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Open Access Publications from the University of California

Scholarly Works (313 results)

  • Article
CSW Update Newsletter (2006)

In the popular romantic comedy Sleepless in Seattle (Ephron, 1993), a pivotal scene in the middle of the film sums up the crux of the dilemma faced by Annie (Meg Ryan), the female protagonist. She is having difficulty making an important decision about her love life and, as she always does, turns to the classic film An Affair to Remember (McCarey, 1957) for guidance. As she watches the film with her best friend Becky (Rosie O’Donnell), she says, “Now those were the days when people knew how to be in love, time, distance, nothing could separate them because they knew.” In response, Becky observes, “That’s your problem, you don’t want to be in love, you want to be in love in a movie.” This interaction between Annie and Becky is meant to elicit a sense of recognition among Sleepless in Seattle’s audience because the text assumes that by nature of the fact that they are watching the film, its spectators must empathize with, if not share, Annie’s desire to fall in love in a way that is completely removed from the mundane realities of everyday life. However, the text also assumes that the audience will find equally familiar Becky’s pointed critique of Annie’s misguided preoccupation.

    Cover page: "You Don't Want to Be in Love... You Want to Be in Love in a Movie": Romance and Postfeminism in Contemporary Film and Television
    • Article
    • Peer Reviewed
    American Indian Culture and Research Journal , Volume 27, Issue 4 (2003)
    INTRODUCTION In October of 2001, the Leggatt Inquiry into salmon farming traveled to four small communities (Port Hardy, Tofino, Alert Bay, and Campbell River) close to the centers of operation for the finfish aquaculture industry in British Columbia (see fig. 1). In doing so, it gave local people, particularly First Nations people, an opportunity to speak about salmon farming using their own vocabularies, styles of speaking, and forms of knowledge. Their testimony, however, was about much more than salmon farming. In fact, most of the talk at the inquiry focused upon people’s sense of place and community, and their understandings of their way of life. In particular, the inquiry brought to light the legal and political context in which the salmon farming industry operates. This paper focuses on narratives that in technical and scientific circles would probably be considered rambling, anecdotal, and off the subject. Much of the background needed to make sense of these accounts of fish farming lies hidden in the colonial context of the industry and the ongoing struggles of Native people in British Columbia for recognition of their rights to land and resources. In particular, the material practices of the colonizers seem to produce Native identities quite different from the ones Native people themselves know and rely on. My analysis of the Leggatt Inquiry tries to give voice to the Native people who appeared at the inquiry by showing that, while they are certainly the victims of continued intrusions into their territories and ways of life—and, as I hope to demonstrate, salmon farming represents such an intrusion—they are not passive bystanders in the process. Instead, the aboriginal people who spoke about salmon farming at the inquiry creatively and strategically employed a variety of devices that would help others see the controversy over salmon farming as they themselves did.
      Cover page: Salmon Farming and Salmon People: Identity and Environment in the Leggatt InquiryCreative Commons 'BY-NC' version 4.0 license
      • Article
      • Peer Reviewed
      American Indian Culture and Research Journal , Volume 30, Issue 4 (2006)
      The coast of British Columbia (BC) is host to runs of salmon that have been the economic, social, and cultural basis of Northwest Coast Native societies for millennia. Wild salmon hatch in streams and spend varying amounts of time there before migrating to the ocean. After spending up to several years in the ocean, these fish return to their natal streams to spawn once, then die. These spawning cycles facilitated productive Native fisheries over the centuries and, since the 1870s, industrial fisheries for global markets. Today, industrial salmon aquaculture sites can be found almost everywhere in the protected waters near shore, along the migration routes of what were once flourishing populations of Pacific salmon. Fish farms compound the destructive effects of more than a century of logging, overfishing, and urbanization on the wild salmon fisheries. The most direct and striking impacts of fish farms—ones that are directly observed by many local Native people—are the spread of fish diseases and waste materials into the surrounding habitat. Sea lice infestations of wild stocks are on the rise: these parasites and other disease organisms concentrate in the densely stocked net pens and appear to spread easily to passing wild salmon. Although a few fish farms are stocked with chinook salmon, a species that is native to the region, most farm sites contain Atlantic salmon. The reality of salmon escapes from net pens and the fact that Atlantic salmon originating from fish farms have been shown to spawn successfully in BC’s rivers have raised grave concerns about the ecological consequences of the invasion of local streams by this exotic species of salmon. Furthermore, the effects of the sewage emanating from fish farms are often noted by Native people using traditional clam digging and fishing spots.
        Cover page: First Nations, Consultation, and the Rule of Law: Salmon Farming and Colonialism in British ColumbiaCreative Commons 'BY-NC' version 4.0 license
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2015)

        Importance

        The applicability of β-amyloid peptide (Aβ) positron emission tomography (PET) as a biomarker in clinical settings to aid in selection of individuals at preclinical and prodromal Alzheimer disease (AD) will depend on the practicality of PET image analysis. In this context, visual-based Aβ PET assessment seems to be the most feasible approach.

