Browse publications by year: 2021

  1. Yen J, Tam CL, Lee SL
    Psych J, 2021 Aug;10(4):574-586.
    PMID: 33928765 DOI: 10.1002/pchj.450
    This study examined the perceptions of parental bonding, depressive experiences of self-criticism and dependency, and the current level of depressive symptomology among 212 college students from Sabah, Malaysia. The participants completed the brief version of the Parental Bonding Instrument, the Reconstructed Depressive Experiences Questionnaire, and the Patient Health Questionnaire. The results showed significant direct effects of maternal care, maternal overprotection, paternal care, self-criticism, and dependency on depressive symptomology. In contrast, the indirect effects of self-criticism and dependency on the relationship between parental bonding and depressive symptomology were not significant. These findings were in line with previous studies that have highlighted the significance of parent-child bonding, self-criticism, and dependency in the development of depressive symptomology. However, they contradicted previous results on the significant indirect effects of self-criticism and dependency. This study highlights the importance of parental care and overprotection, as they can predict the manifestation of depressive symptomology at a later stage in life.
    MeSH terms: Humans; Malaysia; Object Attachment*; Parents*; Surveys and Questionnaires; Students
  2. Ahmed Z, Yusoff MS, Kamal NHM, Aziz HA
    Waste Manag Res, 2021 Nov;39(11):1396-1405.
    PMID: 33928820 DOI: 10.1177/0734242X211012775
    The removal of concentrated colour (around 5039 Pt-Co) and chemical oxygen demand (COD; around 4142 mg L-1) from matured landfill leachate through a novel combination of humic acid extraction and coagulation with natural oil palm trunk starch (OPTS) was investigated in this study. Central composite design from response surface methodology of Design Expert-10 software executed the experimental design to correlate experimental factors with desired responses. Analysis of variance developed the quadratic model for four factors (e.g. coagulant dosage, slow mixing speed and time and centrifugation duration) and two responses (% removal of colour, COD). The model confirmed the highest colour (84.96%) and COD (48.84%) removal with a desirability function of 0.836 at the optimum condition of 1.68 g L-1 coagulant dose, 19.11 rpm slow mixing speed, 16.43 minutes for mixing time and 35.75 minutes for centrifugation duration. Better results of correlation coefficient (R2 = 0.98 and 0.96) and predicted R2 (0.94 and 0.84) indicates the model significance. Electron microscopic images display the amalgamation of flocs through bridging. Fourier transforms infrared spectra confirmed the existence of selected organic groups in OPTS, which eventually signifies the applied method.
    MeSH terms: Color; Humic Substances*; Starch; Biological Oxygen Demand Analysis
  3. Lye JX, Kow RY, Ismail R, Khalid KA
    J Hand Surg Asian Pac Vol, 2021 Jun;26(2):166-179.
    PMID: 33928864 DOI: 10.1142/S2424835521500156
    Background: The Michigan Hand Outcomes Questionnaire (MHQ), a self-reported questionnaire for patients with hand disorders, has been widely used globally. It has been cross-culturally adapted into different languages across all continents. Aims of this study were to translate the MHQ into Malay language and to evaluate its reliability and validity compared with Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire in a Malay-speaking population. Methods: The MHQ was cross-culturally adapted into a Malay version based on the guidelines. A pre-testing involving thirty patients with hand disorders was performed to assess whether it was comprehensible to the target population. One hundred patients with hand disorders were recruited in this study to answer the MHQ and DASH questionnaires. The MHQ was tested twice with an interval of two weeks in between. Statistical analysis was performed to assess the reproducibility and internal consistency via the test-retest method and Cronbach's alpha calculation, respectively. The association between MHQ and DASH questionnaire was assessed with Spearman's correlation calculation. Results: In the pre-testing, twenty-six patients (86.7%) understood all the questions in the Malay version of MHQ. The test-retest analysis showed a good reliability across the duration of two weeks with the intraclass correlation coefficient of all subscales ranging from 0.925 to 0.984. Cronbach's alpha values of the Malay version MHQ ranged from 0.82 to 0.97, indicating a good internal consistency. Spearman's correlation factor of the MHQ in comparison with DASH showed a fair to moderately strong correlation with the values ranging from 0.513 to 0.757. Conclusions: The Malay version of MHQ was successfully translated and culturally-adapted with excellent reliability (reproducibility and internal consistency) and good construct validity.
    MeSH terms: Cross-Sectional Studies; Disability Evaluation*; Female; Hand Injuries/physiopathology*; Humans; Malaysia; Male; Middle Aged; Surveys and Questionnaires; Translations; Reproducibility of Results
  4. Lim LL, Lau ESH, Fu AWC, Ray S, Hung YJ, Tan ATB, et al.
    JAMA Netw Open, 2021 04 01;4(4):e217557.
    PMID: 33929522 DOI: 10.1001/jamanetworkopen.2021.7557
    Importance: Many health care systems lack the efficiency, preparedness, or resources needed to address the increasing number of patients with type 2 diabetes, especially in low- and middle-income countries.

