana G, Juahir H, Joseph B, Shazili NAM
    Mar Pollut Bull, 2017 Oct 15;123(1-2):232-240.
    PMID: 28865793 DOI: 10.1016/j.marpolbul.2017.08.055
    The present study aims to define the possible sources that contribute to the level of Pb into the Brunei Bay, Borneo. The cluster analysis has classified the bay into the northern part with heavy and agriculture-related industries; the southern area with a moderate rural human settlement as well as the southwestern area with a more pristine environment and a low level of human settlement. The score plot of spatial discriminant analysis verified a significant influence of the river system toward the estuary, whereas the temporal discriminant analysis has discriminated the seasonal changes. In comparison to elsewhere, the stable Pb isotopic ratios in Brunei Bay showed a fingerprint similar to coal-related sources and of aerosol input. Briefly, even though Pb in the Brunei Bay ecosystem proved to be at a low level, the stable Pb isotopic ratios showed that human and industrial activities are slowly contributing Pb into the bay ecosystem.
  4. Gammie AJ, Lopez JB, Scott S
    Clin Chem Lab Med, 2023 Mar 28;61(4):634-637.
    PMID: 36343330 DOI: 10.1515/cclm-2022-1052
    Clinical laboratories are significant contributors to the environmental burden of the planet. They have been slow to address the issues with a few exceptions, but it is highly encouraging to see the current impetus and ambition in this direction. This paper describes some of these initiatives and provides the rationale as to why clinical laboratories should become sustainable. It also describes the economic and intangible benefits that labs will accrue in achieving sustainability.
  5. Lopez JB, Peng CL
    Clin Chem Lab Med, 2003 Oct;41(10):1369-72.
    PMID: 14580168
    The concentration of homocysteine (Hcy) rises rapidly after the collection of blood. This feature requires blood to be collected into the anticoagulants EDTA or heparin and the plasma to then be immediately separated; alternatively, the blood may be kept on ice and centrifuged within 1 hour. The use of chemical preservatives has been proposed as a means of stabilising Hcy levels in whole blood after collection. The objective of this study was to determine whether the commonly available fluoride-oxalate (Fl-Ox) and sodium citrate (Na-Cit) containers could stabilise Hcy levels in blood. Our results showed that when blood was collected into potassium EDTA (K-EDTA) tubes, Hcy levels rose from initial levels, on standing at room temperature (approximately 25 degrees C), by an average of 21% after 3 hours and 32% after 5 hours. The initial Hcy levels of blood collected into Fl-Ox and Na-Cit containers, however, were lower, at averages of 89% and 91%, respectively, compared to that of the same samples when collected into K-EDTA tubes. Hcy in these samples subsequently rose on standing, and after 5 hours was, on the average, 10 and 13% higher, respectively, compared with the initial levels in K-EDTA tubes. We conclude that Fl-Ox and Na-Cit do not stabilise Hcy in blood after collection and should not be used as preservatives.
  6. Joseph B, Sithambaresan M, Kurup MR, Ng SW
    Acta Crystallogr Sect E Struct Rep Online, 2014 Jun 1;70(Pt 6):m211-2.
    PMID: 24940200 DOI: 10.1107/S1600536814010150
    The molecule of the title complex, [Ni2(C21H15N3O5)2(H2O)4]·4C3H7NO, is located on an inversion centre. This results in a dimeric Ni(II) complex, with the two Ni(II) atoms bridged by phenolate O atoms. The tridentate ligand is chelated to each Ni(II) atom via one N and two O atoms of the imino-late form of the hydrazide moiety, which has the same conformation as the free ligand. The coordination geometry around each Ni(II) ion is slightly distorted octa-hedral. A supra-molecular three-dimensional architecture is created by dominant inter-molecular O-H⋯N, O-H⋯O and C-H⋯O hydrogen-bonding inter-actions. These are augmented by two C-H⋯π inter-actions and a π-π inter-action with a centroid-centroid distance of 3.681 (2) Å.
  7. Mahmud MR, Khan AM, Nadol JB
    Ann Otol Rhinol Laryngol, 2003 Nov;112(11):979-86.
    PMID: 14653368
