Incorporating Science,Technology, Fairness,and Accountability in Environmental,Health, and Safety Decisions

The Precautionary Principle is in sharp political focus today because (1) the nature of scientific uncertainty is changing and (2) there is increasing pressure to base governmental action on more “rational” schemes, such as cost-benefit analysis and quantitative risk assessment, the former being an embodiment of ‘rational choice theory’ promoted by the Chicago school of law and economics. The Precautionary Principle has been criticized as being both too vague and too arbitrary to form a basis for rational decision making. The assumption underlying this criticism is that any scheme not based on cost-benefit analysis and risk assessment is both irrational and without secure foundation in either science or economics. This paper contests that view and makes explicit the rational tenets of the Precautionary Principle within an analytical framework as rigorous as uncertainties permit, and one that mirrors democratic values embodied in regulatory, compensatory, and common law. Unlike other formulations that reject risk assessment, this paper argues that risk assessment can be used within the formalism of tradeoff analysis—a more appropriate alternative to traditional cost-benefit analysis and one that satisfies the need for well-grounded public policy decision making. This paper will argue that the precautionary approach is the most appropriate basis for policy, even when large uncertainties do not exist, especially where the fairness of the distributions of costs and benefits of hazardous activities and products are a concern. Furthermore, it will offer an approach to making decisions within an analytic framework, based on equity and justice, to replace the economic paradigm of utilitarian cost-benefit analysis.     

Pathway analysis for genome-wide genetic variation data: Analytic principles,latest developments,and new opportunities

Pathway analysis, also known as gene-set enrichment analysis, is a multilocus analytic strategy that integrates a priori, biological knowledge into the statistical analysis of high-throughput genetics data. Originally developed for the studies of gene expression data, it has become a powerful analytic procedure for indepth mining of genome-wide genetic variation data. Astonishing discoveries were made in the past years,uncovering genes and biological mechanisms underlying common and complex disorders. However, as massive amounts of diverse functional genomics data accrue, there is a pressing need for newer generations of pathway analysis methods that can utilize multiple layers of high-throughput genomics data. In this review, we provide an intellectual foundation of this powerful analytic strategy, as well as an update of the state-of-the-art in recent method developments. The goal of this review is threefold:(1) introduce the motivation and basic steps of pathway analysis for genome-wide genetic variation data;(2) review the merits and the shortcomings of classic and newly emerging integrative pathway analysis tools; and(3)discuss remaining challenges and future directions for further method developments.     

Sexing adult Northern Shrikes using DNA, morphometrics, and plumage

ABSTRACT.   Northern Shrikes ( Lanius excubitor ) are predatory songbirds found primarily in taiga regions throughout their Holarctic breeding range. The species is poorly known, especially in North America, and is generally thought to be sexually monomorphic. From 2004 to 2007, we captured 50 adults in northern Wisconsin during the nonbreeding season (December–March) and determined sex using DNA extracted from feather samples. Males had significantly longer wings, longer tails, and less black in the outer rectrix than females, but body mass did not differ between the sexes. A discriminant function equation using tail length and extent of black on the outer rectrix correctly assigned the sex of 97.4% of captured adults. Plumage dimorphism was also evident, with males having paler gray heads and backs without brown tones, whiter underparts with lighter barring, and a more distinct and horizontal border at the base of the sixth primary feather. The ability to accurately determine sex will provide opportunities to examine possible inter- and intrasexual differences in the behavior and ecology of adult Northern Shrikes.     

Development, Characterization, and Use of Monoclonal and Polyclonal Antibodies against the Myxosporean, Ceratomyxa shasta

Both monoclonal and polyclonal antisera were produced against Ceratomyxa shasta. Ascites containing trophozoites of the parasite was collected from infected fish and used as antigen for immunization of mice. The resulting monoclonal antibodies reacted specifically with trophozoite and sporoblast stages but did not react with C. shasta spores by either indirect fluorescent antibody techniques or in Western blots. This indicates that some C. shasta antigens are specific to certain life stages of the parasite. Polyclonal antiserum was produced in a rabbit by injecting a spore protein electro-eluted from an SDS-polyacrylamide gel. This antiserum reacted with both trophozoites and spores by indirect fluorescent antibody techniques and in Western blots. All antisera were tested for cross-reactivity to trout white blood cells, a contaminant of the ascites, and to other myxosporea. Two monoclonal antibodies reacted with white blood cells and myxosporea of the genera Sphaerospora and Myxobilatus. One hybridoma produced antibodies of high specificity for C. shasta pre-spore stages. This is the first report of a monoclonal antibody produced against a myxosporean parasite.     

