Modeling disease incidence data with spatial and spatio temporal dirichlet process mixtures

Disease incidence or mortality data are typically available as rates or counts for specified regions, collected over time. We propose Bayesian nonparametric spatial modeling approaches to analyze such data. We develop a hierarchical specification using spatial random effects modeled with a Dirichlet process prior. The Dirichlet process is centered around a multivariate normal distribution. This latter distribution arises from a log-Gaussian process model that provides a latent incidence rate surface, followed by block averaging to the areal units determined by the regions in the study. With regard to the resulting posterior predictive inference, the modeling approach is shown to be equivalent to an approach based on block averaging of a spatial Dirichlet process to obtain a prior probability model for the finite dimensional distribution of the spatial random effects. We introduce a dynamic formulation for the spatial random effects to extend the model to spatio-temporal settings. Posterior inference is implemented through Gibbs sampling. We illustrate the methodology with simulated data as well as with a data set on lung cancer incidences for all 88 counties in the state of Ohio over an observation period of 21 years.     

The influence of feeding,enrichment, and seasonal context on the behavior of Pacific Walruses (Odobenus rosmarus divergens)

Though some research exists concerning general behavior and activity patterns of Walruses in zoos or aquariums, less is known about how these patterns change in response to various environmental and temporal contexts. This study presents two studies assessing behavioral changes in relation to feeding period, object enrichment (OE), and season in a social group of four Pacific Walruses at the New York Aquarium. Study 1 examined behavior in relation to feeding context (nonfeed, prefeed, postfeed); data were collected over a three‐week period, resulting in 47 observation sessions for each feeding context. Study 2 examined behavior in relation to OE and season; data were collected in two phases resulting in 12 enrichment and 9 no‐enrichment (NE) observation sessions (Phase 1), and 21 enrichment and 18 NE observation sessions (Phase 2). Study 1 showed that after feeding, oral behavior increased while social behavior and total swim frequency decreased. In Study 2, both swim frequency and social behavior were found to interact with OE and phase, while oral behavior remained constant across all conditions. As in the wild, both studies found all animals to be swimming the majority of the time. Though every animal spent much of its swim time engaged in an Individual Swimming Pattern (ISP), both studies showed that the proportion of ISP (in relation to total time swimming) remained stable across all contexts, suggesting a potential functional role of the ISPs. These results are discussed in light of the ongoing debate over the role of stereotypies in welfare assessment. Zoo Biol 29:397–404, 2010. © 2009 Wiley‐Liss, Inc.     

Radiation-induced rectal complications are not influenced by age: a dose fractionation study in the rat

Radiation-induced complications of the rectum are an important dose-limiting factor in radiotherapy of pelvic malignancies. In general, animal studies demonstrated no differences in acute and late normal tissue toxicity with age, but little is known about rectal complications in relation to age. For this purpose, an extensive histological and dose fractionation study was carried out on the rectum of young (12 weeks) and older (77-80 weeks) rats. In this paper, the results of dose fractionation are presented in relation to age at the time of irradiation. Young and older animals were irradiated with single and fractionated doses. After irradiation, rectal complications could lead to occlusion and stenosis, eventually resulting in the clinical symptoms of a megacolon and a possible fistula. For each dose group, cumulative survival rates were obtained with Kaplan-Meier analysis, from which dose-effect curves and the associated LD(50) values for a megacolon/fistula were calculated. The majority of responders died between 8 and 24 weeks after irradiation, irrespective of age. For both age groups, only the fractionation data showed a reduction in the mean latency with increasing dose. In the older age group, 39% of the responders developed a fistula compared to 26% for the younger animals. The LD(50) values increased from around 30 Gy after single doses to nearly 65 Gy after 10 fractions. The increases in LD(50) values with the number of fractions were independent of the age of the rats. For each of the dose fractionation schedules, log-rank testing indicated no significant differences in cumulative survival rates between younger and older animals (P > 0.10). The high alpha/beta ratios obtained for both the young and older animals strongly suggested that the late rectal complications were a consequence of early epithelial injury. Associated histological findings indicated that blood vessel damage, which was already evident at a high incidence at 4 weeks after irradiation, could also play a significant role in the occurrence of consequential late injuries. In conclusion, data obtained for the latent period of rectal occlusion, for the dose-effect curves, for the log-rank testing of cumulative survival rates, and for the alpha/beta ratios strongly support the hypothesis that the incidence of radiation-induced rectal complications is independent of age. Late rectal complications could be a consequence of radiation-induced acute injury.     

