A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

Comparative exergy analysis of direct alcohol fuel cells using fuel mixtures

Within the last years there has been increasing interest in direct liquid fuel cells as power sources for portable devices and, in the future, power plants for electric vehicles and other transport media as ships will join those applications. Methanol is considerably more convenient and easy to use than gaseous hydrogen and a considerable work is devoted to the development of direct methanol fuel cells. But ethanol has much lower toxicity and from an ecological viewpoint ethanol is exceptional among all other types of fuel as is the only chemical fuel in renewable supply. The aim of this study is to investigate the possibility of using direct alcohol fuel cells fed with alcohol mixtures. For this purpose, a comparative exergy analysis of a direct alcohol fuel cell fed with alcohol mixtures against the same fuel cell fed with single alcohols is performed. The exergetic efficiency and the exergy loss and destruction are calculated and compared in each case. When alcohol mixtures are fed to the fuel cell, the contribution of each fuel to the fuel cell performance is weighted attending to their relative proportion in the aqueous solution. The optimum alcohol composition for methanol/ethanol mixtures has been determined.

Space-time analysis of the urban-rural grafient in the metropolitan area of Madrid and ist surroundings -Guadalajara and Toledo.

According to UN provisions in the period from 2007 to 2050 world population will grow up to 9200 million people. In fact, for the first time in history, in the year 2008 world urban population became higher than rural population. The increase of urban areas and their transport infrastructures has influenced agricultural land use due to their irreversible change, especially when they remain as periurban vacant land, losing their character and identity. In the Europe of the nineties, the traditional urban-rural gradient, characterized by a neat contact between both land types, has become so complex that it has change to a gradient in which it is difficult to separate urban and rural land uses. [Antrop 2004]. A literature review has been made on methodologies used for the urban-rural gradient analysis. One of these methodologies was selected that integrates ecological characterization based on the use of spatial metrics and geographical characterization based on spatial components. Cartographical sources used were Corine Land Cover at 1: 100000 scale and the Spanish Land Use Information System at 1:25000 scale. Urban-rural gradient paradigm is an analysis methodology, coming from landscape ecology, which enables to investigate how urbanization provokes changes in ecological patterns and processes into landscape. [Hahs and McDonnell 2006].The present research adapt this methodology to study the urban-rural gradient in the outskirts of Madrid, Toledo and Guadalajara. Both scales (1:25000 and 1:100000) were simultaneously used to reach the next objectives: 1) Analysis of landscape pattern dynamics in relation to distance to the town centre and major infrastructures. 2) Analysis of landscape pattern dynamics in the fringe of protected areas. The paper presents a new approach to the urban-rural relationship which allows better planning and management of urban áreas.

Comparative analysis of passenger transport sustainability in European cities

Sustainable development in its three dimensions – economic, social and environmental – has become a major concern on an international scale. The problem is global, but must be solved locally. Most of the world’s population lives in cities that act as centres of economic growth and productivity, but which – if they develop in the wrong direction – can cause social inequalities, or irreversibly harm the environment. Urban transport causes a number of negative impacts that can affect sustainability targets. The objective of this study is to propose an analysis of sustainability of urban passenger transport systems based on available indicators in most cities. This will serve to benchmark the practices of different cities and manage their transport systems. This work involves the creation of composite indicators (CI) to measure the sustainability of urban passenger transport systems. The methodology is applied to 23 European cities. The indicators are based on a benchmarking approach, and the evaluation of each aspect in each case therefore depends on the performance of the whole sample. The CI enabled us to identify which characteristics have the greatest influence on the sustainability of a city’s transport system, and to establish transport policies that could potentially improve its shortcomings. Finally, the cities are clustered according to the values obtained from the CIs, and thus according to the weaknesses and strengths of their transport systems.

Effects of coaches' timeouts on basketball teams' offensive and defensive performances according to momentary differences in score and game period.

