Prospective sampling based on model ensembles improves the detection of rare species

Identifying the geographic distribution of populations is a basic, yet crucial step in many fundamental and applied ecological projects, as it provides key information on which many subsequent analyses depend. However, this task is often costly and time consuming, especially where rare species are concerned and where most sampling designs generally prove inefficient. At the same time, rare species are those for which distribution data are most needed for their conservation to be effective. To enhance fieldwork sampling, model-based sampling (MBS) uses predictions from species distribution models: when looking for the species in areas of high habitat suitability, chances should be higher to find them. We thoroughly tested the efficiency of MBS by conducting an important survey in the Swiss Alps, assessing the detection rate of three rare and five common plant species. For each species, habitat suitability maps were produced following an ensemble modeling framework combining two spatial resolutions and two modeling techniques. We tested the efficiency of MBS and the accuracy of our models by sampling 240 sites in the field (30 sitesx8 species). Across all species, the MBS approach proved to be effective. In particular, the MBS design strictly led to the discovery of six sites of presence of one rare plant, increasing chances to find this species from 0 to 50%. For common species, MBS doubled the new population discovery rates as compared to random sampling. Habitat suitability maps coming from the combination of four individual modeling methods predicted well the species' distribution and more accurately than the individual models. As a conclusion, using MBS for fieldwork could efficiently help in increasing our knowledge of rare species distribution. More generally, we recommend using habitat suitability models to support conservation plans.

Implementation of guidelines on delirium in a General Hospital: a before-after study of their impact on caregivers' knowledge and clinical skills

INTRODUCTION: Delirium is a highly prevalent disorder, with serious consequences for the hospitalised patient. Nevertheless, it remains under-diagnosed and under-treated. We developed evidence-based clinical practice guidelines (CPGs) focusing on prevention, screening, diagnosis, and treatment of delirium in a general hospital. This article presents the implementation process of these CPGs and a before-after study assessing their impact on healthcare professionals' knowledge and on clinical practice. METHODS: CPGs on delirium were first implemented in two wards (Neurology and Neurosurgery) of the Lausanne university hospital. Interactive one-hour educational sessions for small groups of nurses and physicians were organised. Participants received a summary of the guidelines and completed a multiple choice questionnaire, assessing putative changes in knowledge, before and three months after the educational session. Other indicators such as "diagnosis of delirium" reported in the discharge letters, and mean duration of patients' hospital stay before and after implementation were compared. RESULTS: Eighty percent of the nurses and physicians from the Neurology and Neurosurgery wards attended the educational sessions. Both nurses and physicians significantly improved their knowledge after the implementation (+9 percentage-points). Other indicators were not modified by the intervention. CONCLUSION: A single interactive intervention improved both nurses' and physicians' knowledge on delirium. Sustained and repeated interventions are probably needed to demonstrate changes in clinical practice.

The INTERNORM Project: Bridging Two Worlds of Expert- and Lay-Knowledge in Standardization

This paper presents a pilot project to reinforce participatory practices in standardization. The INTERNORM project creates an interactive knowledge center based on the sharing of academic skills and experiences accumulated by the civil society, especially consumer associations, environmental associations and trade unions to strengthen the participatory process of standardization. The first objective of the project is action-oriented: INTERNORM provides a common knowledge pool supporting the participation of civil society actors to international standard-setting activities by bringing them together with academic experts in working groups and providing logistic and financial support to their participation in meetings of national and international technical committees. The second objective is analytical: the standardization action provides a research field for a better understanding of the participatory dynamics underpinning international standardization. This paper presents three incentives that explain civil society (non-)involvement in standardization that overcome conventional resource-based hypotheses: an operational incentive related to the use of standards in the selective goods provided by associations to their membership; a thematic incentive provided by the setting of priorities by strategic committees created in some standardization organization; and a rhetorical incentive related to the discursive resource that civil society concerns offers to the different stakeholders.

