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- ItemA data quality framework for process mining of electronic health record data(Institute of Electrical and Electronics Engineers (IEEE), 2018-07) Fox, Frank; Aggarwal, Vishal R.; Whelton, Helen; Johnson, OwenReliable research demands data of known quality. This can be very challenging for electronic health record (EHR) based research where data quality issues can be complex and often unknown. Emerging technologies such as process mining can reveal insights into how to improve care pathways but only if technological advances are matched by strategies and methods to improve data quality. The aim of this work was to develop a care pathway data quality framework (CP-DQF) to identify, manage and mitigate EHR data quality in the context of process mining, using dental EHRs as an example. Objectives: To: 1) Design a framework implementable within our e-health record research environments; 2) Scale it to further dimensions and sources; 3) Run code to mark the data; 4) Mitigate issues and provide an audit trail. Methods: We reviewed the existing literature covering data quality frameworks for process mining and for data mining of EHRs and constructed a unified data quality framework that met the requirements of both. We applied the framework to a practical case study mining primary care dental pathways from an EHR covering 41 dental clinics and 231,760 patients in the Republic of Ireland. Results: Applying the framework helped identify many potential data quality issues and mark-up every data point affected. This enabled systematic assessment of the data quality issues relevant to mining care pathways. Conclusion: The complexity of data quality in an EHR-data research environment was addressed through a re-usable and comprehensible framework that met the needs of our case study. This structured approach saved time and brought rigor to the management and mitigation of data quality issues. The resulting metadata is being used within cohort selection, experiment and process mining software so that our research with this data is based on data of known quality. Our framework is a useful starting point for process mining researchers to address EHR data quality concerns.
- ItemDevelopment of an observational protocol for reducing and mitigating workload and the risk of Retained Foreign Objects(Technological University Dublin, 2018) Kay, Alison; O'Byrne, Katie; Corrigan, Siobhan; Callari, Tiziana C.; Slattery, Dubhfeasa; Smyth, David; Turner, Michael; Bennett, Deirdre; Logan, Jamie; Cromie, Sam; Health Research BoardRetained Foreign Objects are an uncommon but costly problem in today's healthcare. It regards the outcome after an unintended item is left behind in a patient after an invasive procedure. This paper presents the development of an observational protocol used for surgical observations in the FOR_RaM Project. The FOR_RaM or Foreign Object Retention - Reduction and Mitigation project aims to analyze and understand the problem of retained foreign objects in surgery and maternity settings in Ireland, develop hospital specific foreign object management processes and implementation roadmaps, with a focus on reducing and mitigating the risk of foreign object retention. This paper discusses the methodology used for developing an observational protocol as part of a socio-technical multi-methods approach in order to gain a better understanding of the existing practices that take place in these settings, including workload, operational processes and collaboration. Emphasis is placed on the observational template development and design, observational tasks, critical points, procedures and protocols followed throughout. This observation protocol has facilitated the collection of critical data and been successful in identifying good practices and potential areas for improvement.
- ItemIn-hospital adverse drug reactions in hospitalised older adults - a systematic review(Oxford University Press, 2018-09-17) Jennings, Emma L. M.; Murphy, Kevin D.; Gallagher, Paul F.; O'Mahony, Denis; Horizon 2020Background: Recent studies indicate that 1 in 4 older people experience an ADR in hospital. This systematic review [SR] aims to evaluate in-hospital ADRs in hospitalised older-adults in terms of incidence and prevalence, most commonly involved drug classes, severity, and consequences. Methods: Using PRISMA methodology [PROSPERO registration CRD42018079095], we systematically searched PubMed, Embase and Ebsco-CINAHL, Cochrane Library and library hosted academic sources, Google® scholar, and ‘grey’ literature. Search terms included aged, ADRs, hospitalized, multi-morbid, polypharmacy and hospital-acquired. A hand search of bibliography lists from relevant editorials and systematic reviews was conducted. We included studies of all languages and all dates up to and including the date of the final search [15/01/2018]. We included all studies that reported ADRs either as a primary or secondary outcome in patients aged ≥ 65 years who were hospitalised at time of ADR occurrence. Two researchers screened all papers for inclusion, risk of bias and data extraction. Results: Initial search yielded 1721 abstracts, 200 underwent full text screening. 60 papers were potentially suitable for inclusion; 48 papers contained pooled all-ages data, 12 papers reported directly on ADRs in our age cohort [2 papers reported the same data]. 11 studies were analysed, involving 4424 patients; 24%  had experienced ADRs. 7 studies reported severity (n = 707); 31%  of ADRs were described as severe. 5 papers reported on post-ADR outcomes i.e. hospital length of stay [LOS, n = 3], death [n = 1] and functional decline [n = 1]. Frequency of culprit drug-groups by system were described in 6 papers [672 ADRs]; 43%  cardiovascular system, 17%  central nervous system, 16%  clotting pathways, 13%  anti-microbials. Conclusion: One in four over 65 years experience an ADR during hospitalisation, one third being severe, and almost half cardiovascular system drugs. Clinical outcomes associated with ADRs are generally poorly described in the literature.
