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  1. Dirong G, Nematbakhsh S, Selamat J, Chong PP, Idris LH, Nordin N, et al.
    Molecules, 2021 Oct 28;26(21).
    PMID: 34770913 DOI: 10.3390/molecules26216502
    Chicken is known to be the most common meat type involved in food mislabeling and adulteration. Establishing a method to authenticate chicken content precisely and identifying chicken breeds as declared in processed food is crucial for protecting consumers' rights. Categorizing the authentication method into their respective omics disciplines, such as genomics, transcriptomics, proteomics, lipidomics, metabolomics, and glycomics, and the implementation of bioinformatics or chemometrics in data analysis can assist the researcher in improving the currently available techniques. Designing a vast range of instruments and analytical methods at the molecular level is vital for overcoming the technical drawback in discriminating chicken from other species and even within its breed. This review aims to provide insight and highlight previous and current approaches suitable for countering different circumstances in chicken authentication.
    Matched MeSH terms: Workflow
  2. Zulkapli NA, Sobi S, Mohd Zubaidi NA, Abdullah JM
    Malays J Med Sci, 2016 Jul;23(4):1-4.
    PMID: 27660539 DOI: 10.21315/mjms2016.23.4.1
    The Malaysian Journal of Medical Sciences (MJMS) has conducted a simple analysis of its scholarly publication, based on the auto-generated data compiled from ScholarOne Manuscripts(™), an innovative, web-based, submission and peer-review workflow solution for scholarly publishers. The performance of the MJMS from 2014-2015 is reported on in this editorial, with a focus on the pattern of manuscript submission, geographical contributors and the acceptance-rejection rate. The total number of manuscript submissions has increased from 264 in 2014, to 272 in 2015. Malaysians are the main contributors to the MJMS. The total number of manuscript rejections following the review process was 79 (29.9%) in 2014, increasing to 92 (33.8%) the following year, in accordance with the exacting quality control criteria applied by the journal's editor to the submitted manuscripts.
    Matched MeSH terms: Workflow
  3. Fletcher E, Burns A, Wiering B, Lavu D, Shephard E, Hamilton W, et al.
    BMC Prim Care, 2023 Jan 20;24(1):23.
    PMID: 36670354 DOI: 10.1186/s12875-023-01973-2
    BACKGROUND: Electronic clinical decision support tools (eCDS) are increasingly available to assist General Practitioners (GP) with the diagnosis and management of a range of health conditions. It is unclear whether the use of eCDS tools has an impact on GP workload. This scoping review aimed to identify the available evidence on the use of eCDS tools by health professionals in general practice in relation to their impact on workload and workflow.

    METHODS: A scoping review was carried out using the Arksey and O'Malley methodological framework. The search strategy was developed iteratively, with three main aspects: general practice/primary care contexts, risk assessment/decision support tools, and workload-related factors. Three databases were searched in 2019, and updated in 2021, covering articles published since 2009: Medline (Ovid), HMIC (Ovid) and Web of Science (TR). Double screening was completed by two reviewers, and data extracted from included articles were analysed.

    RESULTS: The search resulted in 5,594 references, leading to 95 full articles, referring to 87 studies, after screening. Of these, 36 studies were based in the USA, 21 in the UK and 11 in Australia. A further 18 originated from Canada or Europe, with the remaining studies conducted in New Zealand, South Africa and Malaysia. Studies examined the use of eCDS tools and reported some findings related to their impact on workload, including on consultation duration. Most studies were qualitative and exploratory in nature, reporting health professionals' subjective perceptions of consultation duration as opposed to objectively-measured time spent using tools or consultation durations. Other workload-related findings included impacts on cognitive workload, "workflow" and dialogue with patients, and clinicians' experience of "alert fatigue".

    CONCLUSIONS: The published literature on the impact of eCDS tools in general practice showed that limited efforts have focused on investigating the impact of such tools on workload and workflow. To gain an understanding of this area, further research, including quantitative measurement of consultation durations, would be useful to inform the future design and implementation of eCDS tools.

    Matched MeSH terms: Workflow
  4. Farook TH, Jamayet NB, Abdullah JY, Asif JA, Rajion ZA, Alam MK
    Comput Biol Med, 2020 03;118:103646.
    PMID: 32174323 DOI: 10.1016/j.compbiomed.2020.103646
    OBJECTIVE: To design and compare the outcome of commercial (CS) and open source (OS) software-based 3D prosthetic templates for rehabilitation of maxillofacial defects using a low powered personal computer setup.