    Although hearing loss is the most common presenting symptom in patients with acoustic neuroma, the pathophysiology of hearing loss associated with acoustic neuroma is unknown. Although primary dysfunction of the auditory nerve is intuitively logical, available histopathologic and clinical data suggest that although neural degeneration is common, it alone does not adequately account for hearing loss in many cases. The purpose of this study was to evaluate 11 cases of unoperated unilateral acoustic neuromas. Temporal bones were identified by means of a search mechanism provided by the National Temporal Bone, Hearing, and Balance Pathology Resource Registry and were prepared for light microscopy by standard techniques. Quantification of spiral ganglion cells, hair cells, stria vascularis, and spiral ligament was accomplished for each specimen. In addition, the maximum diameter and volume of each tumor were calculated from histopathologic sections. Increasing tumor size did predict a reduced spiral ganglion count. However, although there was a tendency for decreasing spiral ganglion cell count and for increasing tumor size to predict a higher pure tone average and lower speech discrimination score, these correlations did not reach statistical significance. In tumor ears in which the speech discrimination score was 50% or less, there was always significant degeneration of other structures of the inner ear in addition to neurons, including hair cells, the stria vascularis, and the spiral ligament. Endolymphatic hydrops and eosinophilic precipitate in the perilymphatic spaces were found in 2 of 3 such cases. It is concluded that acoustic neuromas appear to cause hearing loss, not only by causing degeneration of the auditory nerve, but also by inducing degenerative changes in the inner ear. It is hypothesized that the proteinaceous material seen histologically may represent the products of up-regulated genes in acoustic neuroma, some of which may interfere with normal cochlear function.
  8. Eleazu C, Suleiman JB, A Othman Z, Zakaria Z, Nna VU, Mohamed M
    J Food Biochem, 2021 02;45(2):e13626.
    PMID: 33492697 DOI: 10.1111/jfbc.13626
    The effect of bee bread (BB) on the biochemical parameters-body weights, calorie intake, Lee obesity indices, serum amylase, aspartate and alanine amino transferases, skeletal muscle activities of creatine kinase, superoxide dismutase, glutathione peroxidase, catalase, malondialdehyde, glutathione-S-transferase, total antioxidant activity, endogenous secretory receptor for advanced glycation end products (esRAGE), and muscle histology of high-fat diet (HFD) obese rats-was studied. Thirty-six male Sprague-Dawley rats were divided into six groups: Control: received rat feed and water (1 ml/kg); HFD: received HFD and water (1 ml/kg): BB or orlistat preventive: received HFD and BB (0.5 g/kg) or HFD and orlistat (10 mg/kg; weeks 1 to 12); BB or orlistat treated: received HFD and BB (0.5 g/kg) or HFD and orlistat (10 mg/kg; weeks 6 to 12), following obesity induction. At week 12, HFD group had altered (p 
  9. Sivathasan C, Hayward C, Jansz P, Sibal AK, ChenChen, Cally HKL, et al.
    J Heart Lung Transplant, 2020 11;39(11):1195-1198.
    PMID: 32950381 DOI: 10.1016/j.healun.2020.08.022
  10. Lopez JB
    Clin Biochem Rev, 2005 Aug;26(3):65-79.
    PMID: 16450014
    Hepatocellular carcinoma (HCC) ranks fifth in frequency of cancers worldwide. The main aetiological factor is hepatitis B virus (HBV) although the importance of hepatitis C virus (HCV) is growing. The most important tumour marker for HCC is alpha-fetoprotein (AFP). The common method of screening high risk patients by AFP and ultrasonography has been shown to result in earlier detection and consequently more easily treatable tumours and longer survival. Proposed screening interval varies from once every 3 months to annually to "as indicated' but, most commonly, is once every 6 months. AFP is a fairly specific but insensitive marker for HCC. Sensitivity of HCC detection by blood markers is improved by combining various other markers with AFP. Of the other markers, the newer high sensitivity des-gamma-carboxy-prothrombin (DCP) has been found to be useful. In addition the AFP fractions L3, P4/5 and the +II band are highly specific for HCC. Among routinely assayed tumour markers in the laboratory, CA 125 is more sensitive for HCC than AFP but far less specific. Various other enzymes, isoenzymes, growth factors, adhesion molecules, other proteins such as interleukin-2 receptor (IL-2R), human cervical cancer oncogene protein (HCCR) and glypican-3 (GPC3), p15 and p16 hypermethylation and nitrite/nitrate ratio have been tested; some of these show promise but none is presently in routine use. The value of other newer markers such as the HBx protein that is produced by HBV, and what are thought to be specific proteins and signatures identified by proteomics remain to be determined.
  11. Shiesh SC, Wiedmeyer HM, Kao JT, Vasikaran SD, Lopez JB, Laboratory Management Committee for the Asian-Pacific Federation of Clinical Biochemistry
    Clin Chem, 2009 Oct;55(10):1876-80.
    PMID: 19617287 DOI: 10.1373/clinchem.2009.129726
    BACKGROUND: The correlation between hemoglobin A(1c) (Hb A(1c)) and risk for complications in diabetic patients heightens the need to measure Hb A(1c) with accuracy. We evaluated the current performance for measuring Hb A(1c) in the Asian and Pacific region by examining data submitted by laboratories participating in the Taiwan proficiency-testing program.

