Spatial modelling of biodiversity at the community level

1. Statistical modelling is often used to relate sparse biological survey data to remotely derived environmental predictors, thereby providing a basis for predictively mapping biodiversity across an entire region of interest. The most popular strategy for such modelling has been to model distributions of individual species one at a time. Spatial modelling of biodiversity at the community level may, however, confer significant benefits for applications involving very large numbers of species, particularly if many of these species are recorded infrequently. 2. Community-level modelling combines data from multiple species and produces information on spatial pattern in the distribution of biodiversity at a collective community level instead of, or in addition to, the level of individual species. Spatial outputs from community-level modelling include predictive mapping of community types (groups of locations with similar species composition), species groups (groups of species with similar distributions), axes or gradients of compositional variation, levels of compositional dissimilarity between pairs of locations, and various macro-ecological properties (e.g. species richness). 3. Three broad modelling strategies can be used to generate these outputs: (i) 'assemble first, predict later', in which biological survey data are first classified, ordinated or aggregated to produce community-level entities or attributes that are then modelled in relation to environmental predictors; (ii) 'predict first, assemble later', in which individual species are modelled one at a time as a function of environmental variables, to produce a stack of species distribution maps that is then subjected to classification, ordination or aggregation; and (iii) 'assemble and predict together', in which all species are modelled simultaneously, within a single integrated modelling process. These strategies each have particular strengths and weaknesses, depending on the intended purpose of modelling and the type, quality and quantity of data involved. 4. Synthesis and applications. The potential benefits of modelling large multispecies data sets using community-level, as opposed to species-level, approaches include faster processing, increased power to detect shared patterns of environmental response across rarely recorded species, and enhanced capacity to synthesize complex data into a form more readily interpretable by scientists and decision-makers. Community-level modelling therefore deserves to be considered more often, and more widely, as a potential alternative or supplement to modelling individual species.

Monthly wages in the Swiss Household Panel

This paper describes the construction of monthly income from employment and self employment in the Swiss Household Panel (SHP). It documents the assumptions that have to be taken and addresses possibilities and difficulties when relating monthly income variables with the number of working hours. Finally, some descriptive statistics of the monthly wages are provided from 1999 to 2008. These show a high correlation of wages across the years, which is higher than correlation from yearly wages. This underlies the suitability of these variables on monthly wages for labour market research with the SHP. Median and average hourly wages have increased slightly from 2002 to 2008. The inequality of wages has remained stable for the total population.

Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

Binge drinking in 19 year old men.

QUESTION UNDER STUDY: To describe alcohol use, binge drinking and drinking consequences in 19 year old men. METHODS: During a one-day army recruitment process mandatory for all Swiss males, a convenience sample of 1,004 men completed the "Health and Lifestyle Questionnaire", assessing demographics, alcohol use, binge drinking, and drinking consequences over the last 12 months. Binge drinking was defined as having 5 or more drinks on a single occasion at least once over the last 12 months. Among the 1,004 subjects, binge drinking could not be defined in 123 (12.3%) due to "don't know" responses, leaving 881 subjects with complete data. RESULTS: Of the 881 subjects, 690 (78.3%) reported binge drinking at least once over the last 12 months, 269 (30.5%) with infrequent binge drinking (< or = 1x/month) and 421 (47.8%) with frequent binge drinking (> or = 2x/month). In addition, 379 (43.0%) of the subjects experienced 3 or more drinking consequences over the last 12 months and the number of these consequences increased as the frequency of binge drinking increased (trend analyses significant for 9 of the 12 consequences evaluated). Among the 687 subjects with moderate average alcohol intake (< 14 drinks per week), 252 (36.7%) reported infrequent binge drinking, of whom 82 (32.5%) experienced 3 or more adverse drinking consequences over the last 12 months, whereas 246 (35.8%) reported frequent binge drinking and 128 (52.0%) of these experienced 3 or more adverse drinking consequences. CONCLUSIONS: Binge drinking in this sample of young men is frequent and is associated with numerous consequences, even among those consuming moderate amounts of alcohol.

Asthme a début tardif [Late-onset asthma].

Late-onset asthma is a common disease, with characteristics that differentiate it from childhood asthma persisting in adults, including a heterogeneity of underlying mechanism, a correlation with occupational exposure and the tendency to chronicize. Inadequate perception of the disease importance and difficulties in diagnosis, due to the association to COPD, the broad differential diagnosis spectrum and an atypical clinical manifestation, make this disease entity underdiagnosed and under-treated, with consequences for morbidity and mortality. The treatment of adults with asthma follows the usual guidelines, but must take into account an occasional poor therapeutic response and the risk of side effects in polymorbid patients.

