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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2019)

Programmers often write code with similarity to existing code written somewhere. Code search tools can help developers find similar solutions and identify possible improvements. For code search tools, good search results rely on valid data collection. Social coding websites, such as Question & Answer forum Stack Overflow (SO) and project repository GitHub, are popular destinations when programmers look for how to achieve certain programming tasks. Over the years, SO and GitHub have accumulated an enormous knowledge base of, and around, code. Since these software artifacts are publicly available, it is possible to leverage them in code search tools. This dissertation explores the opportunities of leveraging software artifacts from the social coding websites in searching for not just similar, but related, code.

Programmers query SO and GitHub extensively to search for suitable code for reuse, however, not much is known about the usability or quality of the available code from each website. This dissertation first investigates under what circumstances the software artifacts found in social coding websites can be leveraged for purposes other than their immediate use by developers. It points out a number of problems that need to be addressed before those artifacts can be leveraged for code search and development tools. Specifically, triviality, fragility, and duplication, dominate these artifacts. However, when these problems are addressed, there is still a considerable amount of good quality artifacts that can be leveraged.

SO and GitHub are not only two separate data resources, moreover, they together, belong to a larger system of software development process: the same users that rely on facilities of GitHub often seeks support on SO for their problems, and return to GitHub to apply the knowledge acquired. This dissertation further studies the crossover of software artifacts between SO and GitHub, and categorizes the adaptations from a SO code snippet to its GitHub counterparts.

Existing search tools only recommend other code locations that are syntactically or semantically similar to the given code but do not reason about other kinds of relevant code that a developer should also pay attention to, e.g., auxiliary code to accomplish a complete task. With the good quality software artifacts and crossover between the two systems available, this dissertation presents two approaches that leverage these artifacts in searching for related code. Aroma indexes GitHub projects, takes a partial code snippet as input, searches the corpus for methods containing the partial code snippet, and clusters and intersects the results of the search to recommend. Aroma is evaluated on randomly selected queries created from the GitHub corpus, as well as queries derived from SO code snippets. It recommends related code for error checking and handling, objects configuring, etc. Furthermore, a user study is conducted where industrial developers are asked to complete programming tasks using Aroma and provide feedback. The results indicate that Aroma is capable of retrieving and recommending relevant code snippets efficiently. CodeAid reuses the crossover between SO and GitHub and recommends related code outside of a method body. For each SO snippet as a query, CodeAid retrieves the co-occurring code fragments for its GitHub counterparts and clusters them to recommend common ones. 74% of the common co-occurring code fragments represent related functionality that should be included in code search results. Three major types of relevancy--complementary, supplementary, and alternative methods, are identified.

