CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.

BACKGROUND: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. RESULTS: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. CONCLUSION: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

Adapting global conservation strategies to climate change at the European scale: the otter as a flagship species

Climate change has created the need for new strategies in conservation planning that account for the dynamics of factors threatening endangered species. Here we assessed climate change threat to the European otter, a flagship species for freshwater ecosystems, considering how current conservation areas will perform in preserving the species in a climatically changed future. We used an ensemble forecasting approach considering six modelling techniques applied to eleven subsets of otter occurrences across Europe. We performed a pseudo-independent and an internal evaluation of predictions. Future projections of species distribution were made considering the A2 and B2 scenarios for 2080 across three climate models: CCCMA-CGCM2, CSIRO-MK2 and HCCPR HAD-CM3. The current and the predicted otter distributions were used to identify priority areas for the conservation of the species, and overlapped to existing network of protected areas. Our projections show that climate change may profoundly reshuffle the otter's potential distribution in Europe, with important differences between the two scenarios we considered. Overall, the priority areas for conservation of the otter in Europe appear to be unevenly covered by the existing network of protected areas, with the current conservation efforts being insufficient in most cases. For a better conservation, the existing protected areas should be integrated within a more general conservation and management strategy incorporating climate change projections. Due to the important role that the otter plays for freshwater habitats, our study further highlights the potential sensitivity of freshwater habitats in Europe to climate change.

Adaptation en français et en allemand d'une échelle de pression des pairs pour jeunes adultes : le Peer Pressure Inventory [Adaptation of a peer pressure scale in French and German: the Peer Pressure Inventory].

BACKGROUND: Peer pressure is regarded as an important determinant of substance use, sexual behavior and juvenile delinquency. However, few peer pressure scales are validated, especially in French or German. Little is known about the factor structure of such scales or the kind of scale needed: some scales takes into account both peer pressure to do and peer pressure not to do, while others consider only peer pressure to do. The aim of the present study was to adapt French and German versions of the Peer Pressure Inventory, which is one of the most widely used scales in this field. We considered its factor structure and concurrent validity. METHODS: Five thousand eight hundred and sixty-seven young Swiss men filled in a questionnaire on peer pressure, substance use, and other variables (conformity, involvement) in a cohort study. RESULTS: We identified a four-factor structure, with the three factors of the initial Peer Pressure Inventory (involvement, conformity, misconduct) and adding a new one (relationship with girls). A non-valued scale (from no peer pressure to peer pressure to do only) showed stronger psychometric qualities than a valued scale (from peer pressure not to do to peer pressure to do). Concurrent validity was also good. Each behavior or attitude was significantly associated with peer pressure. CONCLUSION: Peer pressure seems to be a multidimensional concept. In this study, peer pressure to do showed the strongest influence on participants. Indeed, peer pressure not to do did not add anything useful. Only peer pressure to do affected young Swiss men's behaviors and attitudes and was reliable.

Flow-R, a model for susceptibility mapping of debris flows and other gravitational hazards at a regional scale

The development of susceptibility maps for debris flows is of primary importance due to population pressure in hazardous zones. However, hazard assessment by processbased modelling at a regional scale is difficult due to the complex nature of the phenomenon, the variability of local controlling factors, and the uncertainty in modelling parameters. A regional assessment must consider a simplified approach that is not highly parameter dependant and that can provide zonation with minimum data requirements. A distributed empirical model has thus been developed for regional susceptibility assessments using essentially a digital elevation model (DEM). The model is called Flow-R for Flow path assessment of gravitational hazards at a Regional scale (available free of charge under www.flow-r.org) and has been successfully applied to different case studies in various countries with variable data quality. It provides a substantial basis for a preliminary susceptibility assessment at a regional scale. The model was also found relevant to assess other natural hazards such as rockfall, snow avalanches and floods. The model allows for automatic source area delineation, given user criteria, and for the assessment of the propagation extent based on various spreading algorithms and simple frictional laws.We developed a new spreading algorithm, an improved version of Holmgren's direction algorithm, that is less sensitive to small variations of the DEM and that is avoiding over-channelization, and so produces more realistic extents. The choices of the datasets and the algorithms are open to the user, which makes it compliant for various applications and dataset availability. Amongst the possible datasets, the DEM is the only one that is really needed for both the source area delineation and the propagation assessment; its quality is of major importance for the results accuracy. We consider a 10m DEM resolution as a good compromise between processing time and quality of results. However, valuable results have still been obtained on the basis of lower quality DEMs with 25m resolution.