- ItemIn-hospital adverse drug reactions in hospitalised older adults - a systematic review(Springer, 2018-10) Jennings, Emma L. M.; Murphy, Kevin D.; Gallagher, Paul F.; O'Mahony, Denis; Horizon 2020Introduction: Studies indicate 1 in 4 older people experience hospital-related adverse drug reactions [ADRs]. This systematic-review aims to evaluate in-hospital ADRs in hospitalised older-adults in terms of incidence, prevalence, most commonly involved drug classes, severity, and consequences. Methods: Using PRISMA methodology [PROSPERO CRD42018079095], we searched PubMed, Embase, Ebsco-CINAHL, Cochrane Library, library hosted sources, Google scholar, and ‘grey’ literature, using terms; aged, ADRs, hospitalized, multi-morbid, polypharmacy and hospital-acquired. References of editorials and systematic reviews were hand searched. Studies of all languages and dates until 15/01/2018 were included. All studies reporting ADRs outcomes, ≥65 years, hospitalised at time of ADR occurrence were included. Two researchers screened all papers for inclusion, risk of bias and data extraction. Results: Initial search yielded 1721 abstracts, 200 underwent full text screening. 60 were potentially suitable for inclusion; 48 papers reported combined ages, 12 papers reported directly on ADRs in our age cohort [2 papers reported the same data]. 11 studies [4424 patients] were analysed; 24%  experienced ADRs. 7 reported severity (n = 707); 31%  being severe. 5 reported on post-ADR outcomes i.e. length of stay [n = 3], death [n = 1] and functional decline [n = 1]. Frequency of culprit drug-groups were described in 6 [672 ADRs]; 43%  cardiovascular system, 17%  central nervous system, 16%  clotting pathways, 13%  anti-microbials. Conclusions: One in four over 65 years experience an ADR during hospitalisation, one third being severe, and almost half cardiovascular system drugs. Clinical outcomes associated with ADRs are generally poorly described in the literature.
- ItemMechanical catheter navigation with electromagnetic tracking to peripheral airway targets(International Society for Medical Innovation and Technology (iSMIT), 2017) Trauzettel, Fabian; Jaeger, Herman A.; Hofstad, Erlend Fagertun; Kennedy, Marcus P.; Leira, Håkon; Langø, Thomas; Cantillon-Murphy, PádraigLung cancer remains the single most deadly cancer in men and women due to low rates of early detection and treatment. Since non-small cell lung cancer usually starts in the outer airways, targeted minimally invasive biopsy which limits radiation exposure and avoids surgery is highly desirable. Current commercial solutions such as the superDimension (Medtronic Inc., Dublin, Ireland), and SpIN (Veran Medical, St. Louis, USA) systems rely on electromagnetic tracking for virtual navigation. However, clinical outcomes have been unconvincing due to poor accuracy, limitations in instrumentation and the lack of tracked catheters. This work proposes a novel mechanical catheter design with embedded electromagnetic tracking to facilitate tip-tracked navigation without the need for proprietary instruments or probe exchange. The catheter was used to reach peripheral airway targets by multiple users in pre-clinical studies.