    Cover page: Beyond Similar Code: Leveraging Social Coding Websites
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2019)
    Material transport in the ocean mixed layer (OML) is an important component of natural processes such as gas and nutrient exchanges. It is also important in the context of pollution (oil droplets, microplastics, etc.). Observational studies of small-scale three-dimensional turbulence in the OML are difficult, especially if one aims at a systematic coverage of relevant parameters and their effects, under controlled conditions. Numerical studies are also challenging due to the large-scale separation between the physical processes dominating transport in the horizontal and vertical directions. Despite this difficulty, the application of large eddy simulation (LES) to study OML turbulence and, more specifically, its effects on material transport has resulted in major advances in the field in recent years. In this paper we review the use of LES to study material transport within the OML and then summarize and synthesize the advances it has enabled in the past decade or so. In the first part we describe the LES technique and the most common approaches when applying it in OML material transport investigations. In the second part we review recent results on material transport obtained using LES and comment on implications.
      Cover page: Material Transport in the Ocean Mixed Layer: Recent Developments Enabled by Large Eddy Simulations
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2018)
      Pharmacological dosing of all-trans-retinoic acid (atRA) controls adiposity in rodents by inhibiting adipogenesis and inducing fatty acid oxidation. Retinol dehydrogenases (Rdh) catalyze the first reaction that activates retinol into atRA. This study examined postnatal contributions of Rdh10 to atRA biosynthesis and physiological functions of endogenous atRA. Embryonic fibroblasts from Rdh10 heterozygote hypomorphs or with a total Rdh10 knockout exhibit decreased atRA biosynthesis and escalated adipogenesis. atRA or a retinoic acid receptor (RAR) pan-agonist reversed the phenotype. Eliminating one Rdh10 copy in vivo (Rdh10+/- ) yielded a modest decrease (≤25%) in the atRA concentration of liver and adipose but increased adiposity in male and female mice fed a high-fat diet (HFD); increased liver steatosis, glucose intolerance, and insulin resistance in males fed an HFD; and activated bone marrow adipocyte formation in females, regardless of dietary fat. Chronic dosing with low-dose atRA corrected the metabolic defects. These data resolve physiological actions of endogenous atRA, reveal sex-specific effects of atRA in vivo, and establish the importance of Rdh10 to metabolic control by atRA. The consequences of a modest decrease in tissue atRA suggest that impaired retinol activation may contribute to diabesity, and low-dose atRA therapy may ameliorate adiposity and its sequelae of glucose intolerance and insulin resistance.
        Cover page: Modest Decreases in Endogenous All-Trans-Retinoic Acid Produced by a Mouse Rdh10 Heterozygote Provoke Major Abnormalities in Adipogenesis and Lipid Metabolism
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2020)
        The abundant yet widely distributed methane resources require efficient conversion of methane into liquid chemicals, whereas an ambient selective process with minimal infrastructure support remains to be demonstrated. Here we report selective electrochemical oxidation of CH4 to methyl bisulfate (CH3OSO3H) at ambient pressure and room temperature with a molecular catalyst of vanadium (V)-oxo dimer. This water-tolerant, earth-abundant catalyst possesses a low activation energy (10.8 kcal mol‒1) and a high turnover frequency (483 and 1336 hr-1 at 1-bar and 3-bar pure CH4, respectively). The catalytic system electrochemically converts natural gas mixture into liquid products under ambient conditions over 240 h with a Faradaic efficiency of 90% and turnover numbers exceeding 100,000. This tentatively proposed mechanism is applicable to other d0 early transition metal species and represents a new scalable approach that helps mitigate the flaring or direct emission of natural gas at remote locations.
          Cover page: Ambient methane functionalization initiated by electrochemical oxidation of a vanadium (V)-oxo dimer.
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2017)
          All-trans-retinoic acid (RA) inhibits adipogenesis in established preadipocyte cell lines. Dosing pharmacological amounts of RA reduces weight gain in mice fed a high-fat diet, i.e. counteracts diet-induced obesity (DIO). The aldehyde dehydrogenase Raldh1 (Aldh1a1) functions as one of three enzymes that converts the retinol metabolite retinal into RA, and one of many proteins that contribute to RA homeostasis. Female Raldh1-ablated mice resist DIO. This phenotype contrasts with ablations of other enzymes and binding-proteins that maintain RA homeostasis, which gain adiposity. The phenotype observed prompted the conclusion that loss of Raldh1 causes an increase in adipose tissue retinal, and therefore, retinal functions independently of RA to prevent DIO. A second deduction proposed that low nM concentrations of RA stimulate adipogenesis, in contrast to higher concentrations. Using peer-reviewed LC/MS/MS assays developed and validated for quantifying tissue RA and retinal, we show that endogenous retinal and RA concentrations in adipose tissues from Raldh1-null mice do not correlate with the phenotype. Moreover, male Raldh1-null mice resist weight gain regardless of dietary fat content. Resistance to weight gain occurs during adolescence in both sexes. We show that RA concentrations as low as 1 nM, i.e. in the sub-physiological range, impair adipogenesis of embryonic fibroblasts from wild-type mice. Embryonic fibroblasts from Raldh1-null mice resist differentiating into adipocytes, but retain ability to generate RA. These fibroblasts remain sensitive to an RA receptor pan-agonist, and are not affected by an RA receptor pan-antagonist. Thus, the data do not support the hypothesis that retinal itself represses weight gain and adipogenesis independently of RA. Instead, the data indicate that Raldh1 functions as a retinal and atRA-independent promoter of adiposity during adolescence, and enhances adiposity through pre-adipocyte cell autonomous actions.
            Cover page: Raldh1 promotes adiposity during adolescence independently of retinal signaling.
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2020)
