Isomorphic chain graphs for modeling spatial dependence in ecological data

Graphical models (alternatively, Bayesian belief networks, path analysis models) are increasingly used for modeling complex ecological systems (e.g., Lee, In: Ferson S, Burgman M(eds) Quantative methods for conservation biology. Springer, Berlin Heilin Heideslperk New York, pp.127–147, 2000; Borsuk et al., J Water Res Plann Manage 129:271–282, 2003). Their implementation in this context leverages their utility in modeling interrelationships in multivariate systems, and in a Bayesian implementation, their intuitive appeal of yielding easily interpretable posterior probability estimates. However, methods for incorporating correlational structure to account for observations collected through time and/or space—features of most ecological data—have not been widely studied; Haas et al. (AI Appl 8:15–27, 1994) is one exception. In this paper, an “isomorphic” chain graph (ICG) model is introduced to account for correlation between samples by linking site-specific Bayes network models. Several results show that the ICG preserves many of the Markov properties (conditional and marginal dependencies) of the site-specific models. The ICG model is compared with a model that does not account for spatial correlation. Data from several stream networks in the Willamette River valley, Oregon (USA) are used. Significant correlation between sites within the same stream network is shown with an ICG model.     

Zero-inflated models with application to spatial count data

Count data arises in many contexts. Here our concern is with spatial count data which exhibit an excessive number of zeros. Using the class of zero-inflated count models provides a flexible way to address this problem. Available covariate information suggests formulation of such modeling within a regression framework. We employ zero-inflated Poisson regression models. Spatial association is introduced through suitable random effects yielding a hierarchical model. We propose fitting this model within a Bayesian framework considering issues of posterior propriety, informative prior specification and well-behaved simulation based model fitting. Finally, we illustrate the model fitting with a data set involving counts of isopod nest burrows for 1649 pixels over a portion of the Negev desert in Israel.     

Prenatal diagnosis of the derivative chromosome 22 associated with cat eye syndrome by fluorescence in situ hybridization

Cytogenetic studies of cultured amniocytes demonstrated a karyotype of 46, XX/47, XX,+mar. A bisatellited, dicentric, distamycin-DAPI negative, NOR-positive marker was present in 76 per cent of the metaphases examined. Similar markers have been associated with cat eye syndrome (CES). We report on the utilization of fluorescence in situ hybridization (FISH) with a 14/22 a-satellite probe and a chromosome 22-specific cosmid for locus D22S9 to determine the origin of the prenatally detected supernumerary marker chromosome. FISH studies demonstrated that the marker is a derivative of chromosome 22 and enabled us to provide the family with additional prognostic information.     

Chorionic villus sampling for prenatal diagnosis in wales using DNA probes—5 years' experience

Chorionic villi were sampled from 125 women who requested prenatal diagnosis, either for genetic disorders or because of advanced maternal age. Of these, 105 samples were obtained by the transcervical route and 20 were obtained by the transabdominal approach. The sampling success rate was 97 per cent (122/125). The mean maternal age of the patients was 31 years (range 17–44) and the mean gestational age at which the chorionic villus sampling was performed was 10 weeks (range 7–13 weeks). Seventy-four of these diagnoses involved the use of DNA markers. The minimal size of the sample used for DNA diagnosis was 5 mg. Maternal contamination was detected in two samples. A diagnosis was provided on all but two samples. The fetal loss rate was high initially but fell to 1·9 per cent in 1988.     

Mosaicism of autosomes and sex chromosomes in morphologically normal,monospermic preimplantation human embryos

