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Open Access Publications from the University of California

Scholarly Works (27 results)

  • Article
  • Peer Reviewed
Proceedings of the Annual Meeting of the Cognitive Science Society, Volume 32 (2010)
    Cover page: Simulating the Elimination and Enhancement of the Plosivity Effect in Reading Aloud
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2014)

    Probabilistic graphical models such as Markov random fields, Bayesian networks and decision networks (a.k.a. influence diagrams) provide powerful frameworks for representing and exploiting dependence structures in complex systems. However, making predictions or decisions using graphical models involve challenging computational problems of optimization and/or estimation in high dimensional spaces. These include combinatorial optimization tasks such as maximum a posteriori (MAP), which finds the most likely configuration, or marginalization tasks that calculate the normalization constants or marginal probabilities. Even more challenging tasks require a hybrid of both: marginal MAP tasks find the optimal MAP prediction while marginalizing over missing information or latent variables, while decision-making problems search for optimal policies over decisions in single- or multi-agent systems, in order to maximize expected utility in uncertain environments.

    All these problems are generally NP-hard, creating a need for efficient approximations. The last two decades have witnessed significant progress on traditional optimization and marginalization problems, especially via the development of variational message passing algorithms. However, there has been less progress on the more challenging marginal MAP and decision-making problems.

    This thesis presents a unified variational representation for all these problems. Based on our framework, we derive a class of efficient algorithms that combines the advantages of several existing algorithms, resulting in improved performance on traditional marginalization and optimization tasks. More importantly, our framework allows us to easily extend most or all existing variational algorithms to hybrid inference and decision-making tasks, and significantly improves our ability to solve these difficult problems. In particular, we propose a spectrum of efficient belief propagation style algorithms with "message passing" forms, which are simple, fast and amenable to parallel or distributed computation. We also propose a set of convergent algorithms based on proximal point methods, which have the nice form of transforming the hybrid inference problem into a sequence of standard marginalization problems. We show that our algorithms significantly outperform existing approaches in terms of both empirical performance and theoretical properties.