Validación chilena del cuestionario de evaluación de apego en el adulto CAMIR

El objetivo de esta investigación fue examinar la confiabilidad y validez del instrumento de evaluación de apego en el adulto, "Cartes: Modèles Individuels de Relation (CAMIR), en la realidad sociocultural chilena. Este instrumento, basado en la teoría del apego, es un cuestionario de auto-reporte que evalúa los modelos operativos internos en adultos y otras escalas relacionadas al apego. Los participantes fueron 578 sujetos, 204 hombres y 374 mujeres, con edades entre 14 y 80 años. Los sujetos completaron el CAMIR y medidas de vínculo y sintomatología actual, a través del Parental Bonding Instrument (PBI) and Outcome Questionnaire OQ-45.2. A través del análisis estadístico de los resultados se evaluaron las características psicométricas del test y de analiz ó la posibilidad de generar normas locales para la prueba. Los resultados confirmaron que el CAMIR es un instrumento confiable y válido en la evaluación de los modelos internos de relación en adultos. This study was designed to estimate the validity and reliability of the "Cartes: Modèles Individuels de Relation (CAMIR), in Chile. This inventory, based on attachment's theory, it's a auto-questionnaire evaluates the working models in adults and other scales relating to attachment. Participants were 578 individuals, 204 males and 374 females, 14 a 80 years old. Individuals completed the CAMIR and measures of bond and actual symptoms, with the Parental Bonding Instrument (PBI) and Outcome Questionnaire OQ-45.2. The general norms were obtained according to a statistical analysis of the results and to an evaluation of the psychometric characteristics of the test. The results confirmed that the psychometric characteristics of the CAMIR make it a reliable and valid tool to assess working models in adults.

Identification of new MHC class I-restricted human tumor antigens for immunotherapy

Summary Cancer is a leading cause of morbidity and mortality in Western countries (as an example, colorectal cancer accounts for about 300'000 new cases and 200'000 deaths each year in Europe and in the USA). Despite that many patients with cancer have complete macroscopic clearance of their disease after resection, radiotherapy and/or chemotherapy, many of these patients develop fatal recurrence. Vaccination with immunogenic peptide tumor antigens has shown encouraging progresses in the last decade; immunotherapy might therefore constitute a fourth therapeutic option in the future. We dissect here and critically evaluate the numerous steps of reverse immunology, a forecast procedure to identify antigenic peptides from the sequence of a gene of interest. Bioinformatic algorithms were applied to mine sequence databases for tumor-specific transcripts. A quality assessment of publicly available sequence databanks allowed defining strengths and weaknesses of bioinformatics-based prediction of colon cancer-specific alternative splicing: new splice variants could be identified, however cancer-restricted expression could not be significantly predicted. Other sources of target transcripts were quantitatively investigated by polymerase chain reactions, as cancer-testis genes or reported overexpressed transcripts. Based on the relative expression of a defined set of housekeeping genes in colon cancer tissues, we characterized a precise procedure for accurate normalization and determined a threshold for the definition of significant overexpression of genes in cancers versus normal tissues. Further steps of reverse immunology were applied on a splice variant of the Melan¬A gene. Since it is known that the C-termini of antigenic peptides are directly produced by the proteasome, longer precursor and overlapping peptides encoded by the target sequence were synthesized chemically and digested in vitro with purified proteasome. The resulting fragments were identified by mass spectroscopy to detect cleavage sites. Using this information and based on the available anchor motifs for defined HLA class I molecules, putative antigenic peptides could be predicted. Their relative affinity for HLA molecules was confirmed experimentally with functional competitive binding assays and they were used to search patients' peripheral blood lymphocytes for the presence of specific cytolytic T lymphocytes (CTL). CTL clones specific for a splice variant of Melan-A could be isolated; although they recognized peptide-pulsed cells, they failed to lyse melanoma cells in functional assays of antigen recognition. In the conclusion, we discuss advantages and bottlenecks of reverse immunology and compare the technical aspects of this approach with the more classical procedure of direct immunology, a technique introduced by Boon and colleagues more than 10 years ago to successfully clone tumor antigens.

Quelle place pour la psychologie positive dans le champ de la psychothérapie ? Perspectives théoriques et empiriques

Ce travail vise à exposer le courant de la psychologie positive et à présenter une tentative d'articulation entre ce courant et le champ de la pratique psychothérapeutique. Nous présenterons, dans un premier temps, les fondements de la psychologie positive et les axes principaux qui la constituent. Dans cette perspective, la théorie des émotions positives de Fredrickson et la classification des vertus et des forces de caractères de Peterson et Seligman sont exposées plus en détails. Dans un second temps et à partir des travaux récents, deux facçons d'établir un pont entre psychologie positive et la psychothérapie sont discutées : (i) le développement de nouvelles stratégies thérapeutiques issues de la psychologie positive et (ii) une relecture des principaux modèles psychothérapeutiques au regard de la psychologie positive. / This article aims to present the field of positive psychology and the way it could be integrated in the area of psychotherapy. First, the historical grounding and the main contributions of positive psychology are presented. In this perspective, the Fredrickson's theory of positive emotions and the Peterson's classification of character strengths and virtues are particularly detailed. Secondly, based on recent research, two ways to link positive psychology to clinical practice emerged: (i) the development of new therapeutic strategies anchored in the positive psychology, and (ii) a critical look at different psychotherapeutic modalities based on positive psychology.

