Searching biomedical ontologies based on content

As more ontologies become publicly available, finding the 'right' ontologies becomes much harder. In this paper, we introduce a new ontology search technique which is based on corpus analysis. In particular, we look at the case when users search for ontologies relevant to a particular topic (e.g., an ontology about anatomy). Our experiments demonstrate that using our method for query expansion improves retrieval results by a 113%, compared to the tools that search only for the user query terms and consider only class and property names

Searching Ontologies Based on Content: Experiments in the Biomedical Domain

As more ontologies become publicly available, finding the "right" ontologies becomes much harder. In this paper, we address the problem of ontology search: finding a collection of ontologies from an ontology repository that are relevant to the user's query. In particular, we look at the case when users search for ontologies relevant to a particular topic (e.g., an ontology about anatomy). Ontologies that are most relevant to such query often do not have the query term in the names of their concepts (e.g., the Foundational Model of Anatomy ontology does not have the term "anatomy" in any of its concepts' names). Thus, we present a new ontology-search technique that helps users in these types of searches. When looking for ontologies on a particular topic (e.g., anatomy), we retrieve from the Web a collection of terms that represent the given domain (e.g., terms such as body, brain, skin, etc. for anatomy). We then use these terms to expand the user query. We evaluate our algorithm on queries for topics in the biomedical domain against a repository of biomedical ontologies. We use the results obtained from experts in the biomedical-ontology domain as the gold standard. Our experiments demonstrate that using our method for query expansion improves retrieval results by a 113%, compared to the tools that search only for the user query terms and consider only class and property names (like Swoogle). We show 43% improvement for the case where not only class and property names but also property values are taken into account

Mutational Analysis Among Patients with Duchenne Muscular Dystrophy

Background and objective: Duchenne Muscular Dystrophy is caused by mutations in dystrophin gene that include deletion, duplication and small mutations. Introduction to newer drug therapies in DMD is based on the type of mutation. The objective of this study was to assess distribution and percentage of different mutations among DMD patients. Methods: This retrospective cross-sectional study was conducted in Pediatric Neurology department of UCHS & Children Hospital Lahore. All the cases of Duchenne Muscular Dystrophy confirmed through genetic analysis from January 2022 to June 2022 through MLPA method were enrolled in the study. Data was recorded on detailed history and physical examination of the subjects and all lab investigations along with genetic study was reviewed to collect the data on given Performa. All the collected data was saved for final analysis. Results: Total 60 patients were enrolled in the study. The most common mutation was deletion, detected in 32 (56%) cases, duplication was detected in 10 (17.5%) cases and genetic study of 15 (26.5 ) patients was turned out to be normal. The most common deletion was found to be at 45-52 (43%) exons. Conclusion: The most common mutation among genetically confirmed cases of DMD was found to be deletion at 45-52 exons. This mutational evaluation is the first step toward trial of new medicines while treating DMD, as mechanism of action of new drugs is based on the type of mutation

Patient Communication Simulators for Interprofessional Healthcare Education:Work in Progress - Poster Presentation

Background and aim: The use of virtual technology has increased in clinical education since the pandemic, which necessitated a rapid shift to computer-generated experiences [1]. Whilst student placements have essentially returned to a face-to-face model, plans to continue an element of virtual simulation remain [2]. One area where virtual simulation remains of benefit is interprofessional education (IPE). Online delivery can overcome timetabling challenges that present when coordinating multiple programmes across different disciplines [3]. This project aims to build an IPE scenario that follows a virtual patient journey using an extended reality (XR) platform. Method: An existing scenario based on a service user encountered during a physiotherapy placement, was developed into an IPE resource. Collaboration occurred between the university research team, the simulation department and the IPE working groups, in conjunction with the software creation team. Multiple professional scripts were added to the scenario. Two time points were built into a virtual patient with frailty syndrome, to facilitate student interviews with paramedics, emergency clinicians, diagnostic radiographers, geriatricians, physiotherapists, occupational therapists, nurses, operating department practitioners, dietetics, and social workers. Results: To date, 68 user testing sessions have been conducted to allow the software developers to refine the conversational artificial intelligence (AI).Discussion: There were two key lessons. Firstly, the information's volume, complexity and interrelatedness lend best to data collection via a co-creation process, rather than approaching each profession separately (effectively building scenarios in silos). Secondly, appropriate training and setting user testers’ expectations are recommended to maximise participation and engagement.There are three future research directions. Stakeholder interviews of the contributors, co-creation to develop the allied health scripting and recruiting larger numbers of user testers to develop the conversational AI. This is the first custom case of this size and complexity. The resource will be available within the university to support IPE activities. Conclusion: This project is an example of how XR technology can be developed in a clinical context. The resource is intended to illustrate the value of a joined up care pathway, to develop a systems mindset in healthcare students