    Objective: To examine the effects of a quality improvement intervention comprising information and communications technology and contact with nonphysician personnel on the care and cardiometabolic risk factors of patients with type 2 diabetes in 8 Asia-Pacific countries.

    Design, Setting, and Participants: This 12-month multinational open-label randomized clinical trial was conducted from June 28, 2012, to April 28, 2016, at 50 primary care or hospital-based diabetes centers in 8 Asia-Pacific countries (India, Indonesia, Malaysia, the Philippines, Singapore, Taiwan, Thailand, and Vietnam). Six countries were low and middle income, and 2 countries were high income. The study was conducted in 2 phases; phase 1 enrolled 7537 participants, and phase 2 enrolled 13 297 participants. Participants in both phases were randomized on a 1:1 ratio to intervention or control groups. Data were analyzed by intention to treat and per protocol from July 3, 2019, to July 21, 2020.

    Interventions: In both phases, the intervention group received 3 care components: a nurse-led Joint Asia Diabetes Evaluation (JADE) technology-guided structured evaluation, automated personalized reports to encourage patient empowerment, and 2 or more telephone or face-to-face contacts by nurses to increase patient engagement. In phase 1, the control group received the JADE technology-guided structured evaluation and automated personalized reports. In phase 2, the control group received the JADE technology-guided structured evaluation only.

    Main Outcomes and Measures: The primary outcome was the incidence of a composite of diabetes-associated end points, including cardiovascular disease, chronic kidney disease, visual impairment or eye surgery, lower extremity amputation or foot ulcers requiring hospitalization, all-site cancers, and death. The secondary outcomes were the attainment of 2 or more primary diabetes-associated targets (glycated hemoglobin A1c <7.0%, blood pressure <130/80 mm Hg, and low-density lipoprotein cholesterol <100 mg/dL) and/or 2 or more key performance indices (reduction in glycated hemoglobin A1c≥0.5%, reduction in systolic blood pressure ≥5 mm Hg, reduction in low-density lipoprotein cholesterol ≥19 mg/dL, and reduction in body weight ≥3.0%).

