Efficient implementation of the Metropolis-Hastings algorithm,with application to the Cormack–Jolly–Seber model

Judicious choice of candidate generating distributions improves efficiency of the Metropolis-Hastings algorithm. In Bayesian applications, it is sometimes possible to identify an approximation to the target posterior distribution; this approximate posterior distribution is a good choice for candidate generation. These observations are applied to analysis of the Cormack–Jolly–Seber model and its extensions.     

Analysis of the ph in Europe during the period 1986–1997

The annual averages (1986–1997) of pH are analysed for the most important European Monitoring and Evaluation Programme stations in Europe. The first objective is to discover the different temporal patterns and trends for the pH. To do this, a cluster analysis is developed. The trends are analysed by linear regression for the annual averages. In general, the pH shows an increasing trend significant at 0.05 level and the annual change ranging from +0.01 to +0.05 pH‐units per year for the different clusters obtained. The second objective is to examine the spatial variability of pH in precipitation through the use of principal component analysis. Six statistically significant modes of variability are obtained for the pH which represent the 84.5% of the total variance.     

Rethinking the study of human–wildlife coexistence

Although coexistence with wildlife is a key goal of conservation, little is known about it or how to study it. By coexistence we mean a sustainable though dynamic state in which humans and wildlife coadapt to sharing landscapes, where human interactions with wildlife are effectively governed to ensure wildlife populations persist in socially legitimate ways that ensure tolerable risk levels. Problems that arise from current conflict-oriented framing of human–wildlife interactions include reinforcing a human–nature dichotomy as fundamentally oppositional, suggesting coexistence requires the absence of conflict, and skewing research and management toward direct negative impacts over indirect impacts and positive aspects of living with wildlife. Human behavior toward wildlife is framed as rational calculus of costs and benefits, sidelining emotional and cultural dimensions of these interactions. Coexistence is less studied due to unfamiliarity with relevant methodologies, including qualitative methods, self-reflexivity and ethical rigor, and constraints on funding and time. These challenges are illustrated with examples from fieldwork in India and Africa. We recommend a basic approach to case studies aimed at expanding the scope of inquiries into human–wildlife relations beyond studies of rational behavior and quantification of costs and benefits of wildlife to humans.     

A note on the thyroid function of the pregnant females in the USA: data from NHANES 1999–2002 and 2007–2012

Thyroid dysfunction during pregnancy has been shown to be associated with adverse pregnancy outcomes. Consequently, this study was undertaken to assess the thyroid health of the pregnant females in the United States. Publically available data from National Health and Nutrition Examination Survey for the cycles 1999–2002 and 2007–2012 were analyzed for this purpose. Over 22% (SE: 5.7%) of the pregnant females based on the unweighted data in their first trimester had higher than the recommended levels of thyroid-stimulating hormone (TSH) or 2.5 mIU/L. Free triiodothyronine (FT3) and free thyroxine (FT4) levels decreased over pregnancy trimesters. Based on unweighted data, about 6% (SE: 2.6%) pregnant females were positive for thyroglobulin antibodies and 34.9% (SE: 5.2%) pregnant females were positive for thyroid peroxidase antibodies. Over 55% (SE: 3.5%) pregnant females based on the unweighted data were iodine deficient. As many as 41% (SE: 3%) first trimester pregnant females having TSH > 2.5 mIU/L is of concern. Future research should concentrate on developing educational and other materials that can advise pregnant females during their prenatal care and other appointments about the adverse effects of high TSH levels and what they can do to keep their TSH levels within the recommended levels.     

Problems of the coasts erosion in the North–Eastern Black Sea Region

The seacoasts protection does not stand standard solutions. Every part of a shore needs to be creatively approached and its hydrodynamic, lithodynamic, geological, geomorphological and other peculiarities must be thoroughly studied for each particular situation. It takes a complex scientific approach considering not only local features, but also the reaction of the whole lithodynamic system in limits of which the coast protective activity is planned with consideration of calculated hydrodynamic parameters (waves, sea level, etc.).     