    METHOD: Medical image data for five types of defects were selected, segmented, converted and decimated to 3D polygon models on a personal computer. The models were transferred to a computer aided design (CAD) software which aided in designing the prosthesis according to the virtual models. Two templates were designed for each defect, one by an OS (free) system and one by CS. The parameters for analyses were the virtual volume, Dice similarity coefficient (DSC) and Hausdorff's distance (HD) and were executed by the OS point cloud comparison tool.

    RESULT: There was no significant difference (p > 0.05) between CS and OS when comparing the volume of the template outputs. While HD was within 0.05-4.33 mm, evaluation of the percentage similarity and spatial overlap following the DSC showed an average similarity of 67.7% between the two groups. The highest similarity was with orbito-facial prostheses (88.5%) and the lowest with facial plate prosthetics (28.7%).

    CONCLUSION: Although CS and OS pipelines are capable of producing templates which are aesthetically and volumetrically similar, there are slight comparative discrepancies in the landmark position and spatial overlap. This is dependent on the software, associated commands and experienced decision-making. CAD-based templates can be planned on current personal computers following appropriate decimation.

    Matched MeSH terms: Workflow
  5. Ahmed N, Abbasi MS, Haider S, Ahmed N, Habib SR, Altamash S, et al.
    Biomed Res Int, 2021;2021:3194433.
    PMID: 34532499 DOI: 10.1155/2021/3194433
    Objective: Analyzing and comparing the fit and accuracy of removable partial denture (RPDs) frameworks fabricated with CAD/CAM and rapid prototyping methods with conventional techniques.

    Materials and Methods: The present systematic review was carried out according to PRISMA guidelines. The search was carried out on PubMed/MEDLINE, Cochrane collaboration, Science direct, and Scopus scientific engines using selected MeSH keywords. The articles fulfilling the predefined selection criteria based on the fit and accuracy of removable partial denture (RPD) frameworks constructed from digital workflow (CAD/CAM; rapid prototyping) and conventional techniques were included.

    Results: Nine full-text articles comprising 6 in vitro and 3 in vivo studies were included in this review. The digital RPDs were fabricated in all articles by CAD/CAM selective laser sintering and selective laser melting techniques. The articles that have used CAD/CAM and rapid prototyping technique demonstrated better fit and accuracy as compared to the RPDs fabricated through conventional techniques. The least gaps between the framework and cast (41.677 ± 15.546 μm) were found in RPDs constructed through digital CAD/CAM systems.

    Conclusion: A better accuracy was achieved using CAD/CAM and rapid prototyping techniques. The RPD frameworks fabricated by CAD/CAM and rapid prototyping techniques had clinically acceptable fit, superior precision, and better accuracy than conventionally fabricated RPD frameworks.