Petrophysics based Reservoir Evaluation of the Cretaceous Lower Goru “C” Sands, Middle Indus Basin, Sindh, Pakistan

This study demonstrates the reservoir investigation of the Cretaceous Lower Goru “C” sand interval using exploratory well data from the middle Indus basin of Sindh. The petrophysical parameters including volume of shale, effective porosity, and water saturation of the investigated reservoir interval were calculated. The shale volume calculation results in 30–35% of non-clean (shale) lithology, which is high as compared to Sawan-01 and Sawan-08 wells. The effective porosity ranges from 12–16%, while the average value of water saturation in the complete interval of “C” sand falls in the range of 50–60%. However, certain zones with relatively lower water saturation values of around 30-50% are also observed. These zones are considered better pay zones in comparison to the other intervals. A “gas effect” phenomenon observed on cross plots represents the area of neutron-density cross-over indicating the presence of lighter hydrocarbons in this reservoir zone interva

Missed Opportunities for Diagnosing HIV via Routine Screening in an Inner- City Primary Care Clinic

Background: Although routine, opt-out HIV screening has been recommended for nearly a decade, clinical practice has not kept pace. Here, we examine missed opportunities for HIV screening among patients newly diagnosed with HIV via a routine non-targeted opt-out HIV screening program in a primary care clinic at an inner-city safety-net hospital. Methods: Select demographic and clinical data were analyzed for all persons with a new HIV diagnosis between July 9, 2013 and August 31, 2015. Retrospective reviews of medical records were performed to identify missed opportunities for HIV screening in the year prior to HIV diagnosis. Results: Among 6,582 patients tested for HIV as part of the screening program, 27 patients had a new HIV diagnosis (0.41%). In the year prior to diagnosis, 19 (70%) of these had contact with the healthcare system but were not tested for HIV. At the visit associated with the new HIV diagnosis, 70% of patients did not present with an indication for risk-based HIV screening or symptoms potentially associated with HIV-related infections. Conclusions: Despite CDC recommendations for routine, non-targeted, opt-out HIV screening in all healthcare settings, 70% of patients newly diagnosed with HIV via routine screening in a primary care clinic had contact with the healthcare system in the year prior to the new HIV diagnosis but were not tested for HIV. These findings highlight the importance of routine, nontargeted screening to identify patients with HIV as well as continued provider and patient education about the value of routine HIV screening

Combined protein C and protein S deficiency with pregnancy

A 35 year old female patient, married since 8 years, G6P1L1SA4 was registered with our unit since 8th week of gestation. She was a known case of protein C and protein S deficiency diagnosed 7 years ago (thrombotic profile- protein C: 70% normal: 70-100%, protein S: 55% normal: 70/140%, AT-III: 116% normal 70/140%, factor V leiden: no mutation detected) which was detected on evaluation for her bad obstetric history. ACLA was also positive. She was started on injection low molecular weight heparin 0.6 mg s/c OD, in addition to continuing Tb. Aspirin 75 mg which had been started when the pregnancy was registered. Foleys induction was done at 39 weeks of gestation in view of previous LSCS with pre-eclampsia. Emergency LSCS was done in view of previous LSCS with non-progress of labour. Male child weighing 2.4 kg was born which is doing well. A patient having combined deficiency of both factors protein C and protein S is very rare. Anticoagulation therapy is the cornerstone in the management of patients with inherited coagulation defects

