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Open Access Publications from the University of California

Scholarly Works (11 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2013)

This thesis introduces and explores the idea of ``user-guided inverse 3D modeling'' -- an interactive approach to shape construction and redesign that extracts well-structured, parameterized, procedural descriptions from unstructured, hierarchically flat input data, such as point clouds, boundary representation meshes, or even multiple pictorial views of a given inspirational prototype. This approach combines traditional ``forward'' 3D modeling tools with a system of user-guided extraction modules and optimization routines. With a few cursor strokes users can express their preferences regarding the type of modeling primitives to be used in a particular area of the given prototype to be approximated, and they can also select the degree of parameterization associated with each modeling routine. The results are then pliable, structured descriptions that are well suited to implement the particular design modifications intended by the user.

We present research on the components that make up an inverse 3D modeling system. Our research focuses have been (1) fitting of modeling primitives to data; (2) fitting higher-level structure (CSG expressions, symmetry, and hierarchy) to data; (3) minimal user interactions that guide these fitting processes; and finally (4) shape editing using the fitted structure. We also explore what is necessary to ultimately arrive at a clean, exportable result. A key research question guiding the design of our system has been how bringing the user into the loop affects the problem: i.e., where can the user's inputs simplify, accelerate, or otherwise improve the fitting process? What simple inputs can the user provide to unambiguously extract a desired primitive fit? And how can we let the user immediately begin using their fitted primitives to edit the shape? Answering these questions leads us to many new research findings, including: (1) We identify simple, lightweight inputs that allow the system to extract primitives with a great deal of user control, and we present detailed analysis of how these inputs can be ambiguous and what additional inputs may be needed to exactly capture the user's desired primitive fit. (2) We show multiple improvements to the state of the art in fast, effective fitting methods for sweeps and quadric surfaces. These improvements include identifying and fixing a major problem with previously-standard methods for kinematic surface fitting that led to grossly wrong results for data with small noise, and a new insight into the nature of direct, algebraic fitting that leads us to more accurate type-specific quadric fitting. (3) We show how the user can guide a boundary-to-CSG reverse-engineering process: Specifically, we identify cases where the best result of such a process depends on the user's intent, and we show how simple user interactions can let users specify their intents. (4) In addition to the diverse problems faced by individual structure-fitting and shape editing modules, the combination of these modules also presents new research opportunities; we identify new interactions between these diverse modules, including transformations between primitive types and hierarchies that can be imposed across modules.

    Cover page: User-Guided Inverse 3D Modeling
    • Article
    Recent Work (2005)

    During fieldwork for the Vermont Reptile and Amphibian Atlas Project, a population of Eastern Racers (Coluber constrictor) was found utilizing a parcel of state land managed by the Vermont Agency of Transportation (VTrans) in southeastern Vermont along Interstate 91. This species was thought to have been extirpated from Vermont for nearly 20 years. Until 2003, the last positively identified Racer in Vermont was a road-killed specimen in Putney in 1985. But the recent discovery along I-91, resulting in the species being listed as State Threatened in Vermont, proves that a few hardy individuals are making their way back to the northern fringes of their geographic range. To date, a minimum of eight individuals have been identified in Vermont, and researchers feel that this is a very encouraging sign that the Racer is making a comeback in Vermont.

      Cover page: The return of the Eastern Racer to Vermont; successful conservation through proactive project development and interagency collaboration
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2021)

      Objective

      The association of sarcopenia with development of knee osteoarthritis (OA) or knee pain in older adults is uncertain. We examined the relationship of grip strength and appendicular lean mass (ALM) with the likelihood of developing knee OA and knee pain in older adults in the Health ABC (Health, Aging, and Body Composition) Study.

      Methods

      ALM and grip strength were assessed at baseline by dual-energy x-ray absorptiometry and handheld dynamometry, respectively. Incident clinically diagnosed, symptomatic knee OA, defined as new participant report of physician-diagnosed knee OA and concurrent frequent knee pain, and incident frequent knee pain over 5 years of follow-up were examined. Separate regression analyses, stratified by sex, modeled associations of baseline ALM and grip strength with the likelihood of incident clinically diagnosed, symptomatic knee OA and incident knee pain over follow-up, adjusting for covariates.