Comparative Environmental Assessment in the Studies of Benthic Diatom,Macroinvertebrate, and Fish Communities

Community response to environmental gradients operating at hierarchical scales was assessed in studies of benthic diatoms, macroinvertebrates and fish from 44 stream sites in the New York City watershed. Hierarchical cluster analysis (TWINSPAN) of diatoms and fish partitioned the study sites into four groups, i.e., acid streams, reservoir outlets and wetland streams, large eutrophic streams, and small eutrophic streams; macroinvertebrate TWINSPAN distinguished an additional group of silty eutrophic streams. The correspondence among the three assemblage TWINSPAN groupings was moderate, ranging from 51 to 57%. The similarity across the four major group types was the highest among large eutrophic stream and acid stream assemblages, and the lowest among small eutrophic stream assemblages. Stepwise discriminant function analysis revealed that environmental factors discriminated most effectively the diatom grouping and least effectively the fish grouping. The best environmental predictors for diatom and macroinvertebrate grouping were conductance and percent surface water, while population density was most powerful in separating the fish groups. Carbaryl was the only pesticide that correlated with macroinvertebrate grouping. Partial redundancy analyses suggested a differential dependence of freshwater communities on the scale of the environmental factors to which they respond. The role of small‐scale habitat and habitatland cover/land use interaction steadily increased across the diatom, macroinvertebrate, and fish assemblages, whereas the effect of large‐scale land cover/land use declined.     

Aquatic microorganisms: processes,populations, and molecular solutions to environmental problems

Studies on aquatic ecosystems at the trophic level of bacteria include population succession and the movement of species through the water column. Factor and path analysis of environmental parameters and the bacterial profiles indicate that the bacterial populations are under the control of environmental factors. The most important environmental factors in the Canadian study reported here are temperature followed by oxygen levels, nutrient levels, and ion concentrations. A major revolution in investigative approaches has begun in aquatic bacterial population studies using technology based on molecular methods. Finger print analysis of bacterial 16S RNA (molecular phylogeny) has not only changed the classification of bacteria but also the approach to solving environmental problems. The bacterial groups have been placed into species that are more functionally and ecologically aligned. Uncultured mixed biomass can be examined by gene probes for both procaryotes and eucaryotes to identify specific nucleotide sequences. Aquatic ecosystem health is maintained by the balanced biota and the process of biodegradation is an important stage in bioremediation. Control of toxic wasters in the waters and groundwaters can be accomplished byin situ bioremediation using indigenous microorganisms as demonstrated by the field study reported by Litchfieldet al. (1990).     

Enzyme immunoassay determination of atrazine degradation in soil: Moisture,sterilization, and storage effects

Enzyme immunoassay (EIA) microtiter plate analysis was used to quantify atrazine (2‐chloro‐4‐ethylamino‐6‐isopropylamino‐1,3,5 triazine), fortified at 0, 50, and 500 or 549 ng/g, to Baxter and Maury silt loam soil sampled in 1965 and 1991. In the first experiment, aged soils (sampled in 1965 and stored air‐dried) were fortified with atrazine and then incubated in the dark at 0, 75, 150, 225 and 300 g/kg moisture for 15, 80, 154, and 289 d. In a second experiment, fresh soils were fortified with atrazine and incubated in the dark at 0, 150, and 300 g/kg moisture for 9, 15, 35, 55, 83, and 145 d. One half of the treatments in the second experiment were sterilized with 497 ng/g HgCl₂. Twenty milliliters of acetonitrile: water (9: 1) was used to extract 4 or 5 g of soil by vortex mixing at each sampling date. The soil extract was diluted, 80 μl incubated with antibody‐coated wells, and color development read using a microtiter plate reader. Recovery of atrazine from soil was 98% 5 d after fortification. Pesticide recoveries and first‐order degradation rates were dependent on the freshness and moisture content of the soil sample. Pesticide degradation was slower and recoveries higher in soil that had been air dried and stored since 1965, prior to fortification. More atrazine was extracted from soil maintained at 0 g/kg moisture than from soil maintained at 300 g/kg moisture over time.     