    Matched MeSH terms: Workflow
  6. Farook TH, Jamayet NB, Asif JA, Din AS, Mahyuddin MN, Alam MK
    Sci Rep, 2021 04 19;11(1):8469.
    PMID: 33875672 DOI: 10.1038/s41598-021-87240-9
    Palatal defects are rehabilitated by fabricating maxillofacial prostheses called obturators. The treatment incorporates taking deviously unpredictable impressions to facsimile the palatal defects into plaster casts for obturator fabrication in the dental laboratory. The casts are then digitally stored using expensive hardware to prevent physical damage or data loss and, when required, future obturators are digitally designed, and 3D printed. Our objective was to construct and validate an economic in-house smartphone-integrated stereophotogrammetry (SPINS) 3D scanner and to evaluate its accuracy in designing prosthetics using open source/free (OS/F) digital pipeline. Palatal defect models were scanned using SPINS and its accuracy was compared against the standard laser scanner for virtual area and volumetric parameters. SPINS derived 3D models were then used to design obturators by using (OS/F) software. The resultant obturators were virtually compared against standard medical software designs. There were no significant differences in any of the virtual parameters when evaluating the accuracy of both SPINS, as well as OS/F derived obturators. However, limitations in the design process resulted in minimal dissimilarities. With further improvements, SPINS based prosthetic rehabilitation could create a viable, low cost method for rural and developing health services to embrace maxillofacial record keeping and digitised prosthetic rehabilitation.
    Matched MeSH terms: Workflow
  7. Abd Elaziz M, Abualigah L, Ibrahim RA, Attiya I
    Comput Intell Neurosci, 2021;2021:9114113.
    PMID: 34976046 DOI: 10.1155/2021/9114113
    Instead of the cloud, the Internet of things (IoT) activities are offloaded into fog computing to boost the quality of services (QoSs) needed by many applications. However, the availability of continuous computing resources on fog computing servers is one of the restrictions for IoT applications since transmitting the large amount of data generated using IoT devices would create network traffic and cause an increase in computational overhead. Therefore, task scheduling is the main problem that needs to be solved efficiently. This study proposes an energy-aware model using an enhanced arithmetic optimization algorithm (AOA) method called AOAM, which addresses fog computing's job scheduling problem to maximize users' QoSs by maximizing the makespan measure. In the proposed AOAM, we enhanced the conventional AOA searchability using the marine predators algorithm (MPA) search operators to address the diversity of the used solutions and local optimum problems. The proposed AOAM is validated using several parameters, including various clients, data centers, hosts, virtual machines, tasks, and standard evaluation measures, including the energy and makespan. The obtained results are compared with other state-of-the-art methods; it showed that AOAM is promising and solved task scheduling effectively compared with the other comparative methods.
    Matched MeSH terms: Workflow
  8. Halim N, Kuntom A, Shinde R, Banerjee K
    J AOAC Int, 2020 Sep 01;103(5):1237-1242.
    PMID: 33241391 DOI: 10.1093/jaoacint/qsaa041
    BACKGROUND: Indaziflam (IND) is a herbicide that is used in palm oil plantations for broad spectrum management of weeds. Until now, no validated method has been available for residue estimation of this herbicide in palm oil products.

    OBJECTIVE: In this study, we report a rapid method for the residue analysis of IND and its metabolites, viz., IND-carboxylic acid, diaminotriazine, and triazine indanone in a wide range of palm oil matrices using liquid chromatography-tandem mass spectrometry (LC-MS/MS).

    METHOD: The optimized sample preparation workflows included two options: (1) acetonitrile extraction (QuEChERS workflow), followed by freezing at -80°C and (2) acetonitrile extraction, followed by cleanup through a C18 solid phase extraction (SPE) cartridge. The optimized LC runtime was 7 min. All these analytes were estimated by LC-MS/MS multiple reaction monitoring.

    RESULTS: Both sample preparation methods provided similar method performance and acceptable results. The limit of quantification (LOQ) of IND, IND-carboxylic acid, and triazine indanone was 0.001 mg/kg. For diaminotriazine, the LOQ was 0.005 mg/kg. The method accuracy and precision complied with the SANTE/12682/2019 guidelines of analytical quality control.

    CONCLUSIONS: The potentiality of the method lies in a high throughput analysis of IND and its metabolites in a single chromatographic run with high selectivity and sensitivity. Considering its fit-for-purpose performance, the method can be implemented in regulatory testing of IND residues in a wide range of palm oil matrices that are consumed and traded worldwide.

    HIGHLIGHTS: This work has provided a validated method for simultaneous residue analysis of indaziflam and its metabolites in crude palm oil and its derived matrices with high sensitivity, selectivity, and throughput.

