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Open Access Publications from the University of California

Scholarly Works (30 results)

  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2005)

1. Past studies on phenotypic plasticity usually focus on ultimate (evolutionary) issues. More recently, proximate (developmental) factors explaining how plasticity is achieved are starting to be addressed. 2. Here, we examine the importance of resource level and temperature on growth rate and burst swimming speed in tadpoles of Spea hammondii (Western Spadefoot Toad). 3. Food and temperature manipulations alter growth rate via different developmental processes (cell growth and cell recruitment, respectively) and these processes appear to have consequences for swimming performance in tadpoles. 4. Tadpoles reared at warm temperatures were slower swimmers than those reared at cooler temperatures while food level had no effect on size-specific burst speed. Tadpoles reared at warm temperatures also had more fibres in the tail muscle, probably due to an earlier onset of recruitment. Tadpoles reared at higher food levels had larger muscle fibres, but little differences in fibre number compared to those reared at low food levels. 5. These results indicate that growth by adding cells comes at a performance cost not seen when growth is due to increasing cell size. This developmental difference also has implications for how body size manipulations are carried out in behavioural and ecological studies.

    Cover page: Effect of food level and rearing temperature on burst speed and muscle composition of Western Spadefoot Toad (Spea hammondii)
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2005)

    Recent theoretical and empirical work argues that growth rate can evolve and be optimized, rather than always being maximized. Chronically low resource availability is predicted to favour the evolution of slow growth, whereas attaining a size-refuge from mortality risk is predicted to favor the evolution of rapid growth. Guppies (Poecilia reticulata) evolve difference in behaviour, morphology and life-history traits in response to predation, thus demonstrating that predators are potent agents of selection. Predators in low-predation environments prey preferentially on small guppies, but hose in high-predation environments appear to be non-selective. Because guppies can outgrow their main predator in low- but not high-predation localities, we predict that predation will select for higher growth rate in the low-predation environments. However, low-predation localities also tend to have lower productivity than high-predation localities, yielding the prediction that guppies from these sites should have slower growth rate. Here, we compare the growth rates of the second laboratory-born generation of guppies from paired high- and low-predation localities from four different drainages. In two out of four comparisons, guppies from high-predation sites grew significantly faster than their low-predation counterparts. We also compare laboratory born descendants from a field introduction experiment and show that guppies introduced to a low-predation environment evolved slower growth rates after 13 years, although this was evident only at the high food level. The weight of the evidence suggests that resource availability plays a more important role than predation in shaping the evolution of growth rates.

      Cover page: Evolution of juvenile growth rates in female guppies (Poecilia reticulata): predator regime or resource level?
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      There is an urgent requirement to minimize food waste and create more sustainable food systems that address global increases in malnutrition and hunger. The nutritional value of brewers spent grain (BSG) makes it attractive for upcycling into value-added ingredients rich in protein and fiber having a lower environmental impact than comparable plant-based ingredients. BSG is predictably available in large quantities globally and can therefore play a role in addressing hunger in the developing world via the fortification of humanitarian food aid products. Moreover, addition of BSG-derived ingredients can improve the nutritional profile of foods commonly consumed in more developed regions, which may aid in reducing the prevalence of dietary-related disease and mortality. Challenges facing the widespread utilization of upcycled BSG ingredients include regulatory status, variability of raw material composition, and consumer perception as low-value waste products; however, the rapidly growing upcycled food market suggests increasing consumer acceptability and opportunities for significant market growth via effective new product innovation and communication strategies.
        Cover page: Brewers Spent Grain: An Unprecedented Opportunity to Develop Sustainable Plant-Based Nutrition Ingredients Addressing Global Malnutrition Challenges.
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)
          Cover page: Language Training and Refugees' Integration
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2014)

          Background

          Mild cognitive impairment is often a precursor to dementia due to Alzheimer's disease, but many patients with mild cognitive impairment never develop dementia. New diagnostic criteria may lead to more patients receiving a diagnosis of mild cognitive impairment.

          Objective

          To develop a prediction index for the 3-year risk of progression from mild cognitive impairment to dementia relying only on information that can be readily obtained in most clinical settings.

          Design and participants

          382 participants diagnosed with amnestic mild cognitive impairment enrolled in the Alzheimer's Disease Neuroimaging Initiative (ADNI), a multi-site, longitudinal, observational study.

