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Search Results: 1 - 10 of 330121 matches for " Devin S. Johnson "
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Bayesian Multimodel Inference for Geostatistical Regression Models
Devin S. Johnson, Jennifer A. Hoeting
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0025677
Abstract: The problem of simultaneous covariate selection and parameter inference for spatial regression models is considered. Previous research has shown that failure to take spatial correlation into account can influence the outcome of standard model selection methods. A Markov chain Monte Carlo (MCMC) method is investigated for the calculation of parameter estimates and posterior model probabilities for spatial regression models. The method can accommodate normal and non-normal response data and a large number of covariates. Thus the method is very flexible and can be used to fit spatial linear models, spatial linear mixed models, and spatial generalized linear mixed models (GLMMs). The Bayesian MCMC method also allows a priori unequal weighting of covariates, which is not possible with many model selection methods such as Akaike's information criterion (AIC). The proposed method is demonstrated on two data sets. The first is the whiptail lizard data set which has been previously analyzed by other researchers investigating model selection methods. Our results confirmed the previous analysis suggesting that sandy soil and ant abundance were strongly associated with lizard abundance. The second data set concerned pollution tolerant fish abundance in relation to several environmental factors. Results indicate that abundance is positively related to Strahler stream order and a habitat quality index. Abundance is negatively related to percent watershed disturbance.
A Hierarchical Modeling Framework for Multiple Observer Transect Surveys
Paul B. Conn, Jeffrey L. Laake, Devin S. Johnson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042294
Abstract: Ecologists often use multiple observer transect surveys to census animal populations. In addition to animal counts, these surveys produce sequences of detections and non-detections for each observer. When combined with additional data (i.e. covariates such as distance from the transect line), these sequences provide the additional information to estimate absolute abundance when detectability on the transect line is less than one. Although existing analysis approaches for such data have proven extremely useful, they have some limitations. For instance, it is difficult to extrapolate from observed areas to unobserved areas unless a rigorous sampling design is adhered to; it is also difficult to share information across spatial and temporal domains or to accommodate habitat-abundance relationships. In this paper, we introduce a hierarchical modeling framework for multiple observer line transects that removes these limitations. In particular, abundance intensities can be modeled as a function of habitat covariates, making it easier to extrapolate to unsampled areas. Our approach relies on a complete data representation of the state space, where unobserved animals and their covariates are modeled using a reversible jump Markov chain Monte Carlo algorithm. Observer detections are modeled via a bivariate normal distribution on the probit scale, with dependence induced by a distance-dependent correlation parameter. We illustrate performance of our approach with simulated data and on a known population of golf tees. In both cases, we show that our hierarchical modeling approach yields accurate inference about abundance and related parameters. In addition, we obtain accurate inference about population-level covariates (e.g. group size). We recommend that ecologists consider using hierarchical models when analyzing multiple-observer transect data, especially when it is difficult to rigorously follow pre-specified sampling designs. We provide a new R package, hierarchicalDS, to facilitate the building and fitting of these models.
Estimating demographic parameters using a combination of known-fate and open N-mixture models
Joshua H. Schmidt,Devin S. Johnson,Mark S. Lindberg,Layne G. Adams
Quantitative Biology , 2015,
Abstract: 1. Accurate estimates of demographic parameters are required to infer appropriate ecological relationships and inform management actions. Recently developed N-mixture models use count data from unmarked individuals to estimate demographic parameters, but a joint approach combining the strengths of both analytical tools has not been developed. 2. We present an integrated model combining known-fate and open N-mixture models, allowing the estimation of detection probability, recruitment, and the joint estimation of survival. We first use a simulation study to evaluate the performance of the model relative to known values. We then provide an applied example using 4 years of wolf survival data consisting of relocations of radio-collared wolves within packs and counts of associated pack-mates. The model is implemented in both maximum-likelihood and Bayesian frameworks using a new R package kfdnm and the BUGS language. 3. The simulation results indicated that the integrated model was able to reliably recover parameters with no evidence of bias, and estimates were more precise under the joint model as expected. Results from the applied example indicated that the marked sample of wolves was biased towards individuals with higher apparent survival rates (including losses due to mortality and emigration) than the unmarked pack-mates, suggesting estimates of apparent survival based on joint estimation could be more representative of the overall population. Estimates of recruitment were similar to direct observations of pup production, and overlap of the credible intervals suggested no clear differences in recruitment rates. 4. Our integrated model is a practical approach for increasing the amount of information gained from future and existing radio-telemetry and other similar mark-resight datasets.
