Displaying publications 1 - 20 of 364 in total

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  1. Mustafa MG, Rajaee AH, Hamli H, A Rahim KA
    PeerJ, 2021;9:e12183.
    PMID: 34721960 DOI: 10.7717/peerj.12183
    The length-weight relationships (LWRs), condition factor (Kn), growth, mortality and exploitation status of three polynemid fishes, i.e., Filimanus xanthonema (Valenciennes, 1831), Polynemus melanochir (Valenciennes, 1831) and Polynemus paradiseus (Linnaeus, 1758) from Batang Lassa River estuary were estimated. Fish samples were caught during April 2019 to September 2020 using the ESBN (locally called Gnian) having 1.25 to 4.00 cm mesh size. The total length (TL) and body weight of each individual fish was measured to the nearest 0.1 cm and 0.01 g respectively. The growth coefficients (b) for F. xanthonema, P. melanochir and P. paradiseus, were 2.880, 2.717 and 2.724 with the R 2 values 0.956, 0.972 and 0.936 respectively. Estimated growth coefficients indicated a negative allometric growth pattern for all three threadfin fishes. To date, information regarding length-weight relationships for F. xanthonema and P. melanochir is insufficient whereas the information is available for P. paradiseus. About 40-48% of fishes exhibited flat or thin body shape (Kn < 1), 48-50% were rounded or fat (Kn > 1) and only 1-3% of fishes showed proportional body shape (Kn = 1). The growth parameters L∞ , K and ϕ' were estimated at 15.75 cm, 0.95 yr-1 and 2.37 for F. xanthonema; 27.61 cm 0.87 yr-1 and 2.82 for P. melanochir; and 27.30 cm, 0.58 yr-1 and 2.64 for P. paradiseus; respectively. The estimated natural mortality (M) included 2.10, 1.69 and 1.30 yr-1; the fishing mortality (F) 0.57, 0.67 and 0.60 yr-1; and exploitation ratio (E) 0.21, 0.28 and 0.31 for F. xanthonema, P. melanochir and P. paradiseus respectively. The study concluded that the stocks are still under exploitation (E < 0.5) condition. However, the studied Batang Lassa estuary could be a potential nursery ground considering the minimum lengths of 5.0, 3.8 and 4.0 cm for F. xanthonema, P. melanochir and P. paradiseus respectively. Therefore, management initiatives are needed to escape juvenile catches.
  2. Hoque KE, Hoque KF, A/P Thanabalan R
    PeerJ, 2018;6:e4563.
    PMID: 29736328 DOI: 10.7717/peerj.4563
    Background: Building healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents' educations and incomes on building students' healthy eating habits.

    Methods: A survey on building students' eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students' gender, parents' educations and incomes.

    Results: The study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students' gender and parents' educations are not found significantly related to students' knowledge, attitude and practices towards healthy eating habits, parents' incomes have significant influence on promoting the healthy eating habit.

    Discussion: Findings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits.

  3. Dewi R, Yusoff NA, Abdul Razak SR, Abd Hamid Z
    PeerJ, 2023;11:e15608.
    PMID: 37456886 DOI: 10.7717/peerj.15608
    BACKGROUND: HSPCs are targets for benzene-induced hematotoxicity and leukemogenesis. However, benzene toxicity targeting microRNAs (miRNAs) and transcription factors (TF) that are involve in regulating self-renewing and differentiation of HSPCs comprising of different hematopoietic lineages remains poorly understood. In this study, the effect of a benzene metabolite, 1,4-benzoquinone (1,4-BQ) exposure, in HSPCs focusing on the self-renewing (miRNAs: miR-196b and miR-29a; TF: HoxB4, Bmi-1) and differentiation (miRNAs: miR-181a, TF: GATA3) pathways were investigated.

    METHODS: Freshly isolated mouse BM cells were initially exposed to 1,4-BQ at 1.25 to 5 µM for 24 h, followed by miRNAs and TF studies in BM cells. Then, the miRNAs expression was further evaluated in HSPCs of different lineages comprised of myeloid, erythroid and pre-B lymphoid progenitors following 7-14 days of colony forming unit (CFU) assay.

