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Fulltext Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, et al.

F1000Res, 2019;8:1441.
PMID: 32399182 DOI: 10.12688/f1000research.20144.2

Background: Some Ebola vaccines have been developed and tested in phase III clinical trials. However, assessment of whether public have willingness to purchase or not, especially in unaffected areas, is lacking. The aim of this study was to determine willingness to pay (WTP) for a hypothetical Ebola vaccine in Indonesia. Methods: A cross-sectional study was conducted from 1 August to 30 December 2015 in five cities in Aceh province of Indonesia. Patients' family members who visited outpatient departments were approached and interviewed about their sociodemographic characteristics, knowledge of Ebola, attitude towards vaccination practice and their WTP for a hypothetical Ebola vaccine. A multivariable linear regression model assessed the relationship between these explanatory variables and WTP. Results: During the study, 500 participants were approached and interviewed. There were 424 (84.8%) respondents who completed the interview and 74% (311/424) expressed their acceptance for an Ebola vaccine. There were 288 participants who were willing to pay for an Ebola vaccine (92.6% out of 311). The mean of WTP was US$2.08 (95% CI: 1.75-2.42). The final multivariable model indicated that young age, high educational attainment, working as a private employee, entrepreneur or civil servant (compared to farmers), being unmarried, and residing in a suburb (compared to a city) were associated with higher WTP. Conclusions: Although the proportion of the participants who would accept the Ebola vaccine was relatively high, the amount they were willing to pay for Ebola vaccine was very low. This finding would indicate the need of subsidies for Ebola vaccine in the country.
Fulltext Weak and strong ties and its connection to experts' problem-solving styles in scaffolding students' PBL activities on social media

Abdullah AH, Neo TK, Low JH

F1000Res, 2021;10:1076.
PMID: 35035894 DOI: 10.12688/f1000research.73210.2

Background: Studies have acknowledged that social media enables students to connect with and learn from experts from different ties available in the students' personal learning environment (PLE). Incorporating experts into formal learning activities such as scaffolding problem-solving tasks through social media, allows students to understand how experts solve real-world problems. However, studies that evaluate experts' problem-solving styles on social media in relation to the tie strength of the experts with the students are scarce in the extant literature. This study aimed to explore the problem-solving styles that the experts portrayed based on their ties with the students in problem-based learning (PBL) on Facebook. Methods: This study employed a simultaneous within-subject experimental design which was conducted in three closed Facebook groups with 12 final year management students, six business experts, and one instructor as the participants. The experts were invited by the students from the weak and strong ties in their PLE. Hinging on the Strength of Weak Ties Theory (Granovetter, 1973) and problem-solving styles (Selby et al., 2004), this study employed thematic analysis using the ATLAS.ti qualitative data analysis software to map the experts' comments on Facebook. Results: The experts from strong and weak ties who had a prior relationship with the students showed people preference style by being more sensitive to the students' learning needs and demonstrating firmer scaffolding compared to the weak ties' experts who had no prior relationship with the students. Regardless of the types of ties, all experts applied all manner of processing information and orientation to change but the degree of its applications are correlated with the working experience of the experts. Conclusion: The use of weak or strong ties benefited the students as it expedited their problem-solving tasks since the experts have unique expertise to offer depending on the problem-solving styles that they exhibited.
Fulltext Visual acuity measured with luminance-modulated and contrast-modulated noise letter stimuli in young adults and adults above 50 years old

