Displaying publications 41 - 60 of 451 in total

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  1. Gilmore B, Gerlach N, Abreu Lopes C, Diallo AA, Bhattacharyya S, de Claro V, et al.
    BMJ Open, 2022 Sep 20;12(9):e063057.
    PMID: 36127122 DOI: 10.1136/bmjopen-2022-063057
    INTRODUCTION: Widespread vaccination against COVID-19 is one of the most effective ways to control, and ideally, end the global COVID-19 pandemic. Vaccine hesitancy and vaccine rates vary widely across countries and populations and are influenced by complex sociocultural, political, economic and psychological factors. Community engagement is an integral strategy within immunisation campaigns and has been shown to improve vaccine acceptance. As evidence on community engagement to support COVID-19 vaccine uptake is emerging and constantly changing, research that lessens the knowledge-to-practice gap by providing regular and up-to-date evidence on current best-practice is essential.

    METHODS AND ANALYSIS: A living systematic review will be conducted which includes an initial systematic review and bimonthly review updates. Searching and screening for the review and subsequent updates will be done in four streams: a systematic search of six databases, grey literature review, preprint review and citizen sourcing. The screening will be done by a minimum of two reviewers at title/abstract and full-text in Covidence, a systematic review management software. Data will be extracted across predefined fields in an excel spreadsheet that includes information about article characteristics, context and population, community engagement approaches, and outcomes. Synthesis will occur using the convergent integrated approach. We will explore the potential to quantitatively synthesise primary outcomes depending on heterogeneity of the studies.

    ETHICS AND DISSEMINATION: The initial review and subsequent bimonthly searches and their results will be disseminated transparently via open-access methods. Quarterly briefs will be shared on the reviews' social media platforms and across other interested networks and repositories. A dedicated web link will be created on the Community Health-Community of Practice site for sharing findings and obtaining feedback. A mailing list will be developed and interested parties can subscribe for updates.

    PROSPERO REGISTRATION NUMBER: CRD42022301996.