          Main predictors measures

          Demographics, comorbid conditions, caregiver report of participant symptoms and function, and participant performance on individual items from basic neuropsychological scales.

          Main outcome measure

          Progression to probable Alzheimer's disease.

          Key results

          Subjects had a mean (SD) age of 75 (7) years and 43% progressed to probable Alzheimer's disease within 3 years. Important independent predictors of progression included being female, resisting help, becoming upset when separated from caregiver, difficulty shopping alone, forgetting appointments, number of words recalled from a 10-word list, orientation and difficulty drawing a clock. The final point score could range from 0 to 16 (mean [SD]: 4.2 [2.9]). The optimism-corrected Harrell's c-statistic was 0.71(95% CI: 0.68-0.75). Fourteen percent of subjects with low risk scores (0-2 points, n = 124) converted to probable Alzheimer's disease over 3 years, compared to 51% of those with moderate risk scores (3-8 points, n = 223) and 91% of those with high risk scores (9-16 points, n = 35).

          Conclusions

          An index using factors that can be obtained in most clinical settings can predict progression from amnestic mild cognitive impairment to probable Alzheimer's disease and may help clinicians differentiate between mild cognitive impairment patients at low vs. high risk of progression.
            Cover page: A clinical index to predict progression from mild cognitive impairment to dementia due to Alzheimer's disease.
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2023)
            Coloration facilitates evolutionary investigations in nature because the interaction between genotype, phenotype and environment is relatively accessible. In a landmark set of studies, Endler addressed this complexity by demonstrating that the evolution of male Trinidadian guppy coloration is shaped by the local balance between selection for mate attractiveness versus crypsis. This became a textbook paradigm for how antagonistic selective pressures may determine evolutionary trajectories in nature. However, recent studies have challenged the generality of this paradigm. Here, we respond to these challenges by reviewing five important yet underappreciated factors that contribute to colour pattern evolution: (i) among-population variation in female preference and correlated variation in male coloration, (ii) differences in how predators versus conspecifics view males, (iii) biased assessment of pigmentary versus structural coloration, (iv) the importance of accounting for multi-species predator communities, and (v) the importance of considering the multivariate genetic architecture and multivariate context of selection and how sexual selection encourages polymorphic divergence. We elaborate these issues using two challenging papers. Our purpose is not to criticize but to point out the potential pitfalls in colour research and to emphasize the depth of consideration necessary for testing evolutionary hypotheses using complex multi-trait phenotypes such as guppy colour patterns.
              Cover page: How to generate and test hypotheses about colour: insights from half a century of guppy research
              • Article
              • Peer Reviewed
              LBL Publications (2019)
              Model predictive control (MPC) for buildings is attracting significant attention in research and industry due to its potential to address a number of challenges facing the building industry, including energy cost reduction, grid integration, and occupant connectivity. However, the strategy has not yet been implemented at any scale, largely due to the significant effort required to configure and calibrate the model used in the MPC controller. While many studies have focused on methods to expedite model configuration and improve model accuracy, few have studied the impact a wide range of factors have on the accuracy of the resulting model. In addition, few have continued on to analyze these factors’ impact on MPC controller performance in terms of final operating costs. Therefore, this study first identifies the practical factors affecting model setup, specifically focusing on the thermal envelope. The seven that are identified are building design, model structure, model order, data set, data quality, identification algorithm and initial guesses, and software tool-chain. Then, through a large number of trials, it analyzes each factor's influence on model accuracy, focusing on grey-box models for a single zone building envelope. Finally, this study implements a subset of the models identified with these factor variations in heating, ventilating, and air conditioning MPC controllers, and tests them in simulation of a representative case that aims to optimally cool a single-zone building with time-varying electricity prices. It is found that a difference of up to 20% in cooling cost for the cases studied can occur between the best performing model and the worst performing model. The primary factors attributing to this were model structure and initial parameter guesses during parameter estimation of the model.
                • Article
                • Peer Reviewed
                LBL Publications (2022)
                Detecting and anticipating global proliferation expertise and capability evolution from unstructured, noisy, and incomplete public data streams is a highly desired, but extremely challenging task. In this article, we present our pioneering data-driven approach to support the non-proliferation mission to detect and explain the evolution of proliferation expertise and capability development globally from terabytes of publicly available information (PAI), focusing on our knowledge extraction pipeline and descriptive analytics. We first discuss how we fuse nine open-source data streams, including multilingual data, to convert 4 TB of unstructured data to structured knowledge and encode dynamically evolving proliferation expertise representations - content and context graphs. For this, we rely on natural language processing (NLP) and deep learning (DL) models to perform information extraction, topic modeling, and distributed text representation (aka embedding) learning. We then present interactive, usable, and explainable descriptive analytics to refine domain knowledge and present it in a human-understandable form. Finally, we introduce future work avenues that will leverage our dynamic knowledge representations and descriptive analytics to enable predictive and prescriptive inferences to achieve real-time domain understanding and contextual reasoning about global proliferation expertise and capability evolution.
                  Cover page: Learning Global Proliferation Expertise Evolution Using AI-Driven Analytics and Public InformationCreative Commons 'BY-NC' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2006)