    RESULTS: Exposure to 1,4-BQ in BM cells significantly (p 

  4. Lim YK, Keng FS, Phang SM, Sturges WT, Malin G, Abd Rahman N
    PeerJ, 2019;7:e6758.
    PMID: 31041152 DOI: 10.7717/peerj.6758
    Marine algae have been reported as important sources of biogenic volatile halocarbons that are emitted into the atmosphere. These compounds are linked to destruction of the ozone layer, thus contributing to climate change. There may be mutual interactions between the halocarbon emission and the environment. In this study, the effect of irradiance on the emission of halocarbons from selected microalgae was investigated. Using controlled laboratory experiments, three tropical marine microalgae cultures, Synechococcus sp. UMACC 371 (cyanophyte), Parachlorella sp. UMACC 245 (chlorophyte) and Amphora sp. UMACC 370 (diatom) were exposed to irradiance of 0, 40 and 120 µmol photons m-2s-1. Stress in the microalgal cultures was indicated by the photosynthetic performance (Fv/Fm, maximum quantum yield). An increase in halocarbon emissions was observed at 120 µmol photons m-2s-1, together with a decrease in Fv/Fm. This was most evident in the release of CH3I by Amphora sp. Synechococcus sp. was observed to be the most affected by irradiance as shown by the increase in emissions of most halocarbons except for CHBr3 and CHBr2Cl. High positive correlation between Fv/Fm and halocarbon emission rates was observed in Synechococcus sp. for CH2Br2. No clear trends in correlation could be observed for the other halocarbons in the other two microalgal species. This suggests that other mechanisms like mitochondria respiration may contribute to halocarbon production, in addition to photosynthetic performance.
  5. Mithoo-Singh PK, Keng FS, Phang SM, Leedham Elvidge EC, Sturges WT, Malin G, et al.
    PeerJ, 2017;5:e2918.
    PMID: 28149690 DOI: 10.7717/peerj.2918
    Five tropical seaweeds, Kappaphycus alvarezii (Doty) Doty ex P.C. Silva, Padina australis Hauck, Sargassum binderi Sonder ex J. Agardh (syn. S. aquifolium (Turner) C. Agardh), Sargassum siliquosum J. Agardh and Turbinaria conoides (J. Agardh) Kützing, were incubated in seawater of pH 8.0, 7.8 (ambient), 7.6, 7.4 and 7.2, to study the effects of changing seawater pH on halocarbon emissions. Eight halocarbon species known to be emitted by seaweeds were investigated: bromoform (CHBr3), dibro-momethane (CH2Br2), iodomethane (CH3I), diiodomethane (CH2I2), bromoiodomethane (CH2BrI), bromochlorometh-ane (CH2BrCl), bromodichloromethane (CHBrCl2), and dibro-mochloromethane (CHBr2Cl). These very short-lived halocarbon gases are believed to contribute to stratospheric halogen concentrations if released in the tropics. It was observed that the seaweeds emit all eight halocarbons assayed, with the exception of K. alvarezii and S. binderi for CH2I2 and CH3I respectively, which were not measurable at the achievable limit of detection. The effect of pH on halocarbon emission by the seaweeds was shown to be species-specific and compound specific. The highest percentage changes in emissions for the halocarbons of interest were observed at the lower pH levels of 7.2 and 7.4 especially in Padina australis and Sargassum spp., showing that lower seawater pH causes elevated emissions of some halocarbon compounds. In general the seaweed least affected by pH change in terms of types of halocarbon emission, was P. australis. The commercially farmed seaweed K. alvarezii was very sensitive to pH change as shown by the high increases in most of the compounds in all pH levels relative to ambient. In terms of percentage decrease in maximum quantum yield of photosynthesis (Fv∕Fm) prior to and after incubation, there were no significant correlations with the various pH levels tested for all seaweeds. The correlation between percentage decrease in the maximum quantum yield of photosynthesis (Fv∕Fm) and halocarbon emission rates, was significant only for CH2BrCl emission by P. australis (r = 0.47; p ≤ 0.04), implying that photosynthesis may not be closely linked to halocarbon emissions by the seaweeds studied. Bromine was the largest contributor to the total mass of halogen emitted for all the seaweeds at all pH. The highest total amount of bromine emitted by K. alvarezii (an average of 98% of total mass of halogens) and the increase in the total amount of chlorine with decreasing seawater pH fuels concern for the expanding seaweed farming activities in the ASEAN region.
  6. El Tantawi M, Sabbagh HJ, Alkhateeb NA, Quritum M, Abourdan J, Qureshi N, et al.
    PeerJ, 2022;10:e13555.
    PMID: 35860046 DOI: 10.7717/peerj.13555
    BACKGROUND: Oral manifestations and lesions could adversely impact the quality of people's lives. COVID-19 infection may interact with smoking and the impact on oral manifestations is yet to be discovered.