    METHODS: Five fresh-pooled blood samples were sent to participating laboratories twice each year. The results were evaluated against target values assigned by the National Glycohemoglobin Standardization Program network laboratories; a passing criterion of +/-7% of the target value was used. Measurement uncertainty at Hb A(1c) concentrations of 7.0% and 8.0% were determined.

    RESULTS: A total of 276 laboratories from 11 countries took part in the Hb A(1c) survey. At the Hb A(1c) concentrations tested method-specific interlaboratory imprecision (CVs) were 1.1%-13.9% in 2005, 1.3%-10.1% in 2006, 1.2%-8.2% in 2007, and 1.1%-6.1% in 2008. Differences between target values and median values from the commonly used methods ranged from -0.24% to 0.22% Hb A(1c) in 2008. In 2005 83% of laboratories passed the survey, and in 2008 93% passed. At 7.0% Hb A(1c), measurement uncertainty was on average 0.49% Hb A(1c).

    CONCLUSIONS: The use of accuracy-based proficiency testing with stringent quality criteria has improved the performance of Hb A(1c) testing in the Asian and Pacific laboratories during the 4 years of assessment.

  12. Pandya A, Yu YJ, Ge Y, Nagel E, Kwong RY, Bakar RA, et al.
    J Cardiovasc Magn Reson, 2022 01 06;24(1):1.
    PMID: 34986851 DOI: 10.1186/s12968-021-00833-1
    BACKGROUND: Although prior reports have evaluated the clinical and cost impacts of cardiovascular magnetic resonance (CMR) for low-to-intermediate-risk patients with suspected significant coronary artery disease (CAD), the cost-effectiveness of CMR compared to relevant comparators remains poorly understood. We aimed to summarize the cost-effectiveness literature on CMR for CAD and create a cost-effectiveness calculator, useable worldwide, to approximate the cost-per-quality-adjusted-life-year (QALY) of CMR and relevant comparators with context-specific patient-level and system-level inputs.

    METHODS: We searched the Tufts Cost-Effectiveness Analysis Registry and PubMed for cost-per-QALY or cost-per-life-year-saved studies of CMR to detect significant CAD. We also developed a linear regression meta-model (CMR Cost-Effectiveness Calculator) based on a larger CMR cost-effectiveness simulation model that can approximate CMR lifetime discount cost, QALY, and cost effectiveness compared to relevant comparators [such as single-photon emission computed tomography (SPECT), coronary computed tomography angiography (CCTA)] or invasive coronary angiography.

    RESULTS: CMR was cost-effective for evaluation of significant CAD (either health-improving and cost saving or having a cost-per-QALY or cost-per-life-year result lower than the cost-effectiveness threshold) versus its relevant comparator in 10 out of 15 studies, with 3 studies reporting uncertain cost effectiveness, and 2 studies showing CCTA was optimal. Our cost-effectiveness calculator showed that CCTA was not cost-effective in the US compared to CMR when the most recent publications on imaging performance were included in the model.

    CONCLUSIONS: Based on current world-wide evidence in the literature, CMR usually represents a cost-effective option compared to relevant comparators to assess for significant CAD.

  13. Fadilah NIM, Riha SM, Mazlan Z, Wen APY, Hao LQ, Joseph B, et al.
    Front Bioeng Biotechnol, 2023;11:1160577.
    PMID: 37292094 DOI: 10.3389/fbioe.2023.1160577
    Skin tissue engineering possesses great promise in providing successful wound injury and tissue loss treatments that current methods cannot treat or achieve a satisfactory clinical outcome. A major field direction is exploring bioscaffolds with multifunctional properties to enhance biological performance and expedite complex skin tissue regeneration. Multifunctional bioscaffolds are three-dimensional (3D) constructs manufactured from natural and synthetic biomaterials using cutting-edge tissue fabrication techniques incorporated with cells, growth factors, secretomes, antibacterial compounds, and bioactive molecules. It offers a physical, chemical, and biological environment with a biomimetic framework to direct cells toward higher-order tissue regeneration during wound healing. Multifunctional bioscaffolds are a promising possibility for skin regeneration because of the variety of structures they provide and the capacity to customise the chemistry of their surfaces, which allows for the regulated distribution of bioactive chemicals or cells. Meanwhile, the current gap is through advanced fabrication techniques such as computational designing, electrospinning, and 3D bioprinting to fabricate multifunctional scaffolds with long-term safety. This review stipulates the wound healing processes used by commercially available engineered skin replacements (ESS), highlighting the demand for a multifunctional, and next-generation ESS replacement as the goals and significance study in tissue engineering and regenerative medicine (TERM). This work also scrutinise the use of multifunctional bioscaffolds in wound healing applications, demonstrating successful biological performance in the in vitro and in vivo animal models. Further, we also provided a comprehensive review in requiring new viewpoints and technological innovations for the clinical application of multifunctional bioscaffolds for wound healing that have been found in the literature in the last 5 years.
  14. Rahman MA, Islam SMS, Tungpunkom P, Sultana F, Alif SM, Banik B, et al.
    Global Health, 2021 10 01;17(1):117.
    PMID: 34598720 DOI: 10.1186/s12992-021-00768-3
    BACKGROUND: The current pandemic of COVID-19 impacted the psychological wellbeing of populations globally.