Clinical Learning Environment and Supervision. Development and Validation of the CLES Evaluation Scale

The purpose of the study is: (1) to describe how nursing students' experienced their clinical learning environment and the supervision given by staff nurses working in hospital settings; and (2) to develop and test an evaluation scale of Clinical Learning Environment and Supervision (CLES). The study has been carried out in different phases. The pilot study (n=163) explored the association between the characteristics of a ward and its evaluation as a learning environment by students. The second version of research instrument (which was developed by the results of this pilot study) were tested by an expert panel (n=9 nurse teachers) and test-retest group formed by student nurses (n=38). After this evaluative phase, the CLES was formed as the basic research instrument for this study and it was tested with the Finnish main sample (n=416). In this phase, a concurrent validity instrument (Dunn & Burnett 1995) was used to confirm the validation process of CLES. The international comparative study was made by comparing the Finnish main sample with a British sample (n=142). The international comparative study was necessary for two reasons. In the instrument developing process, there is a need to test the new instrument in some other nursing culture. Other reason for comparative international study is the reflecting the impact of open employment markets in the European Union (EU) on the need to evaluate and to integrate EU health care educational systems. The results showed that the individualised supervision system is the most used supervision model and the supervisory relationship with personal mentor is the most meaningful single element of supervision evaluated by nursing students. The ward atmosphere and the management style of ward manager are the most important environmental factors of the clinical ward. The study integrates two theoretical elements - learning environment and supervision - in developing a preliminary theoretical model. The comparative international study showed that, Finnish students were more satisfied and evaluated their clinical placements and supervision with higher scores than students in the United Kingdom (UK). The difference between groups was statistical highly significant (p= 0.000). In the UK, clinical placements were longer but students met their nurse teachers less frequently than students in Finland. Arrangements for supervision were similar. This research process has produced the evaluation scale (CLES), which can be used in research and quality assessments of clinical learning environment and supervision in Finland and in the UK. CLES consists of 27 items and it is sub-divided into five sub-dimensions. Cronbach's alpha coefficient varied from high 0.94 to marginal 0.73. CLES is a compact evaluation scale and user-friendliness makes it suitable for continuing evaluation.

Ability for self-care and its association with sociodemographic factors of people with spinal cord injury

This study aimed to verify the association between self-care ability and sociodemographic factors of people with spinal cord injury (SCI). It was a cross-sectional study, conducted in 2012, in all 58 Basic Health Units of Natal/RN, Brazil. Seventy-three subjects completed a sociodemographic form andSelf-Care Agency Scale. Statistical analyses were performed using SPSS,including Cronbach’s Alpha, Chi-square, Fisher’s and contingency coefficient tests. The Cronbach's alpha was 0.788. The result verified that sex (p = 0.028), religion (p <0.001), education (p = 0.046), current age (p = 0.027), SCI time (p = 0.020) and the SCI type (p = 0.012) were variables associated with self-care ability of the subjects. It was concluded that sociodemographic factors may interfere with the self-care ability of persons with SCI, and nurses should consider this aspect during the execution of the nursing process.

Burnout and associated factors in employees of a Swiss teaching hospital

Background Working in a teaching hospital is a highly stressful occupation, which can lead to burnout. The consequences of burnout in health professionals can be very serious, both for themselves and patients. The aim of this cross-sectional study was to assess the extent of burnout and associated factors in hospital employees. Methods In the Fall of 2007, all employees of a Swiss teaching hospital were invited to complete a job satisfaction survey. It included the work-related burnout scale (scored 0-100) of the Copenhagen Burnout Inventory (CBI-French version), measuring the degree of physical and psychological fatigue and exhaustion perceived as related to the person's work; a high degree of burnout was defined as a score _50. Logistic regression analyses were used to determine factors associated with a high degree of burnout. Results A total of 4575 individuals returned the questionnaire (response rate 54%). Of them, 1503 (33%) had a high degree of burnout. The rate of burnout was higher among women (34.3% versus 30.5%, P = 0.012) and respondents younger than 40 years (37.7% versus 28.6%, P < 0.001). Executives were less prone to burnout than employees (27.1% versus 33.9%, P < 0.0019). Rates of burnout differed by profession: nurses and physicians had higher rates than administrative and logistic staff (42.8% and 37.4% versus 25.6% and 20.9%, respectively P < 0.001). Burnout was inversely associated with job satisfaction. In multivariate analysis, factors associated with burnout were overall dissatisfaction (OR 3.23; 95% CI 2.66-3.91), dissatisfaction with workload (OR 2.09; 95% CI 1.74-2.51) and work-life balance (OR 2.25; 95% CI 1.83-2.77), being a woman (OR 1.56; 95% CI 1.28-1.90), working fulltime (OR 1.41; 95% CI 1.08-1.85) and working as a nurse, a physician or in the psychosocial sector. Conclusions One-third of respondents, mostly nurses and physicians, experienced burnout and had lower levels of job satisfaction. The factors associated with burnout may help to tailor programmes aiming at reducing burnout at both the individual and organizational level within the hospital.