Velocity-Based Movement Modeling for Individual and Population Level Inference
Ephraim M. Hanks, Mevin B. Hooten, Devin S. Johnson, Jeremy T. Sterling
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022795
Abstract: Understanding animal movement and resource selection provides important information about the ecology of the animal, but an animal's movement and behavior are not typically constant in time. We present a velocity-based approach for modeling animal movement in space and time that allows for temporal heterogeneity in an animal's response to the environment, allows for temporal irregularity in telemetry data, and accounts for the uncertainty in the location information. Population-level inference on movement patterns and resource selection can then be made through cluster analysis of the parameters related to movement and behavior. We illustrate this approach through a study of northern fur seal (Callorhinus ursinus) movement in the Bering Sea, Alaska, USA. Results show sex differentiation, with female northern fur seals exhibiting stronger response to environmental variables.
Dynamic social networks based on movement
Henry R. Scharf,Mevin B. Hooten,Bailey K. Fosdick,Devin S. Johnson,Josh M. London,John W. Durban
Statistics , 2015,
Abstract: Network modeling techniques provide a means for quantifying social structure in populations of individuals. Data used to define social connectivity are often expensive to collect and based on case-specific, ad hoc criteria. Moreover, in applications involving animal social networks, collection of these data is often opportunistic and can be invasive. Frequently, the social network of interest for a given population is closely related to the way individuals move. Thus telemetry data, which are minimally-invasive and relatively inexpensive to collect, present an alternative source of information. We develop a framework for using telemetry data to infer social relationships among animals. To achieve this, we propose a Bayesian hierarchical model with an underlying dynamic social network controlling movement of individuals via two mechanisms: an attractive effect, and an aligning effect. We demonstrate the model and its ability to accurately identify complex social behavior in simulation, and apply our model to telemetry data arising from killer whales. Using auxiliary information about the study population, we investigate model validity and find the inferred dynamic social network is consistent with killer whale ecology and expert knowledge.
The Sun, Moon, Wind, and Biological Imperative–Shaping Contrasting Wintertime Migration and Foraging Strategies of Adult Male and Female Northern Fur Seals (Callorhinus ursinus)
Jeremy T Sterling, Alan M. Springer, Sara J. Iverson, Shawn P. Johnson, Noel A. Pelland, Devin S. Johnson, Mary-Anne Lea, Nicholas A. Bond
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0093068
Abstract: Adult male and female northern fur seals (Callorhinus ursinus) are sexually segregated in different regions of the North Pacific Ocean and Bering Sea during their winter migration. Explanations for this involve interplay between physiology, predator-prey dynamics, and ecosystem characteristics, however possible mechanisms lack empirical support. To investigate factors influencing the winter ecology of both sexes, we deployed five satellite-linked conductivity, temperature, and depth data loggers on adult males, and six satellite-linked depth data loggers and four satellite transmitters on adult females from St. Paul Island (Bering Sea, Alaska, USA) in October 2009. Males and females migrated to different regions of the North Pacific Ocean: males wintered in the Bering Sea and northern North Pacific Ocean, while females migrated to the Gulf of Alaska and California Current. Horizontal and vertical movement behaviors of both sexes were influenced by wind speed, season, light (sun and moon), and the ecosystem they occupied, although the expression of the behaviors differed between sexes. Male dive depths were aligned with the depth of the mixed layer during daylight periods and we suspect this was the case for females upon their arrival to the California Current. We suggest that females, because of their smaller size and physiological limitations, must avoid severe winters typical of the northern North Pacific Ocean and Bering Sea and migrate long distances to areas of more benign environmental conditions and where prey is shallower and more accessible. In contrast, males can better tolerate often extreme winter ocean conditions and exploit prey at depth because of their greater size and physiological capabilities. We believe these contrasting winter behaviors 1) are a consequence of evolutionary selection for large size in males, important to the acquisition and defense of territories against rivals during the breeding season, and 2) ease environmental/physiological constraints imposed on smaller females.