    Matched MeSH terms: Research Design
  2. Nor Shafizah I, Irmawati R, Omar H, Yahaya M, Alia Aina A
    Food Chem, 2022 Mar 30;373(Pt B):131668.
    PMID: 34848088 DOI: 10.1016/j.foodchem.2021.131668
    In this study, potassium oxide supported on dolomite adsorbent was used as an adsorbent for free fatty acids (FFAs) treatment in crude palm oil (CPO). The characteristics of the adsorbent were determined by TGA, XRD, SEM, BET and TPD-CO2. Taguchi method was utilized for experimental design and optimum condition determination. There were four parameters and three levels involved in this study: time (30, 60, 90 min), stirring rate (300, 500, 700 rpm), adsorbent dosage (1, 3, 5 wt%) and K2O concentration (5, 10, 15 wt%). The adsorbent had a larger pore size, higher basic strength, and more basic sites in greater efficiency (63%) in FFAs removal from CPO. The optimum conditions were at 30 min time, 700 rpm stirring rate, 5 wt% adsorbent dosage and 15 wt% K2O concentration. Taguchi method simplified determination of experimental parameters and minimized the operating costs.
    Matched MeSH terms: Research Design
  3. Sanjeevannavar MB, Banapurmath NR, Soudagar MEM, Atgur V, Hossain N, Mujtaba MA, et al.
    Chemosphere, 2022 Feb;288(Pt 2):132450.
    PMID: 34624353 DOI: 10.1016/j.chemosphere.2021.132450
    Biodiesel commercialization is questionable due to poor brake thermal efficiency. Biodiesel utilization should be improved with the addition of fuel additives. Hydrogen peroxide is a potential fuel additive due to extra hydrogen and oxygen content, which improves the combustion process. In this experimental study, biodiesel has been produced from Jatropha oil employing catalyzed transesterification homogeneously to examine its influence on the performance and emissions at engine loads with 1500 rpm utilizing a four-stroke single-cylinder diesel engine. D60B40 (having 60% diesel and 40% biodiesel) and D60B30A10 (60% diesel, 30% biodiesel and 10% hydrogen peroxide (H2O2)), are the fuel mixtures in the current study. The addition of H2O2 reduces emissions and enhances the combustion process. This effect occurred due to the micro-explosion of the injected fuel particles (which increases in-cylinder pressure and heat release rate (HRR)). An increase of 20% in BTE and 25% reduction in BSFC for D60B30A10 was observed compared to D60B40. Significant reduction in emissions of HC up to 17.54%, smoke by 24.6% CO2 by 3.53%, and an increase in NOx was noticed when the engine is operated with D60B30A10. The HRR increased up to 18.6%, ID reduced by 10.82%, and in-cylinder pressure increased by 8.5%. Test runs can be minimized as per Taguchi's design of experiments. It is possible to provide the estimates for the full factorial design of experiments. Exhaust gas temperature standards are evaluated and examined for all fuel blends.
    Matched MeSH terms: Research Design
  4. Armijo-Olivo S, de Castro-Carletti EM, Calixtre LB, de Oliveira-Souza AIS, Mohamad N, Fuentes J
    Am J Phys Med Rehabil, 2022 Jan 01;101(1):64-77.
    PMID: 34091470 DOI: 10.1097/PHM.0000000000001799
    The objective of this review was to summarize the concept of clinical significance and associated methods focusing on the area of rehabilitation to provide a resource to rehabilitation researchers and clinicians. Studies were searched on electronic databases from inception until July 28, 2020, with no date or language limits. Manual searches as well as Scopus forward citation for relevant references were performed. Narrative synthesis of study results was performed. Definitions of the concepts related to clinical significance, ways of calculating, and interpreting each method were provided using rehabilitation examples. An explanation of methods to evaluate clinical significance (distribution, anchor, and opinion-based methods) and their advantages and disadvantages were also provided. Considering the limitations of statistical significance in assuring meaningfulness of results, clinical interpretation of research outcomes and the report of clinical significance in intervention trials should be a priority in rehabilitation research. When possible, the use of multiple methods (distribution, anchor, and opinion based) is recommended. Thus, clinical researchers are encouraged to present results in a manner that allow the rehabilitation professionals to easily interpret and implement those results in their clinical practice.
    Matched MeSH terms: Research Design
  5. Widiastuti T, Prasetyo A, Robani A, Mawardi I, Rosida R, Al Mustofa MU
    PLoS One, 2022;17(11):e0276876.
    PMID: 36413519 DOI: 10.1371/journal.pone.0276876
