Impact of imperfect test sensitivity on determining risk factors : the case of bovine tuberculosis

Background Imperfect diagnostic testing reduces the power to detect significant predictors in classical cross-sectional studies. Assuming that the misclassification in diagnosis is random this can be dealt with by increasing the sample size of a study. However, the effects of imperfect tests in longitudinal data analyses are not as straightforward to anticipate, especially if the outcome of the test influences behaviour. The aim of this paper is to investigate the impact of imperfect test sensitivity on the determination of predictor variables in a longitudinal study. Methodology/Principal Findings To deal with imperfect test sensitivity affecting the response variable, we transformed the observed response variable into a set of possible temporal patterns of true disease status, whose prior probability was a function of the test sensitivity. We fitted a Bayesian discrete time survival model using an MCMC algorithm that treats the true response patterns as unknown parameters in the model. We applied our approach to epidemiological data of bovine tuberculosis outbreaks in England and investigated the effect of reduced test sensitivity in the determination of risk factors for the disease. We found that reduced test sensitivity led to changes to the collection of risk factors associated with the probability of an outbreak that were chosen in the ‘best’ model and to an increase in the uncertainty surrounding the parameter estimates for a model with a fixed set of risk factors that were associated with the response variable. Conclusions/Significance We propose a novel algorithm to fit discrete survival models for longitudinal data where values of the response variable are uncertain. When analysing longitudinal data, uncertainty surrounding the response variable will affect the significance of the predictors and should therefore be accounted for either at the design stage by increasing the sample size or at the post analysis stage by conducting appropriate sensitivity analyses

Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis.

Hox genes play crucial roles in establishing regional identity along the anterior-posterior axis in bilaterian animals, and have been implicated in generating morphological diversity throughout evolution. Here we report the identification, expression, and initial genomic characterization of the complete set of Hox genes from the amphipod crustacean Parhyale hawaiensis. Parhyale is an emerging model system that is amenable to experimental manipulations and evolutionary comparisons among the arthropods. Our analyses indicate that the Parhyale genome contains a single copy of each canonical Hox gene with the exception of fushi tarazu, and preliminary mapping suggests that at least some of these genes are clustered together in the genome. With few exceptions, Parhyale Hox genes exhibit both temporal and spatial colinearity, and expression boundaries correlate with morphological differences between segments and their associated appendages. This work represents the most comprehensive analysis of Hox gene expression in a crustacean to date, and provides a foundation for functional studies aimed at elucidating the role of Hox genes in arthropod development and evolution

Managing conflict between bats and humans: The response of soprano pipistrelles (pipistrellus pygmaeus) to exclusion from roosts in houses

Copyright: © 2015 Stone et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict can arise when bats roost in human dwellings and householders are affected adversely by their presence. In the United Kingdom, the exclusion of bats from roosts can be licensed under exceptional circumstances to alleviate conflict, but the fate of excluded bats and the impact on their survival and reproduction is not well understood. Using radiotracking, we investigated the effects of exclusion on the soprano pipistrelle Pipistrellus pygmaeus, a species that commonly roosts in buildings in Europe. Exclusions were performed under licence at five roosts in England in spring, when females were in the early stages of pregnancy. Following exclusion, all bats found alternative roosts and colonies congregated in nearby known roosts that had been used by radio-tagged bats prior to exclusion. We found no difference in roosting behaviour before and after exclusion. Both the frequency of roost switching and the type of roosts used by bats remained unchanged. We also found no change in foraging behaviour. Bats foraged in the same areas, travelled similar distances to reach foraging areas and showed similar patterns of habitat selection before and after exclusion. Population modelling suggested that any reduction in survival following exclusion could have a negative impact on population growth, whereas a reduction in productivity would have less effect. While the number of soprano pipistrelle exclusions currently licensed each year is likely to have little effect on local populations, the cumulative impacts of licensing the destruction of large numbers of roosts may be of concern

The impact of Hurricane Sandy on the shoreface and inner shelf of Fire Island, New York : large bedform migration but limited erosion

© The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution.. The definitive version was published in Continental Shelf Research 98 (2015): 13-25, doi:10.1016/j.csr.2015.03.001.We investigate the impact of superstorm Sandy on the lower shoreface and inner shelf offshore the barrier island system of Fire Island, NY using before-and-after surveys involving swath bathymetry, backscatter and CHIRP acoustic reflection data. As sea level rises over the long term, the shoreface and inner shelf are eroded as barrier islands migrate landward; large storms like Sandy are thought to be a primary driver of this largely evolutionary process. The “before” data were collected in 2011 by the U.S. Geological Survey as part of a long-term investigation of the Fire Island barrier system. The “after” data were collected in January, 2013, ~two months after the storm. Surprisingly, no widespread erosional event was observed. Rather, the primary impact of Sandy on the shoreface and inner shelf was to force migration of major bedforms (sand ridges and sorted bedforms) 10’s of meters WSW alongshore, decreasing in migration distance with increasing water depth. Although greater in rate, this migratory behavior is no different than observations made over the 15-year span prior to the 2011 survey. Stratigraphic observations of buried, offshore-thinning fluvial channels indicate that long-term erosion of older sediments is focused in water depths ranging from the base of the shoreface (~13-16 m) to ~21 m on the inner shelf, which is coincident with the range of depth over which sand ridges and sorted bedforms migrated in response to Sandy. We hypothesize that bedform migration regulates erosion over these water depths and controls the formation of a widely observed transgressive ravinement; focusing erosion of older material occurs at the base of the stoss (upcurrent) flank of the bedforms. Secondary storm impacts include the formation of ephemeral hummocky bedforms and the deposition of a mud event layer.This work was funded primarily by a rapid response grant from the Jackson School of Geosciences, The University of Texas/Austi