      Results

      Among the 2779 subjects without OA at baseline, 95 men (6.9%) and 158 women (11.3%) developed clinically diagnosed, symptomatic knee OA, and, among the 2182 subjects without knee pain at baseline, 315 men (28.3%) and 385 women (36.1%) developed knee pain over follow-up. Among men only, each SD decrement of ALM was associated with decreasing likelihood of incident knee OA (odds ratio [OR] per SD decrement: 0.68; 95% confidence interval [CI]: 0.47-0.97), and each SD decrement of grip strength was associated with increasing likelihood of incident knee pain (OR per SD decrement: 1.20; 95% CI: 1.01-1.42).

      Conclusion

      In older men, ALM and grip strength may be associated with the development of knee OA and knee pain, respectively.
        Cover page: Appendicular Lean Mass, Grip Strength, and the Development of Knee Osteoarthritis and Knee Pain Among Older Adults
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2013)

        Objectives

        To determine whether pain predicts future activity of daily living (ADL) disability or death in individuals aged 60 and older.

        Design

        Prospective cohort study.

        Setting

        The 1998 to 2008 Health and Retirement Study (HRS), a nationally representative study of older community-living individuals.

        Participants

        Twelve thousand six hundred thirty-one participants in the 1998 HRS aged 60 and older who did not need help in any ADL.

        Measurements

        Participants reporting that they had moderate or severe pain most of the time were defined as having significant pain. The primary outcome was time to development of ADL disability or death over 10 yrs, assessed at five successive 2-year intervals. ADL disability was defined as needing help performing any ADL: bathing, dressing, transferring, toileting, eating, or walking across a room. A discrete hazards survival model was used to examine the relationship between pain and incident disability over each 2-year interval using only participants who started the interval with no ADL disability. Several potential confounders were adjusted for at the start of each interval: demographic factors, seven chronic health conditions, and functional limitations (ADL difficulty and difficulty with five measures of mobility).

        Results

        At baseline, 2,283 (18%) participants had significant pain. Participants with pain were more likely (all P < .001) to be female (65% vs 54%), have ADL difficulty (e.g., transferring 12% vs 2%, toileting 11% vs 2%), have difficulty walking several blocks (60% vs 21%), and have difficulty climbing one flight of stairs (40% vs 12%). Over 10 years, participants with pain were more likely to develop ADL disability or death (58% vs 43%, unadjusted hazard ratio (HR) = 1.67, 95% confidence interval (CI) = 1.57-1.79), although after adjustment for confounders, participants with pain were not at greater risk for ADL disability or death (HR = 0.98, 95% CI = 0.91-1.07). Adjustment for functional status almost entirely explained the difference between the unadjusted and adjusted results.

        Conclusion

        Although there are strong cross-sectional relationships between pain and functional limitations, individuals with pain are not at higher risk of subsequent disability or death after accounting for functional limitations. Like many geriatric syndromes, pain and disability may represent interrelated phenomena that occur simultaneously and require unified treatment paradigms.
          Cover page: Pain as a Risk Factor for Disability or Death
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2017)

          Objectives

          Muscle strength is an important determinant of physical function in women with systemic lupus erythematosus (SLE). Serum biomarkers of inflammation, including interleukin-6 (IL-6) and C-Reactive Protein (CRP), are associated with differences in muscle strength among individuals without rheumatologic disease. We examined whether serum levels of IL-6 and CRP are associated with upper and lower extremity muscle strength among adult women with SLE.

          Methods

          One hundred thirty-six women with SLE participated in this cross-sectional study. High-sensitivity CRP was analyzed by nephelometry. IL-6 serum levels were analyzed by high sensitivity enzyme-linked immunosorbent assay. Upper and lower extremity muscle strength were assessed by grip strength and peak torque of knee extension and flexion, respectively. Regression analyses modeled associations of CRP and IL-6 with upper and lower extremity muscle strength controlling for age, SLE duration, physical activity, prednisone use, BMI, plaquenil use, and pain.

          Results

          Higher serum levels of IL-6 and CRP were associated with significantly weaker upper and lower extremity muscle strength even when controlling for covariates.