Age and hormonal status as determinants of cataractogenesis induced by ionizing radiation. I. Densely ionizing (high-LET) radiation

Astronauts participating in extended lunar missions or the projected mission to Mars would likely be exposed to significant doses of high-linear energy transfer (LET) heavy energetic charged (HZE) particles. Exposure to even relatively low doses of such space radiation may result in a reduced latent period for and an increased incidence of lens opacification. However, the determinants of cataractogenesis induced by densely ionizing radiation have not been clearly elucidated. In the current study, we show that age at the time of exposure is a key determinant of cataractogenesis in rats whose eyes have been exposed to 2 Gy of (56)Fe ions. The rate of progression of cataractogenesis was significantly greater in the irradiated eyes of 1-year-old rats compared to young (56-day-old) rats. Furthermore, older ovariectomized rats that received exogenous estrogen treatment (17-β-estradiol) commencing 1 week prior to irradiation and continuing throughout the period of observation of up to approximately 600 days after irradiation showed an increased incidence of cataracts and faster progression of opacification compared to intact rats with endogenous estrogen or ovariectomized rats. The same potentiating effect (higher incidence, reduced latent period) was observed for irradiated eyes of young rats. Modulation of estrogen status in the 1-year-old animals (e.g., removal of estrogen by ovariectomy or continuous exposure to estrogen) did not increase the latent period or reduce the incidence to that of intact 56-day-old rats. Since the rapid onset and progression of cataracts in 1-year-old compared to 56-day-old rats was independent of estrogen status, we conclude that estrogen cannot account for the age-dependent differences in cataractogenesis induced by high-LET radiation.     

Reactivation of Latent Tuberculosis in Cynomolgus Macaques Infected with SIV Is Associated with Early Peripheral T Cell Depletion and Not Virus Load

HIV-infected individuals with latent Mycobacterium tuberculosis (Mtb) infection are at significantly greater risk of reactivation tuberculosis (TB) than HIV-negative individuals with latent TB, even while CD4 T cell numbers are well preserved. Factors underlying high rates of reactivation are poorly understood and investigative tools are limited. We used cynomolgus macaques with latent TB co-infected with SIVmac251 to develop the first animal model of reactivated TB in HIV-infected humans to better explore these factors. All latent animals developed reactivated TB following SIV infection, with a variable time to reactivation (up to 11 months post-SIV). Reactivation was independent of virus load but correlated with depletion of peripheral T cells during acute SIV infection. Animals experiencing reactivation early after SIV infection (<17 weeks) had fewer CD4 T cells in the periphery and airways than animals reactivating in later phases of SIV infection. Co-infected animals had fewer T cells in involved lungs than SIV-negative animals with active TB despite similar T cell numbers in draining lymph nodes. Granulomas from these animals demonstrated histopathologic characteristics consistent with a chronically active disease process. These results suggest initial T cell depletion may strongly influence outcomes of HIV-Mtb co-infection.     

Chloramphenicol and dextramycin, inhibitors of mammary carcinogenesis induced by 7,12-dimethylbenz(a)anthracene]

In noninbred rats chloramphenicol and its optical isomer dextramycin diminished the blastomogenic effect of 7,12-dimethylbenz(a)anthracene on mammary glands. The protective effect was shown by a decreased tumor incidence at all periods of observation and an increase in the life span of rats and in the case of dextramycin this action consisted in a prolongation of the latent period of tumor emergence.     

A general framework for modeling population abundance data

Time-series data resulting from surveying wild animals are often described using state-space population dynamics models, in particular with Gompertz, Beverton-Holt, or Moran-Ricker latent processes. We show how hidden Markov model methodology provides a flexible framework for fitting a wide range of models to such data. This general approach makes it possible to model abundance on the natural or log scale, include multiple observations at each sampling occasion and compare alternative models using information criteria. It also easily accommodates unequal sampling time intervals, should that possibility occur, and allows testing for density dependence using the bootstrap. The paper is illustrated by replicated time series of red kangaroo abundances, and a univariate time series of ibex counts which are an order of magnitude larger. In the analyses carried out, we fit different latent process and observation models using the hidden Markov framework. Results are robust with regard to the necessary discretization of the state variable. We find no effective difference between the three latent models of the paper in terms of maximized likelihood value for the two applications presented, and also others analyzed. Simulations suggest that ecological time series are not sufficiently informative to distinguish between alternative latent processes for modeling population survey data when data do not indicate strong density dependence.     