    Several previous studies state that the Islamic Social Finance program has not fully succeeded in creating prosperity, and there are no definite measurements to show the sustainability impact of the program. Thus, a measurement is needed to analyze various aspects in achieving the success and sustainability of Islamic social finance programs. This study developed an index for performance evaluation with an emphasis on the success and sustainability of the Islamic Social Finance program. The study used the Analytical Network Process to determine and analyze priority components. Furthermore, the Multistage Weighted Index method was used to calculate the final index score. The index was built by taking into consideration various factors, stakeholders, aspects, and indicators. This study indicates that aspects of funding contribution from donors (0.22), involvement of donors in giving advice (0.99), and controlling of supervisor (0.08) are priority aspects in the success and sustainability of the program. An empirical investigation was performed on three different programs in Indonesia: A, B, and C. Program A (0.81) and C (0.80) have succeeded in improving the beneficiaries' quality of life to the level of economic resilience, although at a low level of sustainability (76-84.33). On the other hand, program B (0.73) is at the economic reinforcement and has not yet achieved sustainability. This index can be seen as a comprehensive tool for measuring the success and sustainability of the program at several levels.
    Matched MeSH terms: Research Design*
  6. Abdul Manaf SA, Mohamad Fuzi SFZ, Low KO, Hegde G, Abdul Manas NH, Md Illias R, et al.
    Appl Microbiol Biotechnol, 2021 Nov;105(21-22):8531-8544.
    PMID: 34611725 DOI: 10.1007/s00253-021-11616-0
    Carbon nanomaterials, due to their catalytic activity and high surface area, have potential as cell immobilization supports to increase the production of xylanase. Recombinant Kluyveromyces lactis used for xylanase production was integrated into a polymeric gel network with carbon nanomaterials. Carbon nanomaterials were pretreated before cell immobilization with hydrochloric acid (HCl) treatment and glutaraldehyde (GA) crosslinking, which contributes to cell immobilization performance. Carbon nanotubes (CNTs) and graphene oxide (GO) were further screened using a Plackett-Burman experimental design. Cell loading and agar concentration were the most important factors in xylanase production with low cell leakage. Under optimized conditions, xylanase production was increased by more than 400% compared to free cells. Immobilized cell material containing such high cell densities may exhibit new and unexplored beneficial properties because the cells comprise a large fraction of the component. The use of carbon nanomaterials as a cell immobilization support along with the entrapment method successfully enhances the production of xylanase, providing a new route to improved bioprocessing, particularly for the production of enzymes. KEY POINTS: • Carbon nanomaterials (CNTs, GO) have potential as cell immobilization supports. • Entrapment in a polymeric gel network provides space for xylanase production. • Plackett-Burman design screen for the most important factor for cell immobilization.
    Matched MeSH terms: Research Design
  7. Lim GP, Soon CF, Ma NL, Morsin M, Nayan N, Ahmad MK, et al.
    Environ Res, 2021 10;201:111592.
    PMID: 34175291 DOI: 10.1016/j.envres.2021.111592
    MXene based nanomaterial is an uprising two-dimensional material gaining tremendous scientific attentions due to its versatile properties for the applications in electronic devices, power generation, sensors, drug delivery, and biomedicine. However, the cytotoxic effects of MXene still remained a huge concern. Therefore, stringent analysis of biocompatibility of MXene is an essential requirement before introduction to human physiological system. Several in vitro and in vivo toxicological studies have been reported to investigate the interactions between MXenes with living organisms such as microbes, mammalian cells and animal models. The biological response and cytotoxicity reported were dependent on the physicochemical properties of MXene. The biocompatibility and cytotoxicity of MXene were dependent on size, dose, and surface coating. This review demystifies the in vitro and in vivo biocompatibility studies associated with MXene. Various methods proposed to mitigate the cytotoxicity of MXene for in vivo applications were revealed. The machine learning methods were developed to predict the cytotoxicity of experimentally synthesized MXene compounds. Finally, we also discussed the current research gaps of applying MXenes in biomedical interventions.