Assessing medication adherence: options to consider.

Background Adherence to chronic therapy is a key determinant of patient health outcomes in chronic disease. However, only about 50 % of patients adhere to chronic therapy. One of the challenges in promoting adherence is having an accurate understanding of adherence rates and the factors that contribute to non-adherence. There are many measures available to assess patient medication adherence. Aim of the review This review aims to present the commonly used indirect methods available for measuring medication adherence in routine healthcare and research studies. Method A literature review on medication adherence measures in patient populations with chronic conditions taking chronic medications was conducted through Medline (2003-2013). A complementary manual search of references cited in the retrieved studies was performed in order to identify any additional studies. Results Of the 238 initial Medline search results, 57 full texts were retrieved. Forty-seven articles were included as a result of the manual search. Adherence measures identified were: self-report (reported in 50 publications), electronic measures (33), pharmacy refills and claims data (26) and pill counts (25). Patient self-report, electronic measures, pharmacy refill and claims data were the most commonly used measures of adherence in research, routine practice, epidemiological and intervention studies. These methods, and their strengths and limitations have been described in this paper. Conclusion A multitude of indirect measures of adherence exist in the literature, however, there is no "gold" standard for measuring adherence to medications. Triangulation of methods increases the validity and reliability of the adherence data collected. To strengthen the adherence data collected and allow for comparison of data, future research and practice interventions should use an internationally accepted, operational standardized definition of medication adherence and clearly describe the medication adherence methods used.

Désir de mort, désir de vie et fin de vie [Desire to die, desire to live at the end of life]

Since a couple of years, physicians are confronted with an increasing request of end of life patients asking for a dying facilitated process. The reasons for this are multiple and complex. Existential suffering, increased by depression, a feeling of loss of meaning or dignity and/or being a burden, seems to be a significant factor. Social isolation and physical symptoms seem to be only contributory. The identification of "protecting elements" such as spiritual well-being or a preserved sense of dignity offers new opportunities for care. Providing a space for dialogue by exploring the patient's expectations and fears, his knowledge of care options available at the end of life, his own resources and difficulties frequently contribute to decrease suffering.

Neuron-to-neuron wild-type Tau protein transfer through a trans-synaptic mechanism: relevance to sporadic tauopathies.

BACKGROUND: In sporadic Tauopathies, neurofibrillary degeneration (NFD) is characterised by the intraneuronal aggregation of wild-type Tau proteins. In the human brain, the hierarchical pathways of this neurodegeneration have been well established in Alzheimer's disease (AD) and other sporadic tauopathies such as argyrophilic grain disorder and progressive supranuclear palsy but the molecular and cellular mechanisms supporting this progression are yet not known. These pathways appear to be associated with the intercellular transmission of pathology, as recently suggested in Tau transgenic mice. However, these conclusions remain ill-defined due to a lack of toxicity data and difficulties associated with the use of mutant Tau. RESULTS: Using a lentiviral-mediated rat model of hippocampal NFD, we demonstrated that wild-type human Tau protein is axonally transferred from ventral hippocampus neurons to connected secondary neurons even at distant brain areas such as olfactory and limbic systems indicating a trans-synaptic protein transfer. Using different immunological tools to follow phospho-Tau species, it was clear that Tau pathology generated using mutated Tau remains near the IS whereas it spreads much further using the wild-type one. CONCLUSION: Taken together, these results support a novel mechanism for Tau protein transfer compared to previous reports based on transgenic models with mutant cDNA. It also demonstrates that mutant Tau proteins are not suitable for the development of experimental models helpful to validate therapeutic intervention interfering with Tau spreading.