Epidemiological characterization of Plasmodium falciparum in the Republic of Cabo Verde: implications for potential large-scale re-emergence of malaria

Background: Malaria has come near eradication at archipelago of Cabo Verde in 1970. Infections are now only observed in Santiago, where outbreaks occur. In these islands, malaria is considered by the international community as being of limited risk and, therefore, no prophylaxis is recommended. Since the understanding of factors that determine malaria outbreaks are crucial for controlling the disease, the present study aimed to investigate if the malaria infections observed in Santiago Island are maintained in isolated foci and in asymptomatic individuals.

Factors influencing adherence to standard precautions among nursing professionals in psychiatric hospitals

OBJECTIVE Evaluate and correlate individual, work-related and organizational factors that influence adherence to standard precautions among nursing professionals of psychiatric hospitals in São Paulo. METHOD An exploratory cross-sectional study conducted with 35 nursing professionals, using the assessment tool for adherence to standard precautions through the Likert scale, ranging from 1 to 5. RESULTS Knowledge of the precautions received a high score (4.69); adherence received (3.86) and obstacles (3.78), while intermediaries and the scales of organizational factors received low scores (2.61). There was a strong correlation between the magnitude adherence scale and the personal protective equipment availability (r = 0.643; p = 0.000). The training scale for prevention of HIV exposure (p = 0.007) was statistically different between the nurses and nursing assistants. CONCLUSION The organizational factors negatively contributed to adherence to standard precautions, indicating that psychiatric institutions lack safe working conditions, ongoing training and management actions to control infections.

An experimental test of loss aversion and scale compatibility

This paper studies two important reasons why people violate procedure invariance, loss aversion and scale compatibility. The paper extends previous research on loss aversion and scale compatibility by studying loss aversion and scale compatibility simultaneously, by looking at a new decision domain, medical decision analysis, and by examining the effect of loss aversion and scale compatibility on "well-contemplated preferences." We find significant evidence both of loss aversion and scale compatibility. However, the sizes of the biases due to loss aversion and scale compatibility vary over trade-offs and most participants do not behave consistently according to loss aversion or scale compatibility. In particular, the effect of loss aversion in medical trade-offs decreases with duration. These findings are encouraging for utility measurement and prescriptive decision analysis. There appear to exist decision contexts in which the effects of loss aversion and scale compatibility can be minimized and utilities can be measured that do not suffer from these distorting factors.

Local-scale spatial variation in diversity of social wasps in an Amazonian rain forest in Caxiuanã, Pará, Brazil (Hymenoptera, Vespidae, Polistinae)

Polistine wasps are important in Neotropical ecosystems due to their ubiquity and diversity. Inventories have not adequately considered spatial attributes of collected specimens. Spatial data on biodiversity are important for study and mitigation of anthropogenic impacts over natural ecosystems and for protecting species. We described and analyzed local-scale spatial patterns of collecting records of wasp species, as well as spatial variation of diversity descriptors in a 2500-hectare area of an Amazon forest in Brazil. Rare species comprised the largest fraction of the fauna. Close range spatial effects were detected for most of the more common species, with clustering of presence-data at short distances. Larger spatial lag effects could also be identified in some species, constituting probably cases of exogenous autocorrelation and candidates for explanations based on environmental factors. In a few cases, significant or near significant correlations were found between five species (of Agelaia, Angiopolybia, and Mischocyttarus) and three studied environmental variables: distance to nearest stream, terrain altitude, and the type of forest canopy. However, association between these factors and biodiversity variables were generally low. When used as predictors of polistine richness in a linear multiple regression, only the coefficient for the forest canopy variable resulted significant. Some level of prediction of wasp diversity variables can be attained based on environmental variables, especially vegetation structure. Large-scale landscape and regional studies should be scheduled to address this issue.