            Yes-associated protein (YAP) and its homolog transcriptional coactivator with PDZ-binding motif (TAZ) are key effectors of the Hippo pathway to control cell growth and organ size, of which dysregulation yields to tumorigenesis or hypertrophy. Upon activation, YAP/TAZ translocate into the nucleus and bind to TEAD transcription factors to promote transcriptional programs for proliferation or cell specification. Immediate early genes, represented by AP-1 complex, are rapidly induced and control later-phase transcriptional program to play key roles in tumorigenesis and organ maintenance. Here, we report that YAP/TAZ directly promote FOS transcription that in turn contributes to the biological function of YAP/TAZ. YAP/TAZ bind to the promoter region of FOS to stimulate its transcription. Deletion of YAP/TAZ blocks the induction of immediate early genes in response to mitogenic stimuli. FOS induction contributes to expression of YAP/TAZ downstream target genes. Genetic deletion or chemical inhibition of AP-1 suppresses growth of YAP-driven cancer cells, such as Lats1/2-deficient cancer cells as well as Gαq/11 mutated uveal melanoma. Furthermore, AP-1 inhibition almost completely abrogates the hepatomegaly induced by YAP overexpression. Our findings reveal a feed-forward interplay between immediate early transcription of AP-1 and Hippo pathway function.
              Cover page: Induction of AP-1 by YAP/TAZ contributes to cell proliferation and organ growth
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2017)
              All-trans-retinoic acid (RA) inhibits adipogenesis in established preadipocyte cell lines. Dosing pharmacological amounts of RA reduces weight gain in mice fed a high-fat diet, i.e. counteracts diet-induced obesity (DIO). The aldehyde dehydrogenase Raldh1 (Aldh1a1) functions as one of three enzymes that converts the retinol metabolite retinal into RA, and one of many proteins that contribute to RA homeostasis. Female Raldh1-ablated mice resist DIO. This phenotype contrasts with ablations of other enzymes and binding-proteins that maintain RA homeostasis, which gain adiposity. The phenotype observed prompted the conclusion that loss of Raldh1 causes an increase in adipose tissue retinal, and therefore, retinal functions independently of RA to prevent DIO. A second deduction proposed that low nM concentrations of RA stimulate adipogenesis, in contrast to higher concentrations. Using peer-reviewed LC/MS/MS assays developed and validated for quantifying tissue RA and retinal, we show that endogenous retinal and RA concentrations in adipose tissues from Raldh1-null mice do not correlate with the phenotype. Moreover, male Raldh1-null mice resist weight gain regardless of dietary fat content. Resistance to weight gain occurs during adolescence in both sexes. We show that RA concentrations as low as 1 nM, i.e. in the sub-physiological range, impair adipogenesis of embryonic fibroblasts from wild-type mice. Embryonic fibroblasts from Raldh1-null mice resist differentiating into adipocytes, but retain ability to generate RA. These fibroblasts remain sensitive to an RA receptor pan-agonist, and are not affected by an RA receptor pan-antagonist. Thus, the data do not support the hypothesis that retinal itself represses weight gain and adipogenesis independently of RA. Instead, the data indicate that Raldh1 functions as a retinal and atRA-independent promoter of adiposity during adolescence, and enhances adiposity through pre-adipocyte cell autonomous actions.
                Cover page: Raldh1 promotes adiposity during adolescence independently of retinal signalingCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2022)
                Semaphorins were originally identified as axonal guidance molecules, but they also control processes such as vascular development and tumorigenesis. The downstream signaling cascades of Semaphorins in these biological processes remain unclear. Here, we show that the class 3 Semaphorins (SEMA3s) activate the Hippo pathway to attenuate tissue growth, angiogenesis, and tumorigenesis. SEMA3B restoration in lung cancer cells with SEMA3B loss of heterozygosity suppresses cancer cell growth via activating the core Hippo kinases LATS1/2 (large tumor suppressor kinase 1/2). Furthermore, SEMA3 also acts through LATS1/2 to inhibit angiogenesis. We identified p190RhoGAPs as essential partners of the SEMA3A receptor PlexinA in Hippo regulation. Upon SEMA3 treatment, PlexinA interacts with the pseudo-guanosine triphosphatase (GTPase) domain of p190RhoGAP and simultaneously recruits RND GTPases to activate p190RhoGAP, which then stimulates LATS1/2. Disease-associated etiological factors, such as genetic lesions and oscillatory shear, diminish Hippo pathway regulation by SEMA3. Our study thus discovers a critical role of Hippo signaling in mediating SEMA3 physiological function.
                  Cover page: The Hippo pathway mediates Semaphorin signaling
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2022)
                  Macrosystem-scale research is supported by many ecological networks of people, infrastructure, and data. However, no network is sufficient to address all macrosystems ecology research questions, and there is much to be gained by conducting research and sharing resources across multiple networks. Unfortunately, conducting macrosystem research across networks is challenging due to the diversity of expertise and skills required, as well as issues related to data discoverability, veracity, and interoperability. The ecological and environmental science community could substantially benefit from networking existing networks to leverage past research investments and spur new collaborations. Here, we describe the need for a “network of networks” (NoN) approach to macrosystems ecological research and articulate both the challenges and potential benefits associated with such an effort. We describe the challenges brought by rapid increases in the volume, velocity, and variety of “big data” ecology and highlight how a NoN could build on the successes and creativity within component networks, while also recognizing and improving upon past failures. We argue that a NoN approach requires careful planning to ensure that it is accessible and inclusive, incorporates multimodal communications and ways to interact, supports the creation, testing, and promulgation of community standards, and ensures individuals and groups receive appropriate credit for their contributions. Additionally, a NoN must recognize important trade-offs in network architecture, including how the degree of centralization of people, infrastructure, and data influence network scalability and creativity. If implemented carefully and thoughtfully, a NoN has the potential to substantially advance our understanding of ecological processes, characteristics, and trajectories across broad spatial and temporal scales in an efficient, inclusive, and equitable manner.
                    Creative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2021)
                    It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building.
                      Creative Commons 'BY' version 4.0 license
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