Study on the marine agarolytic bacterium–infusorium association

Physiological and biochemical properties of a marine agarolytic association of the bacterium Cytophaga diffluens and the infusorium Uronema marinum were investigated. The agarase activity of the association was shown to be higher than that of the pure bacterial culture at all growth stages under identical conditions. Maximum agarase activity of the association, and of the pure bacterial culture, was observed in a medium containing a small amount of organic nitrogen (0.1% yeast extract). Received: 12 October 1998 / Accepted: 11 June 1999     

A fair comparison between the spatial scan and the Besag–Newell Disease clustering tests

Routine surveillance of a large geographic region for clusters of adverse health events, particularly cancers, often involves small area health data, possibly controlling for exposure information. Many different methods have been proposed to test for the presence of geographical clusters. Two of the most popular methods are the spatial scan method proposed by Kulldorff and that using a fixed number of cases within scanning circles proposed by Besag and Newell. Although the second test is very popular, it has some difficulties. While the scan test controls for the multiple testing problem, the Besag and Newell test does not. Additionally, the latter method requires the setting of several tuning parameters whose values affect the test performance and are subjectively chosen by the user. This creates a difficulty to make a fair comparison between the two methods and it explains why there have been few formal studies evaluating their relative performances. In this paper, we modify the Besag and Newell test allowing for the control of the error type I probability and compare its power with respect to that of the spatial scan test. We used data sets from a publicly available simulated benchmark. We found that the two methods have similar results, except for clusters located in sparsely populated regions, where the spatial scan method presented a better performance.     

Body and resource size at the land–sea interface

Body size in animals varies with many parameters, amongst them taxonomic affiliation, lifestyle and ambient environment oxygen levels. Size has considerable implication to possibilities for animals; for example, parasites need to be small and top predators large. Body size and resource requirements (shell size) were investigated across the land–sea interface in hermit crabs (Crustacea: Malacostraca: Decapoda) and snails (Mollusca: Gastropoda: Prosobranchia). These are two of the few taxa to occur in the sea, on the shore and on land as residents. Both taxa are also appropriate for such an analysis as they are abundant, speciose, cohabit the same environments and are linked—gastropod shells are a critical resource to hermit crabs. Both the maximum and mean sizes of hermit crab species showed parabolic relationships with shore height, decreasing from the sublittoral and supralittoral to the eulittoral. Average maximum size of gastropods exhibited a similar intertidal minimum although variability was high. It is suggested that this pattern is robust: not only did two distantly related taxa show the same pattern, but neither region nor site contributed significantly to total variability. The mass of resources (gastropod shells) used by hermit crabs, however, showed a converse pattern. The smallest shells (relative to hermit crab body size) were used in the sublittoral and supralittoral. Response to environmental stress and predation pressure are offered as two alternate theories to explain the observed body dwarfism and resource gigantism in the intertidal zone.Communicated by J.P. Thorpe, Port Erin     

An assessment of air pollution episodes in the urban area of athensfor the period 1984–1994

Air pollution episodes in the greater Athens area for the period 1984–1994 were examined to assess the type, frequency and repetitivity of air pollution in the examined area. The assessment depends strongly on the definition of an air pollution episode (APE), namely if it is the narrow or broad one. Results from the statistical analysis of the data record‐on the basis of the broad definition of the APE‐show a declining trend in the number of APEs especially for non‐photochemical species, a sharp increase of APEs from 1987 to 1993 due to high ozone levels and a similarly sharp decrease thereafter, and a decreasing trend of nitrogen dioxide episodes from the year 1992 thereon. Interannual examination of APEs shows that they occur in higher numbers during the period November to January and in the period May to July. Finally an examination of the number of days for which urgent‐short term‐measures were taken to reduce high levels of atmospheric pollution, shows a decreasing trend from 1989, with the exception of 1994 where the sharp increase in the number of days is due to the application of the urgent measures at a precautionary mode, i.e. when pollution loads exceed the alert levels, air pollution increases in rapid rates and meteorological conditions are supportive for an enhanced APE.     

