Towards Unsupervised Detection of Process Models in Healthcare

Process mining techniques can play a significant role in understanding healthcare processes by supporting analysis of patient records in electronic health record systems. Healthcare processes are complex and patterns of care may vary considerably within similar cohorts of patients. Process mining often creates "spaghetti" models and require significant domain expert input to refine. Machine learning approaches such as Hidden Markov Models (HMM) may assist this refinement process. HMMs have been advocated for patient pathways clustering purposes; however these models can also be utilized for detecting hidden processes to help event abstraction. We explore use of an unsupervised method for detecting hidden healthcare sub-processes using HMMs, in particular the Viterbi algorithm. We describe an approach to enrich the event log with HMM-derived states and remodeling the healthcare processes as state transitions using a process mining tool. Our method is applied to event data for 'Altered Mental Status' patients that was extracted from a US hospital database (MIMIC-III). The results are promising and show a successful reduction of model complexity and detection of several hidden processes unsupervised by a domain expert

Molecular identification of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010.

BACKGROUND: Human adenoviruses of species B, C, and E (HAdV-B, -C, -E) are frequent causative agents of acute respiratory infections worldwide. As part of a surveillance program aimed at identifying the etiology of influenza-like illness (ILI) in Egypt, we characterized 105 adenovirus isolates from clinical samples collected between 2003 and 2010. METHODS: Identification of the isolates as HAdV was accomplished by an immunofluorescence assay (IFA) and confirmed by a set of species and type specific polymerase chain reactions (PCR). RESULTS: Of the 105 isolates, 42% were identified as belonging to HAdV-B, 60% as HAdV-C, and 1% as HAdV-E. We identified a total of six co-infections by PCR, of which five were HAdV-B/HAdV-C co-infections, and one was a co-infection of two HAdV-C types: HAdV-5/HAdV-6. Molecular typing by PCR enabled the identification of eight genotypes of human adenoviruses; HAdV-3 (n = 22), HAdV-7 (n = 14), HAdV-11 (n = 8), HAdV-1 (n = 22), HAdV-2 (20), HAdV-5 (n = 15), HAdV-6 (n = 3) and HAdV-4 (n = 1). The most abundant species in the characterized collection of isolates was HAdV-C, which is concordant with existing data for worldwide epidemiology of HAdV respiratory infections. CONCLUSIONS: We identified three species, HAdV-B, -C and -E, among patients with ILI over the course of 7 years in Egypt, with at least eight diverse types circulating

Medical genetics in developing countries in the Asia-Pacific region: challenges and opportunities

Advances in genetic and genomic technology changed health-care services rapidly in low and middle income countries (LMICs) in the Asia-Pacific region. While genetic services were initially focused on population-based disease prevention strategies, they have evolved into clinic-based and therapeutics-oriented service. Many LMICs struggled with these noncommunicable diseases and were unprepared for the needs of a clinical genetic service. The emergence of a middle class population, the lack of regulatory oversight, and weak capacity-building in medical genetics expertise and genetic counseling services led to a range of genetic services of variable quality with minimal ethical oversight. Some of the current shortcomings faced include the lack of awareness of cultural values in genetic health care, the variable stages of socioeconomic development and educational background that led to increased demand and abuse of genetics, the role of women in society and the crisis of gender selection, the lack of preventive and care services for genetic and birth defects, the issues of gene ethics in medicine, and the lack of understanding of some religious controversies. These challenges provide opportunities for both developing and developed nations to work together to reduce the inequalities and to ensure a caring, inclusive, ethical, and cost-effective genetic service in the region

Staphylococcus aureus Induced Wound Infections Which Antimicrobial Resistance, Methicillin- and Vancomycin-Resistant: Assessment of Emergence and Cross Sectional Study

Mohammed S Almuhayawi,1 Mohammed H Alruhaili,1,2 Hattan S Gattan,2,3 Mohanned Talal Alharbi,4 Mohammed Nagshabandi,4 Soad Al Jaouni,5,6 Samy Selim,7 Awadh Alanazi,7 Yasir Alruwaili,7 Osama Ahmed Faried,8 Mohamed E Elnosary9 1Department of Clinical Microbiology and Immunology, Faculty of Medicine, King AbdulAziz University, Jeddah, Saudi Arabia; 2Special Infectious Agents Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah, Saudi Arabia; 3Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; 4Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Jeddah, Jeddah, 23218, Saudi Arabia; 5Department of Hematology/Oncology, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia; 6Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia; 7Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia; 8Medical Microbiology and Immunology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt; 9Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, EgyptCorrespondence: Mohammed S Almuhayawi; Samy Selim, Email [email protected]; [email protected]: Wound infection is a prevalent concern in the medical field, being is a multi-step process involving several biological processes. Methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) infections often occur in areas of damaged skin, such as abrasions and open wounds.Methods: This research aims to light the incidence of MRSA and VRSA in wound swabs, the antimicrobial susceptibility configuration of isolated S. aureus patterns in pus/wound samples collected from Saudi Arabian tertiary hospital. The cross section study, β- lactamase detection, VRSA genotyping, MAR index, D-test and VRSA genotyping are methods, which used for completed this research.Results: Patients of several ages and genders delivered specimens from two hospitals in the Al jouf area, in the northern province of Saudi Arabia. S. aureus was found in 188 (34.7%) of the 542 wounds. The traumatized wounds provided 71 isolates (38.8%), surgical wound provided 49 isolates (26.8%) and abscess were represented 16 by isolates (8.7%). In the study, 123 (65.4%) out of 188 were MRSA, 60 (31.9%) were MSSA, and five (2.7%) were VRSA. Linezolid and rifampin were found to be the most effective antimicrobials with 100% in vitro antibacterial activity against S. aureus isolates. The Multiple antimicrobials resistance (MAR) index revealed 73 isolates (38.9%) with a MAR index greater than 0.2, and 115 (61.1%) less than 0.2. The D-test showed that of MLSb phenotypes among S. aureus, 22 (11.7%) strains were D-test positive (MLSbi phenotype), 53 (28.2%) strains were constitutive MLSc phenotypes, and 17 (9%) strains were shown to have MSb phenotypes. All VRSA isolates (n=5) were found to be positive for vanA, and no vanB positive isolates were detected in the study.Conclusion: Regular monitoring and an antimicrobials stewardship program should be in place to provide critical information that can be utilized for empirical therapy and future prevention strategies.Keywords: methicillin, vancomycin, resistant, Staphylococcus aureus, emergence, virulent, wound infection, MAR index, D-test, tertiary hospital, Saudi Arabi