    OBJECTIVES: The aim of this study was to assess the self-reported presence of oral lesions by COVID-19-infected young adults and the differences in the association between oral lesions and COVID-19 infection in smokers and non-smokers.

    METHODS: This cross-sectional multi-country study recruited 18-to-23-year-old adults. A validated questionnaire was used to collect data on COVID-19-infection status, smoking and the presence of oral lesions (dry mouth, change in taste, and others) using an online platform. Multi-level logistic regression was used to assess the associations between the oral lesions and COVID-19 infection; the modifying effect of smoking on the associations.

    RESULTS: Data was available from 5,342 respondents from 43 countries. Of these, 8.1% reported COVID-19-infection, 42.7% had oral manifestations and 12.3% were smokers. A significantly greater percentage of participants with COVID-19-infection reported dry mouth and change in taste than non-infected participants. Dry mouth (AOR=, 9=xxx) and changed taste (AOR=, 9=xxx) were associated with COVID-19- infection. The association between COVID-19-infection and dry mouth was stronger among smokers than non-smokers (AOR = 1.26 and 1.03, p = 0.09) while the association with change in taste was stronger among non-smokers (AOR = 1.22 and 1.13, p = 0.86).

    CONCLUSION: Dry mouth and changed taste may be used as an indicator for COVID-19 infection in low COVID-19-testing environments. Smoking may modify the association between some oral lesions and COVID-19-infection.

  7. Ramli NSF, Mat Junit S, Leong NK, Razali N, Jayapalan JJ, Abdul Aziz A
    PeerJ, 2017;5:e3365.
    PMID: 28584708 DOI: 10.7717/peerj.3365
    BACKGROUND: Synthesis of thyroid hormones and regulation of their metabolism involve free radicals that may affect redox balance in the body. Thyroid disorders causing variations in the levels of thyroid hormones may alter cellular oxidative stress. The aim of this study was to measure the antioxidant activities and biomarkers of oxidative stress in serum and red blood cells (RBC) of patients with benign and malignant thyroid disorders and to investigate if changes in the antioxidant activities in these patients were linked to alterations in genes encoding the antioxidant enzymes.

    METHODS: Forty-one patients with thyroid disorders from University of Malaya Medical Centre were recruited. They were categorised into four groups: multinodular goitre (MNG) (n = 18), follicular thyroid adenoma (FTA) (n = 7), papillary thyroid cancer (PTC) (n = 10), and follicular thyroid cancer (FTC) (n = 6). Serum and RBC of patients were analysed for antioxidant activities, antioxidant enzymes, and biomarkers of oxidative stress. Alterations in genes encoding the antioxidant enzymes were analysed using whole exome sequencing and PCR-DNA sequencing.

    RESULTS: Patients with thyroid disorders had significantly higher serum superoxide dismutase (SOD) and catalase (CAT) activities compared to control, but had lower activities in RBC. There were no significant changes in serum glutathione peroxidase (GPx) activity. Meanwhile, GPx activity in RBC was reduced in PTC and FTC, compared to control and the respective benign groups. Antioxidant activities in serum were decreased in the thyroid disorder groups when compared to the control group. The levels of malondialdehyde (MDA) were elevated in the serum of FTA group when compared to controls, while in the RBC, only the MNG and PTC groups showed higher MDA equivalents than control. Serum reactive oxygen species (ROS) levels in PTC group of both serum and RBC were significantly higher than control group. Whole exome sequencing has resulted in identification of 49 single nucleotide polymorphisms (SNPs) in MNG and PTC patients and their genotypic and allelic frequencies were calculated. Analyses of the relationship between serum enzyme activities and the total SNPs identified in both groups revealed no correlation.

    DISCUSSION: Different forms of thyroid disorders influence the levels of antioxidant status in the serum and RBC of these patients, implying varying capability of preventing oxidative stress. A more comprehensive study with a larger target population should be done in order to further evaluate the relationships between antioxidant enzymes gene polymorphisms and thyroid disorders, as well as strengthening the minor evidences provided in literatures.