    Matched MeSH terms: Research Design
  8. Nagendrababu V, Murray PE, Ordinola-Zapata R, Peters OA, Rôças IN, Siqueira JF, et al.
    Int Endod J, 2021 Sep;54(9):1491-1515.
    PMID: 33982298 DOI: 10.1111/iej.13565
    Guidance to authors is needed to prevent their waste of talent, time and resources in writing manuscripts that will never be published in the highest-quality journals. Laboratory studies are probably the most common type of endodontic research projects because they make up the majority of manuscripts submitted for publication. Unfortunately, most of these manuscripts fail the peer-review process, primarily due to critical flaws in the reporting of the methods and results. Here, in order to guide authors, the Preferred Reporting Items for study Designs in Endodontology (PRIDE) team developed new reporting guidelines for laboratory-based studies: the Preferred Reporting Items for Laboratory studies in Endodontology (PRILE) 2021 guidelines. The PRILE 2021 guidelines were developed exclusively for the area of Endodontology by integrating and adapting the modified CONSORT checklist of items for reporting in vitro studies of dental materials and the Clinical and Laboratory Images in Publications (CLIP) principles. The process of developing the PRILE 2021 guidelines followed the recommendations of the Guidance for Developers of Health Research Reporting Guidelines. The aim of the current document is to provide authors with an explanation for each of the items in the PRILE 2021 checklist and flowchart with examples from the literature, and to provide advice from peer-reviewers and editors about how to solve each problem in manuscripts prior to their peer-review. The Preferred Reporting Items for study Designs in Endodontology (PRIDE) website (http://pride-endodonticguidelines.org/prile/) provides a link to the PRILE 2021 explanation and elaboration document as well as to the checklist and flowchart.
    Matched MeSH terms: Research Design
  9. Nagendrababu V, Murray PE, Ordinola-Zapata R, Peters OA, Rôças IN, Siqueira JF, et al.
    Int Endod J, 2021 Sep;54(9):1482-1490.
    PMID: 33938010 DOI: 10.1111/iej.13542
    Reproducible, skilfully conducted and unbiased laboratory studies provide new knowledge, which can inform clinical research and eventually translate into better patient care. To help researchers improve the quality and reproducibility of their research prior to a publication peer-review, this paper describes the process that was followed during the development of the Preferred Reporting Items for Laboratory studies in Endodontology (PRILE) 2021 guidelines and which used a well-documented consensus-based methodology. A steering committee was created with eight individuals (PM, RO, OP, IR, JS, EP, JJ and SP), plus the project leaders (PD, VN). The steering committee prepared an initial checklist by combining and adapting items from the modified Consolidated Statement of Reporting Trials checklist for reporting in vitro studies of dental materials and the Clinical and Laboratory Images in Publications principles as well as adding several new items. The steering committee then formed a PRILE Delphi Group (PDG) and PRILE Online Meeting Group (POMG) to provide expert advice and feedback on the initial draft checklist and flowchart. The members of the PDG participated in an online Delphi process to achieve consensus on the items within the PRILE 2021 checklist and the accompanying flowchart for clarity and suitability. The PRILE checklist and flowchart developed by the online Delphi process were discussed further by the POMG. This online meeting was conducted on 12 February 2021 via the Zoom platform. Following this meeting, the steering committee developed a final version of the PRILE 2021 guidelines and flowchart, which was piloted by several authors when writing up a laboratory study for publication. Authors are encouraged to use the PRILE 2021 guidelines and flowchart to improve the clarity, completeness and quality of reports describing laboratory studies in Endodontology. The PRILE 2021 checklist and flowchart are freely available and downloadable from the Preferred Reporting Items for study Designs in Endodontology website (http://pride-endodonticguidelines.org/prile/).
    Matched MeSH terms: Research Design
  10. Ali SH, Ahmad Rahman NH, Mohd Shariff N, Karim J, Chin KY
    J Adv Nurs, 2021 Sep;77(9):3933-3939.
    PMID: 34028853 DOI: 10.1111/jan.14880
    AIMS: To determine the challenges perceived by final-year nursing students in the clinical learning environment.