Étude des sédiments quaternaires, de la molasse et sa tectonique, dans le Grand Lac (Léman) à partir de données sismiques 2D et 3D

RESUME L'Institut de Géophysique de l'Université de Lausanne a développé au cours de ces dernières années un système d'acquisition de sismique réflexion multitrace à haute résolution 2D et 3D. L'objectif de cette thèse était de poursuivre ce développement tout améliorant les connaissances de la géologie sous le lac Léman, en étudiant en particulier la configuration des grands accidents sous-lacustres dans la Molasse (Tertiaire) qui forme l'essentiel du substratum des formations quaternaires. En configuration 2D, notre système permet d'acquérir des profils sismiques avec une distance inter-CDP de 1,25 m. La couverture varie entre 6 et 18 selon le nombre de traces et la distance inter-tir. Le canon à air (15/15 eu. in.), offre une résolution verticale de 1,25 ni et une pénétration maximale de 300 m sous le fond de l'eau. Nous avons acquis au total plus de 400 km de sections 2D dans le Grand Lac et le Haut Lac entre octobre 2000 et juillet 2004. Une campagne de sismique 3D a fourni des données au large d'Evian sur une surface de 442,5 m sur 1450 m, soit 0,64 km2. La navigation ainsi que le positionnement des hydrophones et de la source ont été réalisés avec des GPS différentiels. Nous avons utilisé un traitement sismique conventionnel, sans appliquer d'AGC et en utilisant une migration post-stack. L'interprétation du substratum antéquaternaire est basée sur l'identification des sismofaciès, sur leurs relations avec les unités géologiques adjacentes au lac, ainsi que sur quelques données de forages. Nous obtenons ainsi une carte des unités géologiques dans le Grand Lac. Nous précisons la position du chevauchement subalpin entre la ville de Lausanne, sur la rive nord, et le bassin de Sciez, sur la rive sud. Dans la Molasse de Plateau, nous avons identifié les décrochements de Pontarlier et de St. Cergue ainsi que plusieurs failles non reconnues jusqu'ici. Nous avons cartographié les accidents qui affectent la Molasse subalpine ainsi que le plan de chevauchement du flysch sur la Molasse près de la rive sud du lac. Une nouvelle carte tectonique de la région lémanique a ainsi pu être dressée. L'analyse du substratum ne montre pas de failles suggérant une origine tectonique de la cuvette lémanique. Par contre, nous suggérons que la forme du creusement glaciaire, donc de la forme du lac Léman, a été influencée par la présence de failles dans le substratum antéquaternaire. L'analyse des sédiments quaternaires nous a permis de tracer des cartes des différentes interfaces ou unités qui les composent. La carte du toit du substratum antéquaternaire montre la présence de chenaux d'origine glaciaire dont la profondeur maximale atteint la cote -200 ni. Leur pente est dirigée vers le nord-est, à l'inverse du sens d'écoulement actuel des eaux. Nous expliquons cette observation par l'existence de circulations sous-glaciaires d'eau artésienne. Les sédiments glaciaires dont l'épaisseur maximale atteint 150 ni au centre du lac ont enregistré les différentes récurrences glaciaires. Dans la zone d'Evian, nous mettons en évidence la présence de lentilles de sédiments glaciolacustres perchées sur le flanc de la cuvette lémanique. Nous avons corrélé ces unités avec des données de forage et concluons qu'il s'agit du complexe inférieur de la pile sédimentaire d'Evian. Celui-ci, âgé de plus de 30 000 ans, serait un dépôt de Kame associé à un lac périglaciaire. La sismique réflexion 3D permet de préciser l'orientation de l'alimentation en matériel détritique de l'unité. La finesse des images obtenues nous permet également d'établir quels types d'érosion ont affecté certaines unités. Les sédiments lacustres, dont l'épaisseur maximale imagée atteint plus de 225 m et sans doute 400 ni sous le delta du Rhône, indiquent plusieurs mécanismes de dépôts. A la base, une mégaturbidite, épaisse d'une trentaine de mètres en moyenne, s'étend entre l'embouchure de la Dranse et le delta du Rhône. Au-dessus, la décantation des particules en suspension d'origine biologique et détritique fournit l'essentiel des sédiments. Dans la partie orientale du lac, les apports détritiques du Rhône forment un delta qui prograde vers l'ouest en s'imbriquant avec les sédiments déposés par décantation. La structure superficielle du delta a brutalement évolué, probablement à la suite de l'évènement catastrophique du Tauredunum (563 A.D.). Sa trace probable se marque par la présence d'une surface érosive que nous avons cartographiée. Le