Woi PJ, Kaur S, Waugh SJ, Hairol MI

F1000Res, 2016;5:1961.
PMID: 28184281 DOI: 10.12688/f1000research.9410.1

The human visual system is sensitive in detecting objects that have different luminance level from their background, known as first-order or luminance-modulated (LM) stimuli. We are also able to detect objects that have the same mean luminance as their background, only differing in contrast (or other attributes). Such objects are known as second-order or contrast-modulated (CM), stimuli. CM stimuli are thought to be processed in higher visual areas compared to LM stimuli, and may be more susceptible to ageing. We compared visual acuities (VA) of five healthy older adults (54.0±1.83 years old) and five healthy younger adults (25.4±1.29 years old) with LM and CM letters under monocular and binocular viewing. For monocular viewing, age had no effect on VA [F(1, 8)= 2.50, p> 0.05]. However, there was a significant main effect of age on VA under binocular viewing [F(1, 8)= 5.67, p< 0.05]. Binocular VA with CM letters in younger adults was approximately two lines better than that in older adults. For LM, binocular summation ratios were similar for older (1.16±0.21) and younger (1.15±0.06) adults. For CM, younger adults had higher binocular summation ratio (1.39±0.08) compared to older adults (1.12±0.09). Binocular viewing improved VA with LM letters for both groups similarly. However, in older adults, binocular viewing did not improve VA with CM letters as much as in younger adults. This could reflect a decline of higher visual areas due to ageing process, most likely higher than V1, which may be missed if measured with luminance-based stimuli alone.
Fulltext Validation of EuroSCORE II in patients undergoing coronary artery bypass grafting (CABG) surgery at the National Heart Institute, Kuala Lumpur: a retrospective review

Musa AF, Cheong XP, Dillon J, Nordin RB

F1000Res, 2018;7:534.
PMID: 32913630 DOI: 10.12688/f1000research.14760.2

Background: The European System for Cardiac Operative Risk (EuroSCORE) II was developed in 2011 to replace the aging EUROScore for predicting in-house mortality after cardiac surgery. Our aim was to validate EuroSCORE II in Malaysian patients undergoing coronary artery bypass graft (CABG) surgery at our Institute. Methods: A retrospective single-center study was performed. A database was created to include EuroSCORE II values and actual mortality of 1718 patients undergoing CABG surgery in Malaysia from 1st January to 31st December 2016. The goodness-of-fit of EuroSCORE II was determined by the Hosmer-Lemeshow goodness-of-fit test and discriminatory power with the areas under the receiver operating characteristics (ROC) curve (AUC). Results: Observed mortality rate was 4.66% (80 out of 1718 patients). The median EuroSCORE II value was 2.06% (Inter Quartile Range: 1.94%) (1st quartile: 1.45%, 3rd quartile: 3.39%). The AUC for EuroSCORE II was 0.7 (95% CI 0.640 - 0.759) indicating good discriminatory power. The Hosmer-Lemeshow goodness-of-fit test did not show significant difference between expected and observed mortality in accordance to the EuroSCORE II model (Chi-square = 13.758, p = 0.089) suggesting good calibration of the model in this population. Cross-tabulation analysis showed that there is slight overestimation of EuroSCORE II in low-risk groups (0-10%) and slight underestimation in high-risk groups (>20%). Multivariate logistic regression analysis showed that gender, age, total hospital stay, serum creatinine and critical pre-operative state are significant predictors of mortality post-CABG surgery. Conclusion: This study indicated that the EuroSCORE II is a good predictor of post-operative mortality in the context of Malaysian patients undergoing CABG surgery. Our study also showed that certain independent variables might possess higher weightage in predicting mortality among this patient group. Therefore, it is suggested that EuroSCORE II can be safely used for risk assessment while ideally, clinical consideration should be applied on an individual basis.
Thermal performance of gasifier cooking stoves: A systematic literature review

Rabby MII, Uddin MW, Sheikh MR, Bhuiyan HK, Mumu TA, Islam F, et al.

F1000Res, 2023;12:38.
PMID: 37484517 DOI: 10.12688/f1000research.126890.2

A systematic literature review was conducted to summarize the overall thermal performance of different gasified cooking stoves from the available literature. For this purpose, available studies from the last 14 years (2008 to 2022) were searched using different search strings. After screening, a total of 28 articles were selected for this literature review. Scopus, Google Scholar, and Web of Science databases were used as search strings by applying "Gasifier cooking stove" AND "producer gas cooking stove" AND "thermal performance" keywords. This review uncovers different gasified cooking stoves, cooking fuels, and fabrication materials besides overall thermal performances. The result shows that the overall thermal performance of different gasified cooking stoves was 5.88% to 91% depending on the design and burning fuels. The premixed producer gas burner with a swirl vane stove provided the highest overall thermal performance range, which was 84% to 91%, and the updraft gasified stove provided the lowest performance, which was 5.88% to 8.79%. The result also demonstrates that the wood pellets cooking fuel provided the highest thermal performance and corn straw briquette fuel provided the lowest for gasified cooking stoves. The overall thermal performance of wood pellets was 38.5% and corn straw briquette was 10.86%.
The utility of salivary CRP and IL-6 as a non-invasive measurement evaluated in patients with COVID-19 with and without diabetes

Bachtiar E, Bachtiar BM, Kusumaningrum A, Sunarto H, Soeroso Y, Sulijaya B, et al.