Constant risk differences in the analysis of animal tumorigenicity data

In a typical tumorigenicity study, most tumors are not observable in live animals and only a single (terminal) sacrifice is performed. This paper proposes a nonparametric, survival-adjusted analysis for these data that focuses on tumor incidence and yet does not require data on cause of death or assumptions about the tumor's lethality. The tumor onset/death process is most naturally characterized in terms of the tumor incidence rate and the death rates for tumor-free and tumor-bearing animals. The proposed approach, however, reparameterizes the problem in terms of the incidence rate, the death rate for tumor-free animals, and the difference between the death rates for tumor-free and tumor-bearing animals (i.e., the risk difference). The advantage of this alternative formulation is that a full likelihood analysis is possible with as few as one sacrifice time if the risk difference is assumed to be constant with respect to time. Data from the large ED01 study suggest that reasonable results can be obtained under the assumption of constant risk differences.     

Estrous cycle synchronization in dairy heifers with the prostaglandin analog alfaprostol (I)

The prostaglandin F(2alpha) analog (PGFA) alfaprostol was used in 277 cyclic dairy heifers for the purpose of estrous cycle synchronization. A dose of 5 mg was used in all the trials during spring 1979 and 1.5 mg 100 kg body weight were used during winter 1979/80. Animals were treated according to 3 schedules: two doses 11 days apart without prior examination (Schedule I), one dose without prior observation and a second dose 11 days later only for those animals that failed to show estrus after the first treatment (Schedule II) and one dose for animals not showing estrus after a 5-day observation period (Schedule III). Estrus synchronization was achieved with peak estrus activity occurring form 32 to 72 h after treatment in 95% of the responding animals. Of the animals treated according to schedules I, II and III, 93%, 100% and 100% showed synchronized estrus activities respectively. Conception rates in all trials, from insemination at observed heat (Schedules I, II and III) or from fixed time insemination at 48 and 72 h after the first or second treatments in schedules III and I, respectively, compared well with that of untreated contemporary controls with a range of 34.2 to 66.7% for animals in these trials, and an overall conception rate of 49.48% for treated and of 48.30% for control animals. This observation, together with the pregnancy rate at 60 days after breeding (78.30% for all treated animals and 73.50% for all untreated controls), indicates that alfaprostol had no adverse effects on fertility.     

Social behaviour of the slender Loris (Loris tardigradus lydekkerianus)

The social behaviour of the nocturnal prosimian Loris tardigradus lydekkerianus in its natural habitat was studied for 21 months in a scrub jungle in Dindigul, southern India. A total of 22834 scans were collected during 2656 hours of observation on identified and unidentified lorises. Social interactions were observed between individuals of all age-sex classes, both during the night and at dawn, when the animals met to sleep together. The majority of aggressive encounters between individuals occurred in territorial and mating contexts. Individuals also communicated with each other through chemical and vocal signals. Adults and sub-adults of both sexes were observed to immigrate into the study area, leading to social interactions with resident individuals.     

New evidence for pre-Columbian Muscovy Duck Cairina moschata from Ecuador

The archaeological record of the large lowland neotropical Muscovy Duck Cairina moschata , one of the few native animals known to have been domesticated by pre-Columbian peoples, is poorly known. Only a few specimens have been recovered in different cultural, temporal and depositional contexts from throughout the neotropics, and differentiating between wild and domesticated forms on the basis of osteological evidence has proved to be difficult. Archaeological specimens are mainly recorded from sites in western Panama and South America, including the western lowlands of Ecuador where two new locations are described and evaluated. It is suggested that at least some of these Ecuadorian specimens belong to domesticated forms, and that the cultural contexts in which they are found at archaeological sites suggest that prehispanic trade may have influenced their geographical distribution prior to the arrival of Europeans.     