delta a ensuite changé de géométrie, avec notamment un déplacement des chenaux sous-lacustres. Sur l'ensemble de nos sections sismiques, nous n'observons aucune faille dans les sédiments quaternaires qui attesterait d'une tectonique postglaciaire du substratum. ABSTRACT During the last few years the institute of Geophysics of the University of Lausanne cleveloped a 2D and 3D high-resolution multichannel seismic reflection acquisition system. The objective of the present work was to carry on this development white improving our knowledge of the geology under Lake Geneva, in particular by studying the configuration of the large accidents affecting the Tertiary Molasse that makes up the basement of most Quaternary deposits. In its 2D configuration, our system makes it possible to acquire seismic profiles with a CDP interval of 1.25 m. The fold varies from 6 to 18 depending on the number of traces and the shooting interval. Our air gun (15/15 cu. in.) provides a vertical resolution of 1.25 m and a maximum penetration depth of approximately 300 m under water bottom. We acquired more than 400 km of 2D sections in the Grand Lac and the Haut Lac between October 2000 and July 2004. A 3D seismic survey off the city of Evian provided data on a surface of 442.5 m x 1450 m (0.64 km2). Ship's navigation as well as hydrophone- and source positioning were carried out with differential GPS. The seismic data were processed following a conventional sequence without .applying AGC and using post-stack migration. The interpretation of the pre-Quaternary substratum is based on sismofacies, on their relationships with terrestrial geological units and on some borehole data. We thus obtained a map of the geological units in the Grand Lac. We defined the location of the subalpine thrust from Lausanne, on the north shore, to the Sciez Basin, on the south shore. Within the Molasse de Plateau, we identified the already know Pontarlier and St Cergue transforms Fault as well as faults. We mapped faults that affect subalpine Molasse as well as the thrust fault plane between alpine flysch and Molasse near the lake's south shore. A new tectonic map of the Lake Geneva region could thus be drawn up. The substratum does not show faults indicating a tectonic origin for the Lake Geneva Basin. However, we suggest that the orientation of glacial erosion, and thus the shape of Lake Geneva, vas influenced by the presence of faults in the pre-Quaternary basement. The analysis of Quaternary sediments enabled us to draw up maps of various discontinuities or internal units. The top pre-Quaternary basement map shows channels of glacial origin, the deepest of them reaching an altitude of 200 m a.s.l. The channel's slopes are directed to the North-East, in opposite direction of the present water flow. We explain this observation by the presence of artesian subglacial water circulation. Glacial sediments, the maximum thickness of which reaches 150 m in the central part of the lake, record several glacial recurrences. In the Evian area, we found lenses of glacio-lacustrine sediments set high up on the flank of the Lake Geneva Bassin. We correlated these units with on-land borehole data and concluded that they represent the lower complex of the Evian sedimentary pile. The lower complex is aider than 30 000 years, and it could be a Kame deposit associated with a periglacial lake. Our 3D seismic reflexion survey enables us to specify the supply direction of detrital material in this unit. With detailed seismic images we established how some units were affected by different erosion types. The lacustrine sediments we imaged in Lake Geneva are thicker than 225 m and 400 m or more Linder the Rhone Delta. They indicate several depositional mechanisms. Their base is a major turbidite, thirty meters thick on average, that spreads between the Dranse mouth and the Rhone delta. Above this unit, settling of suspended biological and detrital particles provides most of the sediments. In the eastern part of the lake, detrital contribution from the Rhone builds a delta that progrades to the west and imbricates with the settling sediments. The shallow structure of the Rhone delta abruptly evolved, probably after the catastrophic Tauredunum event (563 A.D.). It probably coincides with an erosive surface that we mapped. As a result, the delta geometry changed, in particular associated with a displacement of water bottom channels. In all our seismic sections, we do not observe fault in the Quaternary sediments that would attest postglacial tectonic activity in the basement.