    DESIGN: Data-based convergent mixed-method systematic review.

    METHODS: Three electronic databases (Web of Science, Scopus, and Cumulative Index to Nursing and Allied Health Literature) will be used in the identification stage. The first search will use the search string for each database to identify relevant studies. The articles retrieved will be screened by year of publication, article type and language. Abstracts and full-text of selected studies will be screened for eligibility independently by a minimum of two reviewers. The reference lists will be manually screened to identify additional publications. The quality assessment will be conducted by two reviewers using the Mixed Methods Appraisal Tools. Quantitative and mixed-method studies will be transformed into qualitative. A thematic approach will be used to synthesize and report the data. Ethics approval and funding have been approved in April 2020.

    DISCUSSION: This study will synthesize the types of challenges perceived by final-year undergraduate nursing students in different clinical learning environments across the country.

    IMPACT: The proposed study findings will help nursing education stakeholders and faculty provide assistance to final-year nursing students in their transition year to become registered nurses.

    Matched MeSH terms: Research Design
  11. Eu CY, Tang TB, Lin CH, Lee LH, Lu CK
    Sensors (Basel), 2021 Aug 20;21(16).
    PMID: 34451072 DOI: 10.3390/s21165630
    Colorectal cancer has become the third most commonly diagnosed form of cancer, and has the second highest fatality rate of cancers worldwide. Currently, optical colonoscopy is the preferred tool of choice for the diagnosis of polyps and to avert colorectal cancer. Colon screening is time-consuming and highly operator dependent. In view of this, a computer-aided diagnosis (CAD) method needs to be developed for the automatic segmentation of polyps in colonoscopy images. This paper proposes a modified SegNet Visual Geometry Group-19 (VGG-19), a form of convolutional neural network, as a CAD method for polyp segmentation. The modifications include skip connections, 5 × 5 convolutional filters, and the concatenation of four dilated convolutions applied in parallel form. The CVC-ClinicDB, CVC-ColonDB, and ETIS-LaribPolypDB databases were used to evaluate the model, and it was found that our proposed polyp segmentation model achieved an accuracy, sensitivity, specificity, precision, mean intersection over union, and dice coefficient of 96.06%, 94.55%, 97.56%, 97.48%, 92.3%, and 95.99%, respectively. These results indicate that our model performs as well as or better than previous schemes in the literature. We believe that this study will offer benefits in terms of the future development of CAD tools for polyp segmentation for colorectal cancer diagnosis and management. In the future, we intend to embed our proposed network into a medical capsule robot for practical usage and try it in a hospital setting with clinicians.
    Matched MeSH terms: Research Design
  12. Masseran N
    PMID: 34444503 DOI: 10.3390/ijerph18168751
    This study proposes the concept of duration (D) and severity (S) measures, which were derived from unhealthy air pollution events. In parallel with that, the application of a copula model is proposed to evaluate unhealthy air pollution events with respect to their duration and severity characteristics. The bivariate criteria represented by duration and severity indicate their structural dependency, long-tail, and non-identically marginal distributions. A copula approach can provide a good statistical tool to deal with these issues and enable the extraction of valuable information from air pollution data. Based on the copula model, several statistical measurements are proposed for describing the characteristics of unhealthy air pollution events, including the Kendall's τ correlation of the copula, the conditional probability of air pollution severity based on a given duration, the joint OR/AND return period, and the conditional D|S and conditional S|D return periods. A case study based on air pollution data indices was conducted in Klang, Malaysia. The results indicate that a copula approach is beneficial for deriving valuable information for planning and mitigating the risks of unhealthy air pollution events.
    Matched MeSH terms: Research Design
  13. Mamikutty R, Aly AS, Marhazlinda J
    Int J Environ Res Public Health, 2021 Aug 15;18(16).
    PMID: 34444374 DOI: 10.3390/ijerph18168623
    In conducting a systematic review, assessing the risk of bias of the included studies is a vital step; thus, choosing the most pertinent risk of bias (ROB) tools is crucial. This paper determined the most appropriate ROB tools for assessing observational studies in a systematic review assessing the association between anthropometric measurements and dental caries among children. First, we determined the ROB tools used in previous reviews on a similar topic. Subsequently, we reviewed articles on ROB tools to identify the most recommended ROB tools for observational studies. Of the twelve ROB tools identified from the previous steps, three ROB tools that best fit the eight criteria of a good ROB tool were the Newcastle-Ottawa Scale (NOS) for cohort and case-control studies, and Agency for Healthcare Research and Quality (AHRQ) and the Effective Public Health Practice Project (EPHPP) for a cross-sectional study. We further assessed the inter-rater reliability for all three tools by analysing the percentage agreement, inter-class correlation coefficient (ICC) and kappa score. The overall percentage agreements and reliability scores of these tools ranged from good to excellent. Two ROB tools for the cross-sectional study were further evaluated qualitatively against nine of a tool's advantages and disadvantages. Finally, the AHRQ and NOS were selected as the most appropriate ROB tool to assess cross-sectional and cohort studies in the present review.
    Matched MeSH terms: Research Design
  14. Al-Ziftawi NH, Shafie AA, Mohamed Ibrahim MI
    Expert Rev Pharmacoecon Outcomes Res, 2021 Aug;21(4):655-666.
    PMID: 32657174 DOI: 10.1080/14737167.2020.1794826
    BACKGROUND: Pharmacoeconomic evaluation is important for breast-cancer medications due to their high costs. To our knowledge, no systematic literature reviews of pharmacoeconomic studies for breast-cancer medication use are present in developing-countries.

