Browsing by Subject "Models, Theoretical"

Now showing 1 - 6 of 6
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    Menopause and Big Data: Word Adjacency Graph Modeling of Menopause-Related ChaCha® Data
    (Wolters Kluwer, 2017-07) Carpenter, Janet S.; Groves, Doyle; Chen, Chen X.; Otte, Julie L.; Miller, Wendy; School of Nursing
    OBJECTIVE: To detect and visualize salient queries about menopause using Big Data from ChaCha. METHODS: We used Word Adjacency Graph (WAG) modeling to detect clusters and visualize the range of menopause-related topics and their mutual proximity. The subset of relevant queries was fully modeled. We split each query into token words (ie, meaningful words and phrases) and removed stopwords (ie, not meaningful functional words). The remaining words were considered in sequence to build summary tables of words and two and three-word phrases. Phrases occurring at least 10 times were used to build a network graph model that was iteratively refined by observing and removing clusters of unrelated content. RESULTS: We identified two menopause-related subsets of queries by searching for questions containing menopause and menopause-related terms (eg, climacteric, hot flashes, night sweats, hormone replacement). The first contained 263,363 queries from individuals aged 13 and older and the second contained 5,892 queries from women aged 40 to 62 years. In the first set, we identified 12 topic clusters: 6 relevant to menopause and 6 less relevant. In the second set, we identified 15 topic clusters: 11 relevant to menopause and 4 less relevant. Queries about hormones were pervasive within both WAG models. Many of the queries reflected low literacy levels and/or feelings of embarrassment. CONCLUSIONS: We modeled menopause-related queries posed by ChaCha users between 2009 and 2012. ChaCha data may be used on its own or in combination with other Big Data sources to identify patient-driven educational needs and create patient-centered interventions.
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    Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin
    (American Chemical Society, 2014-06-19) Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L.; Marqusee, Susan; Bustamante, Carlos; Dill, Ken; Department of Physics, School of Science
    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others.
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    Titer estimation for quality control (TEQC) method: A practical approach for optimal production of protein complexes using the baculovirus expression vector system
    (Public Library of Science, 2018-04-03) Imasaki, Tsuyoshi; Wenzel, Sabine; Yamada, Kentaro; Bryant, Megan L.; Takagi, Yuichiro; Biochemistry and Molecular Biology, School of Medicine
    The baculovirus expression vector system (BEVS) is becoming the method of choice for expression of many eukaryotic proteins and protein complexes for biochemical, structural and pharmaceutical studies. Significant technological advancement has made generation of recombinant baculoviruses easy, efficient and user-friendly. However, there is a tremendous variability in the amount of proteins made using the BEVS, including different batches of virus made to express the same proteins. Yet, what influences the overall production of proteins or protein complexes remains largely unclear. Many downstream applications, particularly protein structure determination, require purification of large quantities of proteins in a repetitive manner, calling for a reliable experimental set-up to obtain proteins or protein complexes of interest consistently. During our investigation of optimizing the expression of the Mediator Head module, we discovered that the 'initial infectivity' was an excellent indicator of overall production of protein complexes. Further, we show that this initial infectivity can be mathematically described as a function of multiplicity of infection (MOI), correlating recombinant protein yield and virus titer. All these findings led us to develop the Titer Estimation for Quality Control (TEQC) method, which enables researchers to estimate initial infectivity, titer/MOI values in a simple and affordable way, and to use these values to quantitatively optimize protein expressions utilizing BEVS in a highly reproducible fashion.
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    Treatment of Adolescent Substance Use Disorders and Co-Occurring Internalizing Disorders: A Critical Review and Proposed Model
    (Bentham Science Publishers, 2015) Hulvershorn, Leslie A.; Quinn, Patrick D.; Scott, Eric L.; Department of Psychiatry, IU School of Medicine
    BACKGROUND: The past several decades have seen dramatic growth in empirically supported treatments for adolescent substance use disorders (SUDs), yet even the most well-established approaches struggle to produce large or long-lasting improvements. These difficulties may stem, in part, from the high rates of comorbidity between SUDs and other psychiatric disorders. METHOD: We critically reviewed the treatment outcome literature for adolescents with co-occurring SUDs and internalizing disorders. RESULTS: Our review identified components of existing treatments that might be included in an integrated, evidence-based approach to the treatment of SUDs and internalizing disorders. An effective program may involve careful assessment, inclusion of parents or guardians, and tailoring of interventions via a modular strategy. CONCLUSIONS: The existing literature guides the development of a conceptual evidence-based, modular treatment model targeting adolescents with co-occurring internalizing and SUDs. With empirical study, such a model may better address treatment outcomes for both disorder types in adolescents.
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    Use of impact fees to incentivize low-impact development and promote compact growth
    (2013-07-15) Lu, Zhongming; Noonan, Douglas S.; Crittenden, John C.; Jeong, Hyunju; Wang, Dali
    Low-impact development (LID) is an innovative stormwater management strategy that restores the predevelopment hydrology to prevent increased stormwater runoff from land development. Integrating LID into residential subdivisions and increasing population density by building more compact living spaces (e.g., apartment homes) can result in a more sustainable city by reducing stormwater runoff, saving infrastructural cost, increasing the number of affordable homes, and supporting public transportation. We develop an agent-based model (ABM) that describes the interactions between several decision-makers (i.e., local government, a developer, and homebuyers) and fiscal drivers (e.g., property taxes, impact fees). The model simulates the development of nine square miles of greenfield land. A more sustainable development (MSD) scenario introduces an impact fee that developers must pay if they choose not to use LID to build houses or apartment homes. Model simulations show homeowners selecting apartment homes 60% or 35% of the time after 30 years of development in MSD or business as usual (BAU) scenarios, respectively. The increased adoption of apartment homes results from the lower cost of using LID and improved quality of life for apartment homes relative to single-family homes. The MSD scenario generates more tax revenue and water savings than does BAU. A time-dependent global sensitivity analysis quantifies the importance of socioeconomic variables on the adoption rate of apartment homes. The top influential factors are the annual pay rates (or capital recovery factor) for single-family houses and apartment homes. The ABM can be used by city managers and policymakers for scenario exploration in accordance with local conditions to evaluate the effectiveness of impact fees and other policies in promoting LID and compact growth.