                  Background

                  The human retinoblastoma susceptibility gene encodes a nuclear phosphoprotein RB, which is a negative regulator of cell proliferation. The growth suppression function of RB requires an evolutionarily conserved A/B domain that contains two distinct peptide-binding pockets. At the A/B interface is a binding site for the C-terminal trans-activation domain of E2F. Within the B-domain is a binding site for proteins containing the LxCxE peptide motif.

                  Methodology/principle findings

                  Based on the crystal structure of the A/B domain, we have constructed an RB-K530A/N757F (KN) mutant to disrupt the E2F- and LxCxE-binding pockets. The RB-K530A (K) mutant is sufficient to inactivate the E2F-binding pocket, whereas the RB-N757F (N) mutant is sufficient to inactivate the LxCxE-binding pocket. Each single mutant inhibits cell proliferation, but the RB-KN double mutant is defective in growth suppression. Nevertheless, the RB-KN mutant is capable of reducing etoposide-induced apoptosis.

                  Conclusion/significance

                  Previous studies have established that RB-dependent G1-arrest can confer resistance to DNA damage-induced apoptosis. Results from this study demonstrate that RB can also inhibit apoptosis independent of growth suppression.
                    Cover page: Separation of Anti-Proliferation and Anti-Apoptotic Functions of Retinoblastoma Protein through Targeted Mutations of Its A/B Domain
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2021)

                    Background

                    Certolizumab pegol (CZP) is an Fc-free, PEGylated anti-tumor necrosis factor biologic.

                    Objectives

                    To report 3-year outcomes from the CIMPACT (NCT02346240) phase 3, CZP in moderate to severe plaque psoriasis, randomized controlled trial.

                    Methods

                    Adults were randomized 3:3:3:1 to CZP 200 mg every other week (Q2W), CZP 400 mg Q2W, etanercept biweekly or placebo. At Week 16, CZP- and etanercept-treated PASI 75 responders were re-randomized to CZP 200 mg Q2W, CZP 400 mg Q4W, CZP 400 mg Q2W or placebo for maintenance treatment; PASI 75 non-responders entered an open-label escape CZP 400 mg Q2W arm. Patients entering the open-label extension (OLE; Weeks 48-144) from blinded treatment received CZP 200 mg Q2W.

                    Results

                    Double-blinded results have been reported previously. 261 patients received 200 mg Q2W upon OLE entry. PASI 75 response was maintained in patients continuing 200 mg Q2W treatment through Weeks 16-144 (Week 144: 96.2%). In patients dosed down at Week 48 (double-blinded 400 mg to 200 mg Q2W), PASI 75 decreased (Week 48: 98.7%; Week 144: 85.9%). In patients who received placebo through Weeks 16-48, PASI 75 response decreased (Week 48: 60.4%), then increased following Week 48 switch to 200 mg Q2W (Week 144: 95.1%). 48 and 36 patients initially randomized to 200 and 400 mg Q2W, respectively, were Week 16 PASI 75 non-responders and entered the escape arm; at Week 144, 71.8% and 78.2% achieved PASI 75. No new safety signals were identified.

                    Conclusions

                    Response to CZP was durable over three years; no new safety signals were identified.
                      Cover page: Three‐year efficacy and safety of certolizumab pegol for the treatment of plaque psoriasis: results from the randomized phase 3 CIMPACT trial
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