    OBJECTIVES: To systematically review the existing cost-effectiveness evaluations of breast-cancer medication in developing-countries.

    METHODOLOGY: A systematic literature search was performed in PubMed, EMBASE, SCOPUS, and EconLit. Two researchers determined the final articles, extracted data, and evaluated their quality using the Quality of Health-Economic Studies (QHES) tool. The interclass-correlation-coefficient (ICC) was calculated to assess interrater-reliability. Data were summarized descriptively.

    RESULTS: Fourteen pharmacoeconomic studies published from 2009 to 2019 were included. Thirteen used patient-life-years as their effectiveness unit, of which 10 used quality-adjusted life-years. Most of the evaluations focused on trastuzumab as a single agent or on regimens containing trastuzumab (n = 10). The conclusion of cost-effectiveness analysis varied among the studies. All the studies were of high quality (QHES score >75). Interrater reliability between the two reviewers was high (ICC = 0.76).

    CONCLUSION: In many studies included in the review, the use of breast-cancer drugs in developing countries was not cost-effective. Yet, more pharmacoeconomic evaluations for the use of recently approved agents in different disease stages are needed in developing countries.

    Matched MeSH terms: Research Design
  15. Ooi CP, Yusof Khan AHK, Abdul Manaf R, Mustafa N, Sukor N, Williamson PR, et al.
    BMJ Open, 2021 Jul 28;11(7):e050231.
    PMID: 34321306 DOI: 10.1136/bmjopen-2021-050231
    INTRODUCTION: Thyroid dysfunctions (TD) are common medical conditions affecting all global populations. Improved healthcare leading to increasing survival rates and delayed diagnosis rendered significant burden of the disease in the increasing number of patients with TD with comorbid illnesses. Therefore, reducing the burden of TD and improving the quality of care are crucial. Existing poor-quality data that guide evidence-based decisions only provide a fragmented picture of clinical care. The different outcomes across studies assessing the effectiveness of treatments impede our ability to synthesise results for determining the most efficient treatments. This project aims to produce a core outcome set (COS), which embeds the multiple complex dimensions of routine clinical care for the effectiveness studies and clinical care of adult patients with TD.

    METHODS AND ANALYSIS: This mixed-method project has two phases. In phase 1, we will identify a list of patient-reported and clinical outcomes through qualitative research and systematic reviews. In phase 2, we will categorise the identified outcomes using the Core Outcome Measures in Effectiveness Trials taxonomy of core domains and the International Classification of Functioning, Disability and Health. We will develop questionnaires from the list of outcomes identified from each domain for the two-round online Delphi exercise, aiming to reach a consensus on the COS. The Delphi process will include patients, carers, researchers and healthcare participants. We will hold an online consensus meeting involving representatives of all key stakeholders to establish the final COS.

    ETHICS AND DISSEMINATION: The study has been reviewed and approved by the Ethics Committee for Research Involving Human Subjects, Universiti Putra Malaysia and the Research Ethics Committee, National University of Malaysia. This proposed COS in TD will improve the value of data, facilitate high-quality evidence synthesis and evidence-based decision-making. Furthermore, we will present the results to participants, in peer-reviewed academic journals and conferences.

    REGISTRATION DETAILS: Core Outcome Measures in Effectiveness Trials (COMET) Initiative database registration: http://www.comet-initiative.org/studies/details/1371.

    Matched MeSH terms: Research Design*
  16. Jayaraman J, Dhar V, Donly KJ, Priya E, Raggio DP, Childers NK, et al.
    BMC Oral Health, 2021 07 23;21(1):369.
    PMID: 34301229 DOI: 10.1186/s12903-021-01698-7
    BACKGROUND: Reporting guidelines for different study designs are currently available to report studies with accuracy and transparency. There is a need to develop supplementary guideline items that are specific to areas within Pediatric Dentistry. This study aims to develop Reporting stAndards for research in PedIatric Dentistry (RAPID) guidelines using a pre-defined expert consensus-based Delphi process.