      Cover page: Reasoning and Decisions in Probabilistic Graphical Models - A Unified Framework
      • Article
      • Peer Reviewed
      Proceedings of the Annual Meeting of the Cognitive Science Society, Volume 29 (2007)
        Cover page: A Unified Account of Segment Duration and Coarticulatory Effects in Speech Production
        • Article
        • Peer Reviewed
        UC Merced Previously Published Works (2015)
        Speech production and reading aloud studies have much in common, especially the last stages involved in producing a response. We focus on the minimal planning unit (MPU) in articulation. Although most researchers now assume that the MPU is the syllable, we argue that it is at least as small as the segment based on negative response latencies (i.e., response initiation before presentation of the complete target) and longer initial segment durations in a reading aloud task where the initial segment is primed. We also discuss why such evidence was not found in earlier studies. Next, we rebut arguments that the segment cannot be the MPU by appealing to flexible planning scope whereby planning units of different sizes can be used due to individual differences, as well as stimulus and experimental design differences. We also discuss why negative response latencies do not arise in some situations and why anticipatory coarticulation does not preclude the segment MPU. Finally, we argue that the segment MPU is also important because it provides an alternative explanation of results implicated in the serial vs. parallel processing debate.
          Cover page: The segment as the minimal planning unit in speech production and reading aloud: evidence and implications
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2019)
          A central issue in the study of speech production is whether phonological encoding occurs sequentially or in parallel. Some of the strongest evidence for sequential phonological encoding comes from the number of segments primed effect-response latencies decrease when increasing the number of primed segments from 0 to 1 to 2 (e.g., Meyer, 1991). Although it is often assumed that all participants adopt the same response criterion in the naming task, standard instructions can lead to the strategic adoption of different response criteria (such as an initial segment-based criterion or a syllable-based criterion). Furthermore, the number of segments primed effect might be driven by the manner of the initial segment such as the acoustic characteristics of plosives. In this study, participants named monosyllabic words varying in initial segment plosivity in a 0, 1, or 2 segments primed naming task and were instructed in ways to induce either a segment or syllable criterion. Data were analyzed by acoustic latency, articulatory latency, and initial segment duration, as distinguishing between a segment and syllable criterion and sequential and parallel encoding requires more than just a single point in the time-course of articulation. Shorter acoustic latencies when priming 2 segments over 1 were contingent on the manner of the initial segment and the adoption of a segment criterion, clarifying the nature of the number of segments primed effect. Moreover, the similar acoustic latencies found across priming conditions when a syllable criterion was adopted support parallel phonological encoding. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
            Cover page: Task Demands and Segment Priming Effects in the Naming TaskCreative Commons 'BY-NC-ND' version 4.0 license
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2016)
            Recovery from organ-specific autoimmune diseases largely relies on the mobilization of endogenous repair mechanisms and local factors that control them. Natural killer (NK) cells are swiftly mobilized to organs targeted by autoimmunity and typically undergo numerical contraction when inflammation wanes. We report the unexpected finding that NK cells are retained in the brain subventricular zone (SVZ) during the chronic phase of multiple sclerosis in humans and its animal model in mice. These NK cells were found preferentially in close proximity to SVZ neural stem cells (NSCs) that produce interleukin-15 and sustain functionally competent NK cells. Moreover, NK cells limited the reparative capacity of NSCs following brain inflammation. These findings reveal that reciprocal interactions between NSCs and NK cells regulate neurorepair.
              Cover page: Neural stem cells sustain natural killer cells that dictate recovery from brain inflammation
              • Article
              • Peer Reviewed
              California Breast Cancer Research Program Funded Publications (1997)
              Zinc-finger proteins of the Cys2-His2 type represent a class of malleable DNA-binding proteins that may be selected to bind diverse sequences. Typically, zinc-finger proteins containing three zinc-finger domains, like the murine transcription factor Zif268 and the human transcription factor Sp1, bind nine contiguous base pairs. To create a class of proteins that would be generally applicable to target unique sites within complex genomes, we have utilized structure-based modeling to design a polypeptide linker that fuses two three-finger proteins. Two six-fingered proteins were created and demonstrated to bind 18 contiguous bp of DNA in a sequence-specific fashion. Expression of these proteins as fusions to activation or repression domains allows transcription to be specifically up- or down-modulated within human cells. Polydactyl zinc-finger proteins should be broadly applicable as genome-specific transcriptional switches in gene therapy strategies and the development of novel transgenic plants and animals.
                Cover page: Design of polydactyl zinc-finger proteins for unique addressing within complex genomes
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2020)

                Background

                To assess the association of co-existing MRI lesions with knee pain at rest or on joint loading.

                Methods

                We included participants from Osteoarthritis Initiative whose pain score, measured by WOMAC sub-scales, differed by ≥1 point at rest (in bed at night, sitting/lying down) or on joint loading (walking, stairs) between two knees. Cartilage morphology, bone marrow lesions, meniscus extrusion, meniscus morphology, Hoffa's synovitis and synovitis-effusion were assessed using the compartment-specific MRI Osteoarthritis Knee Score. We performed latent class analyses to identify subgroups of co-existing MRI lesions and fitted a conditional logistic regression model to examine their associations with knee pain.

                Results

                Among 130 eligible participants, we identified five subgroups of knees according to patterns of co-existing MRI lesions: I. minimal lesions; II. mild lesions; III. moderate morphological lesions; IV. moderate multiple reactive lesions; and V. severe lesions. Compared with subgroup I, the odds ratios (ORs) and 95% confidence intervals (CI) of greater pain in bed at night were 1.6 (0.3, 7.2), 2.2 (0.5, 9.5), 6.2 (1.3, 29.6) and 11.2 (2.1, 59.2) for subgroups II-V, respectively. A similar association was observed between aforementioned subgroups and pain with sitting/lying down. The ORs (95% CI) of greater pain with walking were 1.0 (reference), 1.7 (0.5, 6.1), 0.7 (0.2, 2.3), 5.0 (1.4, 18.6) and 7.9 (2.0, 31.5) for subgroup I-V, respectively. The corresponding analysis for pain on stairs showed similar results.