Effects of altitude, ethnicity-religion, geographical distance, and occupation on adult anthropometric characters of eastern Himalayan populations

With a view to estimating the effect of altitude on body dimensions vis-à-vis ethnicity-religion, geographical distance, and occupation, a comprehensive multivariate statistical analysis was performed on data pertaining to 16 anthropometric characters collected from 1,103 individuals (643 males and 460 females) belonging to two ethnic groups-Sherpa and Lepcha. Samples were drawn from several locations in the eastern Himalayan region-Darjeeling and Kalimpong in West Bengal (India), and Nepal, situated at low (1,000-2,000 meters) and high (above 3,500 meters) altitudes. The individuals sampled practice different occupations and follow different religions. Significant age and sex effects were observed. The data were age-adjusted, and sexes were treated separately. A test of equality of mean vectors indicated heterogeneity among population groups. Almost all characters were found to contribute significantly to the ability to discriminate between the groups. The overall probability of correctly classifying an individual based on body dimensions into the group in which she or he actually belongs was high (between 0.64 and 0.77). Shape and size factors could be identified that explained about 50% of the total variance and yielded a reasonable separation of the groups. Results of four different types of multivariate statistical analyses were in agreement, and showed that altitude is most highly associated with body dimensions.     

Mystical dreaming: Patterns in form, content, and meaning.

This article enriches the psychological understanding of religious mysticism by exploring patterns of form, content, and meaning in self-described mystical dreams, drawing on extensive sleep and dream interviews conducted with 100 contemporary Americans. Four major hypotheses regarding mystical experience are tested: mysticism as psychopathological, as culturally constructed, as a mode of pure consciousness, and as characterized by four Jamesian “marks” (ineffability, noesis, transience, passivity). The data from this study indicate that mystical dreams are experienced by around half the population and by women more than men, and their prototypical form involves good fortunes, friendly interactions, and unusual or nonhuman characters. These findings provide only limited validation for the psychopathology and pure consciousness hypotheses and somewhat more support for the Jamesian and cultural construction approaches. Taken together, the results suggest that psychological efforts to understand religious mysticism will remain incomplete without systematic reference to contemporary dream research. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Plant-environment relationships on the Montlake wildlife area,Seattle, Washington,USA

Grassland vegetation on the Montlake fill was analyzed using TWINSPAN. Eight herb communities were recognized. Moisture, proximity to gas vents, and disturbance are the main factors that control species and community distributions. Binary discriminant analysis (BDA) and detrended correspondence analysis (DCA) were used to study species-environment relationships. BDA revealed complex species response patterns and the resultant indicator values were used to interpret the ordination axes. Species distributions are controlled primarily by moisture, but also influenced by soil pH. Multiple regressions revealed little about plant-environment relationships not discovered by BDA. Before robust nonlinear methods are available, BDA, metric ordination with data stratification and nonmetric ordination are methods that can yield satisfactory results in exploratory plant-environment studies. BDA alone is an efficient, useful first approach where response patterns of species are initially unknown.Abbreviations BDA Binary Discriminant Analysis - DCA Detrended Correspondence Analysis     

Chromium,nickel, and arsenic determinations in human samples by thermal and epithermal neutron activation analyses

Both thermal and epithermal neutron activation analyses have been employed to determine chromium and nickel in lung tissue and arsenic in urine. Based on accuracy, precision, and detection limits, these techniques have been successfully used to analyze lung tissue from a deceased welder, who died, from cancer, and to paratake in an interlaboratory toxicological urine program.     