F1000Res, 2023;12:419.
PMID: 38269064 DOI: 10.12688/f1000research.130995.3

BACKGROUND: The available evidence suggests that inflammatory responses, in both systemic and oral tissue, contribute to the pathology of COVID-19 disease. Hence, studies of inflammation biomarkers in oral fluids, such as saliva, might be useful to better specify COVID-19 features.
METHODS: In the current study, we performed quantitative real-time PCR to measure salivary levels of C-reactive protein (CRP) and interleukin-6 (IL-6) in saliva obtained from patients diagnosed with mild COVID-19, in a diabetic group (DG; n = 10) and a non-diabetic group (NDG; n = 13). All participants were diagnosed with periodontitis, while six participants with periodontitis but not diagnosed with COVID-19 were included as controls.
RESULTS: We found increases in salivary total protein levels in both the DG and NDG compared to control patients. In both groups, salivary CRP and IL-6 levels were comparable. Additionally, the levels of salivary CRP were significantly correlated with total proteins, in which a strong and moderate positive correlation was found between DG and NDG, respectively. A linear positive correlation was also noted in the relationship between salivary IL-6 level and total proteins, but the correlation was not significant. Interestingly, the association between salivary CRP and IL-6 levels was positive. However, a moderately significant correlation was only found in COVID-19 patients with diabetes, through which the association was validated by a receiver operating curve.
CONCLUSIONS: These finding suggest that salivary CRP and IL-6 are particularly relevant as potential non-invasive biomarker for predicting diabetes risk in mild cases of COVID-19 accompanied with periodontitis.
Fulltext The protective effects of antigen-specific IgY on pyocyanin-treated human lymphoma Raji cells

Susilowati H, Artanto S, Yulianto HDK, Sosroseno W, Hutomo S

F1000Res, 2019;8:1008.
PMID: 32025288 DOI: 10.12688/f1000research.19327.2

Background: Pyocyanin (PCN), a highly pathogenic pigment produced by Pseudomonas aeruginosa, induces caspase 3-dependent human B cell (Raji cells) death. The aim of the present study, therefore, was to assess whether antigen-specific IgY antibodies may be protective on PCN-induced Raji cell death. Methods: Chickens were subcutaneously immunized with Freund's complete adjuvant containing PCN, and then given two boosted immunizations. Anti-PCN IgY antibodies were purified from egg yolk and detected using an agar gel precipitation test (AGPT) and ELISA. Protective effects of antigen-specific IgY on Raji cells were tested using a cell viability assay. Results: AGPT results showed the formation of strong immune complex precipitates, whilst ELISA further confirmed the presence of IgY antibodies specific to PCN at significant concentration. Further experiments showed that anti-PCN IgY antibodies significantly increased PCN-treated Raji cell viability in a dose-dependent fashion (p<0.05). Conclusions: The results of the present study suggest that anti-PCN IgY antibodies may be protective on PCN-induced Raji cell death.
Fulltext The impact factor of an open access journal does not contribute to an article's citations

Chua SK, Qureshi AM, Krishnan V, Pai DR, Kamal LB, Gunasegaran S, et al.