Understanding Reaction of Potato (Solanum tuberosum) to Ralstonia solanacearum and Relationship of Wilt Incidence to Latent Infection

Bacterial wilt caused by Ralstonia solanacearum is one of the most important diseases affecting more than 200 plant species, including solanaceous crops. The pathogen is known to cause complicated symptoms ranging from visible to latent ones. Understanding crop's reaction to the pathogen and the underlying relatedness of latent infection to wilt incidence is of paramount importance. Thus, a number of potato cultivars including improved and otherwise were evaluated under greenhouse and field conditions. Accordingly, twenty‐eight of the cultivars tested under greenhouse conditions were resistant to the pathogen with scores ranging from 0.77 to 1.17 of 5. Nonetheless, under field conditions, only 2 of 28 cultivars found to be ‘resistant’ under greenhouse conditions, showed adequate resistance to the pathogen, indicating the significant impact of environment on the activity of the pathogen and reaction of the crop. Percentage wilt incidence and latent infection showed significant (P < 0.05) positive correlation, with r = 0.9438. Thus, evaluation of crop's performance based on the combination of the parameters like field wilt incidence and proportion of latent infection gave us better picture of the overall crop feat, than using wilt incidence as a sole parameter of evaluation as has been the case in most studies. Moreover, the established correlation of latent infection with field wilt incidence will also help us understand the disease epidemiology and design effective management measures, accordingly.     

Cryptic sexual dimorphism reveals differing selection pressures on continental islands

Birds are well known for their sexual dimorphism. But not all forms of dimorphism are the same, and differences in morphology can be so subtle that they are not detected by casual observation. We report that this is the case with the Sulawesi Babbler (Pellorneum celebense), the first reported instance of sexual dimorphism in this species or any of the ground babblers of the South‐East Asian islands. Our finding is based on a combination of morphometric analyses, genetic sexing, and observation of breeding condition. We highlight the utility of unsupervised clustering approaches, widely used in the biomedical literature, for the investigation of sexual dimorphism in ecological and evolutionary contexts. The sexual dimorphism was weaker on the mainland of Sulawesi and stronger on the continental islands of Kabaena, Muna, and Buton. This suggests that different evolutionary pressures have led the species to partition niches differently in these habitats, which separated only recently in geological history. This kind of intraspecific niche partitioning is an intrinsic part of the ecological niche of such species, one we must not miss if we are to fully understand these endlessly fascinating organisms and systems. Abstract in Bahasa Indonesian is available with online material     

布拉酵母对小儿重症肺炎患儿 肠黏膜屏障功能的影响

目的探讨布拉酵母对小儿重症肺炎患儿肠黏膜屏障功能的影响。方法将90例重症肺炎患儿按随机数字表分为对照组和观察组各45例。对照组患儿采用常规治疗,观察组患儿在常规治疗的同时加用布拉酵母治疗1周。比较两组患儿治疗前后血浆D-乳酸及肠型脂肪酸结合蛋白变化情况、胃肠功能障碍及腹泻发生率以及患儿不良反应。结果治疗1周后,两组患儿血浆D-乳酸和肠型脂肪酸结合蛋白水平均低于治疗前(均P0.01),且不同时间点观察组指标水平下降幅度大于对照组(均P0.01)。观察组患儿胃肠功能障碍发生率为6.7%、对照组为22.2%;观察组患儿腹泻发生率为15.6%,对照组为33.3%,二者比较差异均有统计学意义(均P0.05)。观察组患儿无药物不良反应发生。结论布拉酵母对重症肺炎患儿肠黏膜屏障具有保护作用,能减少胃肠功能障碍及腹泻发生率。     

The induction of liver tumors by 239Pu citrate or 239PuO2 particles in the Chinese hamster

The influence of radiation dose distribution on the frequency of 239Pu-induced liver tumors was evaluated in the Chinese hamster. Different concentrations of 239Pu citrate 239PuO2 particles of known sizes were injected intravenously via the jugular vein. About 60% of the injected 239Pu citrate was deposited in the liver and 40% in the bone. The 239Pu citrate was rather uniformly distributed throughout the liver parenchyma. Injected plutonium oxide particles were taken up by the reticuloendothelial system with 90% of the body burden deposited in the liver. The 239PuO2 particles were localized in the Kupffer cells and produced nonuniform dose distributions that were dependent on particle size. There was an activity- and dose-dependent increase in the incidence of total liver parenchymal cell tumors following injection with either plutonium particles or citrate. For animals that received 14.0-, 2.7-, 0.3-, and 0.04-Gy dose to liver from 239Pu citrate the cumulative tumor incidence was 39, 32, 5, and 0%, respectively. Animals that were injected with the 0.24 micron 239PuO2 particles had doses of 42.0, 7.2, and 0.8 Gy to the liver and tumor incidences of 34, 26, and 5%, respectively. Plutonium citrate also produced hemangiosarcomas of the liver and tumors in bone and bone marrow. The latent period for liver tumor appearance in animals exposed to 239Pu citrate or 239PuO2 particles increased as the injected activity decreased. For animals injected with a similar total activity (7.4 Bq/g), the lifetime cumulative liver tumor incidence was similar for animals exposed to either 239Pu citrate (32%) or 239PuO2 (26%). There was little effect of particle size on liver tumor incidence. These data indicate that, in Chinese hamster liver, local radiation dose distribution is less important in altering tumor incidence than injected activity or average dose. However, the more uniform irradiation from 239Pu citrate administration was more effective in cancer production than the nonuniform irradiation from 239PuO2 particles.     