    OBJECTIVES: We aimed to examine the extent and identify factors associated with psychological distress, fear of COVID-19 and coping.

    METHODS: We conducted a cross-sectional study across 17 countries during Jun-2020 to Jan-2021. Levels of psychological distress (Kessler Psychological Distress Scale), fear of COVID-19 (Fear of COVID-19 Scale), and coping (Brief Resilient Coping Scale) were assessed.

    RESULTS: A total of 8,559 people participated; mean age (±SD) was 33(±13) years, 64% were females and 40% self-identified as frontline workers. More than two-thirds (69%) experienced moderate-to-very high levels of psychological distress, which was 46% in Thailand and 91% in Egypt. A quarter (24%) had high levels of fear of COVID-19, which was as low as 9% in Libya and as high as 38% in Bangladesh. More than half (57%) exhibited medium to high resilient coping; the lowest prevalence (3%) was reported in Australia and the highest (72%) in Syria. Being female (AOR 1.31 [95% CIs 1.09-1.57]), perceived distress due to change of employment status (1.56 [1.29-1.90]), comorbidity with mental health conditions (3.02 [1.20-7.60]) were associated with higher levels of psychological distress and fear. Doctors had higher psychological distress (1.43 [1.04-1.97]), but low levels of fear of COVID-19 (0.55 [0.41-0.76]); nurses had medium to high resilient coping (1.30 [1.03-1.65]).

    CONCLUSIONS: The extent of psychological distress, fear of COVID-19 and coping varied by country; however, we identified few higher risk groups who were more vulnerable than others. There is an urgent need to prioritise health and well-being of those people through well-designed intervention that may need to be tailored to meet country specific requirements.

  15. Low EV, Lee M, Bauer C, Fisher-Hoch SP, McCormick JB, Abughosh S, et al.
    Metab Syndr Relat Disord, 2022 Oct;20(8):440-450.
    PMID: 35819796 DOI: 10.1089/met.2021.0151
    Background: This retrospective cohort study aimed to examine the interaction effect between puberty stage and weight status on individual and clustering of cardiometabolic risk factors (CMRFs) among Mexican American children and adolescents. A total of 333 children and adolescents (aged 8-18 years) enrolled in the Cameron County Hispanic Cohort (CCHC) from 2014 to 2020 were included in the study. Methods: CCHC is a longitudinal, randomly recruited cohort based on the United States Census tracts/blocks of Mexican Americans living on the Texas-Mexico border. Individual CMRFs, including high blood pressure, central obesity, hypertriglyceridemia, low high-density lipoprotein cholesterol, and insulin resistance (IR) were assessed. Clustering of CMRFs is defined as the presence of three or more individual CMRFs. Puberty stages were assessed using the Tanner criteria. Multivariable logistic regressions were conducted to assess the association of puberty, weight status, and the interaction of the two main exposures with individual and clustering of CMRFs. Results: We observed that weight status had a dominant effect on all CMRF measures. The effect was especially prominent on central obesity and clustering of CMRFs. There were 95.4% of children with central obesity and 98.4% of those with clustering of CMRF were either overweight or obese. Entering puberty was associated with an increased risk of having IR [Tanner stage 2 vs. 1: odds ratio (OR) = 3.25, 95% confidence interval (95% CI) 1.28-8.27; Tanner stage 3 vs. 1: OR = 3.50, 95% CI 1.45-8.46] and hypertriglyceridemia (Tanner stage 2 vs. 1: OR = 2.67, 95% CI 1.11-6.45). However, the effects were not observed among those reaching the end of puberty (Tanner stage 4 and 5). Conclusions: A significant interaction effect between weight status and puberty was not detected on any individual CMRF and in the clustering of CMRFs. Other factors positively associated with individual CMRFs, especially IR, were being female and having a family history of diabetes.
  16. Maynard AJ, Ambrose L, Cooper RD, Chow WK, Davis JB, Muzari MO, et al.
    PLoS Negl Trop Dis, 2017 04;11(4):e0005546.
    PMID: 28410388 DOI: 10.1371/journal.pntd.0005546
    BACKGROUND: Within the last century, increases in human movement and globalization of trade have facilitated the establishment of several highly invasive mosquito species in new geographic locations with concurrent major environmental, economic and health consequences. The Asian tiger mosquito, Aedes albopictus, is an extremely invasive and aggressive daytime-biting mosquito that is a major public health threat throughout its expanding range.