    Matched MeSH terms: Workflow
  9. Belhaj AF, Elraies KA, Alnarabiji MS, Abdul Kareem FA, Shuhli JA, Mahmood SM, et al.
    Chem Eng J, 2021 Feb 15;406:127081.
    PMID: 32989375 DOI: 10.1016/j.cej.2020.127081
    Throughout the application of enhanced oil recovery (EOR), surfactant adsorption is considered the leading constraint on both the successful implementation and economic viability of the process. In this study, a comprehensive investigation on the adsorption behaviour of nonionic and anionic individual surfactants; namely, alkyl polyglucoside (APG) and alkyl ether carboxylate (AEC) was performed using static adsorption experiments, isotherm modelling using (Langmuir, Freundlich, Sips, and Temkin models), adsorption simulation using a state-of-the-art method, binary mixture prediction using the modified extended Langmuir (MEL) model, and artificial neural network (ANN) prediction. Static adsorption experiments revealed higher adsorption capacity of APG as compared to AEC, with sips being the most fitted model with R2 (0.9915 and 0.9926, for APG and AEC respectively). It was indicated that both monolayer and multilayer adsorption took place in a heterogeneous adsorption system with non-uniform surfactant molecules distribution, which was in remarkable agreement with the simulation results. The (APG/AEC) binary mixture prediction depicted contradictory results to the experimental individual behaviour, showing that AEC had more affinity to adsorb in competition with APG for the adsorption sites on the rock surface. The adopted ANN model showed good agreement with the experimental data and the simulated adsorption values for APG and AEC showed a decreasing trend as temperature increases. Simulating the impact of binary surfactant adsorption can provide a tremendous advantage of demonstrating the binary system behaviour with less experimental data. The utilization of ANN for such prediction procedure can minimize the experimental time, operating cost and give feasible predictions compared to other computational methods. The integrated workflow followed in this study is quite innovative as it has not been employed before for surfactant adsorption studies.
    Matched MeSH terms: Workflow
  10. Lim HM, Teo CH, Ng CJ, Chiew TK, Ng WL, Abdullah A, et al.
    JMIR Med Inform, 2021 Feb 26;9(2):e23427.
    PMID: 33600345 DOI: 10.2196/23427
    BACKGROUND: During the COVID-19 pandemic, there was an urgent need to develop an automated COVID-19 symptom monitoring system to reduce the burden on the health care system and to provide better self-monitoring at home.

    OBJECTIVE: This paper aimed to describe the development process of the COVID-19 Symptom Monitoring System (CoSMoS), which consists of a self-monitoring, algorithm-based Telegram bot and a teleconsultation system. We describe all the essential steps from the clinical perspective and our technical approach in designing, developing, and integrating the system into clinical practice during the COVID-19 pandemic as well as lessons learned from this development process.

    METHODS: CoSMoS was developed in three phases: (1) requirement formation to identify clinical problems and to draft the clinical algorithm, (2) development testing iteration using the agile software development method, and (3) integration into clinical practice to design an effective clinical workflow using repeated simulations and role-playing.

    RESULTS: We completed the development of CoSMoS in 19 days. In Phase 1 (ie, requirement formation), we identified three main functions: a daily automated reminder system for patients to self-check their symptoms, a safe patient risk assessment to guide patients in clinical decision making, and an active telemonitoring system with real-time phone consultations. The system architecture of CoSMoS involved five components: Telegram instant messaging, a clinician dashboard, system administration (ie, back end), a database, and development and operations infrastructure. The integration of CoSMoS into clinical practice involved the consideration of COVID-19 infectivity and patient safety.

    CONCLUSIONS: This study demonstrated that developing a COVID-19 symptom monitoring system within a short time during a pandemic is feasible using the agile development method. Time factors and communication between the technical and clinical teams were the main challenges in the development process. The development process and lessons learned from this study can guide the future development of digital monitoring systems during the next pandemic, especially in developing countries.