Satisfaction maternelle de la prise en charge anesthésique durant l'accouchement: une étude de cohorte rétrospective. [Risk factors associated with maternal satisfaction during childbirth: a retrospective cohort study.]

PURPOSE: Factors associated with maternal satisfaction of anesthetic management during labour and delivery are poorly known. The purpose of this study was to assess these factors. METHODS: We performed a retrospective cohort study on parturients admitted between January 2004 and December 2008. Data on patients' demographics, comorbidities, procedures performed and various aspects of their anesthetic experience were retrieved from the anesthetic records. Maternal satisfaction was measured using a numerical scale from 0 to 10 (0 = not satisfied at all, 10 = very satisfied). A cutoff of ≤ 6 was taken as poor satisfaction. We performed a multivariate analysis to identify the different predictors of maternal satisfaction and more specifically those related to pain, overall experience with the technique, delays, and presence of anesthetic, obstetrical and neonatal complications. RESULTS: There were 15,386 parturients admitted during the study period. Of these, 10,034 had complete information in the chart and 761 (7.6%) parturients were dissatisfied with their anesthetic care. Factors decreasing patient satisfaction were high risk pregnancy [odds ratio (OR) 95% confidence interval (CI) 0.59 (0.34-1.02)] and difficult delivery [OR (95% CI) 0.62 (0.52-0.74)]. Pain, a negative experience of the procedure, delays, poor coordination in management, and the presence of complications decreased patient satisfaction [OR (95% CI) 0.07 to 0.71]; P < 0.001. CONCLUSION: Maternal satisfaction with anesthesia care is largely determined by the effectiveness and correct performance of the procedure carried from the technical and human point of view. However, other factors such as a good coordination in patient management and the absence of complications also influence maternal satisfaction.

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation.

Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps.

Coexistence of specialist and generalist species is shaped by dispersal and environmental factors.

Disentangling the mechanisms mediating the coexistence of habitat specialists and generalists has been a long-standing subject of investigation. However, the roles of species traits and environmental and spatial factors have not been assessed in a unifying theoretical framework. Theory suggests that specialist species are more competitive in natural communities. However, empirical work has shown that specialist species are declining worldwide due to habitat loss and fragmentation. We addressed the question of the coexistence of specialist and generalist species with a spatially explicit metacommunity model in continuous and heterogeneous environments. We characterized how species' dispersal abilities, the number of interacting species, environmental spatial autocorrelation, and disturbance impact community composition. Our results demonstrated that species' dispersal ability and the number of interacting species had a drastic influence on the composition of metacommunities. More specialized species coexisted when species had large dispersal abilities and when the number of interacting species was high. Disturbance selected against highly specialized species, whereas environmental spatial autocorrelation had a marginal impact. Interestingly, species richness and niche breadth were mainly positively correlated at the community scale but were negatively correlated at the metacommunity scale. Numerous diversely specialized species can thus coexist, but both species' intrinsic traits and environmental factors interact to shape the specialization signatures of communities at both the local and global scales.

The effects of physiologically plausible connectivity structure on local and global dynamics in large scale brain models.

Functionally relevant large scale brain dynamics operates within the framework imposed by anatomical connectivity and time delays due to finite transmission speeds. To gain insight on the reliability and comparability of large scale brain network simulations, we investigate the effects of variations in the anatomical connectivity. Two different sets of detailed global connectivity structures are explored, the first extracted from the CoCoMac database and rescaled to the spatial extent of the human brain, the second derived from white-matter tractography applied to diffusion spectrum imaging (DSI) for a human subject. We use the combination of graph theoretical measures of the connection matrices and numerical simulations to explicate the importance of both connectivity strength and delays in shaping dynamic behaviour. Our results demonstrate that the brain dynamics derived from the CoCoMac database are more complex and biologically more realistic than the one based on the DSI database. We propose that the reason for this difference is the absence of directed weights in the DSI connectivity matrix.