F1000Res, 2017;6:208.
PMID: 28649365 DOI: 10.12688/f1000research.10892.1

Background Citations of papers are positively influenced by the journal's impact factor (IF). For non-open access (non-OA) journals, this influence may be due to the fact that high-IF journals are more often purchased by libraries, and are therefore more often available to researchers, than low-IF journals. This positive influence has not, however, been shown specifically for papers published in open access (OA) journals, which are universally accessible, and do not need library purchase. It is therefore important to ascertain if the IF influences citations in OA journals too. Methods 203 randomized controlled trials (102 OA and 101 non-OA) published in January 2011 were included in the study. Five-year citations for papers published in OA journals were compared to those for non-OA journals. Source papers were derived from PubMed. Citations were retrieved from Web of Science, Scopus, and Google Scholar databases. The Thompson-Reuter's IF was used. Results OA journals were found to have significantly more citations overall compared to non-OA journals (median 15.5 vs 12, p=0.039). The IF did not correlate with citations for OA journals (Spearman's rho =0.187, p=0.60). The increase in the citations with increasing IF was minimal for OA journals (beta coefficient = 3.346, 95% CI -0.464, 7.156, p=0.084). In contrast, the IF did show moderate correlation with citations for articles published in non-OA journals (Spearman's rho=0.514, p<0.001). The increase in the number of citations was also significant (beta coefficient = 4.347, 95% CI 2.42, 6.274, p<0.001). Conclusion It is better to publish in an OA journal for more citations. It may not be worth paying high publishing fees for higher IF journals, because there is minimal gain in terms of increased number of citations. On the other hand, if one wishes to publish in a non-OA journal, it is better to choose one with a high IF.
Fulltext The effects of touch-screen technology usage on hand skills among preschool children: a case-control study

Daud AZC, Aman NA, Chien CW, Judd J

F1000Res, 2020;9:1306.
PMID: 34950457 DOI: 10.12688/f1000research.25753.1

Background: Little is known on how time spent on touch-screen technology affects the hand skills development of preschool children. This study aimed to investigate the effects of touch-screen technology usage on hand skills among preschool children. Methods: Case-control design was employed to compare the hand skills of children who were engaged in touch-screen technology. A total of 128 participants aged between five and six years old who attended preschool were recruited and divided into two groups: high usage touch-screen technology (HUTSTG) and, low usage touch-screen technology (LUTSTG). Children's Hand Skills ability Questionnaire (CHSQ) and Assessment of Children's Hand Skills (ACHS) were used to evaluate the children's hand skills. Results: There were significant differences in the hand skills of preschool children between HUTSTG and LUTSTG. Results showed that preschool children in LUTSTG had better hand skills in all domains of CHSQ (p≤0.001) and ACHS (p<0.001) as compared to HUTSTG. Conclusion: Frequent use of touch-screen technology might cause disadvantages to the development of hand skills among preschool children.
The effect of electronic and printed module about drug abuse prevention on teachers' beliefs in Indonesia

Ghozali G, Azuhairi A A, Mohd Zulkefli NA, Ibrahim F

F1000Res, 2019;8:115.
PMID: 37767456 DOI: 10.12688/f1000research.17628.2

Background: Drug abuse is a serious global health problem. Globally, 269 million people or 5.3 percent of the population aged 15‒64 years used drugs in 2018. Evidence shows that most drug addicts start using drugs in adolescence (<15-years-old). Adolescents need role models who are able to guide them; teachers have important roles as they are primary role models for students. Therefore, teachers should have positive beliefs to guide students effectively, i.e. they should have good awareness about the threat of drug abuse and high confidence to implement required prevention. This research developed an alternative electronic delivery method of learning material to empower teachers in preventing drug abuse. This study aimed to compare the effect of the electronic and a printed teaching module on teachers' beliefs about drug abuse prevention. Methods: 260 junior high school teachers were selected randomly. These teachers were split into two groups. Before intervention, a questionnaire was completed by both groups. The teachers then completed the learning material: electronic module in the first group and printed module in the second group. One month later, data was collected from both groups using the same questionnaire to assess the beliefs of the teachers Results: There was significant positive effect on teachers' beliefs, both in electronic module and printed module groups. All categories of beliefs at one month after intervention were significantly higher than those at baseline (P<0.001). Based on between group comparison analysis of mean changes, perceived susceptibility in electronic module group was significantly higher than printed module group (P<0.001), while perceived severity, benefits, barriers and efficacy were not significantly different (P>0.05). Conclusions: Electronic and printed module intervention significantly increased teachers' beliefs in drug abuse prevention. The printed module was still effective to be used as learning media, while the electronic module was an alternative with some advantages.
Fulltext The contradictory effects of coffee intake on periodontal health: a systematic review of experimental and observational studies

Bramantoro T, Zulfiana AA, Amir MS, Irmalia WR, Mohd Nor NA, Nugraha AP, et al.