Diet, residential origin, and pathology at Machu Picchu, Peru

Pathological conditions in human skeletal remains provide a wealth of information about archaeological populations, but many are limited in their interpretive significance by their nonspecific etiologies. This study analyzes three common pathological conditions known to manifest in infancy and childhood in the skeletal population from Machu Picchu, Peru (N = 74) with published carbon, nitrogen, oxygen, strontium, and lead isotopic data (Turner et al.: J Archaeol Sci 36 (2009) 317–332; Turner et al.: Chungara: Revista de Antropología Chilena 42 (2010) 515–524) to distinguish early‐life diet from residential origins as significantly associated with pathologies among the site's inhabitants. Analyses of variance indicate highly significant variation between enamel δ¹⁸O values, which serve as a rough proxy of local environment, and both cribra orbitalia (CO) and porotic hyperostosis (PH), generally understood to be markers of anemia. Results tentatively suggest that individuals manifesting these lesions may have lived closer to the arid coasts; however, no significant variation was found in parameters of diet (enamel δ¹³C_carbonate, dentin δ¹³C_collagen, dentin δ¹⁵N) by either CO or PH, suggesting that the primary factors causing anemia may have been more significantly related to residential origin rather than diet. Linear enamel hypoplasia (LEH) frequency significantly varied by both dietary and residential parameters, supporting models of LEH formation from a synergy of dietary and environmental factors. These results support previous research on the etiology of PH in the Andes; they also represent a useful approach to refining site‐specific interpretations of pathological conditions in archaeological populations, and exploring etiological variation between populations. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.     

The association between content of the elements S,Cl, K,Fe, Cu,Zn and Br in normal and cirrhotic liver tissue from Danes and Greenlandic Inuit examined by dual hierarchical clustering analysis

ProjectMeta-analysis of previous studies evaluating associations between content of elements sulphur (S), chlorine (Cl), potassium (K), iron (Fe), copper (Cu), zinc (Zn) and bromine (Br) in normal and cirrhotic autopsy liver tissue samples.ProcedureNormal liver samples from 45 Greenlandic Inuit, median age 60 years and from 71 Danes, median age 61 years. Cirrhotic liver samples from 27 Danes, median age 71 years. Element content was measured using X-ray fluorescence spectrometry. Statistics: Dual hierarchical clustering analysis, creating a dual dendrogram, one clustering element contents according to calculated similarities, one clustering elements according to correlation coefficients between the element contents, both using Euclidian distance and Ward Procedure.ResultsOne dendrogram separated subjects in 7 clusters showing no differences in ethnicity, gender or age. The analysis discriminated between elements in normal and cirrhotic livers. The other dendrogram clustered elements in four clusters: sulphur and chlorine; copper and bromine; potassium and zinc; iron. There were significant correlations between the elements in normal liver samples: S was associated with Cl, K, Br and Zn; Cl with S and Br; K with S, Br and Zn; Cu with Br. Zn with S and K. Br with S, Cl, K and Cu. Fe did not show significant associations with any other element.ConclusionsIn contrast to simple statistical methods, which analyses content of elements separately one by one, dual hierarchical clustering analysis incorporates all elements at the same time and can be used to examine the linkage and interplay between multiple elements in tissue samples.     

BaSIQS - basic scale on insomnia complaints and quality of sleep: reliability,norms, validity,and accuracy studies,based on clinical and community samples

This research focused on the Basic Scale on Insomnia Symptoms and Quality of Sleep (BaSIQS), formerly validated in undergraduates using the Pittsburgh Sleep Quality Index (PSQI), and aimed to expand internal consistency analysis, examine thoroughly its validity, and determine its clinical accuracy. Considering objective and subjective measures, recruiting non-clinical and clinical samples, this research implemented a comprehensive approach to examine convergent and discriminant validity, confirmatory factor analyses, and the BaSIQS sensitivity and specificity. The BaSIQS was filled out along with the Insomnia Severity Index (ISI), questions on sleep-wake schedules, Composite Scale of Morningness (CSM) and Brief Symptom Inventory-18 (BSI-18) by 1198 adults, 18–64 years old, plus another 30 who wore actimeters, recruited in community settings. A clinical group of 30 chronic insomnia disorder patients also participated. Cronbach alpha coefficient was 0.80. A two-factor structure was confirmed. The association between BaSIQS and ISI was large, whereas actigraphy correlations were medium or small. Medium to non-significant correlations were found concerning conceptually different self-report measures. Comparing the clinic and control groups, the former showed poorer sleep, with a large effect size. Receiver operating characteristic analysis revealed an area under curve = 0.9, and an optimal cut-off score >15. In conclusion, results on reliability, validity, and accuracy provide support to the utility of the BaSIQS both in community and clinical settings, for research and practical purposes.     