Effect of external beam irradiation on neointimal hyperplasia after experimental coronary artery injury

AbstractHuman coronary artery restenosis after percutaneous revascularization is a response to mechanical injury. Smooth muscle cell proliferation is a major component of restenosis, resulting in obstructive neointimal hyperplasia. Because ionizing radiation inhibits cellular proliferation, this study tested in a porcine coronary injury model the hypothesis that the hyperplastic response to coronary artery injury would be attenuated by X-irradiation.Deep arterial injury was produced in 37 porcine left anterior descending coronary artery segments with overexpanded, percutaneously delivered tantalum wire coils. Three groups of pigs were irradiated with 300-kV X-rays after coil injury: Group I (n = 10), 400 cGy at 1 day; Group II (n = 10), 400 cGy at 1 day and 400 cGy at 4 days and Group III (n = 9), 800 cGy at 1 day. Eight pigs in the control group underwent identical injury but received no radiation. Treatment efficacy was histologically assessed by measuring neointimal thickness and percent area stenosis.Mean neointimal thickness in all irradiated groups was significantly higher than in the control groups and thickness was proportional to X-ray dose.X-irradiation delivered at these doses and times did not inhibit proliferative neointima. Rather, it accentuated the neointimal response to acute arterial injury and may have potentiated that injury

Pregnant and Nonpregnant Women in Cape Town, South Africa: Drug Use, Sexual Behavior, and the Need for Comprehensive Services

The multiple risks associated with methamphetamine use are of serious concern for women. These risks and consequences are magnified during pregnancy. This secondary analysis of a parent study compared 26 pregnant to 356 nonpregnant women in Cape Town, South Africa, on selected demographic, psychosocial, and HIV-risk domains to identify their treatment service needs. Proportionally, more pregnant than nonpregnant women are using methamphetamine, P = .01, although a very high rate of women used methamphetamine. Women reported similar monthly rates of sexual intercourse, but pregnant women were significantly less likely to report condom use, P < .0001, maintaining their risky behavior. Both groups reported elevated Center for Epidemiological Studies Depression Scale CES-D means, suggesting a need for depression treatment. Results demonstrate a pervasive need for women's comprehensive treatment, regardless of pregnancy status. Moreover, findings support the urgent need for women-focused and pregnancy-specific treatment services for methamphetamine use. Finally, a job-skills training/employment component focus is suggested

Pregnant and Nonpregnant Women in Cape Town, South Africa: Drug Use, Sexual Behavior, and the Need for Comprehensive Services

The multiple risks associated with methamphetamine use are of serious concern for women. These risks and consequences are magnified during pregnancy. This secondary analysis of a parent study compared 26 pregnant to 356 nonpregnant women in Cape Town, South Africa, on selected demographic, psychosocial, and HIV-risk domains to identify their treatment service needs. Proportionally, more pregnant than nonpregnant women are using methamphetamine, P = .01, although a very high rate of women used methamphetamine. Women reported similar monthly rates of sexual intercourse, but pregnant women were significantly less likely to report condom use, P < .0001, maintaining their risky behavior. Both groups reported elevated Center for Epidemiological Studies Depression Scale CES-D means, suggesting a need for depression treatment. Results demonstrate a pervasive need for women's comprehensive treatment, regardless of pregnancy status. Moreover, findings support the urgent need for women-focused and pregnancy-specific treatment services for methamphetamine use. Finally, a job-skills training/employment component focus is suggested

Male mice housed in groups engage in frequent fighting and show a lower response to additional bone loading than females or individually housed males that do not fight

AbstractExperiments to investigate bone's physiological adaptation to mechanical loading frequently employ models that apply dynamic loads to bones in vivo and assess the changes in mass and architecture that result. It is axiomatic that bones will only show an adaptive response if the applied artificial loading environment differs in a significant way from that to which the bones have been habituated by normal functional loading. It is generally assumed that this normal loading is similar between experimental groups. In the study reported here we found that this was not always the case. Male and female 17-week-old C57BL/6 mice were housed in groups of six, and a single episode (40cycles) of non-invasive axial loading, engendering 2,200με on the medial surface of the proximal tibiae in sample mice, was applied to right tibiae on alternate days for two weeks. This engendered an adaptive increase in bone mass in females, but not males. Observation revealed the main difference in behaviour between males and females was that males were involved in fights 1.3 times per hour, whereas the females never fought. We therefore housed all mice individually. In females, there was a similar significant osteogenic response to loading in cortical and trabecular bone of both grouped and individual mice. In contrast, in males, adaptive increases in the loaded compared with non-loaded control bones was only apparent in animals housed individually. Our interpretation of these findings is that the frequent vigorous fighting that occurs between young adult males housed in groups could be sufficient to engender peak strains and strain rates that equal or exceed the stimulus derived from artificial loading. This indicates the importance of ensuring that physical activity is consistent between groups. Reducing the background level of the naturally engendered strain environment allows adaptive responses to artificial loading to be demonstrated at lower loads