Transfection of oral squamous cell carcinoma with human papillomavirus-16 induces proliferative and morphological changes in vitro
Karl Kingsley, Devin Johnson, Susan O'Malley
Cancer Cell International , 2006, DOI: 10.1186/1475-2867-6-14
Abstract: This study found that the oral squamous cell carcinoma cell line, CAL27, transfected with HPV16, exhibited significantly increased proliferation, compared with non-transfected CAL27. The increased proliferation was observed under low density conditions, even in the absence of serum. Moreover, these effects were specific to proliferation, adhesion, and morphology, while cell viability was not affected.This study represents one of the first investigations of the effects of HPV16 infection on the proliferation, adhesion, and morphology of an oral squamous cell carcinoma cell line in vitro. The finding that HPV16 has the ability to measurably alter adhesion and proliferative potential is significant, indicating that HPV may have multiple influences on precancerous and cancerous lesions and should be explored as a risk factor and mediator of cancer phenotypes. These measurements and observations will be of benefit to researchers interested in elucidating the mechanisms of oral cancer transformation and the factors governing carcinogenesis and progression.Human papillomavirus (HPV) has been implicated in many intraepithelial neoplasias and invasive squamous cell carcinomas [1-3]. The worldwide prevalence of HPV in cervical carcinomas has been determined to be as high as 99.7%, with HPV types 16 and 18 implicated most frequently [4,5]. Recent studies indicate that of these two high risk types of HPV, HPV16 is the most prevalent type found in oral cancers, most notably in oral squamous cell carcinomas (OSCC). These studies have also provided evidence that oral infection with HPV is a significant independent risk factor for OSCC, determining that HPV is detected in 46.5% of OSCC, compared with its detection in 10% of normal oral mucosa [6-10].Why HPV is found in virtually all cervical cancers, but only in a subset of OSCC, has yet to be explained. The mechanism of HPV carcinogenesis has been well established for cervical cancers. Early studies have demonstrated that the HPV-
Structured Inquiry-Based Learning: Drosophila GAL4 Enhancer Trap Characterization in an Undergraduate Laboratory Course
Christopher R. Dunne,Anthony R. Cillo,Danielle R. Glick,Katherine John,Cody Johnson,Jaspinder Kanwal,Brian T. Malik,Kristina Mammano,Stefan Petrovic,William Pfister,Alexander S. Rascoe,Diane Schrom,Scott Shapiro,Jeffrey W. Simkins,David Strauss,Rene Talai,John P. Tomtishen III,Josephine Vargas,Tony Veloz,Thomas O. Vogler,Michael E. Clenshaw,Devin T. Gordon-Hamm,Kathryn L. Lee,Elizabeth C. Marin
PLOS Biology , 2014, DOI: 10.1371/journal.pbio.1002030
Abstract: We have developed and tested two linked but separable structured inquiry exercises using a set of Drosophila melanogaster GAL4 enhancer trap strains for an upper-level undergraduate laboratory methods course at Bucknell University. In the first, students learn to perform inverse PCR to identify the genomic location of the GAL4 insertion, using FlyBase to identify flanking sequences and the primary literature to synthesize current knowledge regarding the nearest gene. In the second, we cross each GAL4 strain to a UAS-CD8-GFP reporter strain, and students perform whole mount CNS dissection, immunohistochemistry, confocal imaging, and analysis of developmental expression patterns. We have found these exercises to be very effective in teaching the uses and limitations of PCR and antibody-based techniques as well as critical reading of the primary literature and scientific writing. Students appreciate the opportunity to apply what they learn by generating novel data of use to the wider research community.
