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Search Results: 1 - 10 of 222675 matches for " Joshua C "
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Chapter 13: Mining Electronic Health Records in the Genomics Era
Joshua C. Denny
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002823
Abstract: Abstract: The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped individuals. This chapter reviews several examples of phenotype extraction and their application to genetic research, demonstrating a viable future for genomic discovery using EHR-linked data.
Difficulties in Complex Multiplication and Exponentiation
Joshua C. Sasmor
Mathematics , 2010,
Abstract: During my study of the iteration of functions of the form $f(z)=z^{\alpha}+c$, where $z,c \in \mathbbC$, and $\alpha$ is a rational non-integer larger than 2 (\cite{s1}), I encountered a fundamental difficulty in the exponentiation of a complex number. This paper will explore this difficulty and the problems encountered in trying to resolve it using a Riemann surface which is the direct generalization of the polar form of the complex plane. This paper will also answer two questions raised by Robert Corless in his \emph{E.C.C.A.D.} presentation \cite{co}: "Can a Riemann surface variable be coded? What will the operations be on it?" Unfortunately, the addition operation will be incompatible with the Riemann surface structure.
Detecting the Supernova Breakout Burst in Terrestrial Neutrino Detectors
Joshua Wallace,Adam Burrows,Joshua C. Dolence
Physics , 2015,
Abstract: We calculate the distance-dependent performance of a few representative terrestrial neutrino detectors in detecting and measuring the properties of the $\nu_e$ breakout burst light curve in a Galactic core-collapse supernova. The breakout burst is a signature phenomenon of core collapse and offers a probe into the stellar core through collapse and bounce. We examine cases of no neutrino oscillations and oscillations due to normal and inverted neutrino-mass hierarchies. For the normal hierarchy, other neutrino flavors emitted by the supernova overwhelm the $\nu_e$ signal, making a detection of the breakout burst difficult. For the inverted hierarchy, some detectors at some distances should be able to see the $\nu_e$ breakout burst peak and measure its properties. For the inverted hierarchy, the maximum luminosity of the breakout burst can be measured at 10 kpc to accuracies of $\sim$30% for Hyper-K and $\sim$60% for DUNE. Super-K and JUNO lack the mass needed to make an accurate measurement. IceCube cannot sufficiently account for the other neutrino flavors to discern a clear $\nu_e$ breakout burst signal. For the inverted hierarchy, the time of the maximum luminosity of the breakout burst can be measured in Hyper-K to an accuracy of $\sim$3 ms at 7 kpc, in DUNE $\sim$2 ms at 4 kpc, and JUNO and Super-K can measure the time of maximum luminosity to an accuracy of $\sim$2 ms at 1 kpc. For the inverted hierarchy, a measurement of the maximum luminosity of the breakout burst could be used to differentiate between nuclear equations of state.
The Global Weather Research and Forecasting (GWRF) Model: Model Evaluation, Sensitivity Study, and Future Year Simulation  [PDF]
Yang Zhang, Joshua Hemperly, Nicholas Meskhidze, William C. Skamarock
Atmospheric and Climate Sciences (ACS) , 2012, DOI: 10.4236/acs.2012.23024
Abstract: Global WRF (GWRF) is an extension of the mesoscale Weather Research and Forecasting (WRF) model that was developed for global weather research and forecasting applications. GWRF is being expanded to simulate atmospheric chemistry and its interactions with meteorology on a global scale. In this work, the ability of GWRF to reproduce major boundary layer meteorological variables that affect the fate and transport of air pollutants is assessed using observations from surface networks and satellites. The model evaluation shows an overall good performance in simulating global shortwave and longwave radiation, temperature, and specific humidity, despite large biases at high latitudes and over-Arctic and Antarctic areas. Larger biases exist in wind speed and precipitation predictions. These results are generally consistent with the performance of most current general circulation models where accuracies are often limited by a coarse grid resolution and inadequacies in sub-filter-scale parameterizations and errors in the specification of external forcings. The sensitivity simulations show that a coarse grid resolution leads to worse predictions of surface temperature and precipitation. The combinations of schemes that include the Dudhia shortwave radiation scheme or the Purdue Lin microphysics module, or the Grell-Devenyi cumulus parameterization lead to a worse performance for predictions of downward shortwave radiation flux, temperature, and specific humidity, as compared with those with respective alternative schemes. The physical option with the Purdue Lin microphysics module leads to a worse performance for precipitation predictions. The projected climate in 2050 indicates a warmer and drier climate, which may have important impacts on the fate and lifetime of air pollutants.
Sensitivity and Specificity Determinations with Isoelectric Focusing Fractions of Blastomyces dermatitidis for Antibody Detection in Serum Specimens from Infected Dogs  [PDF]
Joshua C. Wright, Terrick E. Harrild, Gene M. Scalarone
Open Journal of Veterinary Medicine (OJVM) , 2012, DOI: 10.4236/ojvm.2012.24038
Abstract: Blastomycosis and histoplasmosis manifest as lung and systemic fungal infections in mammals caused by Histoplasma capsulatum, and Blastomyces dermatitidis. These infections exhibit cross reactivity of antibodies which makes a correct diagnosis potentially elusive. The purpose of this study was to gain an understanding of which isoelectric focusing fractions (RotoforTM) of B. dermatitidis were reactive or cross reactive with serum specimens from dogs infected with B. dermatitidis, H. capsulatum, and Cryptococcus neoformans. Three serum specimens from dogs that were infected with B. dermatitidis, two dogs infected with H. capsulatum, and one dog infected with C. neoformans were assayed against the 20 B. dermatitidis RotoforTM fractions. Reactivity was determined using the indirect enzyme linked immunoassay (ELISA). Reactivity with B. dermatitidis was found predominantly in the protein fractions 1 - 6, and cross reactivity with H. capsulatum, and C. neoformans sera was found within the B. dermatitidis protein fractions 15 - 19.