F1000Res, 2022;11:924.
PMID: 36313542 DOI: 10.12688/f1000research.124547.3

Background: Drinking coffee is known to have both positive and negative aftermath on periodontal health. The current study is aiming to systematically review the impact of coffee consumption on periodontal health status. Methods: An article search was carried out in two electronic databases (PUBMED and Web of Sciences). All type of experimental and observational studies were included. The assessment of the included articles were conducted using Joanna Briggs Institute (JBI) critical appraisal tool. Data were analyzed qualitatively. Result: A total of 10 articles were included in this study. Most (5) of the studies discovered a negative correlation between coffee intake and periodontal health, while 4 other studies found the protective effect of daily coffee consumption against alveolar bone loss. Last, only one study found that coffee intake did not relate with periodontitis. Conclusion: The effect of coffee consumption on periodontal health was fragmented since coffee has complex components that may give either beneficial effects or negative impact on periodontal health.
Fulltext The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, et al.

F1000Res, 2018;7.
PMID: 30026930 DOI: 10.12688/f1000research.14509.2

Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms. In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed. NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced. Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process. This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017. Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a "One Health" approach.
Fulltext Technology readiness and UTAUT2 in e-wallet adoption in a developing country

Leong MY, Kwan JH, Ming Ming L

F1000Res, 2021;10:863.
PMID: 34621517 DOI: 10.12688/f1000research.72853.1

Background: An e-wallet is a digital equivalent of a physical wallet which plays an essential role in payment system transformation. To embrace the concept of a cashless society, the Malaysian Government and central bank have taken various steps to encourage the adoption of e-wallets. Despite the seamless services offered by the e-wallet, it is yet to reach high-scale adoption in Malaysia. This study aims to investigate Malaysians' readiness towards the e-wallet and their perceptions of it by employing the UTAUT2 model. Methods: A total of 309 valid data were gathered and analysed with partial least squares structural equation modelling (PLS-SEM). Results: The findings revealed that the respondents were confident about the new technology and tended to believe that e-wallet was somehow useful for them. The results also disclosed that e-wallet adoption intention was significantly influenced by performance expectancy, price value, facilitating conditions, and followed closely by social influence. Nonetheless, insecurity did not present significant impact on both performance expectancy and effort expectancy of e-wallet. Conclusions: This study provides a substantial contribution to the knowledge domain by combining system-specific and individual-specific models in an e-wallet context. The outcomes of this study would also benefit e-wallet service providers and policymakers by delivering holistic insight into Malaysians' readiness and adoption behaviour of the e-wallet.
Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects

Sama-Ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, et al.

F1000Res, 2022;11:1274.
PMID: 36936052 DOI: 10.12688/f1000research.126227.1

Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of the agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results obtained provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
Fulltext Synchronous online learning during movement control order in higher education institutions: a systematic review

Lee YW, Dorasamy M, Bin Ahmad AA, Jambulingam M, Yeap PF, Harun S

F1000Res, 2021;10:1056.
PMID: 34950456 DOI: 10.12688/f1000research.73342.2

Background: Higher education institutions (HEI) are not spared from the coronavirus disease 2019 (COVID-19) pandemic. The closure of campuses because of the movement control order (MCO) to mitigate the spread of the COVID-19 has forced HEIs to adopt online learning, especially synchronous online learning (SOL). Although teaching and learning can be continued via SOL, retaining students' interest and sustaining their engagement have not been sufficiently explored. This study presents a systematic review of the research pertaining to SOL associated with students' interest and engagement in HEIs during the MCO environment. Methods: Five major online databases, i.e., EBSCOhost, Science Direct, Emerald, Scopus and Springer were searched to collect relevant papers published between 1st January 2010 to 15th June 2021 including conference proceedings, peer-reviewed papers and dissertations. Papers written in the English language, based in full-fledged universities, and with these five keywords: (i) synchronous online learning, (ii) engagement, (iii) interest, (iv) MCO/Covid-19 and (v) HEI, were included. Papers focussing on synchronous and asynchronous online learning in schools and colleges were excluded. Each paper was reviewed by two reviewers in order to confirm the eligibility based on the inclusion and exclusion criteria. Results: We found 31 papers of which six papers were related to SOL, engagement and interest in HEIs in the MCO environment. Our review presents three major findings: (i) limited research has been conducted on SOL associated with students' engagement and interest, (ii) studies related to the context of HEIs in the MCO environment are limited, and (iii) the understanding of the new phenomena through qualitative research is insufficient. We highlight the SOL alignment with students' engagement, interest, style preference, learner interaction effectiveness, behavior and academic performance. Conclusions: We believe that the findings of this study are timely and require attention from the research community.
Fulltext Stability, orientation and position preference of the stem region (residues 689-703) in Hepatitis C Virus (HCV) envelope glycoprotein E2: a molecular dynamics study