  8. Adenan DM, Jaafar Z, Jayapalan JJ, Abdul Aziz A
    PeerJ, 2020;8:e9230.
    PMID: 32477840 DOI: 10.7717/peerj.9230
    INTRODUCTION: A high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses in women of different body mass index (BMI).

    SUBJECTS AND METHODS: Eighty female adults were recruited and divided into three groups; normal weight (n = 23), overweight (n = 28) and obese (n = 29), according to their BMI. Blood samples were obtained prior to cardiopulmonary exercise testing. Plasma samples were separated by centrifugation and analysed for enzymatic antioxidant activity including catalase, glutathione peroxidase and superoxide dismutase. Non-enzymatic antioxidant activities were assessed using 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging and ferric reducing ability of plasma (FRAP) assays. To evaluate the oxidative stress status of subjects, levels of reactive oxygen species and malondialdehyde, the by-product of lipid peroxidation, were measured. Cardiopulmonary responses were analysed using cardiopulmonary exercise testing (CPET) which involved 15 various parameters such as peak oxygen consumption, metabolic equivalents and respiratory exchange ratio.

    RESULTS: The obese group had significantly lower ABTS radical scavenging and FRAP activities than the normal weight group. A higher catalase activity was observed in the obese group than the normal weight group. Spearman's correlation showed an inverse relationship between catalase and peak oxygen consumption, while partial correlation analysis showed inverse correlations between superoxide dismutase and respiratory frequency, ABTS activity and oxygen pulse, and between ABTS activity and cardiac output.

    CONCLUSION: Our results demonstrate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase activity may be a compensatory mechanism. The negative correlations found between these two parameters may indicate the potential effect of antioxidants on the cardiopulmonary system and deserve further analysis in a larger population. Nevertheless, this study provides the basis for future studies to further explore the relationships between redox status and cardiopulmonary responses. This can potentially be used to predict future risk of developing diseases associated with oxidative stress, especially pulmonary and cardiovascular diseases.

  9. Kong KW, Mat-Junit S, Aminudin N, Hassan FA, Ismail A, Abdul Aziz A
    PeerJ, 2016;4:e1628.
    PMID: 26839752 DOI: 10.7717/peerj.1628
    Barringtonia racemosa is a tropical plant with medicinal values. In this study, the ability of the water extracts of the leaf (BLE) and stem (BSE) from the shoots to protect HepG2 cells against oxidative damage was studied. Five major polyphenolic compounds consisting of gallic acid, ellagic acid, protocatechuic acid, quercetin and kaempferol were identified using HPLC-DAD and ESI-MS. Cell viability assay revealed that BLE and BSE were non-cytotoxic (cell viabilities >80%) at concentration less than 250 µg/ml and 500 µg/ml, respectively. BLE and BSE improved cellular antioxidant status measured by FRAP assay and protected HepG2 cells against H2O2-induced cytotoxicity. The extracts also inhibited lipid peroxidation in HepG2 cells as well as the production of reactive oxygen species. BLE and BSE could also suppress the activities of superoxide dismutase and catalase during oxidative stress. The shoots of B. racemosa can be an alternative bioactive ingredient in the prevention of oxidative damage.
  10. Mohd Hanafiah Z, Wan Mohtar WHM, Abd Manan TS, Bachi NA, Abu Tahrim N, Abd Hamid HH, et al.
    PeerJ, 2023;11:e14719.
    PMID: 36748091 DOI: 10.7717/peerj.14719
    The environmental fate of non-steroidal anti-inflammatory drugs (NSAIDs) in the urban water cycle is still uncertain and their status is mainly assessed based on specific water components and information on human risk assessments. This study (a) explores the environmental fate of NSAIDs (ibuprofen, IBU; naproxen, NAP; ketoprofen, KET; diazepam, DIA; and diclofenac, DIC) in the urban water cycle, including wastewater, river, and treated water via gas chromatography-mass spectrophotometry (GCMS), (b) assesses the efficiency of reducing the targeted NSAIDs in sewage treatment plant (STP) using analysis of variance (ANOVA), and (c) evaluates the ecological risk assessment of these drugs in the urban water cycle via teratogenic index (TI) and risk quotient (RQ). The primary receptor of contaminants comes from urban areas, as a high concentration of NSAIDs is detected (ranging from 5.87 × 103 to 7.18 × 104 ng/L). The percentage of NSAIDs removal in STP ranged from 25.6% to 92.3%. The NAP and KET were still detected at trace levels in treated water, indicating the persistent presence in the water cycle. The TI values for NAP and DIA (influent and effluent) were more than 1, showing a risk of a teratogenic effect. The IBU, KET, and DIC had values of less than 1, indicating the risk of lethal embryo effects. The NAP and DIA can be classified as Human Pregnancy Category C (2.1 > TI ≥ 0.76). This work proved that these drugs exist in the current urban water cycle, which could induce adverse effects on humans and the environment (RQ in high and low-risk categories). Therefore, they should be minimized, if not eliminated, from the primary sources of the pollutant (i.e., STPs). These pollutants should be considered a priority to be monitored, given focus to, and listed in the guideline due to their persistent presence in the urban water cycle.
  11. Mohd Shukri MF, Norhayati MN, Badrin S, Abdul Kadir A
    PeerJ, 2022;10:e13992.
    PMID: 36132218 DOI: 10.7717/peerj.13992
    BACKGROUND: Polycystic ovary syndrome (PCOS) is a disorder in reproductive age women and is characterized by hyperandrogenic anovulation and oligo-amenorrhea, which leads to infertility. Anovulation in PCOS is associated with low follicle-stimulating hormone levels and the arrest of antral follicle development in the final stages of maturation. L-carnitine (LC) plays a role in fatty acid metabolism, which is found to be lacking in PCOS patients. This systematic review and meta-analysis aimed to determine the effectiveness of LC supplementation for patients with PCOS.

    METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychological Information Database (PsycINFO), and the World Health Organization International Clinical Trials Registry Platform for all randomized control trials, comparing LC alone or in combination with other standard treatments for the treatment of PCOS from inception till June 2021. We independently screened titles and abstracts to identify available trials, and complete texts of the trials were checked for eligibility. Data on the methods, interventions, outcomes, and risk of bias from the included trials were independently extracted by the authors. The estimation of risk ratios and mean differences with a 95 percent confidence interval (CI) was performed using a random-effects model.

    RESULTS: Nine studies with 995 participants were included in this review. Five comparison groups were involved. In one comparison group, LC reduced the fasting plasma glucose (FPG) (mean differences (MD) -5.10, 95% CI [-6.25 to -3.95]; P = 0.00001), serum low-density lipoprotein (LDL) (MD -25.00, 95% CI [-27.93 to -22.07]; P = 0.00001), serum total cholesterol (MD -21.00, 95% CI [-24.14 to -17.86]; P = 0.00001), and serum triglyceride (TG) (MD -9.00, 95% CI [-11.46 to -6.54]; P = 0.00001) with moderate certainty of evidence. Another comparison group demonstrated that LC lowers the LDL (MD -12.00, 95% CI [-15.80 to -8.20]; P = 0.00001), serum total cholesterol (MD -24.00, 95% CI [-27.61 to -20.39]; P = 0.00001), and serum TG (MD -19.00, 95% CI [-22.79 to -15.21]; P = 0.00001) with moderate certainty of evidence.

    CONCLUSION: There was low to moderate certainty of evidence that LC improves Body Mass Index (BMI) and serum LDL, TG, and total cholesterol levels in women with PCOS.

  12. Wan KS, Sundram ER, Abdul Haddi AA, Dashuki AR, Ahad A, John R, et al.
    PeerJ, 2023;11:e14742.
    PMID: 36915663 DOI: 10.7717/peerj.14742
    BACKGROUND: Long COVID is new or ongoing symptoms at four weeks or more after the start of acute COVID-19. However, the prevalence and factors associated with long COVID are largely unknown in Malaysia. We aim to determine the proportion and factors associated with long COVID among COVID-19 patients in Port Dickson, Malaysia. The positive outcomes of our long COVID active detection initiative were also described.

    METHODS: This was a retrospective analysis of long COVID data collected by the Port Dickson District Health Office between 1 September 2021 to 31 October 2021. Monitoring long COVID symptoms was our quality improvement initiative to safeguard residents' health in the district. The study population was patients previously diagnosed with COVID-19 who resided in Port Dickson. The inclusion criteria were adults aged 18 years and above and were in the fifth week (day 29 to 35) post-COVID-19 diagnosis during the data collection period. We called all consecutive eligible patients to inquire regarding long COVID symptoms. Long COVID was defined as new or ongoing symptoms lasting more than 28 days from the date of positive SARS-CoV-2 by polymerase chain reaction test. Binary multivariate logistic regression was conducted to determine factors associated with long COVID.