A new locus for congenital cataract, microcornea, microphthalmia, and atypical iris coloboma maps to chromosome 2.

OBJECTIVE: To report a novel phenotype of autosomal dominant atypical congenital cataract associated with variable expression of microcornea, microphthalmia, and iris coloboma linked to chromosome 2. Molecular analysis of this phenotype may improve our understanding of anterior segment development. DESIGN: Observational case study, genome linkage analysis, and gene mutation screening. PARTICIPANTS: Three families, 1 Egyptian and 2 Belgians, with a total of 31 affected were studied. METHODS: Twenty-one affected subjects and 9 first-degree relatives underwent complete ophthalmic examination. In the Egyptian family, exclusion of PAX6, CRYAA, and MAF genes was demonstrated by haplotype analysis using microsatellite markers on chromosomes 11, 16, and 21. Genome-wide linkage analysis was then performed using 385 microsatellite markers on this family. In the 2 Belgian families, the PAX6 gene was screened for mutations by direct sequencing of all exons. MAIN OUTCOME MEASURES: Phenotype description, genome-wide linkage of the phenotype, linkage to the PAX6, CRYAA, and MAF genes, and mutation detection in the PAX6 gene. RESULTS: Affected members of the 3 families had bilateral congenital cataracts inherited in an autosomal dominant pattern. A novel form of hexagonal nuclear cataract with cortical riders was expressed. Among affected subjects with available data, 95% had microcornea, 39% had microphthalmia, and 38% had iris coloboma. Seventy-five percent of the colobomata were atypical, showing a nasal superior location in 56%. A positive lod score of 4.86 was obtained at theta = 0 for D2S2309 on chromosome 2, a 4.9-Mb common haplotype flanked by D2S2309 and D2S2358 was obtained in the Egyptian family, and linkage to the PAX6, CRYAA, or MAF gene was excluded. In the 2 Belgian families, sequencing of the junctions and all coding exons of PAX6 did not reveal any molecular change. CONCLUSIONS: We describe a novel phenotype that includes the combination of a novel form of congenital hexagonal cataract, with variably expressed microcornea, microphthalmia, and atypical iris coloboma, not caused by PAX6 and mapping to chromosome 2. FINANCIAL DISCLOSURE(S): The authors have no proprietary or commercial interest in any materials discussed in this article.

ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

A case study of landslides and coping strategies in two villages of central-eastern Nepal

Landslides are an increasing problem in Nepal's Middle Hills due to both natural and human phenomena: mainly increasingly intense monsoon rains and a boom in rural road construction. This problem has largely been neglected due to underreporting of losses and the dispersed nature of landslides. Understanding how populations cope with landslides is a first step toward developing more effective landslide risk management programs. The present research focuses on two villages in Central-Eastern Nepal, both affected by active landslides but with different coping strategies. Research methods are interdisciplinary, based on a geological assessment of landslide risk and a socio-economic study of the villages using household questionnaires, focus group discussions and transect walks. Community risk maps are compared with geological landslide risk maps to better understand and communicate community risk perceptions, priorities and coping strategies. A modified typology of coping strategies is presented, based on previous work by Burton, Kates, and White (1993) that is useful for decision-makers for designing more effective programs for landslide mitigation. Main findings underscore that coping strategies, mainly seeking external assistance and outmigration, are closely linked to access to resources, ethnicity/social status and levels of community organization. Conclusions include the importance of investing in organizational skills, while building on local knowledge about landslide mitigation for reducing landslide risk. There is great potential to increase coping strategies by incorporating skills training on landslide mitigation in existing agricultural outreach and community forest user group training.

A new spin on a compositionalist predictive modelling framework for conservation planning: a tropical case study in Ecuador

Knowledge about spatial biodiversity patterns is a basic criterion for reserve network design. Although herbarium collections hold large quantities of information, the data are often scattered and cannot supply complete spatial coverage. Alternatively, herbarium data can be used to fit species distribution models and their predictions can be used to provide complete spatial coverage and derive species richness maps. Here, we build on previous effort to propose an improved compositionalist framework for using species distribution models to better inform conservation management. We illustrate the approach with models fitted with six different methods and combined using an ensemble approach for 408 plant species in a tropical and megadiverse country (Ecuador). As a complementary view to the traditional richness hotspots methodology, consisting of a simple stacking of species distribution maps, the compositionalist modelling approach used here combines separate predictions for different pools of species to identify areas of alternative suitability for conservation. Our results show that the compositionalist approach better captures the established protected areas than the traditional richness hotspots strategies and allows the identification of areas in Ecuador that would optimally complement the current protection network. Further studies should aim at refining the approach with more groups and additional species information.