All Sugars are Not Sweet

Background: Extravasation is defined as the leakage of drugs from the vessel to the surrounding area with the potential to cause tissue necrosis. Such drugs (known as vesicants) that can extravasate include vasopressors, alkylating chemotherapeutic agents, hyperosmolar or hypo-osmolar agents, and certain antibiotics (vancomycin) [1]. Dextrose, at concentrations of 10% or greater, is also considered to be a vesicant, with rates of extravasation from 50% dextrose (D50) injections varying between 10–30% [2]. Case Report: A cachectic 48-year-old female with a past medical history of HIV, former IV drug use, and alcohol use, presented with lethargy. Upon initial assessment, she had track marks on her arms and was only responsive to sternal rub, with her exam otherwise unremarkable. She briefly improved with intravenous naloxone but ultimately required intensive care unit admission following intubation for airway protection. The toxicology screen was positive for methadone, opioids, and alcohol. Initial labs revealed ALT of 118 units per liter, AST of 94 units per liter, hemoglobin of 9.5 grams per deciliter, and albumin of 2.3 grams per deciliter. She was started on thiamine, multivitamin, and folate supplementation, and despite starting tube feeds, glucose measurements were consistently low (with the lowest reading of 35 milligrams per deciliter). She received 2 ampules of 50 milliliters (25 grams) 50% dextrose through a 22-gauge antecubital peripheral IV line, with fingerstick improving to 220 milligrams per deciliter after 10 minutes. Two hours later, extensive swelling and fluid-filled blisters were noted throughout her right forearm and hand, with Doppler ultrasound revealing the absence of a radial pulse ('Figure 1'). Her arm was elevated, a cold compress was applied, and a local subcutaneous injection of hyaluronidase was administered. Compartment pressures remained within normal limits, and a repeat Doppler ultrasound after one hour revealed reappearance of the right radial pulse. The patient’s swelling and blisters improved gradually over the next few days. Discussion: To the best of our knowledge, there is only one published case on D50 extravasation so far. It describes a 57-year-old female who received D50 in the field for hypoglycemia. She developed extravasation injury and was subsequently diagnosed with compartment syndrome, ultimately requiring fasciotomy. In our case, however, because the incident occurred in-hospital, it was recognized early, the patient was treated with hyaluronidase, and her symptoms self-resolved. Conclusion: This case emphasizes the importance of early detection and treatment when suspecting extravasation of D50 in order to prevent the development of serious complications like compartment syndrome. 10% dextrose (D10) is now emerging as a safer (given the lower concentration) and equally effective alternative to D50 administration and could become the standard of care for hypoglycemia management [3]

The Role of Diffuse Optical Spectroscopy in the Clinical Management of Breast Cancer

Diffuse optical spectroscopy (DOS) of breast tissue provides quantitative, functional information based on optical absorption and scattering properties that cannot be obtained with other radiographic methods. DOS-measured absorption spectra are used to determine the tissue concentrations of deoxyhemoglobin (Hb-R), oxyhemoglobin (Hb-O(2)), lipid, and water (H(2)O), as well as to provide an index of tissue hemoglobin oxygen saturation (S(t)O(2)). Tissue-scattering spectra provide insight into epithelial, collagen, and lipid contributions to breast density. Clinical studies of women with malignant tumors show that DOS is sensitive to processes such as increased tissue vascularization, hypoxia, and edema. In studies of healthy women, DOS detects variations in breast physiology associated with menopausal status, menstrual cycle changes, and hormone replacement. Current research involves using DOS to monitor tumor response to therapy and the co-registration of DOS with magnetic resonance imaging. By correlating DOS-derived parameters with lesion pathology and specific molecular markers, we anticipate that composite “tissue optical indices” can be developed that non-invasively characterize both tumor and normal breast-tissue function