    Results: A total of 20 834 patients with type 2 diabetes were randomized in phases 1 and 2. In phase 1, 7537 participants (mean [SD] age, 60.0 [11.3] years; 3914 men [51.9%]; 4855 patients [64.4%] from low- and middle-income countries) were randomized, with 3732 patients allocated to the intervention group and 3805 patients allocated to the control group. In phase 2, 13 297 participants (mean [SD] age, 54.0 [11.1] years; 7754 men [58.3%]; 13 297 patients [100%] from low- and middle-income countries) were randomized, with 6645 patients allocated to the intervention group and 6652 patients allocated to the control group. In phase 1, compared with the control group, the intervention group had a similar risk of experiencing any of the primary outcomes (odds ratio [OR], 0.94; 95% CI, 0.74-1.21) but had an increased likelihood of attaining 2 or more primary targets (OR, 1.34; 95% CI, 1.21-1.49) and 2 or more key performance indices (OR, 1.18; 95% CI, 1.04-1.34). In phase 2, the intervention group also had a similar risk of experiencing any of the primary outcomes (OR, 1.02; 95% CI, 0.83-1.25) and had a greater likelihood of attaining 2 or more primary targets (OR, 1.25; 95% CI, 1.14-1.37) and 2 or more key performance indices (OR, 1.50; 95% CI, 1.33-1.68) compared with the control group. For attainment of 2 or more primary targets, larger effects were observed among patients in low- and middle-income countries (OR, 1.50; 95% CI, 1.29-1.74) compared with high-income countries (OR, 1.20; 95% CI, 1.03-1.39) (P = .04).

    Conclusions and Relevance: In this 12-month clinical trial, the use of information and communications technology and nurses to empower and engage patients did not change the number of clinical events but did reduce cardiometabolic risk factors among patients with type 2 diabetes, especially those in low- and middle-income countries in the Asia-Pacific region.

    Trial Registration: ClinicalTrials.gov Identifier: NCT01631084.

