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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2017)

Mammalian teeth and bone contain a record of an animal’s health and environment over daily, weekly, and yearly time scales. These tissues have long been used to assess the health and environmental conditions particular to individuals, but they may also preserve characteristics of entire populations, in this case relative population size and behavior. In this dissertation, we draw new inferences from skeletal and dental characters to demonstrate that they preserve 1) unique signals of predatory behavior and 2) relative changes in ungulate population size. Chapter 1 assesses the potential of skeletal pathology to preserve a signal of behavior in extinct species, specifically the hunting modes of two Pleistocene predators reconstructed as ambush and pursuit predators, respectively. To answer this question we analyzed injury rates across thousands of pathological elements and performed quantitative analysis of injury locations, the first such application of spatial analyses. In chapter 2, we documented a correlation between population size, nutritional status and dental/osteological features in extant moose (Alces alces) using mandibles collected over the past five decades from Isle Royale, MI. This is the first attempt to use patterns of dental growth and wear in past or present populations to infer food-limitation and relative density. In chapter 3 we examined incremental growth rates of dentin, the tooth tissue surrounding the pulp cavity, allowing a first look at the responses of tooth enamel, dentin and bone growth to episodes of stress in a wild population. Through this work we developed methods of characterizing past ecosystems to benefit studies that seek to restore national parks to their pre-anthropogenic state or contribute to the long-standing paleontological debate regarding the Pleistocene mammal extinctions. As a result of our efforts, we have a robust set of both macroscopic and microscopic indicators of predatory behavior (Chapter 1) and nutritional stress (Chapter 2-3) that can be applied to extinct and extant carnivoran and ungulate and populations.

    Cover page: Interpreting Pleistocene Predator-Prey Dynamics: Inference from Skeletal Pathology, Dental Growth and Stature
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2018)
    The recovery and persistence of rare and endangered species are often threatened by genetic factors, such as the accumulation of deleterious mutations, loss of adaptive potential, and inbreeding depression [1]. Island foxes (Urocyon littoralis), the dwarfed descendants of mainland gray foxes (Urocyon cinereoargenteus), have inhabited Californias Channel Islands for >9,000 years [2-4]. Previous genomic analyses revealed that island foxes have exceptionally low levels of diversity and elevated levels of putatively deleterious variation [5]. Nonetheless, all six populations have persisted for thousands of generations, and several populations rebounded rapidly after recent severe bottlenecks [6, 7]. Here, we combine morphological and genomic data with population-genetic simulations to determine the mechanism underlying the enigmatic persistence of these foxes. First, through analysis of genomes from 1929 to 2009, we show that island foxes have remained at small population sizes with low diversity for many generations. Second, we present morphological data indicating an absence of inbreeding depression in island foxes, confirming that they are not afflicted with congenital defects common to other small and inbred populations. Lastly, our population-genetic simulations suggest that long-term small population size results in a reduced burden of strongly deleterious recessive alleles, providing a mechanism for the absence of inbreeding depression in island foxes. Importantly, the island fox illustrates a scenario in which genetic restoration through human-assisted gene flow could be a counterproductive or even harmful conservation strategy. Our study sheds light on the puzzle of island fox persistence, a unique success story that provides a model for the preservation of small populations.
      Cover page: Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes.
      • Article
      • Peer Reviewed
      LBL Publications (2021)
      Logistic regression has long been the gold standard for choice modeling in the transportation field. Despite the rising popularity of machine learning (ML), few is applied to predicting the household vehicle transactions. To address the research gap, this paper presents a first use case of ML application to predicting household vehicle transaction decisions by leveraging a newly processed national panel data set. Model performances are reported for four ML models and the traditional multinomial logit model (MNL). Instead of treating the gold standard and ML models as competitors, this paper tries to use ML tools to inform the MNL model building process. We find the two gradient boosting based methods, CatBoost and LightGBM, are the best performing ML models; and improving logistic models with SHAP interpretation tools can achieve similar performance levels to the best performing ML methods.
        Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2018)
        The recovery and persistence of rare and endangered species are often threatened by genetic factors, such as the accumulation of deleterious mutations, loss of adaptive potential, and inbreeding depression [1]. Island foxes (Urocyon littoralis), the dwarfed descendants of mainland gray foxes (Urocyon cinereoargenteus), have inhabited California's Channel Islands for >9,000 years [2-4]. Previous genomic analyses revealed that island foxes have exceptionally low levels of diversity and elevated levels of putatively deleterious variation [5]. Nonetheless, all six populations have persisted for thousands of generations, and several populations rebounded rapidly after recent severe bottlenecks [6, 7]. Here, we combine morphological and genomic data with population-genetic simulations to determine the mechanism underlying the enigmatic persistence of these foxes. First, through analysis of genomes from 1929 to 2009, we show that island foxes have remained at small population sizes with low diversity for many generations. Second, we present morphological data indicating an absence of inbreeding depression in island foxes, confirming that they are not afflicted with congenital defects common to other small and inbred populations. Lastly, our population-genetic simulations suggest that long-term small population size results in a reduced burden of strongly deleterious recessive alleles, providing a mechanism for the absence of inbreeding depression in island foxes. Importantly, the island fox illustrates a scenario in which genetic restoration through human-assisted gene flow could be a counterproductive or even harmful conservation strategy. Our study sheds light on the puzzle of island fox persistence, a unique success story that provides a model for the preservation of small populations.
        • 1 supplemental PDF
        Cover page: Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island FoxesCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 24, Issue 5 (2023)