        Objectives

        To determine the agreement between visual and quantitative Aβ PET analysis and to assess the ability of both techniques to predict conversion from mild cognitive impairment (MCI) to AD.

        Design, setting, and participants

        A longitudinal study was conducted among the Alzheimer's Disease Neuroimaging Initiative (ADNI) sites in the United States and Canada during a 1.6-year mean follow-up period. The study was performed from September 21, 2010, to August 11, 2014; data analysis was conducted from September 21, 2014, to May 26, 2015. Participants included 401 individuals with MCI receiving care at a specialty clinic (219 [54.6%] men; mean [SD] age, 71.6 [7.5] years; 16.2 [2.7] years of education). All participants were studied with florbetapir F 18 [18F] PET. The standardized uptake value ratio (SUVR) positivity threshold was 1.11, and one reader rated all images, with a subset of 125 scans rated by a second reader.

        Main outcomes and measures

        Sensitivity and specificity of positive and negative [18F] florbetapir PET categorization, which was estimated with cerebrospinal fluid Aβ1-42 as the reference standard. Risk for conversion to AD was assessed using Cox proportional hazards regression models.

        Results

        The frequency of Aβ positivity was 48.9% (196 patients; visual analysis), 55.1% (221 patients; SUVR), and 64.8% (166 patients; cerebrospinal fluid), yielding substantial agreement between visual and SUVR data (κ = 0.74) and between all methods (Fleiss κ = 0.71). For approximately 10% of the 401 participants in whom visual and SUVR data disagreed, interrater reliability was moderate (κ = 0.44), but it was very high if visual and quantitative results agreed (κ = 0.92). Visual analysis had a lower sensitivity (79% vs 85%) but higher specificity (96% vs 90%), respectively, compared with SUVR. The conversion rate was 15.2% within a mean of 1.6 years, and a positive [18F] florbetapir baseline scan was associated with a 6.91-fold (SUVR) or 11.38-fold (visual) greater hazard for AD conversion, which changed only modestly after covariate adjustment for apolipoprotein ε4, concurrent fludeoxyglucose F 18 PET scan, and baseline cognitive status.

        Conclusions and relevance

        Visual and SUVR Aβ PET analysis may be equivalently used to determine Aβ status for individuals with MCI participating in clinical trials, and both approaches add significant value for clinical course prognostication.
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2016)
          Single lifestyle factors affect brain biomarkers and cognition. Here, we addressed the covariance of various lifestyle elements and investigated their impact on positron emission tomography-based β-amyloid (Aβ), hippocampal volume, and cognitive function in aged controls. Lower Aβ burden was associated with a lifestyle comprising high cognitive engagement and low vascular risk, particularly in apolipoprotein E ε4 carriers. Although cognitive function was related to high lifetime cognitive engagement and low vascular risk, Aβ load had no relation to current cognitive function. The covariance between high adult socioeconomic status, high education, and low smoking prevalence predicted better cognitive function and this was mediated by larger hippocampal volume. Our data show that lifestyle is a complex construct composed of associated variables, some of which reflect factors operating over the life span and others which may be developmental. These factors affect brain health via different pathways, which may reinforce one another. Our findings moreover support the importance of an intellectually enriched lifestyle accompanied by vascular health on both cognition and presumed cerebral mediators of cognitive function.
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2017)
            Positive density-dependence occurs when individuals experience increased survivorship, growth, or reproduction with increased population densities. Mechanisms leading to these positive relationships include mate limitation, saturating predation risk, and cooperative breeding and foraging. Individuals within these populations may differ in age, size, or geographic location and thereby structure these populations. Here, I study structured population models accounting for positive density-dependence and environmental stochasticity i.e. random fluctuations in the demographic rates of the population. Under an accessibility assumption (roughly, stochastic fluctuations can lead to populations getting small and large), these models are shown to exhibit a dynamical trichotomy: (i) for all initial conditions, the population goes asymptotically extinct with probability one, (ii) for all positive initial conditions, the population persists and asymptotically exhibits unbounded growth, and (iii) for all positive initial conditions, there is a positive probability of asymptotic extinction and a complementary positive probability of unbounded growth. The main results are illustrated with applications to spatially structured populations with an Allee effect and age-structured populations experiencing mate limitation.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2011)
              Understanding under what conditions populations, whether they be plants, animals, or viral particles, persist is an issue of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations are key factors that can facilitate or disrupt persistence. One approach to examining the interplay between these deterministic and stochastic forces is the construction and analysis of stochastic difference equations $X_{t+1}=F(X_t,\xi_{t+1})$ where $X_t \in \R^k$ represents the state of the populations and $\xi_1,\xi_2,...$ is a sequence of random variables representing environmental stochasticity. In the analysis of these stochastic models, many theoretical population biologists are interested in whether the models are bounded and persistent. Here, boundedness asserts that asymptotically $X_t$ tends to remain in compact sets. In contrast, persistence requires that $X_t$ tends to be "repelled" by some "extinction set" $S_0\subset \R^k$. Here, results on both of these proprieties are reviewed for single species, multiple species, and structured population models. The results are illustrated with applications to stochastic versions of the Hassell and Ricker single species models, Ricker, Beverton-Holt, lottery models of competition, and lottery models of rock-paper-scissor games. A variety of conjectures and suggestions for future research are presented.
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2015)
                A number of related changes have evolved over the past 25 years: the development of a truly national disaster mental health service in Israel; progress in the science of risk, resilience and evidence base care for those suffering from traumatic stress related disorders; and the development of conceptual models of population level disaster mental health response in the context of emergency management systems such as the Incident Command System. In a recent IJHPR article, Bodas, et al. report on the dynamic history of disaster mental health response in Israel, which informed by the all too numerous real world events affecting the region. What is most striking is that the system now in place reflects true "lessons learned" in that problems and issues identified in incidents informed deliberative planning, and the current system reflects many iterations of "lessons observed and learned". There appears to be commitment across sectors of government in Israel that the mental health consequences of disasters and terrorism are important and a priority. This is advanced thinking and sound policy. As the system in Israel continues to evolve, additional possibilities are offered for further consideration, based on the author's US-centric experience, to advance emergency response systems in Israel, the Middle East and around the world.
                  Cover page: Toward the way forward: building an emergency mental health system for IsraelCreative Commons 'BY-NC-ND' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2015)

