MS

thesisThe early detection of infectious disease outbreaks is key to their management and initiation of mitigation strategies. This is true whether the disease is naturally occurring or due to intentional release as an act of terrorism. In recent times, this has become evident with the anthrax bioterrorism attacks of October 2001, the occurrence of emerging infections such as West Nile Virus and Severe Acute Respiratory Syndrome of the concern for a new pandemic of influenza based on H5N1 avian influenza. Public health surveillance efforts at the University of Utah have been place for several years and came to the forefront during the 2002 Winter Olympic Games. At that time, an electronic medical record-based system was developed and deployed to perform daily surveillance of patients visiting the clinics and emergency department of the University of Utah Health Care System. This effort was then followed by a detailed validation of the computer rules used in the surveillance system, with special emphasis on the early detection of central nervous system (CNS) syndromes such as meningitis and encephalitis. These syndromes are of importance to both emerging infections such as West Nile Virus and for NIH/CDC Category B threat agents such as Eastern and Western Equine Encephalitis. True CNS syndromes caused by infectious agents represent a small proportion of patients seen at the emergency department of a large tertiary hospital. "Reason for visit" chief complaint data were poor predictors for the early detection of CNS syndromes. Orders and early results from the laboratory testing of cerebro-spinal fluid were useful for the early detection of meningitis and encephalitis. Overall, computer-based surveillance methods have a role to play in the early detection of infectious diseases. In particular, this project has contributed to public health surveillance by moving the field beyond complaint data and has shown the validity of suing computer-based rules for the detection of meningitis and encephalitis

Needles in a haystack: screening and healthcare system evidence for homelessness

Effectiveness of screening for homelessness in a large healthcare system was evaluated in terms of successfully referring and connecting patients with appropriate prevention or intervention services. Screening and healthcare services data from nearly 6 million U.S. military veterans were analyzed. Veterans either screened positive for current or risk of housing instability, or negative for both. Current living situation was used to validate results of screening. Administrative evidence for homelessness-related services was significantly higher among positive-screen veterans who accepted a referral for services compared to those who declined. Screening for current or risk of homelessness led to earlier identification, which led to earlier and more extensive service engagement

Comparing the utilization and cost of health services between veterans experiencing brief and ongoing episodes of housing instability

Housing instability is associated with costly patterns of health and behavioral health service use. However, little prior research has examined patterns of service use associated with higher costs among those experiencing ongoing housing instability. To address this gap, we compared inpatient and outpatient medical and behavioral health service utilization and costs between veterans experiencing brief and ongoing episodes of housing instability. We used data from a brief screening instrument for homelessness and housing instability that has been implemented throughout the US Department of Veterans Affairs (VA) health care system to identify a national sample of veterans experiencing housing instability. Veterans were classified as experiencing either brief or ongoing housing instability, based on two consecutive responses to the instrument, and we used a series of two-part regression models to conduct adjusted comparisons of costs between veterans experiencing brief and ongoing episodes of housing instability. Among 5794 veterans screening positive for housing instability, 4934 (85%) were experiencing brief and 860 (15%) ongoing instability. The average total annual incremental cost associated with ongoing versus brief episodes of housing instability was estimated at $7573, with the bulk of this difference found in inpatient services. Cost differences resulted more from a higher probability of service use among those experiencing ongoing episodes of housing instability than from higher costs among service users. Our findings suggest that VA programmatic efforts aimed at preventing extended episodes of housing instability could potentially result in substantial cost offsets for the VA health care system.This study was supported by funding from the Department of Veterans Affairs (VA) Health Services Research & Development (HSR&D) grant IIR 13-334-3 and from the VA National Center on Homelessness Among Veterans

Rurality or distance to care and the risk of homelessness among Afghanistan and Iraq veterans

INTRODUCTION: To date, no studies have examined the relationship of rurality and distance to nearest VA facility to risk of homelessness. METHODS: We examined differences in the rate of homelessness within a year of a Veteran's first encounter with the VA following last military separation based on rurality and distance to the nearest VA facility using multivariable log-binomial regressions. RESULTS: In our cohort of 708,120 Veterans, 73% were determined to have a forwarding address in urban areas, 59.2% and 86.7% lived within 40 miles of the nearest VA medical center (VAMC), respectively. Veterans living in a rural area and those living between 20+ miles away from the nearest VAMC were at a lower risk for homelessness. CONCLUSIONS: Our unique dataset allowed us to explore the relationship between geography and homelessness. These results are important to policy makers in understanding the risk factors for homelessness among Veterans and planning interventions

Realizing a Robust, Reconfigurable Active Quenching Design for Multiple Types of Single-Photon Avalanche Detectors

Most active quench circuits used for single-photon avalanche photodetectors (APDs) are designed either with discrete components which lack the flexibility of dynamically changing the control parameters, or with custom ASICs which require a long development time and high cost. As an alternative, we present a reconfigurable and robust hybrid design implemented using a System-on-Chip (SoC), which integrates both an FPGA and a microcontroller. We take advantage of the FPGA's speed and reconfiguration capabilities to vary the quench and reset parameters dynamically over a large range, thus allowing our system to operate a variety of APDs without changing the design. The microcontroller enables the remote adjustment of control parameters and calibration of APDs in the field. The ruggedized design uses components with space heritage, thus making it suitable for space-based applications in the fields of telecommunications and quantum key distribution (QKD). We demonstrate our circuit by operating a commercial APD cooled to -20{\deg}C with a deadtime of 35ns while maintaining the after-pulsing probability at close to 3%. We also showcase its versatility by operating custom-fabricated chip-scale APDs, which paves the way for automated wafer-scale characterization.Comment: 6 pages, 6 figures. arXiv admin note: substantial text overlap with arXiv:2205.0022

Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy

Background: Timely information about disease severity can be central to the detection and management of outbreaks of acute respiratory infections (ARI), including influenza. We asked if two resources: 1) free text, and 2) structured data from an electronic medical record (EMR) could complement each other to identify patients with pneumonia, an ARI severity landmark. Methods: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The x-ray reports served as a reference to develop a text classifier using machine-learning software that did not require custom coding. To identify pneumonia cases, the classifier was combined with EMR-based structured data and with text analyses aimed at ARI symptoms in clinical notes. Results: 370 reference cases with Possible Pneumonia and 250 with Pneumonia-in-Plan were identified. The x-ray report text classifier increased the positive predictive value of otherwise identical EMR-based case-detection algorithms by 20–70%, while retaining sensitivities of 58–75%. These performance gains were independent of the case definitions and of whether patients were admitted to the hospital or sent home. Text analyses seeking ARI symptoms in clinical notes did not add further value. Conclusion: Specialized software development is not required for automated text analyses to help identify pneumonia patients. These results begin to map an efficient, replicable strategy through which EMR data can be used to stratify ARI severity

Drugs of Last Resort? The Use of Polymyxins and Tigecycline at US Veterans Affairs Medical Centers, 2005–2010

Multidrug-resistant (MDR) and carbapenem-resistant (CR) Gram-negative pathogens are becoming increasingly prevalent around the globe. Polymyxins and tigecycline are among the few antibiotics available to treat infections with these bacteria but little is known about the frequency of their use. We therefore aimed to estimate the parenteral use of these two drugs in Veterans Affairs medical centers (VAMCs) and to describe the pathogens associated with their administration. For this purpose we retrospectively analyzed barcode medication administration data of parenteral administrations of polymyxins and tigecycline in 127 acute-care VAMCs between October 2005 and September 2010. Overall, polymyxin and tigecycline use were relatively low at 0.8 days of therapy (DOT)/1000 patient days (PD) and 1.6 DOT/1000PD, respectively. Use varied widely across facilities, but increased overall during the study period. Eight facilities accounted for three-quarters of all polymyxin use. The same statistic for tigecycline use was twenty-six VAMCs. There were 1,081 MDR or CR isolates during 747 hospitalizations associated with polymyxin use (1.4/hospitalization). For tigecycline these number were slightly lower: 671 MDR or CR isolates during 500 hospitalizations (1.3/hospitalization) (p = 0.06). An ecological correlation between the two antibiotics and combined CR and MDR Gram-negative isolates per 1000PD during the study period was also observed (Pearson’s correlation coefficient r = 0.55 polymyxin, r = 0.19 tigecycline). In summary, while polymyxin and tigecycline use is low in most VAMCs, there has been an increase over the study period. Polymyxin use in particular is associated with the presence of MDR Gram-negative pathogens and may be useful as a surveillance measure in the future

Exploiting the UMLS Metathesaurus for extracting and categorizing concepts representing signs and symptoms to anatomically related organ systems

AbstractObjectiveTo develop a method to exploit the UMLS Metathesaurus for extracting and categorizing concepts found in clinical text representing signs and symptoms to anatomically related organ systems. The overarching goal is to classify patient reported symptoms to organ systems for population health and epidemiological analyses.Materials and methodsUsing the concepts’ semantic types and the inter-concept relationships as guidance, a selective portion of the concepts within the UMLS Metathesaurus was traversed starting from the concepts representing the highest level organ systems. The traversed concepts were chosen, filtered, and reviewed to obtain the concepts representing clinical signs and symptoms by blocking deviations, pruning superfluous concepts, and manual review. The mapping process was applied to signs and symptoms annotated in a corpus of 750 clinical notes.ResultsThe mapping process yielded a total of 91,000 UMLS concepts (with approximately 300,000 descriptions) possibly representing physical and mental signs and symptoms that were extracted and categorized to the anatomically related organ systems. Of 1864 distinct descriptions of signs and symptoms found in the 750 document corpus, 1635 of these (88%) were successfully mapped to the set of concepts extracted from the UMLS. Of 668 unique concepts mapped, 603 (90%) were correctly categorized to their organ systems.ConclusionWe present a process that facilitates mapping of signs and symptoms to their organ systems. By providing a smaller set of UMLS concepts to use for comparing and matching patient records, this method has the potential to increase efficiency of information extraction pipelines

Osteogenic Activity of Locally Applied Small Molecule Drugs in a Rat Femur Defect Model

The long-term success of arthroplastic joints is dependent on the stabilization of the implant within the skeletal site. Movement of the arthroplastic implant within the bone can stimulate osteolysis, and therefore methods which promote rigid fixation or bone growth are expected to enhance implant stability and the long-term success of joint arthroplasty. In the present study, we used a simple bilateral bone defect model to analyze the osteogenic activity of three small-molecule drug implants via microcomputerized tomography (micro-CT) and histomorphometry. In this study, we show that local delivery of alendronate, but not lovastatin or omeprazole, led to significant new bone formation at the defect site. Since alendronate impedes osteoclast-development, it is theorized that alendronate treatment results in a net increase in bone formation by preventing osteoclast mediated remodeling of the newly formed bone and upregulating osteoblasts