High risk HPV types 18 and 16 are potent modulators of oral squamous cell carcinoma phenotypes in vitro
Nicole Reddout, Todd Christensen, Anthony Bunnell, Dayne Jensen, Devin Johnson, Susan O'Malley, Karl Kingsley
Infectious Agents and Cancer , 2007, DOI: 10.1186/1750-9378-2-21
Abstract: CAL27 cells transfected with HPV18, HPV16, as well as HPV16/18 co-transfectants, demonstrated significant increases in proliferation, adhesion and cell spreading compared with non-transfected controls. These observed differences were correlated with a small level of increased cell survival. SCC-15 cells, however, displayed a differential response to HPV transfection, with only HPV18-transfectants demonstrated changes to proliferation. Interestingly, SCC-25 cells displayed a more complex response, with HPV16-induced increases in cell proliferation, viability and cell spreading, while HPV18- and 16/18-transfectants exhibited reduced adhesion and proliferation.Determining the potential of specific high-risk HPV strains to alter phenotypic behaviors of already transformed oral carcinomas is a critical step in providing more accurate prognosis and treatment options for oral cancer patients. The identification of differential responses to specific HPV strains among oral cancers suggests a more significant, complex and multifactorial role of HPV, not only in transforming, but also in modulating, the phenotype and treatment responsiveness of precancerous and cancerous oral lesions. This study provides some of the first evidence to help identify the important molecular markers for pathways that could be used to determine the most effective and appropriate treatment plans for oral cancer patients with concomitant oral HPV infections.Human papillomavirus (HPV) has been confirmed as the primary etiological factor that transforms cervical epithelia into cancer [1]. Certain HPV types are detected in virtually all invasive cervical cancer biopsies and have thus been designated as oncogenic or high-risk HPV [2,3]. According to epidemiological case-control studies [4], 15 high-risk HPV types have been acknowledged (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 73, and 82), while 3 types have been designated as probable high-risk (types 26, 53, and 66) and 12 types have b
Qualitative Study among African American Parents to Inform an Intervention to Promote Adoption of the Dietary Guidelines for Americans Food and Physical Activity Recommendations  [PDF]
Bernestine B. McGee, Valerie Richardson, Glenda S. Johnson, Crystal Johnson
Food and Nutrition Sciences (FNS) , 2014, DOI: 10.4236/fns.2014.59093
Abstract:

This qualitative study was conducted to enable the research team to culturally tailor an intervention to increase adherence to Dietary Guidelines for Americans (DGA) in African American parents and their children living in Lower Mississippi Delta (LMD) communities. Focus group results guided the planning of an obesity prevention intervention utilizing the We Can! (Ways to Enhance Children’s Activity and Nutrition) obesity prevention program. Main outcome measure was perceptions of approaches to use in culturally tailoring a nutrition and physical activity intervention. Six focus group sessions were conducted with 86 African American adults to identify cultural concerns, intervention strategies in two Louisiana parishes in the LMD. Focus groups discussions were audio recorded, transcribed, and analyzed to identify recurring trends and patterns among focus groups. Major themes that emerged included cultural influences on food habits and physical activity, challenges of meeting the DGA and the CDC physical activity guidelines, facilitators and barriers to adhering to healthy food and physical activity guidelines and program development. Wider acceptance and use of the DGA recommendations are needed by LMD populations, leading to reduced prevalence of overweight and obesity and parallel reductions in the prevalence of chronic diseases. Interventions are needed that will enhance adherence to the DGA particularly for diverse subpopulations in the U.S. This study provides important insights for culturally tailoring an intervention to promote adoption of the DGA in two low-income African American Delta communities.

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