    Matched MeSH terms: Workflow
  11. Khalid H, Hashim SJ, Ahmad SMS, Hashim F, Chaudhary MA
    Sensors (Basel), 2021 Feb 18;21(4).
    PMID: 33670675 DOI: 10.3390/s21041428
    The development of the industrial Internet of Things (IIoT) promotes the integration of the cross-platform systems in fog computing, which enable users to obtain access to multiple application located in different geographical locations. Fog users at the network's edge communicate with many fog servers in different fogs and newly joined servers that they had never contacted before. This communication complexity brings enormous security challenges and potential vulnerability to malicious threats. The attacker may replace the edge device with a fake one and authenticate it as a legitimate device. Therefore, to prevent unauthorized users from accessing fog servers, we propose a new secure and lightweight multi-factor authentication scheme for cross-platform IoT systems (SELAMAT). The proposed scheme extends the Kerberos workflow and utilizes the AES-ECC algorithm for efficient encryption keys management and secure communication between the edge nodes and fog node servers to establish secure mutual authentication. The scheme was tested for its security analysis using the formal security verification under the widely accepted AVISPA tool. We proved our scheme using Burrows Abdi Needham's logic (BAN logic) to prove secure mutual authentication. The results show that the SELAMAT scheme provides better security, functionality, communication, and computation cost than the existing schemes.
    Matched MeSH terms: Workflow
  12. Agbolade O, Nazri A, Yaakob R, Ghani AAA, Cheah YK
    PeerJ Comput Sci, 2020;6:e249.
    PMID: 33816901 DOI: 10.7717/peerj-cs.249
    Over the years, neuroscientists and psychophysicists have been asking whether data acquisition for facial analysis should be performed holistically or with local feature analysis. This has led to various advanced methods of face recognition being proposed, and especially techniques using facial landmarks. The current facial landmark methods in 3D involve a mathematically complex and time-consuming workflow involving semi-landmark sliding tasks. This paper proposes a homologous multi-point warping for 3D facial landmarking, which is verified experimentally on each of the target objects in a given dataset using 500 landmarks (16 anatomical fixed points and 484 sliding semi-landmarks). This is achieved by building a template mesh as a reference object and applying this template to each of the targets in three datasets using an artificial deformation approach. The semi-landmarks are subjected to sliding along tangents to the curves or surfaces until the bending energy between a template and a target form is minimal. The results indicate that our method can be used to investigate shape variation for multiple datasets when implemented on three databases (Stirling, FRGC and Bosphorus).
    Matched MeSH terms: Workflow
  13. Lee BK, Tiong KH, Chang JK, Liew CS, Abdul Rahman ZA, Tan AC, et al.
    BMC Genomics, 2017 01 25;18(Suppl 1):934.
    PMID: 28198666 DOI: 10.1186/s12864-016-3260-7
    BACKGROUND: The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed to enable effective drugs to enter the clinic. Precision medicine has demonstrated that genetic features of cancer cells can be used for predicting drug response, and emerging evidence suggest that gene-drug connections could be predicted more accurately by exploring the cumulative effects of many genes simultaneously.

    RESULTS: We developed DeSigN, a web-based tool for predicting drug efficacy against cancer cell lines using gene expression patterns. The algorithm correlates phenotype-specific gene signatures derived from differentially expressed genes with pre-defined gene expression profiles associated with drug response data (IC50) from 140 drugs. DeSigN successfully predicted the right drug sensitivity outcome in four published GEO studies. Additionally, it predicted bosutinib, a Src/Abl kinase inhibitor, as a sensitive inhibitor for oral squamous cell carcinoma (OSCC) cell lines. In vitro validation of bosutinib in OSCC cell lines demonstrated that indeed, these cell lines were sensitive to bosutinib with IC50 of 0.8-1.2 μM. As further confirmation, we demonstrated experimentally that bosutinib has anti-proliferative activity in OSCC cell lines, demonstrating that DeSigN was able to robustly predict drug that could be beneficial for tumour control.

    CONCLUSIONS: DeSigN is a robust method that is useful for the identification of candidate drugs using an input gene signature obtained from gene expression analysis. This user-friendly platform could be used to identify drugs with unanticipated efficacy against cancer cell lines of interest, and therefore could be used for the repurposing of drugs, thus improving the efficiency of drug development.

    Matched MeSH terms: Workflow
  14. Tiong KH, Chang JK, Pathmanathan D, Hidayatullah Fadlullah MZ, Yee PS, Liew CS, et al.
    Biotechniques, 2018 12;65(6):322-330.
    PMID: 30477327 DOI: 10.2144/btn-2018-0072
    We describe a novel automated cell detection and counting software, QuickCount® (QC), designed for rapid quantification of cells. The Bland-Altman plot and intraclass correlation coefficient (ICC) analyses demonstrated strong agreement between cell counts from QC to manual counts (mean and SD: -3.3 ± 4.5; ICC = 0.95). QC has higher recall in comparison to ImageJauto, CellProfiler and CellC and the precision of QC, ImageJauto, CellProfiler and CellC are high and comparable. QC can precisely delineate and count single cells from images of different cell densities with precision and recall above 0.9. QC is unique as it is equipped with real-time preview while optimizing the parameters for accurate cell count and needs minimum hands-on time where hundreds of images can be analyzed automatically in a matter of milliseconds. In conclusion, QC offers a rapid, accurate and versatile solution for large-scale cell quantification and addresses the challenges often faced in cell biology research.
    Matched MeSH terms: Workflow
  15. Manousopoulou A, Hamdan M, Fotopoulos M, Garay-Baquero DJ, Teng J, Garbis SD, et al.
    Proteomics Clin Appl, 2019 05;13(3):e1800153.
    PMID: 30488576 DOI: 10.1002/prca.201800153
    BACKGROUND: Endometriosis affects about 4% of women in the reproductive age and is associated with subfertility. The aim of the present study is to examine the integrated quantitative proteomic profile of eutopic endometrium and serum from women with endometriosis compared to controls in order to identify candidate disease-specific serological markers.

