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Open Access Publications from the University of California

Scholarly Works (86 results)

  • Article
  • Peer Reviewed
UC Santa Cruz Previously Published Works (2010)
One of the main concepts in quantum physics is a density matrix, which is a symmetric positive definite matrix of trace one. Finite probability distributions can be seen as a special case when the density matrix is restricted to be diagonal. We develop a probability calculus based on these more general distributions that includes definitions of joints, conditionals and formulas that relate these, including analogs of the Theorem of Total Probability and various Bayes rules for the calculation of posterior density matrices. The resulting calculus parallels the familiar “conventional” probability calculus and always retains the latter as a special case when all matrices are diagonal. We motivate both the conventional and the generalized Bayes rule with a minimum relative entropy principle, where the Kullbach-Leibler version gives the conventional Bayes rule and Umegaki’s quantum relative entropy the new Bayes rule for density matrices. Whereas the conventional Bayesian methods maintain uncertainty about which model has the highest data likelihood, the generalization maintains uncertainty about which unit direction has the largest variance. Surprisingly the bounds also generalize: as in the conventional setting we upper bound the negative log likelihood of the data by the negative log likelihood of the MAP estimator.
    Cover page: Bayesian generalized probability calculus for density matrices
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2019)
    It is challenging to predict the docked conformations of two proteins. Current methods are susceptible to errors from treating proteins as rigid bodies and from an inability to compute relative Boltzmann populations of different docked conformations. Here, we show that by using the ClusPro server as a front end to generate possible protein-protein contacts, and using Modeling Employing Limited Data (MELD) accelerated molecular dynamics (MELD × MD) as a back end for atomistic simulations, we can find 16/20 native dimer structures of small proteins as those having the lowest free energy, starting from good-bound-backbone structures. We show that atomistic MD free energies can be used to identify native protein dimer structures.
      Cover page: Predicting Protein Dimer Structures Using MELD × MD.
      • Article
      • Peer Reviewed
      Mediterranean Journal of Emergency Medicine & Acute Care, Volume 3, Issue 4 (2022)

      Introduction: This study aims to assess follow-up behaviors of patients who leave without being seen (LWBS) from a hybrid point of service (POS) collection model Emergency Department (ED).

      Methods: A cross-sectional survey was administered to patients who LWBS from a hybrid POS collection model ED, one-week post-ED visit, at an academic tertiary care medical center in Lebanon, between June 2016 and May 2017.

      Results: LWBS patients were found to be young, males, and present with conditions of lower urgency and presenting mainly with a musculoskeletal chief complaint. Majority (66.8%) left because of third party payer denial of visit coverage followed by cost of visit (12.6%) and wait times (12.6%). A greater percentage of those who LWBS due to financial reasons were male (64.1% vs 33.3%, p <0.001) and waited less (23.4 min vs 30.8 min, p=0.08) compared to those who left for non-financial reasons. The majority of LWBS patients sought medical care within the week after leaving the ED (78.4%), primarily at ambulatory clinics (89.9%) with few at emergency departments (10.1%). Few required admission to hospital (4.2%) and no mortalities were reported. A greater percentage of those who left because of financial barriers, felt the same/better after leaving the ED (82.1% vs 66.7%, p=0.03), sought care at alternate sites (82.1% vs 66.7%, p=0.03), primarily ambulatory clinics (94.1%, p=0.003), with fewer requiring admission to the hospital within one well (1.4% vs 13.3%, p=003). Irrespective of the reason for LWBS, all patients who sought care at an ambulatory clinic, did so at a different institution (100.0%).

      Conclusion: While the majority of patients who left without being seen from a hybrid POS collection ED left for financial reasons, a high percentage sought care at ambulatory clinics after leaving the ED.  Larger-scale studies are needed to adequately assess the outcomes of those patients, especially in areas with limited access to primary care ambulatory services.

       