Blastomyces dermatitidis: Stability studies on different yeast lysate antigens  [PDF]
Tiffany R. Allison, Joshua C. Wright, Gene M. Scalarone
Open Journal of Immunology (OJI) , 2013, DOI: 10.4236/oji.2013.33014
Abstract:

In Trial 1, 19 lots of Blastomyces dermatitidis (T-58; Tennessee dog isolate) were assayed to determine the stability of the reagents following storage. The reactivity of the antigens, produced from 1989 to 2012 and stored at 4°C, was determined by comparing antibody detection (enzyme-linked immunosorbent assay; ELISA) in 12 serum specimens from immunized rabbits. All of the 19 reagents produced during this 23-year period exhibited a high degree of stability and were able to detect antibody in the sera. Mean absorbance values ranged from 0.798 (1989) to 0.827 (2012) and a mean value for all 19 antigens of 0.728. In a related evaluation, Trial 2, B. dermatitidis lysate antigens prepared from 8 isolates (dog, human, soil) at two different time periods were assayed as above to determine reactivity. The time of storage between the first and second reagents varied from 4 to 17 years. The results indicated that all 16 of the lysate antigens detected antibody in the 15 rabbit serum specimens with mean absorbance values ranging from 0.346 to 0.682, but variations in reactivity were observed depending on the lysate and the serum specimen assayed. This comparative study provided evidence that the antigenic reagents do exhibit some lot-to-lot variation in reactivity, but they did not lose any appreciable potency during prolonged storage.

Germination Biology and Occurrence of Polyembryony in Two Forms of Cats Claw Creeper Vine, Dolichandra unguis-cati (Bignoniaceae): Implications for Its Invasiveness and Management  [PDF]
Joshua C. Buru, Kunjithapatham Dhileepan, Olusegun O. Osunkoya, Tanya Scharaschkin
American Journal of Plant Sciences (AJPS) , 2016, DOI: 10.4236/ajps.2016.73058
Abstract: Cat’s claw creeper vine, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry), is a major environmental weed in Australia. Two forms (“long” and “short” pod) of the weed occur in Australia. This investigation aimed to evaluate and compare germination behavior and occurrence of polyembryony (production of multiple seedlings from a single seed) in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20°C, 15/25°C, 20/30°C, 30/45°C and 25°C, representing ambient temperature conditions of the region. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from the short pod form exhibited significantly higher germination rates and higher occurrence of polyembryony than those from the long pod form. Seeds from the long pod form did not germinate at the lowest temperature of 10/20°C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate. Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed form in Australia, while the long pod form is confined to a few localities. The results have implication in predicting future ranges of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.
Enhancing Holistic Identity through Yoga: Investigating Body-Mind-Spirit Interventions on Mental Illness Stigma across Culture–A Case Study  [PDF]
Elizabeth C. McKibben, Kin-Man Joshua Nan
Open Journal of Nursing (OJN) , 2017, DOI: 10.4236/ojn.2017.74038
Abstract: Objective: Mental illness stigma plagues many individuals with mental health issues such as depression. Labels attributed to the mentally ill focus on meeting diagnostic criterion, increase association with mental illness identities, and do not always promote greater wellbeing. Body-Mind-Spirit (BMS) interventions for depression address mental health without promoting stigmatizing labels. This study identifies how yoga can help to reduce mental illness stigma, and examines the effectiveness of a yoga intervention conducted by an expatriate in a cross-cultural context. Methods: This study took a qualitative research approach to examine the effectiveness of a four-week yoga class as an alternative Body-Mind-Spirit (BMS) intervention on participant Jenny (pseudonym) by a licensed yoga instructor and expatriate. Interpretive content analysis of post-intervention interviews, and subjective observational analysis throughout the yoga classes captured the movements of Body-Mind-Spirit as well as their impacts on the participant’s perceptions of mental illness and the change through yoga practice. Results: Some specific themes from the participant’s narratives were identified that could give light to the mechanism of change through yoga that stifles mental illness stigma, transforms identity, and enhances attention. Conclusion and implications for practice: Most notably, changes occurred through the physical to psychological axis of wellbeing, indicating some symbolic mechanism in yoga that facilitates the flow of information from the body to the mind. As Jenny’s awareness of her body deepened, her association with a stigmatizing mental illness identity decreased. Although this study was limited in its generalizability, it shows an increased understanding of how identity is an important link between BMS interventions and mental illness stigma. Furthermore these findings suggest that there is a need for rigorous research in the effectiveness of yoga on mental illnesses such as depression.
A Path to Discovery: The Career of Maclyn McCarty
Joshua Lederberg,Emil C. Gotschlich
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0030341
Abstract:
A path to discovery: the career of Maclyn McCarty.
Lederberg Joshua,Gotschlich Emil C
PLOS Biology , 2005,
Abstract:
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