Mediating male–male interactions: the role of the UV blue crest coloration in blue tits

Badges of status, usually color patches, are hypothesized to serve as important signals within natural populations by communicating an individual’s fighting ability or aggressiveness before an interaction ever takes place. These signals, which may evolve via sexual and/or social selection, mediate intra-specific competition by influencing the outcome or escalation of contests between individuals. The last 10 years saw the rise of interest in the role of ultraviolet (UV)-based coloration in intra-sexual communication. However, the rare experimental studies that tested this hypothesis found opposite results, which may originate from the different methodological procedures used to assess the badge of status theory. We present here the results of an experiment testing whether male blue tits (Cyanistes caeruleus) respond differently to unfamiliar conspecifics presenting contrasted UV crest coloration. In an aviary, we simultaneously presented two caged blue tits with enhanced (UV+) or reduced (UV−) crest coloration to a focal bird. We found that focal males acted more aggressively towards the UV− males than UV+ males. In addition, focal males fed more often close to males that were similar in brightness or duller than themselves. We conclude that, in blue tits, UV blue crest coloration affects both social and aggressive responses towards unfamiliar individuals, and thus it has some properties of a badge of status.     

Mitochondrial DNA evidence for rapid colonisation of the Indo–West Pacific by the mudcrab Scylla serrata

Scylla serrata (Forskål, 1775) is widely distributed throughout mangrove habitats of the Indo-West Pacific (IWP) coastal waters. This study investigated the phylogeographic distribution of S. serrata mitochondrial DNA haplotypes sampled throughout the species range. Adults were sampled from three west Indian Ocean locations (N?=?21), five west Pacific sites (N?=?28) and three sites from northern and eastern Australia (N?=?76). Temperature-gradient gel-electrophoresis and sequencing of 549 base pairs of a mtDNA gene (cytochrome oxidase 1) identified 18 distinct haplotypes. Haplotypes cluster into two clades separated by ?2% sequence-divergence. One clade is widespread throughout the IWP, the other is strictly confined to northern Australia. Genealogical assessment of sequenced haplotypes suggests that the historical spread of S. serrata throughout the IWP has occurred rapidly and recently (<1 million years before present) from a west Pacific origin. The fact that many locations contain a single unique haplotype suggests limited contemporary gene flow between trans-oceanic sites, and that recent historical episodes of population founding and retraction have both determined and affected the current distribution of S. serrata populations. Contrary to that reported for other widespread species of IWP taxa, there is no pattern of regional separation of Indian from Pacific Ocean populations. However, results do suggest a vicariant separation of northern Australian crabs prior to the IWP radiation. We speculate that this separation may have resulted in the formation of a new species of Scylla.     

Mesoscale circulation in the surface layer off the southern and western Sardinia Island in 2000–2002

Five oceanographic cruises were organized in the Sardinian Sea and Channel in May 2000, March 2001, September 2001, May 2002, and November 2002 to study the characterization of the water masses, Atlantic Water (AW) and Winter Intermediate Water (WIW), and their mesoscale variability. In the Sardinian Channel, an Algerian anticyclonic Eddy (AE) was observed in May 2000, along the Tunisian coast. This induced a greater minimum salinity in a wider and deeper layer than in November 2002, when no AE was observed. Some WIW was observed below it; nevertheless, no link could be established between AEs and WIW occurrences. In the Sardinian Sea, two AEs were observed during spring 2000, and a further two during spring 2002. One AE strongly influenced shelf circulation, in contrast to the other three that were off the continental slope. In the same area, during the end of September 2001, a vertical salinity inversion occurred in the first 30–50 m of depth over the whole sampling field, and a W–NW wind induced a coastal upwelling over the western Sardinian coast (south of 41° N). This upwelling increased the salinity from ～20 to 30 m below the surface to the surface and, thereby led to a lower salinity close to the coast than offshore. This was in contrast to a classical upwelling. Consequently, in the Sardinian Sea, the general circulation, mainly driven by AEs, can meet the coastal wind-driven circulation.     