    METHODS: The development of the RAPID guidelines was based on the Guidance for Developers of Health Research Reporting Guidelines. Following a comprehensive search of the literature, the Executive Group identified ten themes in Pediatric Dentistry and compiled a draft checklist of items under each theme. The themes were categorized as: General, Oral Medicine, Pathology and Radiology, Children with Special Health Care Needs, Sedation and Hospital Dentistry, Behavior Guidance, Dental Caries, Preventive and Restorative Dentistry, Pulp Therapy, Traumatology, and Interceptive Orthodontics. A RAPID Delphi Group (RDG) was formed comprising of 69 members from 15 countries across six continents. Items were scored using a 9-point rating Likert scale. Items achieving a score of seven and above, marked by at least 70% of RDG members were accepted into the RAPID checklist items. Weighted mean scores were calculated for each item. Statistical significance was set at p researchers, authors, reviewers and editors, to ensure that all elements relevant to particular studies are adequately reported.

    Matched MeSH terms: Research Design
  17. Deng L, Ma L, Cheng KK, Xu X, Raftery D, Dong J
    J Proteome Res, 2021 06 04;20(6):3204-3213.
    PMID: 34002606 DOI: 10.1021/acs.jproteome.1c00064
    Metabolite set enrichment analysis (MSEA) has gained increasing research interest for identification of perturbed metabolic pathways in metabolomics. The method incorporates predefined metabolic pathways information in the analysis where metabolite sets are typically assumed to be mutually exclusive to each other. However, metabolic pathways are known to contain common metabolites and intermediates. This situation, along with limitations in metabolite detection or coverage leads to overlapping, incomplete metabolite sets in pathway analysis. For overlapping metabolite sets, MSEA tends to result in high false positives due to improper weights allocated to the overlapping metabolites. Here, we proposed an extended partial least squares (PLS) model with a new sparse scheme for overlapping metabolite set enrichment analysis, named overlapping group PLS (ogPLS) analysis. The weight vector of the ogPLS model was decomposed into pathway-specific subvectors, and then a group lasso penalty was imposed on these subvectors to achieve a proper weight allocation for the overlapping metabolites. Two strategies were adopted in the proposed ogPLS model to identify the perturbed metabolic pathways. The first strategy involves debiasing regularization, which was used to reduce inequalities amongst the predefined metabolic pathways. The second strategy is stable selection, which was used to rank pathways while avoiding the nuisance problems of model parameter optimization. Both simulated and real-world metabolomic datasets were used to evaluate the proposed method and compare with two other MSEA methods including Global-test and the multiblock PLS (MB-PLS)-based pathway importance in projection (PIP) methods. Using a simulated dataset with known perturbed pathways, the average true discovery rate for the ogPLS method was found to be higher than the Global-test and the MB-PLS-based PIP methods. Analysis with a real-world metabolomics dataset also indicated that the developed method was less prone to select pathways with highly overlapped detected metabolite sets. Compared with the two other methods, the proposed method features higher accuracy, lower false-positive rate, and is more robust when applied to overlapping metabolite set analysis. The developed ogPLS method may serve as an alternative MSEA method to facilitate biological interpretation of metabolomics data for overlapping metabolite sets.
    Matched MeSH terms: Research Design
  18. Nagendrababu V, Kishen A, Murray PE, Nekoofar MH, de Figueiredo JAP, Priya E, et al.
    Int Endod J, 2021 Jun;54(6):848-857.
    PMID: 33450080 DOI: 10.1111/iej.13477
    Animal testing is crucial in situations when research on humans is not allowed because of unknown health risks and ethical concerns. The current project aims to develop reporting guidelines exclusively for animal studies in Endodontology, using an established consensus-based methodology. The guidelines have been named: Preferred Reporting Items for Animal Studies in Endodontology (PRIASE) 2021. Nine individuals (PD, VN, AK, PM, MN, JF, EP, JJ and SJ), including the project leaders (PD, VN) formed a steering committee. The steering committee developed a novel checklist by adapting and integrating their animal testing and peer review experience with the Animals in Research: Reporting In Vivo