    MeSH terms: Aged; Amputation/statistics & numerical data; Asia, Southeastern; Blood Pressure; Cardiovascular Diseases/epidemiology; Developing Countries; Diabetes Mellitus, Type 2/metabolism; Diabetes Mellitus, Type 2/therapy*; Diabetic Nephropathies/epidemiology; Diabetic Retinopathy/epidemiology; Female; Hemoglobin A, Glycosylated/metabolism; Humans; India; Cholesterol, LDL/metabolism; Male; Middle Aged; Mortality; Neoplasms/epidemiology; Patient Participation; Taiwan; Technology*; Diabetic Foot/epidemiology; Risk Assessment; Evidence-Based Medicine; Disease Management; Decision Support Systems, Clinical*; Renal Insufficiency, Chronic/epidemiology; Quality Improvement
  5. Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, et al.
    Plant Cell Rep, 2021 Jul;40(7):1141-1154.
    PMID: 33929599 DOI: 10.1007/s00299-021-02698-1
    KEY MESSAGE: Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
    MeSH terms: Abscisic Acid/metabolism; Abscisic Acid/pharmacology; Plant Proteins/genetics; Seeds/genetics*; Stress, Physiological/genetics; Gene Expression Regulation, Plant*; Plant Leaves/genetics*; Gene Expression Profiling; Arecaceae/drug effects; Arecaceae/genetics*; Arecaceae/metabolism; Plant Somatic Embryogenesis Techniques/methods*
  6. Nguyen VL, Iatta R, Manoj RRS, Colella V, Bezerra-Santos MA, Mendoza-Roldan JA, et al.
    Acta Trop, 2021 Aug;220:105935.
    PMID: 33930300 DOI: 10.1016/j.actatropica.2021.105935
    Trypanosoma evansi, the causative agent of surra, is a hemoflagellate protozoan mechanically transmitted by hematophagous flies, mainly in tropical and subtropical regions. This protozoan affects several mammalian hosts, including dogs, which are highly susceptible to the infection. To investigate the occurrence of T. evansi in dogs, a total of 672 DNA samples from India (n = 228), Indonesia (n = 57), Malaysia (n = 45), the Philippines (n = 103), Thailand (n = 120), and Vietnam (n = 119) were screened by using species-specific conventional PCR. Of the tested dogs, 10 (1.5%) scored positive to T. evansi. In particular, positive samples were detected in canine blood samples collected from India (n = 4; 1.8%), Indonesia (n = 4; 7%), and Malaysia (n = 2; 4.4%). All tested samples from the Philippines, Thailand and Vietnam were negative. Nucleotide sequence analysis revealed a high variation (i.e. from 0.4% to 6.2%) among the RoTat 1.2 variant surface glycoprotein (vsg) gene. Although the number of sequences included in this analysis is relatively small, this nucleotide variation may indicate the divergence of T. evansi RoTat 1.2 vsg gene among different strains. The high incidence of T. evansi previously reported in cattle and buffaloes in India and Southeast Asia suggests that these animals are the main source of infection to dogs.
    MeSH terms: Animals; Asia, Southeastern/epidemiology; Dog Diseases; Dogs; India/epidemiology; Membrane Glycoproteins; Trypanosoma/genetics*; Trypanosomiasis/veterinary*; Polymerase Chain Reaction/veterinary
  7. Yusuf A, Sarfati D, Booth CM, Pramesh CS, Lombe D, Aggarwal A, et al.
    Lancet Oncol, 2021 06;22(6):749-751.
    PMID: 33930324 DOI: 10.1016/S1470-2045(21)00244-8
    MeSH terms: Female; Humans; Male; Neoplasms/complications; Neoplasms/epidemiology*; Neoplasms/prevention & control; Neoplasms/virology; Global Health
  8. Azmi AAB, Chew KW, Chia WY, Mubashir M, Sankaran R, Lam MK, et al.
    Bioresour Technol, 2021 Aug;333:125197.
    PMID: 33930672 DOI: 10.1016/j.biortech.2021.125197
    The work aimed to study the potential in producing a system with high microalgal protein recovery and separation by utilizing a one-step or integrated downstream process. This in turn enables green biorefinery of protein, contributing to circular bioeconomy whereby less energy, labor, and cost are required for the process. By utilizing electric three phase partitioning flotation system, high protein recovery yield, R of 99.42 ± 0.52% and high separation efficiency, E of 52.72 ± 0.40% system was developed. Scaling up also showed high protein recovery yield with R value of 89.13 ± 1.56%. Total processing duration (extraction, separation, and purification) was also significantly reduced to 10 min. This system showed remarkable potential in reducing processing time, alternatively cost of production, benefiting microalgal downstream processing. Concisely, through this system, microalgal bioprocessing will no longer be complex allowing a wide array of potentials for further studies in this field.
    MeSH terms: Electricity; Biomass; Chlorella vulgaris*; Microalgae*
  9. Fang Wong S, Mei Khor S
    Food Chem, 2021 Apr 20;357:129801.
    PMID: 33930694 DOI: 10.1016/j.foodchem.2021.129801
    Foodborne amides, specifically acrylamide, are vitally important for food safety and security, as they are the most common food toxicants and suspected human carcinogens. A facile and novel differential-based colorimetric nanobiosensor array composed of three surface-bioengineered gold nanoparticles (AuNPs) was developed for the rapid detection, differentiation, and quantification of acrylamide and six analogues. Diverse cross-reactive receptors demonstrated differential binding affinities toward target analytes, resulting in distinctive AuNP aggregation behaviors and distinguishable response patterns. The sensor array, integrated with principal component analysis and hierarchical cluster analysis, accurately discriminated foodborne amides based on their amine subgroups, International Agency for Research on Cancer (IARC) carcinogen classifications, and food additive types, even at ultra-low concentrations (500 pM). Additionally, the sensor array successfully differentiated non-targeted analytes by sweetener and food ingredients types with 100% correct classification. Partial least squares regression outcomes exhibited high correlation coefficients (R2 > 0.95). Thus, the sensor array has practical potential for food safety monitoring in the food and beverage industries.
  10. Lim CC, Chan SK, Lim YY, Ishikawa Y, Choong YS, Nagaoka Y, et al.
    Mol Immunol, 2021 07;135:191-203.
    PMID: 33930714 DOI: 10.1016/j.molimm.2021.04.016
    The murine double minute 2 (MDM2) protein is a major negative regulator of the tumour suppressor protein p53. Under normal conditions, MDM2 constantly binds to p53 transactivation domain and/or ubiquinates p53 via its role as E3 ubiquitin ligase to promote p53 degradation as well as nuclear export to maintain p53 levels in cells. Meanwhile, amplification of MDM2 and appearance of MDM2 spliced variants occur in many tumours and normal tissues making it a prognostic indicator for human cancers. The mutation or deletion of p53 protein in half of human cancers inactivates its tumour suppressor activity. However, cancers with wild type p53 have its function effectively inhibited through direct interaction with MDM2 oncoprotein. Here, we described the construction of a MDM2 spliced variant (rMDM215kDa) consisting of SWIB/MDM2 domain and its central region for antibody generation. Biopanning with a human naïve scFv library generated four scFv clones specific to rMDM215kDa. Additionally, the selected scFv clones were able to bind to the recombinant full length MDM2 (rMDM2-FL). Computational prediction showed that the selected scFv clones potentially bind to exon 7-8 of MDM2 while leaving the MDM2/SWIB domain free for p53 interaction. The developed antibodies exhibit good specificity can be further investigated for downstream biomedical and research applications.
    MeSH terms: Antibodies, Monoclonal/immunology*; Humans; Tumor Suppressor Protein p53/genetics; Tumor Suppressor Protein p53/metabolism; Protein Isoforms/immunology; Proto-Oncogene Proteins c-mdm2/genetics*; Proto-Oncogene Proteins c-mdm2/immunology*; Proto-Oncogene Proteins c-mdm2/metabolism; Ubiquitination; Single-Chain Antibodies/immunology*; Molecular Docking Simulation; Protein Domains/genetics
  11. Kim YE
    BMJ Open, 2021 04 14;11(4):e045070.
    PMID: 33853801 DOI: 10.1136/bmjopen-2020-045070
    OBJECTIVES: Childhood vaccination coverage in Nagaland has lagged almost all states in India for more than two decades. This study aims to find drivers and barriers of childhood vaccination in Nagaland from the perspective of demand, supply and local health governance.