    METHODS: Eutopic endometrium and serum from patients with endometriosis (n = 8 for tissue and n = 4 for serum) are, respectively, compared to endometrium and serum from females without endometriosis (n = 8 for tissue and n = 4 for serum) using a shotgun quantitative proteomics method. All study participants are at the proliferative phase of their menstrual cycle.

    RESULTS: At the tissue and serum level, 1214 and 404 proteins are differentially expressed (DEPs) in eutopic endometrium and serum, respectively, of women with endometriosis versus controls. Gene ontology analysis shows that terms related to immune response/inflammation, cell adhesion/migration, and blood coagulation are significantly enriched in the DEPs of eutopic endometrium, as well as serum. Twenty-one DEPs have the same trend of differential expression in both matrices and can be further examined as potential disease- and tissue-specific serological markers of endometriosis.

    CONCLUSIONS: The present integrated proteomic profiling of eutopic endometrium and serum from women with endometriosis identify promising serological markers that can be further validated in larger cohorts for the minimally invasive diagnosis of endometriosis.

    Matched MeSH terms: Workflow
  16. Vogel K, Karltun J, Yeow PH, Eklund J
    Meat Sci, 2015 Jul;105:81-8.
    PMID: 25828161 DOI: 10.1016/j.meatsci.2015.03.009
    The beef industry worldwide is showing a trend towards increased cutting pace aimed at higher profits. However, prior research in the duck meat industry suggested that a higher cutting pace reduced quality and yield, leading to losses. This study aimed to test this hypothesis by investigating the effects of varying beef-cutting paces on yield, quality and economy. A field experiment was conducted on six workers cutting beef fillet, sirloin and entrecôte. Three types of paces were sequentially tested: Baseline (i.e., status quo), 'Quantity focus' (i.e., pace required to maximise quantity) and 'Quality focus' (i.e., pace required to minimise errors). The results showed a significant drop in yield, increased rate of quality deficiency and economic losses with the change to 'Quantity focus' (from Baseline and 'Quality focus') for all meat types. Workers supported these results and also added health problems to the list. The results confirmed that an increased cutting pace is unprofitable.
    Matched MeSH terms: Workflow
  17. Olufisayo O, Mohd Yusof M, Ezat Wan Puteh S
    Stud Health Technol Inform, 2018;255:112-116.
    PMID: 30306918
    Despite the widespread use of clinical decision support systems with its alert function, there has been an increase in medical errors, adverse events as well as issues regarding patient safety, quality and efficiency. The appropriateness of CDSS must be properly evaluated by ensuring that CDSS provides clinicians with useful information at the point of care. Inefficient clinical workflow affects clinical processes; hence, it is necessary to identify processes in the healthcare system that affect provider's workflow. The Lean method was used to eliminate waste (non-value added) activities that affect the appropriate use of CDSS. Ohno's seven waste model was used to categorize waste in the context of healthcare and information technology.
    Matched MeSH terms: Workflow*
  18. Olakotan O, Mohd Yusof M, Ezat Wan Puteh S
    Stud Health Technol Inform, 2020 Jun 16;270:906-910.
    PMID: 32570513 DOI: 10.3233/SHTI200293
    Clinical decision support systems (CDSSs) provides vital information for managing patients by advising clinicians through an alert or reminders about adverse events and medication errors. Clinicians receive a high number of alerts, resulting in alert override and workflow disruptions. A systematic review was carried out to identify factors affecting CDSS alert appropriateness in supporting clinical workflows using a recently introduced framework. The review findings identified several influencing factors of CDSS alert appropriateness including: technology (usability, alert presentation, workload and data entry), human (training, knowledge and skills, attitude and behavior), organization (rules and regulation, privacy and security) and process (waste, delay, tuning and optimization). The findings can be used to guide the design of CDSS alert and minimise potential safety hazards associated with CDSS use.
    Matched MeSH terms: Workflow
  19. Emrizal R, Hamdani HY, Firdaus-Raih M
    Int J Mol Sci, 2021 Aug 09;22(16).
    PMID: 34445259 DOI: 10.3390/ijms22168553
    The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule's functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.
    Matched MeSH terms: Workflow
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