    RESULTS: Among 452 patients, they were predominantly male (54.2%), Malays (68.8%) and aged 18-29 years (58.6%). A total of 27.4% (95% CI [23.4-31.8]) of patients experienced long COVID symptoms and were referred to government clinics. The most frequent long COVID symptoms experienced were fatigue (54.0%), cough (20.2%), muscle pain (18.5%), headache (17.7%) and sleep disturbance (16.1%). Females, patients with underlying cardiovascular disease, asthma and chronic obstructive airway disease, those who received symptomatic care, and patients with myalgia and headaches at COVID-19 diagnosis were more likely to have long COVID. Three patients with suspected severe mental health problems were referred to the district psychologist, and ten patients with no/incomplete vaccination were referred for vaccination.

    CONCLUSION: Long COVID is highly prevalent among COVID-19 patients in Port Dickson, Malaysia. Long-term surveillance and management of long COVID, especially among the high-risk groups, are needed as we transition to living with COVID-19.

  13. Yaacob N, Mohamad Ali MS, Salleh AB, Abdul Rahman NA
    PeerJ, 2016;4:e1751.
    PMID: 26989608 DOI: 10.7717/peerj.1751
    Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.
  14. Saleem MKM, Lal A, Ahmed N, Abbasi MS, Vohra F, Abduljabbar T
    PeerJ, 2023;11:e14860.
    PMID: 36908817 DOI: 10.7717/peerj.14860
    BACKGROUND: Salivary disturbance is associated with patients who either have an active coronavirus disease 2019 (COVID-19) or have recovered from coronavirus infection along with loss of taste sensation. In addition, COVID-19 infection can drastically compromise quality of life of individuals.

    OBJECTIVE: This study aimed to analyze xerostomia, ageusia and the oral health impact in coronavirus disease-19 patients utilizing the Xerostomia Inventory scale-(XI) and the Oral Health Impact Profile-14.

    METHODS: In this cross-sectional survey-based study, data was collected from 301 patients who suffered and recovered from COVID-19. Using Google Forms, a questionnaire was developed and circulated amongst those who were infected and recovered from coronavirus infection. The Xerostomia Inventory (XI) and Oral Health Impact Profile-14 were used to assess the degree and quality of life. A paired T-test and Chi-square test were used to analyze the effect on xerostomia inventory scale-(XI) and OHIP-14 scale scores. A p-value of 0.05 was considered as statistically significant.

    RESULTS: Among 301 participants, 54.8% were females. The prevalence of xerostomia in participants with active COVID-19 disease was 39.53% and after recovery 34.88%. The total OHIP-14 scores for patients in the active phase of infection was 12.09, while 12.68 in recovered patients. A significant difference was found between the mean scores of the xerostomia inventory scale-11 and OHIP-14 in active and recovered COVID patients.

    CONCLUSION: A higher prevalence of xerostomia was found in COVID-19 infected patients (39.53%) compared to recovered patients (34.88%). In addition, more than 70% reported aguesia. COVID-19 had a significantly higher compromising impact on oral function of active infected patients compared to recovered patients.

  15. Mohamad-Matrol AA, Chang SW, Abu A
    PeerJ, 2018;6:e5579.
    PMID: 30186704 DOI: 10.7717/peerj.5579
    Background: The amount of plant data such as taxonomical classification, morphological characteristics, ecological attributes and geological distribution in textual and image forms has increased rapidly due to emerging research and technologies. Therefore, it is crucial for experts as well as the public to discern meaningful relationships from this vast amount of data using appropriate methods. The data are often presented in lengthy texts and tables, which make gaining new insights difficult. The study proposes a visual-based representation to display data to users in a meaningful way. This method emphasises the relationships between different data sets.

    Method: This study involves four main steps which translate text-based results from Extensible Markup Language (XML) serialisation format into graphs. The four steps include: (1) conversion of ontological dataset as graph model data; (2) query from graph model data; (3) transformation of text-based results in XML serialisation format into a graphical form; and (4) display of results to the user via a graphical user interface (GUI). Ontological data for plants and samples of trees and shrubs were used as the dataset to demonstrate how plant-based data could be integrated into the proposed data visualisation.