          Conclusions

          Increased serum IL-6 and CRP are associated with clinically significant differences in upper and lower extremity muscle strength and may be useful in identifying those at risk for weakness and decreased physical function.
            Cover page: Serum biomarkers of inflammation and muscle strength among women with systemic lupus erythematosus
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2017)
            Reduced physical function and health-related quality of life are common in rheumatoid arthritis (RA), and further studies are needed that examine novel determinates of reduced physical function in RA. This study examines whether frailty, a state of increased vulnerability to stressors, is associated with differences in self-reported physical function among adults with RA. Adults from a longitudinal RA cohort (n = 124) participated in the study. Using an established definition of frailty, individuals with three or more of the following physical deficits were classified as frail: (1) body mass index ≤18.5, (2) low grip strength (adjusted for sex and body mass index (BMI), measured by handheld dynamometer), (3) severe fatigue (measured by the Multidimensional Assessment of Fatigue), (4) slow 4-m walking speed (adjusted for sex and height), and (5) low physical activity (measured by the International Physical Activity Questionnaire). Individuals with one or two deficits were classified as "pre-frail" and those with no deficits as "robust." Self-reported physical function was assessed by the Health Assessment Questionnaire (HAQ) and the Valued Life Activities Difficulty scale. Regression analyses modeled associations of frailty category with HAQ and Valued Life Activities (VLA) Difficulty scores with and without controlling for age, sex, disease duration, C-reactive protein, use of oral steroids, and pain. Among adults with RA, being frail compared to being robust was associated with a 0.44 worse VLA score (p < 0.01) when the effects of covariates are held constant. Being frail, compared to being robust, is associated with clinically meaningful differences in self-reported physical function among adults with RA.
              Cover page: Frailty and reduced physical function go hand in hand in adults with rheumatoid arthritis: a US observational cohort study
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2019)

              Objective

              Reduced physical function and frailty are common in rheumatoid arthritis (RA). However, relationships between frailty and changes in physical function and disease activity over time in RA are unknown. We tested whether frailty is a risk factor for worsening patient-reported physical function and disease activity in RA.

              Methods

              Adults from a longitudinal RA cohort (N = 124) participated. By using an established frailty definition, individuals with three or more of the following deficits were considered frail: 1) body mass index less than or equal to 18.5, 2) low grip strength, 3) severe fatigue, 4) slow 4-m walking speed, and 5) low physical activity. Individuals with one to two or zero deficits were considered "pre-frail" or "robust," respectively. Physical function and RA disease activity were assessed by the Health Assessment Questionnaire (HAQ) and Rheumatoid Arthritis Disease Activity Index (RADAI), respectively, at baseline and follow-up 2 years later. Regression analyses modeled associations of frailty status with change in HAQ and RADAI scores between baseline and follow-up with and without controlling for covariates. Associations of individual frailty components with change in HAQ and RADAI scores were also examined.

              Results

              Among adults with RA, baseline frailty status predicted significant increases, or worsening, in HAQ (β: 0.4; 95% confidence interval: 0.1-0.8; P < 0.01) but not RADAI scores (β: 0.5; 95% confidence interval: -0.4 to 1.5; P > 0.05) between baseline and follow-up in fully adjusted models. Fatigue was an important contributor to this effect.

              Conclusion

              Frailty may be an important risk factor for reduced physical function over time in RA. Future studies should address whether interventions to reduce frailty improve physical function in RA.
                Cover page: The Impact of Frailty on Changes in Physical Function and Disease Activity Among Adults With Rheumatoid Arthritis
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2015)

                Objective

                Cross-sectional studies have observed that muscle weakness is associated with worse physical function among women with systemic lupus erythematosus (SLE). The present study examines whether reduced upper and lower extremity muscle strength predict declines in function over time among adult women with SLE.

                Methods

                One hundred forty-six women from a longitudinal SLE cohort participated in the study. All measures were collected during in-person research visits approximately 2 years apart. Upper extremity muscle strength was assessed by grip strength. Lower extremity muscle strength was assessed by peak knee torque of extension and flexion. Physical function was assessed using the Short Physical Performance Battery (SPPB). Regression analyses modeled associations of baseline upper and lower extremity muscle strength with followup SPPB scores controlling for baseline SPPB, age, SLE duration, SLE disease activity (Systemic Lupus Activity Questionnaire), physical activity level, prednisone use, body composition, and depression. Secondary analyses tested whether associations of baseline muscle strength with followup in SPPB scores differed between intervals of varying baseline muscle strength.

