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Open Access Publications from the University of California

Scholarly Works (11 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2016)

Water scarcity is a global challenge that stifles social and economic growth. There is a growing concern to examine the water-energy nexus to understand the importance of applying energy and water interactions to technology. In developing countries there are many communities that live off-grid in remote region with no access to electricity or clean water. Additionally, there are developed countries that are located in regions with electricity but no access to clean water. Recent developments in renewable energy technology and energy policies have greatly reduced the costs of renewable energy making them more attractive and affordable. The purpose of this dissertation is to evaluate the main barriers to deploying renewables to non-Organization for Economic Co-operation and Development (non-OECD) countries and member countries of the Organization for Economic Co-operation and Development (OECD). This dissertation examines the potential of renewable desalination technology systems across emerging countries. The findings of this research can serve as the basis for investors interested in entering this market. The combined chapters seek to address potential problems regarding the costs, methods, and tools required for the implementation of the appropriate water purification technologies for off-grid, community scale infrastructures.

    Cover page: An integrated approach to scale up the market penetration of low carbon technologies in developing countries and water scarce regions’
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2018)
    Habitat conversion is driving biodiversity loss and restructuring species assemblages across the globe. Responses to habitat conversion vary widely, however, and little is known about the degree to which shared evolutionary history underlies changes in species richness and composition. We analyzed data from 48 studies, comprising 438 species on five continents, to understand how taxonomic and phylogenetic diversity of amphibian assemblages shifts in response to habitat conversion. We found that evolutionary history explains the majority of variation in species' responses to habitat conversion, with specific clades scattered across the amphibian tree of life being favored by human land uses. Habitat conversion led to an average loss of 139 million years of amphibian evolutionary history within assemblages, high species and lineage turnover at landscape scales, and phylogenetic homogenization at the global scale (despite minimal taxonomic homogenization). Lineage turnover across habitats was greatest in lowland tropical regions where large species pools and stable climates have perhaps given rise to many microclimatically specialized species. Together, our results indicate that strong phylogenetic clustering of species' responses to habitat conversion mediates nonrandom structuring of local assemblages and loss of global phylogenetic diversity. In an age of rapid global change, identifying clades that are most sensitive to habitat conversion will help prioritize use of limited conservation resources.
      Cover page: Phylogenetic homogenization of amphibian assemblages in human-altered habitats across the globe
      • Article
      • Peer Reviewed
      Clinical Practice and Cases in Emergency Medicine, Volume 5, Issue 2 (2021)

      Introduction: Amid the global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), chloroquine and hydroxychloroquine were being studied as agents to prevent and treat coronavirus disease 2019. Information about these agents and their effects circulated throughout the general public media, raising the concern for self-directed consumption of both pharmaceutical and non-pharmaceutical products.

      Case Report: We present two cases of chloroquine toxicity that occurred after ingestion of an aquarium disinfectant that contained chloroquine phosphate in a misguided attempt to prevent infection by SARS-CoV-2. One patient had repeated emesis and survived, while the other was unable to vomit, despite attempts, and suffered fatal cardiac dysrhythmias.

      Conclusion: These cases illustrate the spectrum of toxicity, varied presentations, and importance of early recognition and management of chloroquine poisoning. In addition, we can see the importance of sound medical guidance in an era of social confusion compounded by the extremes of public and social media.

