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Open Access Publications from the University of California

Scholarly Works (13 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2010)
In this dissertation the problem of data assimilation in stochastic nonlinear systems is formulated using path integrals. Each path represents a time evolution of the model states, and the time independent model parameters. In the path integral, every possible path is integrated over with each path weighted by P(XIY) ̃exp[-A₀(X,Y)], where A₀(X,Y) is the action, which quantifies how likely it is that the given path X was actually realized in the experiment which produced the observed time series Y. The goal of data assimilation is to combine information from a measurement time series with a dynamical model to make statistical estimates or predictions of model states and parameters. Both the measurements and the dynamical model may be noisy, and this fact is incorporated by using a probabilistic formulation for P(XIY), the posterior path distribution conditioned on the observed time series. With an expression for P(XIY) it is possible to express expectation values, conditioned upon the observations, of any function of the path as a path integral over all possible paths. The path integrals can then be numerically approximated using a Markov chain Monte Carlo method such as the Metropolis method. This method is discussed and applied to two example systems: the Colpitts oscillator circuit, and the Lorenz 96 toy atmosphere model. By studying the characteristics of the action as a function of the path, properties of the data assimilation problem can be deduced. For instance, if the surface in path space defined by the action is rough with many local minima with similar values of action, then the data assimilation problem is not well-defined. If more observations are made which rule out regions of path space that were previously likely, then the surface may become smoother with a single minimum. By examining the shape of the action, the question of how many measurements are needed to fully reconstruct the model state can be answered. It is also important to examine the shape of the action in the vicinity of the global minimum to find the level of uncertainty in state and parameter estimates. These ideas are illustrated with the Lorenz 96 system as an example
    Cover page: A path integral approach to data assimilation in stochastic nonlinear systems
    • Article
    • Peer Reviewed
    Ufahamu: A Journal of African Studies, Volume 21, Issue 1-2 (1993)
    No abstract
      Cover page: The Impact of State Ownership of Resources on Economic and Political Development in Sub-Saharan Africa
      • Thesis
      • Peer Reviewed
      UC Riverside Electronic Theses and Dissertations (2013)

      Abstract: The scale symmetry of self-similarity is a fundamental one in physics and in geometry. We develop a calculus of the scale space evolution of self-similar fractal sets via an analysis of box-counting functions on these structures utilizing the theories of distributions and hyperfunctions. A differential study of the Box-Counting function can account for the oscillations of the local geometry of some examples of such structures, paralleling the theory of the complex dimensions of fractal strings. The algebraic structure on the iterates of the unit interval under an Iterated Function System admits a tensor product representation we develop to define an intrinsic geometry of fractals and an integral calculus on these objects.

        Cover page: Scale Covariance of Fractal Sets and Measures, A Differential Approach to the Box-Counting Function of a Fractal, with Applications
        • Article
        • Peer Reviewed
        Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 24, Issue 2 (2023)

        Introduction: The Standardized Letter of Evaluation (SLOE) is an emergency medicine (EM)-specific assessment designed to help EM residency programs differentiate applicants. We became interested in SLOE-narrative language referencing personality when we observed less enthusiasm for applicants described as “quiet” in their SLOEs. In this study our objective was to compare how quiet-labeled, EM-bound applicants were ranked compared to their non-quiet peers in the global assessment (GA) and anticipated rank list (ARL) categories in the SLOE.

        Methods: We conducted a planned subgroup analysis of a retrospective cohort study of all core EM clerkship SLOEs submitted to one, four-year academic EM residency program in the 2016-2017 recruitment cycle. We compared SLOEs of applicants who were described as “quiet,” “shy,” and/or “reserved” — collectively referred to as “quiet” — to SLOEs from all other applicants, referred to as “non-quiet.” We compared frequencies of quiet to non-quiet students in GA and ARL categories using chi-square goodness-of-fit tests with a rejection criteria (alpha) of 0.05.