Akbar R, Jusoh SA

F1000Res, 2013;2:64.
PMID: 24555044 DOI: 10.12688/f1000research.2-64.v2

Envelope glycoproteins of Hepatitis C Virus (HCV) play an important role in the virus assembly and initial entry into host cells. Conserved charged residues of the E2 transmembrane (TM) domain were shown to be responsible for the heterodimerization with envelope glycoprotein E1. Despite intensive research on both envelope glycoproteins, the structural information is still not fully understood. Recent findings have revealed that the stem (ST) region of E2 also functions in the initial stage of the viral life cycle. We have previously shown the effect of the conserved charged residues on the TM helix monomer of E2. Here, we extended the model of the TM domain by adding the adjacent ST segment. Explicit molecular dynamics simulations were performed for the E2 amphiphilic segment of the ST region connected to the putative TM domain (residues 683-746). Structural conformation and behavior are studied and compared with the nuclear magnetic resonance (NMR)-derived segment of E2 ( 2KQZ.pdb). We observed that the central helix of the ST region (residues 689 - 703) remained stable as a helix in-plane to the lipid bilayer. Furthermore, the TM domain appeared to provide minimal contribution to the structural stability of the amphipathic region. This study also provides insight into the orientation and positional preferences of the ST segment with respect to the membrane lipid-water interface.
Smartic: A smart tool for Big Data analytics and IoT

Sayeed S, Ahmad AF, Peng TC

F1000Res, 2022;11:17.
PMID: 38269303 DOI: 10.12688/f1000research.73613.1

The Internet of Things (IoT) is leading the physical and digital world of technology to converge. Real-time and massive scale connections produce a large amount of versatile data, where Big Data comes into the picture. Big Data refers to large, diverse sets of information with dimensions that go beyond the capabilities of widely used database management systems, or standard data processing software tools to manage within a given limit. Almost every big dataset is dirty and may contain missing data, mistyping, inaccuracies, and many more issues that impact Big Data analytics performances. One of the biggest challenges in Big Data analytics is to discover and repair dirty data; failure to do this can lead to inaccurate analytics results and unpredictable conclusions. We experimented with different missing value imputation techniques and compared machine learning (ML) model performances with different imputation methods. We propose a hybrid model for missing value imputation combining ML and sample-based statistical techniques. Furthermore, we continued with the best missing value inputted dataset, chosen based on ML model performance for feature engineering and hyperparameter tuning. We used k-means clustering and principal component analysis. Accuracy, the evaluated outcome, improved dramatically and proved that the XGBoost model gives very high accuracy at around 0.125 root mean squared logarithmic error (RMSLE). To overcome overfitting, we used K-fold cross-validation.
Fulltext Simulation framework for connected vehicles: a scoping review

Abdul Razak SF, Yogarayan S, Azman A, Abdullah MFA, Muhamad Amin AH, Salleh M

F1000Res, 2021;10:1265.
PMID: 36852011 DOI: 10.12688/f1000research.73398.2

Background: V2V (Vehicle-to-Vehicle) is a booming research field with a diverse set of services and applications. Most researchers rely on vehicular simulation tools to model traffic and road conditions and evaluate the performance of network protocols. We conducted a scoping review to consider simulators that have been reported in the literature based on successful implementation of V2V systems, tutorials, documentation, examples, and/or discussion groups. Methods: Simulators that have limited information were not included. The selected simulators are described individually and compared based on their requirements and features, i.e., origin, traffic model, scalability, and traffic features. This scoping review was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The review considered only research published in English (in journals and conference papers) completed after 2015. Further, three reviewers initiated the data extraction phase to retrieve information from the published papers. Results: Most simulators can simulate system behaviour by modelling the events according to pre-defined scenarios. However, the main challenge faced is integrating the three components to simulate a road environment in either microscopic, macroscopic or mesoscopic models. These components include mobility generators, VANET simulators and network simulators. These simulators require the integration and synchronisation of the transportation domain and the communication domain. Simulation modelling can be run using a different types of simulators that are cost-effective and scalable for evaluating the performance of V2V systems in urban environments. In addition, we also considered the ability of the vehicular simulation tools to support wireless sensors. Conclusions: The outcome of this study may reduce the time required for other researchers to work on other applications involving V2V systems and as a reference for the study and development of new traffic simulators.
Sentiment analysis of Indonesian tweets on COVID-19 and COVID-19 vaccinations