    METHODOLOGY/PRINCIPAL FINDINGS: We used 13 nuclear microsatellite loci (on 911 individuals) and mitochondrial COI sequences to gain a better understanding of the historical and contemporary movements of Ae. albopictus in the Indo-Pacific region and to characterize its population structure. Approximate Bayesian computation (ABC) was employed to test competing historical routes of invasion of Ae. albopictus within the Southeast (SE) Asian/Australasian region. Our ABC results show that Ae. albopictus was most likely introduced to New Guinea via mainland Southeast Asia, before colonizing the Solomon Islands via either Papua New Guinea or SE Asia. The analysis also supported that the recent incursion into northern Australia's Torres Strait Islands was seeded chiefly from Indonesia. For the first time documented in this invasive species, we provide evidence of a recently colonized population (the Torres Strait Islands) that has undergone rapid temporal changes in its genetic makeup, which could be the result of genetic drift or represent a secondary invasion from an unknown source.

    CONCLUSIONS/SIGNIFICANCE: There appears to be high spatial genetic structure and high gene flow between some geographically distant populations. The species' genetic structure in the region tends to favour a dispersal pattern driven mostly by human movements. Importantly, this study provides a more widespread sampling distribution of the species' native range, revealing more spatial population structure than previously shown. Additionally, we present the most probable invasion history of this species in the Australasian region using ABC analysis.

  17. Lopez JB, Jackson D, Gammie A, Badrick T
    Clin Biochem Rev, 2017 Feb;38(1):3-11.
    PMID: 28798502
    Healthcare is a significant contributor to environmental impact but this has received little attention. The typical laboratory uses far more energy and water per unit area than the typical office building. There is a need to sensitise laboratories to the importance of adopting good environmental practices. Since this comes at an initial cost, it is vital to obtain senior management support. Convincing management of the various tangible and intangible benefits that can accrue in the long run should help achieve this support. Many good environmental practices do not have a cost but will require a change in the culture and mind-set of the organisation. Continuing education and training are important keys to successful implementation of good practices. There is a need to undertake a rigorous cost-benefit analysis of every change that is introduced in going green. The adoption of good practices can eventually lead to ISO certification if this is desired. This paper provides suggestions that will allow a laboratory to start going green. It will allow the industry to enhance its corporate citizenship whilst improving its competitive advantage for long-term.
  18. Ong MC, Yong JC, Shaari H, Joseph B, Shazili NAM, Pradit S, et al.
    Environ Geochem Health, 2023 Jun;45(6):3777-3787.
    PMID: 36574138 DOI: 10.1007/s10653-022-01456-w
    Brunei Bay is a unique ecosystem which offers a vast biodiversity. This study was carried out to define the source of metals in the surface sediment of Brunei Bay to ensure the bay's health. The secondary data were analysed using chemometrics analysis to verify the possible factors that influence metals distribution in Brunei Bay sediment. Samples were collected several times during 2013 to 2014 using Ponar grab at 16 stations within the bay. Samples were then dried, pre-treated, digested and analysed using Inductively Coupled Plasma Mass Spectrometry (ICPMS) in the laboratory. Overall, the mean concentration of metal, sediment pH and clay fraction were significantly changed during different sampling periods, as the changes were presumed affected by seasonal changes. The Pearson correlation has pointed that metals were dominantly derived by natural input; however, the total organic carbon was proven to be derived by anthropogenic sources. Moreover, the principal component analysis has verified that the distribution of metals in the bay's sediment was dominantly influenced by natural processes. However, the utilization and manipulation of marine resources are slightly affecting the bay's ecosystem which may deteriorate the ecosystem health soon.
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