The aim of the present study was to assess the effects of game timeouts on basketball teams? offensive and defensive performances according to momentary differences in score and game period. The sample consisted of 144 timeouts registered during 18 basketball games randomly selected from the 2007 European Basketball Championship (Spain). For each timeout, five ball possessions were registered before (n?493) and after the timeout (n?475). The offensive and defensive efficiencies were registered across the first 35 min and last 5 min of games. A k-means cluster analysis classified the timeouts according to momentary score status as follows: losing ( ?10 to ?3 points), balanced ( ?2 to 3 points), and winning (4 to 10 points). Repeated-measures analysis of variance identified statistically significant main effects between pre and post timeout offensive and defensive values. Chi-square analysis of game period identified a higher percentage of timeouts called during the last 5 min of a game compared with the first 35 min (64.999.1% vs. 35.1910.3%; x ?5.4, PB0.05). Results showed higher post timeout offensive and defensive performances. No other effect or interaction was found for defensive performances. Offensive performances were better in the last 5 min of games, with the least differences when in balanced situations and greater differences when in winning situations. Results also showed one interaction between timeouts and momentary differences in score, with increased values when in losing and balanced situations but decreased values when in winning situations. Overall, the results suggest that coaches should examine offensive and defensive performances according to game period and differences in score when considering whether to call a timeout.

Character displacement in some Cnemidophorus lizards revisited: A phylogenetic analysis

Ecological studies have demonstrated the role of competition in structuring communities; however, the importance of competition as a vehicle for evolution by natural selection and speciation remains unresolved. Study systems of insular faunas have provided several well known cases where ecological character displacement, coevolution of competitors leading to increased morphological separation, is thought to have occurred (e.g., anoline lizards and geospizine finches). Whiptail lizards (genus Cnemidophorus) from the islands of the Sea of Cortez and the surrounding mainland demonstrate a biogeographic pattern of morphological variation suggestive of character displacement. Two species of Cnemidophorus occur on the Baja peninsula, one relatively large (Cnemidophorus tigris) and one smaller (Cnemidophorus hyperythrus). Oceanic islands in the Sea of Cortez contain only single species, five of six having sizes intermediate to both species found on the Baja peninsula. On mainland Mexico C. hyperythrus is absent, whereas C. tigris is the smaller species in whiptail guilds. Here we construct a phylogeny using nucleotide sequences of the cytochrome b gene to infer the evolutionary history of body size change and historical patterns of colonization in the Cnemidophorus system. The phylogenetic analysis indicates that (i) oceanic islands have been founded at least five times from mainland sources by relatives of either C. tigris or C. hyperythrus, (ii) there have been two separate instances of character relaxation on oceanic islands for C. tigris, and (iii) there has been colonization of the oceanic island Cerralvo with retention of ancestral size for Cnemidophorus ceralbensis, a relative of C. hyperythrus. Finally, the phylogenetic analysis reveals potential cryptic species within mainland populations of C. tigris.

Ecological factors rather than temporal factors dominate the evolution of vesicular stomatitis virus

Vesicular stomatitis New Jersey virus (VSV-NJ) is a rhabdovirus that causes economically important disease in cattle and other domestic animals in endemic areas from southeastern United States to northern South America. Its negatively stranded RNA genome is capable of undergoing rapid evolution, which allows phylogenetic analysis and molecular epidemiology studies to be performed. Previous epidemiological studies in Costa Rica showed the existence of at least two distinct ecological zones of high VSV-NJ activity, one located in the highlands (premontane tropical moist forest) and the other in the lowlands (tropical dry forest). We wanted to test the hypothesis that the viruses circulating in these ecological zones were genetically distinct. For this purpose, we sequenced the hypervariable region of the phosphoprotein gene for 50 VSV-NJ isolates from these areas. Phylogenetic analysis showed that viruses from each ecological zone had distinct genotypes. These genotypes were maintained in each area for periods of up to 8 years. This evolutionary pattern of VSV-NJ suggests an adaptation to ecological factors that could exert selective pressure on the virus. As previous data indicated an absence of virus adaptation to factors related to the bovine host (including immunological pressure), it appears that VSV genetic divergence represents positive selection to adapt to specific vectors and/or reservoirs at each ecological zone.