Effects of the spatial pattern of disturbance on the patch-occupancy dynamics of juniper–pine open woodland

Typically, studies of the disturbance effect on metapopulation dynamics are limited to understanding the effect of habitat loss although, recently, the spatial pattern of the disturbance has been shown to influence dynamics. In this study, we used a stochastic patch-dynamic model to investigate the effects of spatial disturbance patterns on the persistence of an open woodland community of Juniperus spp. and Pinus spp. First, we estimated patch-occupancy dynamics by using the coefficients that best predicted the occupancy observed in 1998 based on occupancy data from 1957. Next, we evaluated the effects of the rate and pattern of the disturbance on the extinction probability. In modeling the disturbance, we considered (1) the degree of disturbance produced by scenarios of complete destruction or degradation (with the potential for recolonization), (2) the overall rate of disturbance, and (3) the spatial autocorrelation of habitat destruction. Twenty 40-year simulations predicted a 25% increase in the number of patches, and when 50% of the habitat was removed, the impact was more pronounced after complete destruction than it was after degradation of the area. Predictions based on scenarios of complete destruction, including random, contiguous, Brownian, and autoregressive noise, demonstrated that the impact of disturbance depends upon the spatial structure of the disturbance regimen. The autocorrelated structure of the disturbance regimen had the greatest impact on patch persistence. Patch-occupancy was higher after 20 40-year simulations when habitat loss was randomly distributed than when it followed an autocorrelated patch destruction, which was simulated using autoregressive noise to produce 50% habitat destruction. In addition, while habitat loss was negatively linearly correlated with patch persistence when habitat destruction was randomly distributed, a dramatic transition shift occurred when habitat destruction was simulated following an autoregressive spatial distribution after a certain threshold of habitat destruction (40% of the actual open woodland habitat). Our study suggests that the spatial patterns of the disturbance should be considered when predicting the consequences of fragmentation and improving management strategies.     

The As-Contaminated Elqui River Basin: a Long Lasting Perspective (1975–1995) Covering the Initiation and Development of Au–Cu–As Mining in the High Andes of Northern Chile

The Elqui watershed (northern Chile) constitutes a highly contaminated river system, with arsenic exceeding by up to three orders of magnitude the average for river waters. There are three main reasons that explain this contamination: (1) the regional geology and hydrothermal (mineralizing) processes that developed in this realm during Miocene time; (2) the later unroofing–erosion–oxidation–leaching of As–Cu rich sulfide ores, a process that have been taking place for at least 10,000 years; and last but not least (3) mining activities at the high-altitude (>4000 m above sea level) Au–Cu–As El Indio mine, from the late 1970s onwards. The El Indio mineral deposit hosted large veins of massive sulfides, including the important presence of enargite (Cu₃AsS₄). The continuous natural erosion of these veins and their host rocks (also rich in As and Cu) during Holocene time, led to important and widespread metal dispersion along the river system. During the studied pre mining period (1975–1977), the high altitude river Toro waters already showed very large As concentrations (0.36–0.52 mg l⁻¹). The initiation of full scale mining at El Indio (1980 onwards) led to an increase of these values, reaching a concentration of 1.51 mg l⁻¹ As in 1995. During the same year other rivers of the watershed reached peak As concentrations of 0.33 (Turbio) and 0.11 mg l⁻¹ (Elqui). These figures largely exceed the USEPA regulations for drinking water (0.01 mg l⁻¹ As), and about 10% of the total As data from the river Elqui (and 70% from the river Turbio) are above the maximum level allowed by the Chilean law for irrigation water (0.1 mg l⁻¹ As).     

Cytotoxic study in the treatment of tetracycline by using magnetic Fe3O4–PAMAM–antibody complexes

Environmental Chemistry Letters - Antibiotics are widely used as drugs to treat&nbsp;human and animal&nbsp;diseases. However, the widespread use of antibiotics has induced environmental...     

Acid–base regulation in the Dungeness crab (Metacarcinus magister)

Homeostatic regulation allows organisms to secure basic physiological processes in a varying environment. To counteract fluctuations in ambient carbonate system speciation due to elevated seawater pCO₂ (hypercapnia), many aquatic crustaceans excrete/accumulate acid–base equivalents through their gills; however, not much is known about the role of ammonia in this response. The present study investigated the effects of hypercapnia on acid–base and ammonia regulation in the Dungeness crab, Metacarcinus magister on the whole animal and isolated gill levels. Hemolymph pCO₂ and [HCO₃ ^?] increased in M. magister acclimated to elevated pCO₂ (330 Pa), while pH remained stable. Additionally, hemolymph [Na⁺], [Ca²⁺], and [SO₄ ^2?] were significantly increased. When challenged with varying pH during gill perfusion, the pH of the artificial hemolymph remained relatively unchanged. Overall, ammonia production and excretion, as well as oxygen consumption, were reduced in crabs acclimated to elevated pCO₂, demonstrating that either (amino acid) oxidation is reduced in response to this particular stress, or nitrogenous wastes are excreted in an alternative form.     