    DESIGN: A cross-sectional study was designed using a survey conducted by the Directorate of Health and Family in 2015.

    SETTING: Households, community-based health centres and health committees were surveyed.

    PARTICIPANTS: 285 children aged under 2 years with vaccination cards and data on households, health centres and health committees were included.

    OUTCOMES: Variables indicating whether a child received each of bacillus calmette-guérin (BCG), diphtheria-tetanus-pertussis (DTP3), oral polio (OPV3) and measles vaccination and all of them were outcome variables. Associated factors were identified using multilevel logistic regressions.

    RESULTS: Antenatal care at least three times was significantly associated with BCG, DTP3, OPV3 and full vaccination with adjusted ORs ranging from 2.4 (95% CI 1.1 to 5.1) to 3.3 (1.1 to 9.9). The availability of bus to health centre was slightly significant for BCG and OPV3 with the adjusted ORs of 2.0 (0.9 to 4.5) and 2.1 (0.9 to 4.8), respectively. Health committees' budget provision to health centres was significant for OPV3 and full vaccination with the respective adjusted ORs of 15.7 (1.0 to 234.1) and 15.9 (1.2 to 214.7), the wide 95% CIs of which were driven by a small sample size. Health committees' review of expenditure of health centres was significant for measles and full vaccination with the adjusted ORs of 4.0 (1.4 to 11.4) and 5.2 (1.4 to 19.4), respectively.

    CONCLUSION: This study suggests that enhancing the utilisation of antenatal care and providing reliable transportation between villages and health centres are required to improve childhood vaccination coverage. Also, the significant association of budget administration of health committees suggests that supporting local health committees for effective financial management is important.