Experiments (ARRIVE) guidelines and also the Clinical and Laboratory Images in Publications (CLIP) principles. A PRIASE Delphi Group (PDG) and PRIASE Online Meeting Group (POMG) were also formed. Thirty-one PDG members participated in the online Delphi process and achieved consensus on the checklist items and flowchart that were used to formulate the PRIASE guidelines. The novel PRIASE 2021 guidelines were discussed with the POMG on 9 September 2020 via a Zoom online video call attended by 21 individuals from across the globe and seven steering committee members. Following the discussions, the guidelines were modified and then piloted by several authors whilst writing a manuscript involving research on animals. The PRIASE 2021 guidelines are a checklist consisting of 11 domains and 43 individual items together with a flowchart. The PRIASE 2021 guidelines are focused on improving the methodological principles, reproducibility and quality of animal studies in order to enhance their reliability as well as repeatability to estimate the effects of endodontic treatments and usefulness for guiding future clinical studies on humans.
    Matched MeSH terms: Research Design*
  19. Nagendrababu V, Kishen A, Murray PE, Nekoofar MH, de Figueiredo JAP, Priya E, et al.
    Int Endod J, 2021 Jun;54(6):858-886.
    PMID: 33492704 DOI: 10.1111/iej.13481
    Laws and ethics require that before conducting human clinical trials, a new material, device or drug may have to undergo testing in animals in order to minimize health risks to humans, unless suitable supporting grandfather data already exist. The Preferred Reporting Items for Animal Studies in Endodontology (PRIASE) 2021 guidelines were developed exclusively for the specialty of Endodontology by integrating and adapting the ARRIVE (Animals in Research: Reporting In Vivo Experiments) guidelines and the Clinical and Laboratory Images in Publications (CLIP) principles using a validated consensus-based methodology. Implementation of the PRIASE 2021 guidelines will reduce potential sources of bias and thus improve the quality, accuracy, reproducibility, completeness and transparency of reports describing animal studies in Endodontology. The PRIASE 2021 guidelines consist of a checklist with 11 domains and 43 individual items and a flowchart. The aim of the current document is to provide an explanation for each item in the PRIASE 2021 checklist and flowchart and is supplemented with examples from the literature in order for readers to understand their significance and to provide usage guidance. A link to the PRIASE 2021 explanation and elaboration document and PRIASE 2021 checklist and flowchart is available on the Preferred Reporting Items for study Designs in Endodontology (PRIDE) website (http://pride-endodonticguidelines.org/priase/).
    Matched MeSH terms: Research Design*
  20. Walters K, Cox A, Yaacob H
    Genet Epidemiol, 2021 Jun;45(4):386-401.
    PMID: 33410201 DOI: 10.1002/gepi.22375
    The Gaussian distribution is usually the default causal single-nucleotide polymorphism (SNP) effect size prior in Bayesian population-based fine-mapping association studies, but a recent study showed that the heavier-tailed Laplace prior distribution provided a better fit to breast cancer top hits identified in genome-wide association studies. We investigate the utility of the Laplace prior as an effect size prior in univariate fine-mapping studies. We consider ranking SNPs using Bayes factors and other summaries of the effect size posterior distribution, the effect of prior choice on credible set size based on the posterior probability of causality, and on the noteworthiness of SNPs in univariate analyses. Across a wide range of fine-mapping scenarios the Laplace prior generally leads to larger 90% credible sets than the Gaussian prior. These larger credible sets for the Laplace prior are due to relatively high prior mass around zero which can yield many noncausal SNPs with relatively large Bayes factors. If using conventional credible sets, the Gaussian prior generally yields a better trade off between including the causal SNP with high probability and keeping the set size reasonable. Interestingly when using the less well utilised measure of noteworthiness, the Laplace prior performs well, leading to causal SNPs being declared noteworthy with high probability, whilst generally declaring fewer than 5% of noncausal SNPs as being noteworthy. In contrast, the Gaussian prior leads to the causal SNP being declared noteworthy with very low probability.
    Matched MeSH terms: Research Design
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