We have previously detected chromosome abnormalities in human embryos whilst identifying the sex for preimplantation diagnosis of X-linked disease. In this study we assess the incidence of these abnormalities, both for sex chromosomes and autosomes 1 and 17, using dual fluorescent in situ hybridization (FISH). Sixty-nine normally fertilized embryos of good morphology at the 6–10 cell stage (day 3 post-insemination) were examined. The embryos were spread whole using HCl and Tween 20 to dissolve the cytoplasm. Thirty-four embryos were analysed for the sex chromosomes and 35 for autosomes 1 and 17. All probes were directly labelled with fluorochromes allowing analysis in 2 h. Control lymphocytes demonstrated that the probes were of high specificity. For the sex chromosomes, five embryos were mosaic (15 per cent) with the remaining 29 being uniformly XX or XY. In no case was an XX nucleus found in an otherwise XY embryo, indicating that even though mosaicism for the sex chromosomes is present, such abnormalities would not lead to a misdiagnosis of sex. For the autosomes, 16 embryos were abnormal (46 per cent); one embryo was triploid, one was monosomic for chromosome 1, and ten others were diploid mosaics (three diploid/aneuploid, three diploid/polyploid, and four diploid/haploid). A further four embryos had variable chromosome numbers in the majority of nuclei which appeared to be the result of uncontrolled mitotic division. The presence of haploidy or double monosomy, which occurred in 15 per cent of nuclei, has important implications for the diagnosis of trisomies and dominant disorders.     

Syndromes identified in fetuses with prenatally diagnosed cephaloceles

An evaluation of all fetuses from our institution with prenatally diagnosed cephaloceles was conducted to determine the frequency and spectrum of genetic syndromes associated with this abnormality. Review of the sonographic images, postnatal autopsy or pathology reports, delivery room records, paediatric neurosurgical findings, radiographs, and cytogenetic data were collected. Fifteen postnatally confirmed cases of prenatally diagnosed cephaloceles and two misdiagnosed cases were identified. Thirteen were midline occipital lesions, one was frontoparietal, and one was frontoethmoidal. Excluding microcephaly, hydrocephaly, and distortion of intracranial anatomy, 9 of 15 (60 per cent) had other associated anomalies, including two fetuses with aneuploidy. The prenatal diagnosis of a cephalocele should initiate a thorough search for other abnormalities. In this series, there were three multifactorial, two chromosomal, two sporadic, and two autosomal recessive syndromes identified. An accurate diagnosis is critical in determining the prognosis and providing appropriate genetic counselling.     

To see or not to see: does previewing a future opponent affect the contest behavior of green swordtail males (<Emphasis Type="Italic">Xiphophorus helleri</Emphasis>)?

Animals assess the fighting ability of conspecifics either by engaging in aggressive interactions or observing contests between others. However, whether individuals assess physical prowess outside the context of aggressive interactions remains unknown. We examined whether male green swordtails (Xiphophorus helleri) extract information about the fighting ability of solitary individuals via observation and whether acquiring such information elicits behavioral modifications. Contests preceded by mutual visual assessment were significantly shorter than fights where only one or neither of the two individuals was informed in advance. Focal animals initiated aggressive behavior more often against larger opponents only after previewing their adversary, indicating that swordtails can extract information about relative body size from watching solitary conspecifics. When a fighting disadvantage is perceived, observers adopt tactics that increase their probability of winning the contest.     

Stomatal uptake of O3 in aspen and aspen-birch forests under free-air CO2 and O3 enrichment

Rising atmospheric carbon dioxide (CO₂) may alleviate the toxicological impacts of concurrently rising tropospheric ozone (O₃) during the present century if higher CO₂ is accompanied by lower stomatal conductance (g_s), as assumed by many models. We investigated how elevated concentrations of CO₂ and O₃, alone and in combination, affected the accumulated stomatal flux of O₃ (AFst) by canopies and sun leaves in closed aspen and aspen-birch forests in the free-air CO₂-O₃ enrichment experiment near Rhinelander, Wisconsin. Stomatal conductance for O₃ was derived from sap flux data and AFst was estimated either neglecting or accounting for the potential influence of non-stomatal leaf surface O₃ deposition. Leaf-level AFst (AFst_l) was not reduced by elevated CO₂. Instead, there was a significant CO₂ × O₃ interaction on AFst_l, as a consequence of lower values of g_s in control plots and the combination treatment than in the two single-gas treatments. In addition, aspen leaves had higher AFst_l than birch leaves, and estimates of AFst_l were not very sensitive to non-stomatal leaf surface O₃ deposition. Our results suggest that model projections of large CO₂-induced reductions in g_s alleviating the adverse effect of rising tropospheric O₃ may not be reasonable for northern hardwood forests.