    MeSH terms: Child; Child, Preschool; Cross-Sectional Studies; Female; Humans; India/epidemiology; Infant; Pregnancy; Vaccination; Immunization Programs*
  12. Mhd Haniffa MAC, Munawar K, Ching YC, Illias HA, Chuah CH
    Chem Asian J, 2021 Jun 01;16(11):1281-1297.
    PMID: 33871151 DOI: 10.1002/asia.202100226
    New and emerging demand for polyurethane (PU) continues to rise over the years. The harmful isocyanate binding agents and their integrated PU products are at the height of environmental concerns, in particular PU (macro and micro) pollution and their degradation problems. Non-isocyanate poly(hydroxy urethane)s (NIPUs) are sustainable and green alternatives to conventional PUs. Since the introduction of NIPU in 1957, the market value of NIPU and its hybridized materials has increased exponentially in 2019 and is expected to continue to rise in the coming years. The secondary hydroxyl groups of these NIPU's urethane moiety have revolutionized them by allowing for adequate pre/post functionalization. This minireview highlights different strategies and advances in pre/post-functionalization used in biobased NIPU. We have performed a comprehensive evaluation of the development of new ideas in this field to achieve more efficient synthetic biobased hybridized NIPU processes through selective and kinetic understanding.
    MeSH terms: Amines/chemistry; Carbonates/chemistry; Kinetics; Lignin/chemistry; Plant Oils/chemistry; Polyamines/chemistry; Polyurethanes/chemical synthesis*; Polyurethanes/chemistry; Nanoparticles/chemistry
  13. Akhtar A, Hassali MAA, Zainal H, Ali I, Iqbal MS, Khan AH
    Ther Adv Respir Dis, 2021 4 30;15:1753466620971141.
    PMID: 33910420 DOI: 10.1177/1753466620971141
    BACKGROUND: Geriatric individuals are more susceptible to different infections, especially respiratory-tract infections (RTIs) due to their compromised immune system. Hence, the objectives of the present study were to evaluate the prevalence, medication regimen complexity and factors associated with the treatment outcomes of different RTIs among geriatrics.

    METHODS: A retrospective cross-sectional study (5 years) was conducted at the respiratory department, Hospital Pulau Pinang. Patients aged ⩾65 years with confirmed diagnosis of RTI were included in the study.

    RESULTS: A total of 474 patients were included, and the most prevalent RTIs were community-acquired pneumonia (65.6%) followed by chronic obstructive pulmonary disease (20.7%), bronchitis (8.2%) and hospital-acquired pneumonia (5.5%). Amoxicillin/clavulanate (69.8%), ampicillin/sulbactam (9.1%) and cefuroxime (6.5%) are the most common antibiotics prescribed to treat RTIs among geriatrics. Smoking, alcohol consumption, polypharmacy and presence of other co-morbidities are statistically significant factors associated with treatment outcomes of RTIs among geriatrics.

    CONCLUSION: Prevalence of community-acquired pneumonia (65.6%) among older patients aged 65 years and older higher than other RTIs. Smoking, alcohol use, presence of polypharmacy and other co-morbidities are important factors associated with the treatment outcomes of RTIs.The reviews of this paper are available via the supplemental material section.

    MeSH terms: Aged; Cross-Sectional Studies; Humans; Retrospective Studies; Prevalence; Treatment Outcome
  14. Ahmed J, Wong LP, Chua YP, Channa N, Memon UU, Garn JV, et al.
    PMID: 33910486 DOI: 10.1080/10934529.2021.1915653
    The purpose of this study was to characterize the concentrations of lead (Pb), cadmium (Cd), manganese (Mn), and Fe (Fe) in drinking water sources in primary schools in Sindh Province, Pakistan and to quantify potential health risks among those school children. We conducted a representative, cross-sectional study among 425 primary schools in Sindh province of Pakistan. We used risk assessment models to estimate the metal index, pollution index, lifetime cancer risk, and hazard quotient index. Across the 425 sampled schools, the levels of heavy metals in the drinking water often exceeded the WHO permissible limits (67% of schools exceeded Pb limit, 17% for Cd, 15% for Fe). The average incremental lifetime cancer risk (ILCR) for Pb exceeded tolerable limits in all of the districts under study. The findings, particularly for Pb, are of concern, as Pb may negatively influence children's growth, development, school performance, and long-term health.
  15. Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, et al.
    Genome Biol, 2021 04 29;22(1):120.
    PMID: 33910595 DOI: 10.1186/s13059-021-02336-9
    BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

    RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.

    CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

    MeSH terms: Animals; Repetitive Sequences, Nucleic Acid*; Vertebrates/genetics*; Evolution, Molecular; Computational Biology/methods; Computational Biology/standards; Gene Duplication*; Genome, Mitochondrial*; High-Throughput Nucleotide Sequencing
  16. Wong LC, Leh CP, Goh CF
    Carbohydr Polym, 2021 Jul 15;264:118036.
    PMID: 33910744 DOI: 10.1016/j.carbpol.2021.118036
    Hydrogels are an attractive system for a myriad of applications. While most hydrogels are usually formed from synthetic materials, lignocellulosic biomass appears as a sustainable alternative for hydrogel development. The valorization of biomass, especially the non-woody biomass to meet the growing demand of the substitution of synthetics and to leverage its benefits for cellulose hydrogel fabrication is attractive. This review aims to present an overview of advances in hydrogel development from non-woody biomass, especially using native cellulose. The review will cover the overall process from cellulose depolymerization, dissolution to crosslinking reaction and the related mechanisms where known. Hydrogel design is heavily affected by the cellulose solubility, crosslinking method and the related processing conditions apart from biomass type and cellulose purity. Hence, the important parameters for rational designs of hydrogels with desired properties, particularly porosity, transparency and swelling characteristics will be discussed. Current challenges and future perspectives will also be highlighted.
    MeSH terms: Cellulose/chemistry*; Cross-Linking Reagents/chemistry; Humans; Lignin/chemistry; Plants/chemistry; Polysaccharides/chemistry; Solubility; Solvents/chemistry; Wood/chemistry; Porosity; Biomass; Hydrogels/chemistry*
  17. Lee JS, Chieng CH, Martin M, Toh TH
    BMJ Case Rep, 2021 Apr 28;14(4).
    PMID: 33910804 DOI: 10.1136/bcr-2020-241482
    We report a term newborn who presented on day 3 of life with unilateral, tender scrotal swelling with skin discolouration, which was subsequently diagnosed as haemophilia A at about 6 months of age. He received intramuscular vitamin K and hepatitis B vaccine at birth uneventfully. The scrotal swelling was treated as an infected hydrocoele, considering the absence of a family history of bleeding disorder and other risks of bleeding tendency, as well as the ultrasonographic features. He also had congenital pneumonia requiring venepuncture, non-invasive oxygen supplementation and intravenous antibiotics, without any complication. The swelling slowly improved over 2 months. He later developed post-trial vaccine injection haematoma at 4 months of age, and multiple non-traumatic bruises when he was 6 months old, leading to the diagnosis. This case demonstrates an uncommon, but a possible, early manifestation of haemophilia A at birth with a unilateral scrotal haematoma.
    MeSH terms: Genital Diseases, Male*; Hematoma/etiology; Humans; Infant; Infant, Newborn; Male
  18. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.
    Nature, 2021 Apr;592(7856):737-746.
    PMID: 33911273 DOI: 10.1038/s41586-021-03451-0
    High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
    MeSH terms: Animals; Birds; Haplotypes; Sex Chromosomes/genetics; Vertebrates/genetics*; Gene Library; Sequence Alignment; Genome*; Sequence Analysis, DNA; Genomics/methods*; Genome, Mitochondrial; Molecular Sequence Annotation; High-Throughput Nucleotide Sequencing; Genome Size
  19. Yusof EM, Abdullah SA, Mohamed NH
    J Conserv Dent, 2021 02 10;23(5):473-478.
    PMID: 33911356 DOI: 10.4103/JCD.JCD_509_20
    Objective: The objective of this study was to compare the effects of light and laser activation of in-office tooth bleaching systems on enamel microhardness and surface roughness.