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Climate change data and predictions for the Himalayas are very sparse and uncertain, characterized by a ?Himalayan data gap? and difficulties in predicting changes due to topographic complexity. A few reliable studies and climate change models for Nepal predict considerable changes: shorter monsoon seasons, more intensive rainfall patterns, higher temperatures, and drought. These predictions are confirmed by farmers who claim that temperatures have been increasing for the past decade and wonder why the rains have ?gone mad.? The number of hazard events, notably droughts, floods, and landslides are increasing and now account for approximately 100 deaths in Nepal annually. Other effects are drinking water shortages and shifting agricultural patterns, with many communities struggling to meet basic food security before climatic conditions started changing. The aim of this paper is to examine existing gaps between current climate models and the realities of local development planning through a case study on flood risk and drinking water management for the Municipality of Dharan in Eastern Nepal. This example highlights current challenges facing local-level governments, namely, flood and landslide mitigation, providing basic amenities ? especially an urgent lack of drinking water during the dry season ? poor local planning capacities, and limited resources. In this context, the challenge for Nepal will be to simultaneously address increasing risks caused by hazard events alongside the omnipresent food security and drinking water issues in both urban and rural areas. Local planning is needed that integrates rural development and disaster risk reduction (DRR) with knowledge about climate change considerations. The paper concludes with a critical analysis of climate change modeling and the gap between scientific data and low-tech and low capacities of local planners to access or implement adequate adaptation measures. Recommendations include the need to bridge gaps between scientific models, the local political reality and local information needs.

Management of the risk of HIV infection in male homosexual couples.

OBJECTIVES: To study the ways of managing HIV risk within male homosexual steady relationships (gay couples), including factors associated with consistent condom use during anal sex with the steady partner.¦METHOD: An anonymous and standardized questionnaire completed by a convenience sample of homosexuals in Switzerland in 1997 (n = 1097). Information on the couple was provided by the 74% (n = 786) of male respondents who reported having a steady partner in the past 12 months. Data were analysed by contingency tables and logistic regression.¦RESULTS: Different ways of managing HIV risk were reported: negotiated safety (both HIV negative, condoms abandoned) was chosen by one quarter of the couples, but the most frequent solution was reliance on condoms for anal sex, chosen by more than four in 10. Altogether 84% of couples exhibited safe management of HIV risk within their partnership. The 16% of couples showing inadequate management of HIV risk within the couple mostly relied on questionable assumptions about past or present risks. A total of 74% of couples had spoken about managing HIV risk with possible casual partners. Reported behaviour with the steady partner and with casual partners was highly consistent with claimed strategies chosen to manage HIV risk. Consistent condom use with the steady partner was mostly associated with variables characterizing the relationship: initial 2 years of the relationship, discordant or unknown serological HIV status, non-exclusivity.¦CONCLUSION: Gay couples manage HIV risk in a variety of ways. Most strategies provide adequate protection with casual partners, but leave gaps in protection between the steady partners themselves.

Using robots to understand social behaviour.

A major challenge in studying social behaviour stems from the need to disentangle the behaviour of each individual from the resulting collective. One way to overcome this problem is to construct a model of the behaviour of an individual, and observe whether combining many such individuals leads to the predicted outcome. This can be achieved by using robots. In this review we discuss the strengths and weaknesses of such an approach for studies of social behaviour. We find that robots-whether studied in groups of simulated or physical robots, or used to infiltrate and manipulate groups of living organisms-have important advantages over conventional individual-based models and have contributed greatly to the study of social behaviour. In particular, robots have increased our understanding of self-organization and the evolution of cooperative behaviour and communication. However, the resulting findings have not had the desired impact on the biological community. We suggest reasons for why this may be the case, and how the benefits of using robots can be maximized in future research on social behaviour.

Effective continuing professional development for translating shared decision making in primary care: A study protocol.

Background: Shared decision making (SDM) is a process by which a healthcare choice is made jointly by the healthcare professional and the patient. SDM is the essential element of patient-centered care, a core concept of primary care. However, SDM is seldom translated into primary practice. Continuing professional development (CPD) is the principal means by which healthcare professionals continue to gain, improve, and broaden the knowledge and skills required for patient-centered care. Our international collaboration seeks to improve the knowledge base of CPD that targets translating SDM into the clinical practice of primary care in diverse healthcare systems. Methods: Funded by the Canadian Institutes of Health Research (CIHR), our project is to form an international, interdisciplinary research team composed of health services researchers, physicians, nurses, psychologists, dietitians, CPD decision makers and others who will study how CPD causes SDM to be practiced in primary care. We will perform an environmental scan to create an inventory of CPD programs and related activities for translating SDM into clinical practice. These programs will be critically assessed and compared according to their strengths and limitations. We will use the empirical data that results from the environmental scan and the critical appraisal to identify knowledge gaps and generate a research agenda during a two-day workshop to be held in Quebec City. We will ask CPD stakeholders to validate these knowledge gaps and the research agenda. Discussion: This project will analyse existing CPD programs and related activities for translating SDM into the practice of primary care. Because this international collaboration will develop and identify various factors influencing SDM, the project could shed new light on how SDM is implemented in primary care.