        Results: We reviewed 1,582 SLOEs from 696 applicants. Of these, 120 SLOEs described quiet applicants. The distributions of quiet and non-quiet applicants across GA and ARL categories were significantly different (P < 0.001). Quiet applicants were less likely than non-quiet applicants to be ranked in the top 10% and top one-third GA categories combined (31% vs 60%) and more likely to be in the middle one-third category (58% vs 32%). For ARL, quiet applicants were also less likely to be ranked in the top 10% and top one-third categories combined (33% vs 58%) and more likely to be in the middle one-third category (50% vs 31%).

        Conclusion: Emergency medicine-bound students described as quiet in their SLOEs were less likely to be ranked in the top GA and ARL categories compared to non-quiet students. More research is needed to determine the cause of these ranking disparities and address potential biases in teaching and assessment practices.

          Cover page: The Standardized Letter of Evaluation: How We Perceive the Quiet StudentCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2016)

          Introduction

          The demand for total knee arthroplasty (TKA) continues to challenge hospital financial resources. Hospitals have countered this economic demand by reducing patient length of stay (LoS), thus requiring a higher utilization of extended care facilities (ECF) and home with home health care (HHC). With an increase in the number of insured low-income families following the Affordable Care Act (ACA), TKA patients' demographics are anticipated to change. Both trends have significant economic implications, and predicting the discharge destinations of TKA patients would help plan for future health expenditures. The purpose of this study was to determine which variables are significant in predicting discharge destinations of patients treated with TKA.

          Methods

          We utilized the California Hospital Discharge data set of the year 2010. For each hospitalization, the data set includes information about patient demographics (age, gender, race, and ethnicity), insurance type, diagnoses and procedures, and patient disposition. Discharge to home was the reference category. Discharges to a skilled nursing home and discharge to home with home care were the 2 additional alternatives. Independent variables included the Charlson comorbidity index, payer category (private, Medicare, Medical, and other), race, ethnicity, age, and gender.

          Results

          Over 28 611 TKAs were reviewed with 45.9% discharged to HHC, 29.9% going to ECF, and 24.2% going home without home health care. Race, age, insurance, and morbidity proved to be highly significant factors influencing patient discharge destination (P < .001). Medicare coverage relative to private payers was a strong predictor for discharge destination (relative risk ratio (RRR) 1.69, P < .001). The strongest predictors were black and Asian races relative to whites (RRR 1.54, P < .01). Male gender was the only factor that lowered the risk of discharge to a nursing home (RRR 0.43, P < .001).

          Conclusions

          This study provides insight on which patient characteristics influence discharge destination after TKA. Race, age, insurance, and morbidity were highly significant (P < .001) factors on patient discharge destination.
            Cover page: Factors Influencing Discharge Destination After Total Knee ArthroplastyCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 24, Issue 4 (2023)

            Introduction: The Standardized Letter of Evaluation (SLOE) is designed to assist emergency medicine (EM) residency programs in differentiating applicants and in selecting those to interview. The SLOE narrative component summarizes the student’s clinical skills as well as their non-cognitive attributes. The purpose of this qualitative investigation was to explore how students described in the SLOE as quiet are perceived by faculty and to better understand how this may impact their residency candidacy.

            Methods: This retrospective cohort study included all SLOEs submitted to one EM residency program during one application cycle. We analyzed sentences in the SLOE narrative describing students as “quiet,”“shy,” and/or “reserved.” Using grounded theory, thematic content analysis with a constructivist approach, we identified five mutually exclusive themes that best characterized the usage of these target words.

            Results: We identified five themes: 1) quiet traits portrayed as implied-negative attributes (62.4%); 2) quiet students portrayed as overshadowed by more extraverted peers (10.3%); 3) quiet students portrayed as unfit for fast-paced clinical settings (3.4%); 4) “quiet” portrayed as a positive attribute(10.3%); and 5) “quiet” comments deemed difficult to assess due to lack of context (15.6%).