                  Motivation: Nanopore-based sequencing techniques can reconstruct properties of biosequences by analyzing the sequence-dependent ionic current steps produced as biomolecules pass through a pore. Typically this involves alignment of new data to a reference, where both reference construction and alignment have been performed by hand.

                  Results: We propose an automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be simply incorporated into the model. Previously, the M2MspA nanopore was shown to be sensitive enough to distinguish between cytosine, methylcytosine, and hydroxymethylcytosine. We validated our automated methodology on a subset of that data by automatically calculating an error rate for the distinction between the three cytosine variants, and show that the automated methodology produces a 2–3% error rate, lower than the 10% error rate from previous manual segmentation and alignment.

                  Availability: The data, output, scripts, and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/ Data/tree/master/Automation.

                  • 1 supplemental PDF
                  Cover page: Analysis of Nanopore Data using Hidden Markov Models
                  • Thesis
                  • Peer Reviewed
                  UC Santa Barbara Electronic Theses and Dissertations (2019)

                  In the middle of the flatlands of the Cochabamba Central Valley of Bolivia, Piñami, one of many habitation mounds in the valley, is exceptional for producing some of the most extensive Tiwanaku-era evidence from Cochabamba. Over the course of five years, I led an international team in the excavation of a multigenerational mound at Piñami. The excavation yielded over 92,000 ceramics (including potsherds and entire vessels), over 60 funerary contexts, architectural and other household evidence, and four new radiocarbon dates. This dissertation considers the implications this rich mass of evidence has on questions of Central Valley chronology and of Tiwanaku influence on Cochabamba.

                  The findings at Piñami demonstrate the great impact of Tiwanaku on the Central Valley in ceramics and drinking practices, mortuary rituals, and economic and household activities. I use ceramic evidence to argue that the association between the Central Valley and Tiwanaku was strong by the Piñami Phase and that decorated fineware expressed materially and symbolically the transformation of local social identities. Piñami mortuary evidence also reflects the substantial impact of Tiwanaku on the Central Valley as seen in changes in body position, vessel offerings and tomb construction. Further, I use cranial deformation and strontium isotope studies to support a hypothsis of an ethnically diverse population at Piñami that shared the same mortuary space. Finally, I use a variety of household evidence to show the impact of Tiwanaku on daily life at Piñami and to present a picture of a shared essential cosmology with Tiwanaku.

                  As for the nature of Tiwanaku expansion, I argue that Tiwanaku had more corporate state than exclusionary state characteristics: locals actively incorporated a Tiwanaku identity, and markers of Tiwanaku culture were widespread rather than restricted to elites. Further, the strong evidence of local response unearthed at Piñami, showing in a variety of ways the adoption of styles, technology, customs, symbols and everyday household items, supports the view of indirect control and the exercise of soft power in Tiwanaku expansion.

                  Piñami evidence also refines Central Valley chronlogy both by showing artifact changes over time and by providing new radiocarbon dates that more definitively tie Central Valley chronology to Tiwanaku. In short, this dissertation demonstrates that the Central Valley was of great importance to Tiwanaku for hundreds of years and aims to fill a vital gap in Tiwanaku studies that have underestimated Cochabamba in models of Tiwanaku expansion.

                    Cover page: Vessels, Burials and Households: Piñami's Evidence of the Tiwanaku State in the Central Valley of Cochabamba
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