Cancer mortality inequalities in urban areas: a Bayesian small area analysis in Spanish cities

Background: Intra-urban inequalities in mortality have been infrequently analysed in European contexts. The aim of the present study was to analyse patterns of cancer mortality and their relationship with socioeconomic deprivation in small areas in 11 Spanish cities. Methods: It is a cross-sectional ecological design using mortality data (years 1996-2003). Units of analysis were the census tracts. A deprivation index was calculated for each census tract. In order to control the variability in estimating the risk of dying we used Bayesian models. We present the RR of the census tract with the highest deprivation vs. the census tract with the lowest deprivation. Results: In the case of men, socioeconomic inequalities are observed in total cancer mortality in all cities, except in Castellon, Cordoba and Vigo, while Barcelona (RR = 1.53 95%CI 1.42-1.67), Madrid (RR = 1.57 95%CI 1.49-1.65) and Seville (RR = 1.53 95%CI 1.36-1.74) present the greatest inequalities. In general Barcelona and Madrid, present inequalities for most types of cancer. Among women for total cancer mortality, inequalities have only been found in Barcelona and Zaragoza. The excess number of cancer deaths due to socioeconomic deprivation was 16,413 for men and 1,142 for women. Conclusion: This study has analysed inequalities in cancer mortality in small areas of cities in Spain, not only relating this mortality with socioeconomic deprivation, but also calculating the excess mortality which may be attributed to such deprivation. This knowledge is particularly useful to determine which geographical areas in each city need intersectorial policies in order to promote a healthy environment.

Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

No effect of unemployment on intimate partner-related femicide during the financial crisis: a longitudinal ecological study in Spain

Background: Spain’s financial crisis has been characterized by an increase in unemployment. This increase could have produced an increase in deaths of women due to intimate partner-related femicides (IPF). This study aims to determine whether the increase in unemployment among both sexes in different regions in Spain is related to an increase in the rates of IPF during the current financial crisis period. Methods: An ecological longitudinal study was carried out in Spain’s 17 regions. Two study periods were defined: pre-crisis period (2005–2007) and crisis period (2008–2013). IPF rates adjusted by age and unemployment rates for men and women were calculated. We fitted multilevel linear regression models in which observations at level 1 were nested within regions according to a repeated measurements design. Results: Rates of unemployment have progressively increased in Spain, rising above 20 % from 2008 to 2013 in some regions. IPF rates decreased in some regions during crisis period with respect to pre-crisis period. The multilevel analysis does not support the existence of a significant relationship between the increase in unemployment in men and women and the decrease in IPF since 2008. Discussion: The increase in unemployment in men and women in Spain does not appear to have an effect on IPF. The results of the multilevel analysis discard the hypothesis that the increase in the rates of unemployment in women and men are related to an increase in IPF rates. Conclusions: The decline in IPF since 2008 might be interpreted as the result of exposure to other factors such as the lower frequency of divorces in recent years or the medium term effects of the integral protection measures of the law on gender violence that began in 2005.

Main ecological gradients and landscape matrix affect wild rabbit Oryctolagus cuniculus (Linnaeus, 1758) (Mammalia: Leporidae) abundance in a coastal region (South-East Spain)

Landscape analysis with transects, in the Marina Baja area (province of Alicante, Spain), has contributed to establish the influence of different landscape matrices and some environmental gradients on wild rabbit Oryctolagus cuniculus (Linnaeus, 1758) (Mammalia: Leporidae) abundance (kilometric abundance index, KAI). Transects (n = 396) were developed to estimate the abundance of this species in the study area from 2006 to 2008.Our analysis shows that rabbits have preferences for a specific land use matrix (irrigated: KAI = 3.47 ± 1.14 rabbits/km). They prefer the coastal area (KAI = 3.82 ± 1.71 rabbits/km), which coincides with thermo-Mediterranean (a bioclimatic belt with a tempered winter and a hot and dry summer with high human density), as opposed to areas in the interior (continental climate with lower human occupation). Their preference for the southern area of the region was also noted (KAI = 8.22 ± 3.90 rabbits/km), which coincides with the upper semi-arid area, as opposed to the northern and intermediate areas (the north of the region coinciding with the upper dry and the intermediate area with the lower dry). On the other hand, we found that the number of rabbits increased during the 3-year study period, with the highest abundance (KAI = 2.71 ± 1.30 rabbits/km) inMay. Thus, this study will enable more precise knowledge of the ecological factors (habitat variables) that intervene in the distribution of wild rabbit populations in a poorly studied area.