Kalanjati VP, Hasanatuludhhiyah N, d'Arqom A, Arsyi DH, Marchianti ACN, Muhammad A, et al.

F1000Res, 2023;12:1007.
PMID: 38605817 DOI: 10.12688/f1000research.130610.3

BACKGROUND: Sentiments and opinions regarding COVID-19 and the COVID-19 vaccination on Indonesian-language Twitter are scarcely reported in one comprehensive study, and thus were aimed at our study. We also analyzed fake news and facts, and Twitter engagement to understand people's perceptions and beliefs that determine public health literacy.
METHODS: We collected 3,489,367 tweets data from January 2020 to August 2021. We analyzed factual and fake news using the string comparison method. The difflib library was used to measure similarity. The user's engagement was analyzed by averaging the engagement metrics of tweets, retweets, favorites, replies, and posts shared with sentiments and opinions regarding COVID-19 and COVID-19 vaccination.
RESULT: Positive sentiments on COVID-19 and COVID-19 vaccination dominated, however, the negative sentiments increased during the beginning of the implementation of restrictions on community activities (PPKM). The tweets were dominated by the importance of health protocols (washing hands, keeping distance, and wearing masks). Several types of vaccines were on top of the word count in the vaccine subtopic. Acceptance of the vaccination increased during the studied period, and the fake news was overweighed by the facts. The tweets were dynamic and showed that the engaged topics were changed from the nature of COVID-19 to the vaccination and virus mutation which peaked in the early and middle terms of 2021. The public sentiment and engagement were shifted from hesitancy to anxiety towards the safety and effectiveness of the vaccines, whilst changed again into wariness on an uprising of the delta variant.
CONCLUSION: Understanding public sentiment and opinion can help policymakers to plan the best strategy to cope with the pandemic. Positive sentiments and fact-based opinions on COVID-19, and COVID-19 vaccination had been shown predominantly. However, sufficient health literacy levels could yet be predicted and sought for further study.
Fulltext Sea grapes powder with the addition of tempe rich in collagen: An anti-aging functional food

Permatasari HK, Nurkolis F, Vivo CD, Noor SL, Rahmawati R, Radu S, et al.

F1000Res, 2021;10:789.
PMID: 36237995 DOI: 10.12688/f1000research.55307.3

Background: This study aimed to determine the potential anti-aging effects of sea grapes and tempe (fermented soybeans) collagen particle size, by measuring the activities of anti-glycation, antioxidant, and tyrosinase inhibitors. Methods: Collagen was isolated from freeze-dried sea grapes and tempe powder and treated with different NaOH concentrations (0.10 M; 0.20 M; 0.30 M), and CH 3COOH 1 M solution, separately. The collagen particle size was adjusted by stirring at 1000 rpm for 5 and 10 hours. 2,2-diphenyl-1-picrylhydrazyl (DPPH) was used to measure the antioxidant activity, and L-tyrosine and L-DOPA (l-3,4-dihydroxyphenylalanine) was used as a marker of tyrosine inhibition. Results: The collagen treated with 0.10 M NaOH produced the highest collagen yield (11.65%), and the largest particle size (2455 nm). Additionally, this collagen, when treated for 5 hours, exhibited 24.70% antioxidant activity, 62.60% anti-glycation, 8.97% L-tyrosine, and 26.77% L-Dopa inhibition activities. Meanwhile, the collagen treated for 10 hours had a 9.98% antioxidant activity, 41.48% anti-glycation, 7.89% L-tyrosine, and 2.67% L-Dopa inhibition activity. Conclusion: Sea grapes and tempe collagen powder treated with 0.10 M NaOH and stirred for 5 hours, possess the best potential anti-aging properties as a functional food.

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