            Conclusion: We found that quiet personality traits were often portrayed as negative attributes. Further, comments often lacked clinical context, leaving them vulnerable to misunderstanding or bias. More research is needed to determine how quiet students perform compared to their non-quiet peers and to determine what changes to instructional practices may support the quiet student and help create a more inclusive learning environment. [West J Emerg Med. 2023;24(4)1–4.]

              Cover page: Perception of Quiet Students in Emergency Medicine: An Exploration of Narratives in the Standardized Letter of EvaluationCreative Commons 'BY' version 4.0 license
              • Article
              Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 25, Issue 3.1 (2024)
                Cover page: Implementing A Climate Change and Sustainability Curriculum for Emergency Medicine PhysiciansCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2019)
                Mitochondrial dysfunction has been implicated in the etiology of monogenic Parkinson's disease (PD). Yet the role that mitochondrial processes play in the most common form of the disease; sporadic PD, is yet to be fully established. Here, we comprehensively assessed the role of mitochondrial function-associated genes in sporadic PD by leveraging improvements in the scale and analysis of PD GWAS data with recent advances in our understanding of the genetics of mitochondrial disease. We calculated a mitochondrial-specific polygenic risk score (PRS) and showed that cumulative small effect variants within both our primary and secondary gene lists are significantly associated with increased PD risk. We further reported that the PRS of the secondary mitochondrial gene list was significantly associated with later age at onset. Finally, to identify possible functional genomic associations we implemented Mendelian randomization, which showed that 14 of these mitochondrial function-associated genes showed functional consequence associated with PD risk. Further analysis suggested that the 14 identified genes are not only involved in mitophagy, but implicate new mitochondrial processes. Our data suggests that therapeutics targeting mitochondrial bioenergetics and proteostasis pathways distinct from mitophagy could be beneficial to treating the early stage of PD.
                  Cover page: Mitochondria function associated genes contribute to Parkinson’s Disease risk and later age at onset
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2021)
                    Cover page: Leveraging the NEON Airborne Observation Platform for socio‐environmental systems researchCreative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2019)

                    Background

                    PD is a complex polygenic disorder. In recent years, several genes from the endocytic membrane-trafficking pathway have been suggested to contribute to disease etiology. However, a systematic analysis of pathway-specific genetic risk factors is yet to be performed.

                    Objectives

                    To comprehensively study the role of the endocytic membrane-trafficking pathway in the risk of PD.

                    Methods

                    Linkage disequilibrium score regression was used to estimate PD heritability explained by 252 genes involved in the endocytic membrane-trafficking pathway including genome-wide association studies data from 18,869 cases and 22,452 controls. We used pathway-specific single-nucleotide polymorphisms to construct a polygenic risk score reflecting the cumulative risk of common variants. To prioritize genes for follow-up functional studies, summary-data based Mendelian randomization analyses were applied to explore possible functional genomic associations with expression or methylation quantitative trait loci.

                    Results

                    The heritability estimate attributed to endocytic membrane-trafficking pathway was 3.58% (standard error = 1.17). Excluding previously nominated PD endocytic membrane-trafficking pathway genes, the missing heritability was 2.21% (standard error = 0.42). Random heritability simulations were estimated to be 1.44% (standard deviation = 0.54), indicating that the unbiased total heritability explained by the endocytic membrane-trafficking pathway was 2.14%. Polygenic risk score based on endocytic membrane-trafficking pathway showed a 1.25 times increase of PD risk per standard deviation of genetic risk. Finally, Mendelian randomization identified 11 endocytic membrane-trafficking pathway genes showing functional consequence associated to PD risk.

                    Conclusions

                    We provide compelling genetic evidence that the endocytic membrane-trafficking pathway plays a relevant role in disease etiology. Further research on this pathway is warranted given that critical effort should be made to identify potential avenues within this biological process suitable for therapeutic interventions. © 2019 International Parkinson and Movement Disorder Society.
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