                Conclusions

                Distinct patterns of co-existing MRI lesions have different implications for the pathogenesis of osteoarthritic knee pain occurring with/without joint loading.
                  Cover page: Co-existing patterns of MRI lesions were differentially associated with knee pain at rest and on joint loading: a within-person knee-matched case-controls study
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2021)

                  Objective

                  To examine the associations of knee injury, radiographic osteoarthritis severity, and quadriceps strength with knee pain exacerbation during walking.

                  Design

                  Within-person knee-matched case-control study.

                  Methods

                  Participants from the Osteoarthritis Initiative who completed a 20-m walking test at the 24-month visit were included. Pain exacerbation was defined as an increase in pain intensity of 1 or more on a numeric rating scale (0 as no pain and 10 as the worst imaginable pain) while completing the 20-m walking test. We used conditional logistic regression to assess the relation of recent knee injury, Kellgren-Lawrence (KL) grade, and quadriceps strength to unilateral knee pain exacerbation during walking.

                  Results

                  We included 277 people who experienced unilateral knee pain exacerbation during the walking test. Recent knee injury was associated with pain exacerbation during walking, with an odds ratio of 3.4 (95% confidence interval [CI]: 1.3, 9.2). Compared with knees with a KL grade of 0, the odds ratios of pain exacerbation during walking were 1.3 (95% CI: 0.7, 2.7), 3.3 (95% CI: 1.5, 7.1), and 8.1 (95% CI: 3.1, 21.1) for knees with KL grades of 2, 3, and 4, respectively. Painful knees with a deficit in quadriceps strength of greater than or equal to 4% had a 1.4-fold (95% CI: 1.0, 1.9) higher risk of pain exacerbation during walking than their pain-free counterparts.

                  Conclusion

                  Recent knee injury, more severe radiographic osteoarthritis, and lower quadriceps strength were associated with an increased risk of knee pain exacerbation during walking. J Orthop Sports Phys Ther 2021;51(6):298-304. Epub 10 May 2021. doi:10.2519/jospt.2021.9735.
                    Cover page: Recent Injury, Severe Radiographic Change, and Lower Quadriceps Strength Increase Risk of Knee Pain Exacerbation During Walking: A Within-Person Knee-Matched Study.
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2018)

                    Aim

                    To evaluate whether knee alignment explains the higher prevalence of lateral compartment tibiofemoral radiographic osteoarthritis (TFROA) among rural Chinese compared with that among Whites.

                    Methods

                    The Wuchuan OA Study is a population-based longitudinal study of risk factors for knee OA. At baseline 1030 participants had home interviews, clinical examinations and weight-bearing posteroanterior semi-flexed radiographs of the tibiofemoral joints. Anatomic knee alignment was measured using an e-film workstation and divided into three categories: normal (182°-184°), valgus (> 184°), and varus (< 182°) alignment. A knee was defined as having medial or lateral compartmental ROA if its Kellgren and Lawrence grade was ≥ 2 and joint space narrowing ≥ 1 in the medial or lateral compartment, respectively. We examined the association between knee alignment with prevalent medial or lateral knee ROA separately using multiple logistic regression.

                    Results

                    Among 1030 participants, the proportions of knees with normal, valgus and varus alignment were 29.9%, 56.5% and 13.7%, respectively. The prevalence of medial and lateral ROA was 16.0% and 4.3%, respectively. Valgus alignment was associated with prevalence of lateral compartment ROA (odds ratio [OR] = 5.0, 95% CI: 2.4-10.5), while varus alignment was associated with medial compartment ROA (OR = 6.1, 95% CI: 4.4-8.6). The ratio of prevalence of lateral versus medial compartment TFROA was greater in Wuchuan than that in the Framingham OA Study and valgus malalignment was more common in Wuchuan than in the Rotterdam study.

                    Conclusions

                    The prevalence of compartment-specific TFROA differs between rural Chinese and Whites. This difference is likely due to relatively high prevalence of valgus malalignment in rural Chinese compared with that in Whites.
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