The ecological significance of time sense in animals

Time is a fundamental dimension of all biological events and it is often assumed that animals have the capacity to track the duration of experienced events (known as interval timing). Animals can potentially use temporal information as a cue during foraging, communication, predator avoidance, or navigation. Interval timing has been traditionally investigated in controlled laboratory conditions but its ecological relevance in natural environments remains unclear. While animals may time events in artificial and highly controlled conditions, they may not necessarily use temporal information in natural environments where they have access to other cues that may have more relevance than temporal information. Herein we critically evaluate the ecological contexts where interval timing has been suggested to provide adaptive value for animals. We further discuss attributes of interval timing that are rarely considered in controlled laboratory studies. Finally, we encourage consideration of ecological relevance when designing future interval-timing studies and propose future directions for such experiments.     

The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle

Bovine viral diarrhea virus is a major cattle pathogen with a worldwide distribution. Animals may be infected with BVD virus transiently or persistently. Transient infection leads to protective immunity. Persistent infection is unique because it is associated with an immunotolerance that is specific to the infecting strain of BVD virus. Persistent infection results from viral invasion of fetuses between the second and fourth month of development. Such animals are of prime importance in the epidemiology of BVD because they shed large amounts of virus, and thus serve as a constant source of infection for non-immune animals. Infection of pregnant animals during the first two months of gestation may result in an increased rate of return to estrus. Animals infected in the period of five months to birth may abort or give birth to calves with malformations. The effects of BVD virus on fertility and gestation are well documented from experimental infection. However, much less is known of the extent of losses under field conditions. The main reason for this may be the multitude of other causes of increased return rates and gestation failures. In addition, the incidence of infection with BVD virus may vary over time and depends on management practices. In this study, we investigated the impact of BVD virus on gestation failures under field conditions in a large cattle-breeding area of Switzerland, where no specific measures to control BVD are in effect. Our approach consisted of relating seroconversions to BVD virus with the rate of return to estrus, abortion, and birth of calves with apparent malformations. These parameters of fertility were compared to those of animals immune to BVDV infection due to previous exposure to the virus and animals without seroconversion. Our data show that infection with BVD virus during the first 45 days of gestation did not influence the rate of return to estrus. By contrast, we observed a statistically significant increase in the abortion rate in mid-term gestation (Days 46 to 210) while no such effect was observed in the later stages of gestation. No clinically manifest malformations were observed in the offspring of animals that had seroconverted to BVD virus. In our study population the prevalence of BVDV antibody positive cattle varied only slightly between 78% and 80% over the period of observation. Our data showed that 7% (CI: 2.4-14%) of fetal deaths may be attributable to infection with BVD virus.     

Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3' nucleotide to the codon has a context effect.

Codon context can affect translational efficiency by several molecular mechanisms. The base stacking interactions between a codon-anticodon complex and the neighboring nucleotide immediately 3' can facilitate translation by amber suppressors and the tRNA structure is also known to modulate the sensitivity to context. In this study the relative rates of aminoacyl-tRNA selection were measured at four sense codons (UGG, CUC, UUC and UCA), in all four 3' nucleotide contexts, through direct competition with a programmed frameshift at a site derived from the release factor 2 gene. Two codons (UGG and UUC) are read by tRNAs with small variable regions and their rates of aminoacyl-tRNA selection correlated with the potential base stacking strength of the 3' neighboring nucleotide. The other two codons (CUC and UCA) are read by tRNAs with large variable regions and the rate of selection of the aminoacyl-tRNAs in these cases varied little among the four contexts. Re-examination of published data on amber suppression also revealed an inverse correlation between context sensitivity and the size of the variable region. Collectively the data suggest that a large variable loop in a tRNA decreases the influence of the 3' context on tRNA selection, probably by strengthening tRNA-ribosomal interactions.     

Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.