        Cover page: Chloroquine Ingestion to Prevent SARS-CoV-2 Infection: A Report of Two CasesCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2016)
        The fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused the greatest known wildlife pandemic, infecting over 500 amphibian species. It remains unclear why some host species decline from disease-related mortality whereas others persist. We introduce a conceptual model that predicts that infection risk in ectotherms will decrease as the difference between host and pathogen environmental tolerances (i.e. tolerance mismatch) increases. We test this prediction using both local-scale data from Costa Rica and global analyses of over 11 000 Bd infection assays. We find that infection prevalence decreases with increasing thermal tolerance mismatch and with increasing host tolerance of habitat modification. The relationship between environmental tolerance mismatches and Bd infection prevalence is generalisable across multiple amphibian families and spatial scales, and the magnitude of the tolerance mismatch effect depends on environmental context. These findings may help explain patterns of amphibian declines driven by a global wildlife pandemic.
          Cover page: Infection risk decreases with increasing mismatch in host and pathogen environmental tolerances
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2018)
          BACKGROUND: Clinicians are increasingly sharing outpatient visit notes with patients through electronic portals. These open notes may bring about new educational opportunities as well as concerns to physicians-in-training and residency programs. OBJECTIVE: We assessed anticipatory attitudes about open notes and explored factors influencing residents propensity toward note transparency. METHODS: Residents in primary care clinics at 4 teaching hospitals were surveyed prior to implementation of open notes. Main measures included resident attitudes toward open notes and the anticipated effect on patients, resident workload, and education. Data were stratified by site. RESULTS: A total of 176 of 418 (42%) residents responded. Most residents indicated open notes would improve patient engagement, trust, and education but worried about overwhelming patients, residents being less candid, and workload. More than half of residents thought open notes were a good idea, and 32% (56 of 176) indicated they would encourage patients to read these notes. More than half wanted note-writing education and more feedback, and 72% (126 of 175) indicated patient feedback on residents notes could improve communication skills. Attitudes about effects of open notes on safety, quality, trust, and medical education varied by site. CONCLUSIONS: Residents reported mixed feelings about the anticipated effects of sharing clinical notes with patients. They advocate for patient feedback on notes, yet worry about workload, supervision, and errors. Training site was correlated with many attitudes, suggesting local culture drives resident support for open notes. Strategies that address resident concerns and promote teaching and feedback related to notes may be helpful.
            Cover page: Open Notes in Teaching Clinics: A Multisite Survey of Residents to Identify Anticipated Attitudes and Guidance for Programs.
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2019)
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2020)
              We conducted genome sequencing to search for rare variation contributing to early-onset Alzheimer's disease (EOAD) and frontotemporal dementia (FTD). Discovery analysis was conducted on 435 cases and 671 controls of European ancestry. Burden testing for rare variation associated with disease was conducted using filters based on variant rarity (less than one in 10,000 or private), computational prediction of deleteriousness (CADD) (10 or 15 thresholds), and molecular function (protein loss-of-function [LoF] only, coding alteration only, or coding plus non-coding variants in experimentally predicted regulatory regions). Replication analysis was conducted on 16,434 independent cases and 15,587 independent controls. Rare variants in TET2 were enriched in the discovery combined EOAD and FTD cohort (p = 4.6 × 10-8, genome-wide corrected p = 0.0026). Most of these variants were canonical LoF or non-coding in predicted regulatory regions. This enrichment replicated across several cohorts of Alzheimer's disease (AD) and FTD (replication only p = 0.0029). The combined analysis odds ratio was 2.3 (95% confidence interval [CI] 1.6-3.4) for AD and FTD. The odds ratio for qualifying non-coding variants considered independently from coding variants was 3.7 (95% CI 1.7-9.4). For LoF variants, the combined odds ratio (for AD, FTD, and amyotrophic lateral sclerosis, which shares clinicopathological overlap with FTD) was 3.1 (95% CI 1.9-5.2). TET2 catalyzes DNA demethylation. Given well-defined changes in DNA methylation that occur during aging, rare variation in TET2 may confer risk for neurodegeneration by altering the homeostasis of key aging-related processes. Additionally, our study emphasizes the relevance of non-coding variation in genetic studies of complex disease.
                Cover page: Non-coding and Loss-of-Function Coding Variants in TET2 are Associated with Multiple Neurodegenerative Diseases
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2019)
                We assessed the results of genome sequencing for early-onset dementia. Participants were selected from a memory disorders clinic. Genome sequencing was performed along with C9orf72 repeat expansion testing. All returned sequencing results were Sanger-validated. Prior clinical diagnoses included Alzheimer's disease, frontotemporal dementia, and unspecified dementia. The mean age of onset was 54 (41-76). Fifty percent of patients had a strong family history, 37.5% had some, and 12.5% had no known family history. Nine of 32 patients (28%) had a variant defined as pathogenic or likely pathogenic (P/LP) by American College of Medical Genetics and Genomics standards, including variants in APP, C9orf72, CSF1R, and MAPT Nine patients (including three with P/LP variants) harbored established risk alleles with moderate penetrance (odds ratios of ∼2-5) in ABCA7, AKAP9, GBA, PLD3, SORL1, and TREM2 All six patients harboring these moderate penetrance variants but not P/LP variants also had one or two APOE ε4 alleles. One patient had two APOE ε4 alleles with no other established contributors. In total, 16 patients (50%) harbored one or more genetic variants likely to explain symptoms. We identified variants of uncertain significance (VUSs) in ABI3, ADAM10, ARSA, GRID2IP, MME, NOTCH3, PLCD1, PSEN1, TM2D3, TNK1, TTC3, and VPS13C, also often along with other variants. In summary, genome sequencing for early-onset dementia frequently identified multiple established or possible contributory alleles. These observations add support for an oligogenic model for early-onset dementia.
                  Cover page: Genome sequencing for early-onset or atypical dementia: high diagnostic yield and frequent observation of multiple contributory alleles
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2023)
                  PURPOSE: ARF1 was previously implicated in periventricular nodular heterotopia (PVNH) in only five individuals and systematic clinical characterisation was not available. The aim of this study is to provide a comprehensive description of the phenotypic and genotypic spectrum of ARF1-related neurodevelopmental disorder. METHODS: We collected detailed phenotypes of an international cohort of individuals (n=17) with ARF1 variants assembled through the GeneMatcher platform. Missense variants were structurally modelled, and the impact of several were functionally validated. RESULTS: De novo variants (10 missense, 1 frameshift, 1 splice altering resulting in 9 residues insertion) in ARF1 were identified among 17 unrelated individuals. Detailed phenotypes included intellectual disability (ID), microcephaly, seizures and PVNH. No specific facial characteristics were consistent across all cases, however microretrognathia was common. Various hearing and visual defects were recurrent, and interestingly, some inflammatory features were reported. MRI of the brain frequently showed abnormalities consistent with a neuronal migration disorder. CONCLUSION: We confirm the role of ARF1 in an autosomal dominant syndrome with a phenotypic spectrum including severe ID, microcephaly, seizures and PVNH due to impaired neuronal migration.
                    Cover page: ARF1-related disorder: phenotypic and molecular spectrum.
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2023)
                    Animal tolerance towards humans can be a key factor facilitating wildlife-human coexistence, yet traits predicting its direction and magnitude across tropical animals are poorly known. Using 10,249 observations for 842 bird species inhabiting open tropical ecosystems in Africa, South America, and Australia, we find that avian tolerance towards humans was lower (i.e., escape distance was longer) in rural rather than urban populations and in populations exposed to lower human disturbance (measured as human footprint index). In addition, larger species and species with larger clutches and enhanced flight ability are less tolerant to human approaches and escape distances increase when birds were approached during the wet season compared to the dry season and from longer starting distances. Identification of key factors affecting animal tolerance towards humans across large spatial and taxonomic scales may help us to better understand and predict the patterns of species distributions in the Anthropocene.
                      Cover page: Bird tolerance to humans in open tropical ecosystems
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