        Background: There are no randomized trials comparing andexanet alfa and 4 factor prothrombin complex concentrate (4F-PCC) for the treatment of factor Xa inhibitor (FXa-I)-associated bleeds, and observational studies lack important patient characteristics. We pursued this study to demonstrate the feasibility of acquiring relevant patient characteristics from electronic health records. Secondarily, we explored outcomes in patients with life-threatening FXa-I associated bleeds after adjusting forthese variables.

        Methods: We conducted a multicenter, chart review of 100 consecutive adult patients with FXa-I associated intracerebral hemorrhage (50) or gastrointestinal bleeding (50) treated with andexanet alfa or 4F-PCC. We collected demographic, clinical, laboratory, and imaging data including time from last factor FXa-I dose and bleed onset.

        Results: Mean (SD) age was 75 (12) years; 34% were female. Estimated time from last FXa-I dose to bleed onset was present in most cases (76%), and patients treated with andexanet alfa and 4F-PCC were similar in baseline characteristics. Hemostatic efficacy was excellent/good in 88% and 76% of patients treated with andexanet alfa and 4F-PCC, respectively (P = 0.29). Rates of thrombotic events within 90 days were 14% and 16% in andexanet alfa and 4F-PCC patients, respectively (P = 0.80). Survival to hospital discharge was 92% and 76% in andexanet alfa and 4F-PCC patients, respectively (P = 0.25). Inclusion of an exploratory propensity score and treatment in a logistic regression model resulted in an odds ratio in favor of andexanet alfa of 2.01 (95% confidence interval 0.67–6.06) for excellent/good hemostatic efficacy, although the difference was not statistically significant.

        Conclusion: Important patient characteristics are often documented supporting the feasibility of a large observational study comparing real-life outcomes in patients with FXa-I-associated bleeds treated with andexanet alfa or 4F-PCC. The small sample size in the current study precluded definitive conclusions regarding the safety and efficacy of andexanet alfa or 4F-PCC in FXa-I-associated bleeds.

        • 3 supplemental PDFs
        Cover page: Treatment of Factor-Xa Inhibitor-associated Bleeding with Andexanet Alfa or 4 Factor PCC: A Multicenter Feasibility Retrospective StudyCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        LBL Publications (2023)
        What makes you hold on to that old car? While the vast majority of household vehicles are still powered by conventional internal combustion engines, the progress of adopting emerging vehicle technologies will critically depend on how soon the existing vehicles are transacted out of the household fleet. Leveraging a nationally representative longitudinal data set, the Panel Study of Income Dynamics, this study examines how household decisions to dispose of or replace a given vehicle are: 1) influenced by the vehicle’s attributes, 2) mediated by households’ concurrent socio-demographic and economic attributes, and 3) triggered by key life cycle events. Coupled with a newly developed machine learning interpretation tool, TreeExplainer, we demonstrate an innovative use of machine learning models to augment traditional logit modeling to both generate behavioral insights and improve model performance. We find the two gradient-boosting-based methods, CatBoost and LightGBM, are the best performing machine learning models for this problem. The multinomial logistic model can achieve similar performance levels after its model specification is informed by TreeExplainer. Both machine learning and multinomial logit models suggest that while older vehicles are more likely to be disposed of or replaced than newer ones, such probability decreases as the vehicles serve the family longer. Pickup trucks and sport utility vehicles are less likely to be disposed of or replaced than cars, and leased vehicles are more likely to be transacted than owned vehicles. We find that married families, families with higher education levels, homeowners, and older families tend to keep their vehicles longer. Life events such as childbirth, residential relocation, and change of household composition and income are found to increase vehicle disposal and/or replacement. We provide additional insights on the timing of vehicle replacement or disposal, in particular, the presence of children and childbirth events are more strongly associated with vehicle replacement among younger parents.
          Creative Commons 'BY' version 4.0 license
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