    Materials and Methods: Twenty-five enamel slabs were divided into three treatment groups: light-activated bleaching, laser-activated bleaching, and control. The baseline data were recorded for enamel microhardness (Vickers microhardness [VMH]) and surface roughness (Roughness average, Ra). The specimens were cured for 10 min upon hydrogen peroxide application for the light-activated bleaching group and activated with a laser source, 8 cycles, 10 s per cycle for the laser-activated group. The changes in VMH and Ra at days 1, 7, and 28 were evaluated. Kruskal-Wallis, Friedman, Wilcoxon, and Mann-Whitney tests were used to analyze both VMH and Ra between the treatment groups at different time intervals.

    Results: There were a significant reduction in VMH values and significant differences between days 1, 7, and 28 against the baseline in the light-activated bleaching group (P = 0.001). The Ra values revealed significant differences in both light- (P = 0.001) and laser-activated (P = 0.033) groups.

    Conclusion: Light activation of a bleaching agent caused a reduction in enamel microhardness and an increase in surface roughness when compared to laser activation.

    MeSH terms: Dental Enamel; Hardness; Hydrogen Peroxide; Hypochlorous Acid; Lasers; Tooth Bleaching; Bleaching Agents
  20. Ismail IH, Al-Bayaty FH, Yusof EM, Gulam Khan HBS, Hamka FA, Azmi NA
    J Conserv Dent, 2021 02 10;23(5):489-496.
    PMID: 33911359 DOI: 10.4103/JCD.JCD_528_20
    Introduction: Enterococcus faecalis can be found in failed endodontic treatment (FET) even after performing primary endodontic treatment (PET). Calcium hydroxide (Ca(OH)2) cannot fully eliminate this microorganism during PET. Brazilian green propolis (bee glue) was found to be more effective against E. faecalis when compared to Ca(OH)2. A much less studied Malaysian geopropolis (MP) as well as Aloe vera (AV) is antibacterial but is unknown against E. faecalis.

    Objective: The objective of this study is to determine the antimicrobial effects of MP, AV, and MP + AV in comparison with Ca(OH)2 against E. faecalis, as an intracanal medicament.

    Materials and Methods: Antimicrobial activity of MP, AV, MP + AV, Ca(OH)2, and dimethyl sulfoxide was tested against E. faecalis using antimicrobial sensitivity testing, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC). The results were analyzed by Kruskal-Wallis test with Mann-Whitney post hoc test and repeated measures analysis of variance with Bonferroni post hoc test (P < 0.05).

    Results: For agar well-diffusion method, MP + AV gave maximum inhibition zone diameter (mean: 8.11 ± 0.015 mm), MP (mean: 6.21 ± 0.046 mm, Ca(OH)2 (mean: 5.5 ± 0.006), and AV (mean: 5.05 ± 0.012) with P < 0.05. MIC for MP + AV was 2 mg/ml, MP at 8 mg/ml, Ca(OH)2 at 8 mg/ml, and AV at 16 mg/ml. The MBC for MP + AV is at 4 mg/ml, MP at 16 mg/ml, Ca(OH)2 at 16 mg/ml, and AV at 32 mg/ml.

    Conclusion: The combination of MP and AV consistently showed better antimicrobial activity compared to MP and AV alone against E. faecalis. The findings suggest that MP and AV used in combination may be an ideal intracanal medicament in FET and PET.

    MeSH terms: Agar; Aloe; Analysis of Variance; Anti-Infective Agents; Anti-Bacterial Agents; Brazil; Calcium Hydroxide; Dimethyl Sulfoxide; Microbial Sensitivity Tests; Propolis; Enterococcus faecalis
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