- ItemMulti-configuration Raman spectrometer for early stage diagnosis of oral cancer(Society of Photo-Optical Instrumentation Engineers (SPIE), 2022-03-02) Maryam, Siddra; Saito Nogueira, Marcelo; Krishna Moorthy, Shree; Sekar, Sanathana Konugolu Venkata ; Lu, Huihui; Gautam, Rekha; Burke, Ray; Andersson-Engels, Stefan; Ni Riordain, Richeal; Sheahan, Patrick; Huang, Zhiwei; Science Foundation IrelandOral Squamous Cell carcinoma (OSCC) is one of the most common and aggressive oral malignancies. Despite all significant advances in medicine, five-year survival rate is still 40%-60%. Diagnosis in early stages is critical as it can improve the survival rate and the quality of life after treatment. This study aims to develop a strategy for diagnosing oral cancer non-invasively in the early stages and to provide better surgical guidance by differentiating healthy and tumor tissues by using Raman spectroscopy. For this purpose, a multimodal Raman system is developed to detect oral cancer biomarkers in patient’s saliva specimen and to study different tissue types in oral cavity with Raman spectroscopy. The developed system is quite compact, easy to use and portable. It can be easily modified for in vivo and ex vivo analysis and can work in both reflection and transmission mode in case of ex vivo measurements. This paper compares the surface enhancement and background spectra from different plasmonic nanoparticles. Lastly, bovine serum albumin (BSA) and uric acid were used as model analytes to at physiologically relevant concentrations to test the performance of the system.
- ItemNon-invasive multimodal spectroscopic diagnosis for early-stage oral cancer(Optica Publishing Group, 2023) Maryam, Siddra; Ghauri, Daniyal; Sekar, Sanathana Konugolu Venkata; Fahy, Edward; Saito Nogueira, Marcelo; Lu , Huihui; Beffara, Flavien; Humbert, Georges; Burke, Ray; Feeley, Linda; Sheahan, Patrick; Ni Riordain, Richeal; Andersson-Engels, Stefan; Wei Kho, Kiang; Gautam, Rekha; 2023This study aims to develop a multimodal scheme for diagnosing oral cancer non-invasively in its early stages and to assess the performance of an integrated diagnostic platform comprising of Raman and diffuse reflectance spectroscopy systems.
- ItemOpen source airway navigation: initial experiences with CustusX and Anser EMT(International Society for Medical Innovation and Technology (iSMIT), 2017) Jaeger, Herman A.; Trauzettel, Fabian; Hofstad, Erlend Fagertun; Kennedy, Marcus P.; Leira, Håkon; Langø, Thomas; Cantillon-Murphy, PádraigElectromagnetic tracking (EMT) is a common navigation technology used in image guided applications. EMT is particularly useful in procedures where line-of-sight of the operating field is not feasible. We present a major update of the open source electromagnetic tracking platform Anser EMT  and present its results when performing bronchoscopy in a pre-clinical setting using the CustusX navigation suite . The updated system design is open source and free to use and modify under the Berkeley Standard Distribution (BSD) license.
- ItemSparse-denoising methods for extracting desaturation transients in cerebral oxygenation signals of preterm Infants(IEEE, 2021-11) Ashoori, Minoo; Dempsey, Eugene M.; McDonald, Fiona B.; O'Toole, John M.; Science Foundation Ireland
- ItemWorld Workshop on Oral Medicine VIII: Development of a core outcome set for oral lichen planus: The patient perspective(Elsevier Inc., 2023-03-01) Diniz-Freitas, Márcio; López-Pintor, Rosa María; Bissonnette, Caroline; Dan, Hongxia; Kuduva Ramesh, Shilpa Shree; Valdéz, J. Amadeo; Brennan, Michael T.; Burkhart, Nancy W.; Farag, Arwa; Greenberg, Martin S.; Hong, Catherine; Setterfield, Jane F.; Woo, Sook-Bin; Sollecito, Thomas P.; Byrne, Harriet; Robledo-Sierra, Jairo; Taylor, Jennifer; Ni Riordain, RichealObjective: This study aimed to explore the lived experience of patients with oral lichen planus (OLP) and investigate what treatment-related outcomes are the most important to them and should be included in a core outcome set (COS) for OLP. Study Design: A qualitative study involving focus group work with 10 participants was conducted. Interviews with each focus group were held twice: session 1 explored the lived experience of patients with OLP, and session 2 allowed patients to review a summary of the outcome domains used in the OLP literature to date. The discussions were recorded, transcribed verbatim, and analyzed using framework analysis. Results: In session 1, 4 themes and 8 sub-themes emerged from the data analysis. An additional outcome, ‘knowledge of family and friends,’ was suggested in session 2. Conclusions: We have gained valuable insight into the lived experience of patients with OLP via this qualitative study. To our knowledge, this study is the first to explore the patient perspective on what should be measured in clinical trials on OLP, highlighting an important additional suggested outcome. This additional outcome will be voted upon in a consensus process to determine a minimum COS for OLP.