    Results: A visualisation system named plant visualisation system was developed. This system provides a GUI that enables users to perform the query process, as well as a graphical viewer to display the results of the query in the form of a network graph. The efficiency of the developed visualisation system was measured by performing two types of user evaluations: a usability heuristics evaluation, and a query and visualisation evaluation.

    Discussion: The relationships between the data were visualised, enabling the users to easily infer the knowledge and correlations between data. The results from the user evaluation show that the proposed visualisation system is suitable for both expert and novice users, with or without computer skills. This technique demonstrates the practicability of using a computer assisted-tool by providing cognitive analysis for understanding relationships between data. Therefore, the results benefit not only botanists, but also novice users, especially those that are interested to know more about plants.

  16. Woon JS, Mackeen MM, Illias RM, Mahadi NM, Broughton WJ, Murad AMA, et al.
    PeerJ, 2017;5:e3909.
    PMID: 29038760 DOI: 10.7717/peerj.3909
    BACKGROUND: Aspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger.

    METHODS: In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CBHB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CBHB in assisting biomass conversion, CBHB was supplemented into a commercial cellulase preparation (Cellic(®) CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment.

    RESULTS: Recombinant CBHB was over-expressed as a hyperglycosylated protein attached to N-glycans. CBHB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel(®) and Sigmacell cellulose. Characterisation of purified CBHB using MUC as the model substrate revealed that optimum catalysis occurred at 50 °C and pH 4 but the enzyme was stable between pH 3 to 10 and 30 to 80 °C. Although CBHB on its own was unable to digest crystalline substrates, supplementation of CBHB (0.37%) with Cellic(®) CTec2 (30%) increased saccharification of OPEFB by 27%. Compositional analyses of the treated OPEFB samples revealed that CBHB supplementation reduced peak intensities of both crystalline cellulose Iα and Iβ in the treated OPEFB samples.

    DISCUSSION: Since CBHB alone was inactive against crystalline cellulose, these data suggested that it might work synergistically with other components of Cellic(®) CTec2. CBHB supplements were desirable as they further increased hydrolysis of OPEFB when the performance of Cellic(®) CTec2 was theoretically capped at an enzyme loading of 34% in this study. Hence, A. niger CBHB was identified as a potential supplementary enzyme for the enzymatic hydrolysis of OPEFB.

  17. Che Noh I, Avoi R, Abdullah Nurul A, Ahmad I, Abu Bakar R
    PeerJ, 2022;10:e13330.
    PMID: 35469194 DOI: 10.7717/peerj.13330
    BACKGROUND: Chronic hepatitis C virus (HCV) infection is one of the major causes of liver cirrhosis and liver carcinoma. Studies have indicated that an imbalance of cytokine activities could contribute to the pathogenesis of chronic HCV infection. This study aimed to investigate serum levels and gene expression of cytokines (IL-6, TNF-α and TGF-β1) in chronic HCV infection among Malay male subjects.

    METHODS: Thirty-nine subjects were enrolled from various health clinics in Kelantan, Malaysia, and divided into two groups: patients with chronic HCV infection (HP) and healthy control (HS). The serum cytokines IL-6, TNF-a-were measured using Luminex assay, and serum TGF-β1 was measured by ELISA. The mRNA gene expression for IL-6, TNF-α and TGF-β1 was measured by real-time reverse transcriptase polymerase chain reaction (RT-PCR).

    RESULTS: There were statistically significant differences in the mean serum levels of IL-6, and TGF-β1 in HP compared to HS group (p = 0.0180 and p = 0.0005, respectively). There was no significant difference in the mean serum level of TNF-α in HP compared to HS group. The gene expression for the studied cytokines showed no significant differences in HP compared to HS group.

    CONCLUSION: Serum IL-6 was significantly associated with chronic HCV infection.

  18. Hasan M, Hanafiah MM, Alhilfy IHH, Aeyad Taha Z
    PeerJ, 2021;9:e10614.
    PMID: 33520446 DOI: 10.7717/peerj.10614
    Background: Laser applications in agriculture have recently gained much interest due to improved plant characteristics following laser treatment before the sowing of seeds. In this study, maize seeds were exposed to different levels of laser treatment prior to sowing to improve their field performance. The aim of this study is to evaluate the impact of pre-sowing laser photobiomodulation on the field emergence and growth of treated maize seeds.