                Results

                Lower extremity muscle strength strongly predicted changes over 2 years in physical function even when controlling for covariates. The association of reduced lower extremity muscle strength with reduced physical function in the future was greatest among the weakest women.

                Conclusion

                Reduced lower extremity muscle strength predicted clinically significant declines in physical function, especially among the weakest women. Future studies should test whether therapies that promote preservation of lower extremity muscle strength may prevent declines in function among women with SLE.
                  Cover page: Muscle Strength and Changes in Physical Function in Women With Systemic Lupus Erythematosus.
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2015)

                  Objective

                  Data describing relationships between muscle strength, muscle mass, and physical disability among individuals with systemic lupus erythematosus (SLE) are limited. The present study examines the relationship of muscle strength and muscle mass with physical disability among adult women with SLE.

                  Methods

                  A total of 146 women from a longitudinal SLE cohort participated in the study. All measures were collected during an in-person research visit. Lower extremity muscle strength was assessed by peak knee torque of extension and flexion and by chair-stand time. Total lean body mass, appendicular lean mass, and fat mass (kg/m(2) ) were measured by whole-body dual x-ray absorptiometry. Self-reported physical disability was assessed using the Short Form 36 health survey (SF-36) physical functioning subscale, and the Valued Life Activities (VLA) disability scale. Spearman's rank correlation coefficients tested the correlations between muscle strength, muscle mass, and disability scores. Regression analyses modeled the effect of lower extremity muscle strength and mass on SF-36 and VLA disability scores controlling for age, SLE duration, SLE disease activity measured with the Systemic Lupus Activity Questionnaire, physical activity level, prednisone use, body composition, and depression.

                  Results

                  On all measures, reduced lower extremity muscle strength was associated with poorer SF-36 and VLA disability scores. Trends persisted after adjustment for covariates. Muscle mass was moderately correlated with muscle strength, but did not contribute significantly to adjusted regression models.

                  Conclusion

                  Lower extremity muscle strength, but not muscle mass, was strongly associated with physical disability scores. While further studies are needed, these findings suggest that improving muscle strength may reduce physical disability among women with SLE.
                    Cover page: Muscle Strength, Muscle Mass, and Physical Disability in Women With Systemic Lupus Erythematosus
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2023)
                    BACKGROUND: Identification of novel risk factors for dementia in older adults could facilitate development of methods to identify patients most at risk and improve their cognitive outcomes. We aimed to determine whether lower appendicular lean mass (ALM), assessed by dual-energy x-ray absorptiometry (DXA), and lower grip strength are associated with a greater likelihood of incident dementia among older adults in the Health Aging and Body Composition Study (Health ABC). METHODS: Health ABC data from 1997 to 2008 were analyzed (n = 2 704). Baseline ALM to body mass index (BMI) ratio (ALMBMI) was assessed by DXA. Baseline grip strength was assessed by hand-held dynamometry. Incident dementia diagnosis was defined as either (i) dementia-related hospitalization plus a Modified Mini-Mental State Examination (3MS) score of ≤ 90; or (ii) record of prescription for anti-dementia medication; or (iii) decline of at least 1.5 SDs on the 3MS score compared to baseline. Cox proportional hazard models estimated associations of ALMBMI and grip strength with incident dementia over follow-up with and without adjusting for covariates, stratified by sex. RESULTS: Among older men, each standard deviation decrement in ALMBMI (adjusted hazard ratio [aHR]: 1.33; 95% confidence interval [CI]: 1.07, 1.65) or grip strength (aHR 1.22; 95% CI: 1.06, 1.41) was associated with increased likelihood of incident dementia. CONCLUSIONS: Lower ALMBMI and grip strength may be important risk factors for the development of dementia among older men. How these factors may belong to a causal pathway of dementia must be elucidated in future work.
                      Cover page: Appendicular Lean Mass, Grip Strength, and the Incidence of Dementia Among Older Adults in the Health ABC Study.
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