        Cover page: Follow-Up Behavior of Patients Who Leave Without Being Seen from a Hybrid Point of Service Collection Emergency Department
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2016)
        During the first year of life, infants maintain their ability to discriminate faces from their own race but become less able to differentiate other-race faces. Though this is likely due to daily experience with own-race faces, the mechanisms linking repeated exposure to optimal face processing remain unclear. One possibility is that frequent experience with own-race faces generates a selective attention bias to these faces. Selective attention elicits enhancement of attended information and suppression of distraction to improve visual processing of attended objects. Thus attention biases to own-race faces may boost processing and discrimination of these faces relative to other-race faces. We used a spatial cueing task to bias attention to own- or other-race faces among Caucasian 9-month-old infants. Infants discriminated faces in the focus of the attention bias, regardless of race, indicating that infants remained sensitive to differences among other-race faces. Instead, efficacy of face discrimination reflected the extent of attention engagement.
          Cover page: Visual selective attention biases contribute to the other‐race effect among 9‐month‐old infants
          • Article
          Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 25, Issue 3.1 (2024)
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          Cover page: Validity of a Novel Entrustable Professional Activities Based End of Shift Assessment
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
            Cover page: Editorial: Empirical Research at a Distance: New Methods for Developmental Science
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2020)
            The Saccharomyces cerevisiae spindle pole body (SPB) serves as the sole microtubule-organizing center of the cell, nucleating both cytoplasmic and nuclear microtubules. Yeast pericentrin, Spc110, binds to and activates the γ-tubulin complex via its N terminus, allowing nuclear microtubule polymerization to occur. The Spc110 C terminus links the γ-tubulin complex to the central plaque of the SPB by binding to Spc42, Spc29, and calmodulin (Cmd1). Here, we show that overexpression of the C terminus of Spc110 is toxic to cells and correlates with its localization to the SPB. Spc110 domains that are required for SPB localization and toxicity include its Spc42-, Spc29-, and Cmd1-binding sites. Overexpression of the Spc110 C terminus induces SPB defects and disrupts microtubule organization in both cycling and G2/M arrested cells. Notably, the two mitotic SPBs are affected in an asymmetric manner such that one SPB appears to be pulled away from the nucleus toward the cortex but remains attached via a thread of nuclear envelope. This SPB also contains relatively fewer microtubules and less endogenous Spc110. Our data suggest that overexpression of the Spc110 C terminus acts as a dominant-negative mutant that titrates endogenous Spc110 from the SPB causing spindle defects.
              Cover page: Yeast pericentrin/Spc110 contains multiple domains required for tethering the γ-tubulin complex to the centrosome
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2018)
              Working memory (WM) is a central construct in cognitive neuroscience because it comprises mechanisms of active information maintenance and cognitive control that underpin most complex cognitive behavior. Individual variation in WM has been associated with multiple behavioral and health features including demographic characteristics, cognitive and physical traits and lifestyle choices. In this context, we used sparse canonical correlation analyses (sCCAs) to determine the covariation between brain imaging metrics of WM-network activation and connectivity and nonimaging measures relating to sensorimotor processing, affective and nonaffective cognition, mental health and personality, physical health and lifestyle choices derived from 823 healthy participants derived from the Human Connectome Project. We conducted sCCAs at two levels: a global level, testing the overall association between the entire imaging and behavioral-health data sets; and a modular level, testing associations between subsets of the two data sets. The behavioral-health and neuroimaging data sets showed significant interdependency. Variables with positive correlation to the neuroimaging variate represented higher physical endurance and fluid intelligence as well as better function in multiple higher-order cognitive domains. Negatively correlated variables represented indicators of suboptimal cardiovascular and metabolic control and lifestyle choices such as alcohol and nicotine use. These results underscore the importance of accounting for behavioral-health factors in neuroimaging studies of WM and provide a neuroscience-informed framework for personalized and public health interventions to promote and maintain the integrity of the WM network.
                Cover page: An integrated brain–behavior model for working memory
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2021)
                Comorbidity of tuberculosis (TB) and depression may lead to delayed TB treatment initiation. A cross-sectional study was conducted between January and December 2019 to examine the association between depression and delayed TB treatment initiation among newly diagnosed TB patients in Botswana. We used the Patient Health Questionnaire-9 and the ZUNG self-rating anxiety scale to assess depressive and anxiety symptoms, respectively. Delayed TB treatment was defined as experiencing common TB symptoms for more than 2 months before treatment initiation. We used Poisson regression models with robust variance to assess the association between covariates and delayed treatment initiation. Majority of the enrolled 180 study participants were males (n =116, 64.4%). Overall, 99 (55%) were co-infected with HIV; depression and anxiety symptoms were reported by 47.2% and 38.5% of the participants respectively. The prevalence of delayed TB treatment was 42.6% and 18.8% among participants who indicated symptoms of depression and among participants without depression respectively. After adjusting for age, HIV status, gender and anxiety symptoms, depression was still associated with delayed TB treatment (adjusted prevalence ratio [aPR] = 2.09; 95% CI = 1.23-3.57). Integrating management of depressive symptoms during TB treatment may help in improving overall TB treatment outcomes.
                  Cover page: Depression and delayed tuberculosis treatment initiation among newly diagnosed patients in Botswana
                  • Article
                  • Peer Reviewed
                  Adaptive Optics for Extremely Large Telescopes 4 – Conference Proceedings, Volume 1, Issue 1 (2015)
                  In this paper, we discuss the feasibility and the performance assessment of a possible MCAO system for E-ELT, basedon the novel concept of Global MCAO, which takes advantage of a very wide technical FoV to perform adaptive opticscorrection using only natural guide stars, with the aim to increase the sky coverage. The technique envisages thedefinition of Virtual-DMs, as tools for the global reconstruction. This investigation has been carried out during afeasibility study we performed for ESO, in which we combined computations, simulations and literature. The aim of thisanalysis is to identify and review the main parameters and the technical issues, which would act as error sources in a realGMCAO system, evaluating their contribution to the overall performance. The study involves both issues related to thePyramid WFS in general, and to the GMCAO case in particular, including the wavelength and FoV size selection, thenumber of guide stars and reconstructed Virtual-DMs, and actual components parameters.
                    Cover page: GMCAO for E-ELT: a feasibility study
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