    Methods: The maize seeds were first photobiomodulated with two lasers: 1) a helium-neon (He-Ne) red laser (632.8 nm), and 2) a neodymium-doped yttrium aluminum garnet (Nd:YAG) green laser (532 nm). Following three replications of randomized complete block design (RCBD), four irradiation treatments were applied (45 s, 65 s, 85 s, and 105 s) at two power intensities (2 mW/cm2 and 4 mW/cm2).

    Results: Based on the results, maize seeds pretreated with a green laser and 2 mW/cm2 power intensity for 105 s exhibited the highest rate of seed emergence (96%) compared to the untreated control seeds with a lower seed emergence rate (62.5%). Furthermore, maize seeds treated with a red laser for 45 s showed an increased vigor index compared to the other treatment options and the control (P 

  19. Al-Mhanna SB, Wan Ghazali WS, Mohamed M, Rabaan AA, Santali EY, H Alestad J, et al.
    PeerJ, 2022;10:e13664.
    PMID: 35935260 DOI: 10.7717/peerj.13664
    BACKGROUND: Cancer is a huge group of diseases that can affect various body parts of humans but also has a psychological, societal, and economic impact. Physical activity can improve the quality of life (QOL) and immunity, while moderate intensity exercise can reduce the probability of this lethal disease. The current study aimed to determine the effect of physical activity on immune markers and QOL in cancer patients as well as to evaluate cancer-related fatigue (CRF) and its association with physical activity.

    METHODOLOGY: Before starting the study, the study protocol was registered in PROSPERO (registration number CRD42021273292). An electronic literature search was performed by combining MeSH terminology and keywords used with the Boolean operators "OR" and "AND" to find relevant published studies on PubMed, Scopus, Cochrane, and ScienceDirect databases. The Joanna Briggs Institute (JBI) critical evaluation checklist was used to assess the quality of selected studies, while the GRADE approach was used to see the quality of evidence.

    RESULTS: A total of 13,931 studies were retrieved after the search on databases. After the scrutiny of studies by reading the title of articles and the inclusion/exclusion criteria, a total of 54 studies were selected for further screening by reading the full texts. In the final, a total of nine studies were selected for the current systematic review and proceeded for data extraction. The patients who were doing different exercises showed improvements in immunity, QOL, and reduction in CRF. A significant reduction in tumour necrosis factor-α (TNF-α), C reactive protein (CRP), interleukin-8 (IL-8), IL-6, and an increase in natural killer (NK) cells levels was also observed.

    CONCLUSIONS: The exercise program is safe and beneficial to improve the quality of life and immunity markers before, during, and after cancer treatment. Physical exercise may also help patients to overcome the adverse effects of the treatment and to reduce the chance of developing new tumours in the future.

  20. Tran HNT, Thomas JJ, Ahamed Hassain Malim NH
    PeerJ, 2022;10:e13163.
    PMID: 35578674 DOI: 10.7717/peerj.13163
    The exploration of drug-target interactions (DTI) is an essential stage in the drug development pipeline. Thanks to the assistance of computational models, notably in the deep learning approach, scientists have been able to shorten the time spent on this stage. Widely practiced deep learning algorithms such as convolutional neural networks and recurrent neural networks are commonly employed in DTI prediction projects. However, they can hardly utilize the natural graph structure of molecular inputs. For that reason, a graph neural network (GNN) is an applicable choice for learning the chemical and structural characteristics of molecules when it represents molecular compounds as graphs and learns the compound features from those graphs. In an effort to construct an advanced deep learning-based model for DTI prediction, we propose Deep Neural Computation (DeepNC), which is a framework utilizing three GNN algorithms: Generalized Aggregation Networks (GENConv), Graph Convolutional Networks (GCNConv), and Hypergraph Convolution-Hypergraph Attention (HypergraphConv). In short, our framework learns the features of drugs and targets by the layers of GNN and 1-D convolution network, respectively. Then, representations of the drugs and targets are fed into fully-connected layers to predict the binding affinity values. The models of DeepNC were evaluated on two benchmarked datasets (Davis, Kiba) and one independently proposed dataset (Allergy) to confirm that they are suitable for predicting the binding affinity of drugs and targets. Moreover, compared to the results of baseline methods that worked on the same problem, DeepNC proves to improve the performance in terms of mean square error and concordance index.
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