The role of parsimony,outgroup analysis,and theory of evolution in phylogenetic systematics

It is argued that both the principle of parsimony and the theory of evolution, especially that of natural selection, are essential analytical tools in phylogenetic systematics, whereas the widely used outgroup analysis is completely useless and may even be misleading. In any systematic analysis, two types of patterns of characters and character states must be discriminated which are referred to as completely and incompletely resolved. In the former, all known species are presented in which the characters and their states studied occur, whereas in the latter this is not the case. Dependent on its structure, a pattern of characters and their states may be explained by either a unique or by various conflicting, equally most parsimonious hypotheses of relationships. The so-called permutation method is introduced which facilitates finding the conflicting, equally most parsimonious hypotheses of relationships. The utility of the principle of parsimony is limited by the uncertainty as to whether its application in systematics must refer to the minimum number of steps needed to explain a pattern of characterts and their states most parsimoniously or to the minimum number of evolutionary events assumed to have caused these steps. Although these numbers may differ, the former is usually preferred for simplicity. The types of outgroup analysis are shown to exist which are termed parsimony analysis based on test samples and cladistic type of outgroup analysis. Essentially, the former is used for analysing incompletely resolved patterns of characters and their states, the latter for analysing completely resolved ones. Both types are shown to be completely useless for rejecting even one of various conflicting, equally most parsimonious hypotheses of relationships. According to contemporary knowledge, this task can be accomplished only by employing the theory of evolution (including the theory of natural selection). But even then, many phylogenetic-systematic problems will remain unsolved. In such cases, arbitrary algorithms like those offered by phenetics can at best offer pseudosolutions to open problems. Despite its limitations, phylogenetic systematics is superior to any kind of aphylogenetic systematics (transformed cladistics included) in approaching a (not: the) “general reference system” of organisms.     

Pollen and phytolith evidence for rice cultivation during the Neolithic at Longqiuzhuang, eastern Jianghuai, China

Phytolith and pollen analyses were carried out at the archaeological site at Longqiuzhuang in Gaoyou, Jiangsu, southern China. The results indicate that the key morphological phytolith types associated with cultivated rice (Oryza) are common in the Neolithic cultural layers at this site. The evidence strongly suggests that cultivated rice (mainlyO. japonica) was grown locally during the Neolithic. The archaeopalynological record provides information about the impact of human activity and, in particular, farming on the natural vegetation. The evergreen and deciduous broad-leaved forest was substantially altered, and herbaceous taxa, including ruderals, expanded. Based on the results from the phytolith and pollen analyses, two distinct phases of human activity have been recognized, namely (1) phase A (7000-6300 B.P., i.e. early Neolithic) a warm and humid period when arable farming, including rice cultivation, was pursued but the variation in the size of the carbonized rice grains was low, and (2) phase B (6300-5500 B.P., late Neolithic age), a period of relatively cold and/or arid climate when cultivated rice was of major importance and was morphologically similar to present-day rice. Environment, and in particular climate change in the late Neolithic, were important factors affecting the development of rice as a cultivated crop. It was mainly during this period that artificial selection favoured the emergence of forms similar to those of today.     

Molecular Identification of Cryptosporidium spp., Enterocytozoon bieneusi,and Giardia duodenalis in Captive Pet Birds in Henan Province,Central China

Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis are common enteric pathogens that are capable of infecting humans and animals. Total of 1,005 fecal samples from captive pet birds were collected from seven locations in Henan Province, China. The results demonstrated that 9.9% (99/1,005) of the captive birds were infected with one of these three pathogens. Enterocytozoon bieneusi was the most prevalent species among the birds (45/1,005, 4.5%) followed by G. duodenalis (33/1,005, 3.3%) and Cryptosporidium spp. (21/1,005, 2.1%). Five Cryptosporidium species were identified, namely, C. baileyi (10), C. galli (5), C. meleagridis (4), C. andersoni (1), and C. parvum (1). Two known E. bieneusi genotypes were identified: Peru 6 (44) was identified in pigeons (34) and European turtle doves (10); whereas, the genotype PtEb I (1) was only identified in a pigeon. Only G. duodenalis assemblage E (33) was identified in some pet birds. To the best of our knowledge, this study is the first to undertake the molecular identification of G. duodenalis in birds in China. The identification of potentially zoonotic species/genotypes of the pathogens suggests that exposure to the excreta of these birds, either directly or via food and water, may pose a threat to human health.