Meso-scale hydrodynamic and reproductive asynchrony affects the source–sink metapopulation structure of the coastal polychaete Pectinaria koreni

The polychaete Pectinaria koreni exhibits a complex life cycle characterized by non-overlapping generations and widespread larval dispersal. To explore how “local” metapopulation genetic structure varies spatially and temporally during population turnover, we combined observations on demography, larval dispersal through hydrodynamic modelling and population genetics of successive age cohorts in the Baie de Seine (eastern English Channel, France). Mature adults (March), newly settled (July) and later-stage juveniles (September) were sampled in 2003 on the edge and in the main demes of the metapopulation. Demes displayed an asynchronous dynamics due to variations in habitat quality affecting reproductive timing (e.g. three distinct spawning events observed) and in local larval supply linked to temporal fluctuations of hydrodynamism. Two-source populations were identified among dense areas with the greatest larval retention and self-recruitment rates: one with a single recruitment event, stable temporal genetic variation and a strong spatial genetic re-homogenization during turnover, and the other with two recruitment events and significant allele frequency changes over time. Sink habitats displayed single recruitment event and experienced strong inter-generational (juveniles vs adults) genetic changes due to genetic drift associated with strong winter mortalities. Altogether, results suggested that adult spawning asynchrony and sweepstakes reproductive success, together with genetic drift, played a greater role than hydrodynamics itself in determining effective recruitment rates at some sites and generating genetic patchiness.     

Queen–worker–brood coadaptation rather than conflict may drive colony resource allocation in the ant Temnothorax curvispinosus

Conflicts of interest among genetically heterogeneous nestmates in social insect colonies have been emphasized as driving colony resource allocation. However, potential intracolonial conflicts may not actually be realized so that resource allocation could be shaped primarily by among-colony selection that maximizes colony productivity. To elucidate the causal basis of patterns of resource allocation, I experimentally manipulated three fundamental aspects of colony social structure (relatedness among workers, relatedness among larvae, and queen presence) in the ant Temnothorax curvispinosus and measured effects on colony resource allocation to new workers, gynes, and males. The experimental manipulations had widespread effects on patterns of colony resource allocation, but there was little evidence for realized conflicts over the sex ratio and caste ratio. Decreasing nestmate relatedness caused decreased colony productivity, suggesting that more closely related nestmates have more favorably interacting phenotypes. Together, these results suggest that resource allocation in T. curvispinosus may be shaped more by among-colony selection than intracolonial conflict, leading to queen–worker–brood coadaptation.     

Pollution indices as useful tools for the comprehensive evaluation of the degree of soil contamination–A review

The paper provides a complex, critical assessment of heavy metal soil pollution using different indices. Pollution indices are widely considered a useful tool for the comprehensive evaluation of the degree of contamination. Moreover, they can have a great importance in the assessment of soil quality and the prediction of future ecosystem sustainability, especially in the case of farmlands. Eighteen indices previously described by several authors (I_geo, PI, EF, C_f, PI_sum, PI_Nemerow, PLI, PI_ave, PI_Vector, PIN, MEC, CSI, MERMQ, C_deg, RI, mCd and ExF) as well as the newly published Biogeochemical Index (BGI) were compared. The content, as determined by other authors, of the most widely investigated heavy metals (Cd, Pb and Zn) in farmland, forest and urban soils was used as a database for the calculation of all of the presented indices, and this shows, based on statistical methods, the similarities and differences between them. The indices were initially divided into two groups: individual and complex. In order to achieve a more precise classification, our study attempted to further split indices based on their purpose and method of calculation. The strengths and weaknesses of each index were assessed; in addition, a comprehensive method for pollution index choice is presented, in order to best interpret pollution in different soils (farmland, forest and urban). This critical review also contains an evaluation of various geochemical backgrounds (GBs) used in heavy metal soil pollution assessments. The authors propose a comprehensive method in order to assess soil quality, based on the application of local and reference GB.