EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology.

Integrated approaches using different in vitro methods in combination with bioinformatics can (i) increase the success rate and speed of drug development; (ii) improve the accuracy of toxicological risk assessment; and (iii) increase our understanding of disease. Three-dimensional (3D) cell culture models are important building blocks of this strategy which has emerged during the last years. The majority of these models are organotypic, i.e., they aim to reproduce major functions of an organ or organ system. This implies in many cases that more than one cell type forms the 3D structure, and often matrix elements play an important role. This review summarizes the state of the art concerning commonalities of the different models. For instance, the theory of mass transport/metabolite exchange in 3D systems and the special analytical requirements for test endpoints in organotypic cultures are discussed in detail. In the next part, 3D model systems for selected organs--liver, lung, skin, brain--are presented and characterized in dedicated chapters. Also, 3D approaches to the modeling of tumors are presented and discussed. All chapters give a historical background, illustrate the large variety of approaches, and highlight up- and downsides as well as specific requirements. Moreover, they refer to the application in disease modeling, drug discovery and safety assessment. Finally, consensus recommendations indicate a roadmap for the successful implementation of 3D models in routine screening. It is expected that the use of such models will accelerate progress by reducing error rates and wrong predictions from compound testing.

Assessment of skinfold thickness equations in estimating body composition in children with inflammatory bowel

Introduction: Growth is a central process in paediatrics. Weight and height evaluation are therefore routine exams for every child but in some situation, particularly inflammatory bowel disease (IBD), a wider evaluation of nutritional status needs to be performed. The assessment of body composition is essential in order to maintain acceptable growth using the following techniques: Dual-energy X-ray absorptiometry (DEXA), bio-impedance-analysis (BIA) and anthropometric measurements (skinfold thickness skin), the latter being most easily available and most cost effective. Objectives: To assess the accuracy of skinfold equations in estimating percentage body fat (%BF) in children with inflammatory bowel disease (IBD), compared with assessment of body fat dual energy X-ray absorptiometry (DEXA). Methods: Twenty-one patients (11 females, 10 males; mean age: 14.3 years, range 12 - 16 years) with IBD (Crohn's disease n = 15, ulcerative colitis n = 6)). Estimated%BF was computed using 6 established equations based on the triceps, biceps, subscapular and suprailiac skinfolds (Deurenberg, Weststrate, Slaughter, Durnin & Rahaman, Johnston, Brook) and compared to DEXA. Concordance analysis was performed using Lin's concordance correlation and the Bland-Altman limits of agreement method. Results: Durnin & Rahaman's equation shows a higher Lin's concordance coefficient with a small difference amongst raw values for skinfolds and DEXA compared to the other equations. Correlation coefficient between mean and difference is close to zero with a non-significant Bradley-Blackwood test. Conclusion: Body composition in paediatric IBD patients using the Durnin & Rahaman skinfold-equation adequately reflects values obtained by DEXA.

Integrated application of geochemical and geophysical methods for hydrogeological impact assessment for tunneling in fractured rock

The interaction of tunneling with groundwater is a problem both from an environmental and an engineering point of view. In fact, tunnel drilling may cause a drawdown of piezometric levels and water inflows into tunnels that may cause problems during excavation of the tunnel. While the influence of tunneling on the regional groundwater systems may be adequately predicted in porous media using analytical solutions, such an approach is difficult to apply in fractured rocks. Numerical solutions are preferable and various conceptual approaches have been proposed to describe and model groundwater flow through fractured rock masses, ranging from equivalent continuum models to discrete fracture network simulation models. However, their application needs many preliminary investigations on the behavior of the groundwater system based on hydrochemical and structural data. To study large scale flow systems in fractured rocks of mountainous terrains, a comprehensive study was conducted in southern Switzerland, using as case studies two infrastructures actually under construction: (i) the Monte Ceneri base railway tunnel (Ticino), and the (ii) San Fedele highway tunnel (Roveredo, Graubiinden). The chosen approach in this study combines the temporal and spatial variation of geochemical and geophysical measurements. About 60 localities from both surface and underlying tunnels were temporarily and spatially monitored during more than one year. At first, the project was focused on the collection of hydrochemical and structural data. A number of springs, selected in the area surrounding the infrastructures, were monitored for discharge, electric conductivity, pH, and temperature. Water samples (springs, tunnel inflows and rains) were taken for isotopic analysis; in particular the stable isotope composition (δ2Η, δ180 values) can reflect the origin of the water, because of spatial (recharge altitude, topography, etc.) and temporal (seasonal) effects on precipitation which in turn strongly influence the isotopic composition of groundwater. Tunnel inflows in the accessible parts of the tunnels were also sampled and, if possible, monitored with time. Noble-gas concentrations and their isotope ratios were used in selected locations to better understand the origin and the circulation of the groundwater. In addition, electrical resistivity and VLF-type electromagnetic surveys were performed to identify water bearing fractures and/or weathered areas that could be intersected at depth during tunnel construction. The main goal of this work was to demonstrate that these hydrogeological data and geophysical methods, combined with structural and hydrogeological information, can be successfully used in order to develop hydrogeological conceptual models of the groundwater flow in regions to be exploited for tunnels. The main results of the project are: (i) to have successfully tested the application of electrical resistivity and VLF-electromagnetic surveys to asses water-bearing zones during tunnel drilling; (ii) to have verified the usefulness of noble gas, major ion and stable isotope compositions as proxies for the detection of faults and to understand the origin of the groundwater and its flow regimes (direct rain water infiltration or groundwater of long residence time); and (iii) to have convincingly tested the combined application of a geochemical and geophysical approach to assess and predict the vulnerability of springs to tunnel drilling. - L'interférence entre eaux souterraines et des tunnels pose des problèmes environnementaux et de génie civile. En fait, la construction d'un tunnel peut faire abaisser le niveau des nappes piézométriques et faire infiltrer de l'eau dans le tunnel et ainsi créer des problème pendant l'excavation. Alors que l'influence de la construction d'un tunnel sur la circulation régionale de l'eau souterraine dans des milieux poreux peut être prédite relativement facilement par des solution analytiques de modèles, ceci devient difficile dans des milieux fissurés. Dans ce cas-là, des solutions numériques sont préférables et plusieurs approches conceptuelles ont été proposées pour décrire et modéliser la circulation d'eau souterraine à travers les roches fissurées, en allant de modèles d'équivalence continue à des modèles de simulation de réseaux de fissures discrètes. Par contre, leur application demande des investigations importantes concernant le comportement du système d'eau souterraine basées sur des données hydrochimiques et structurales. Dans le but d'étudier des grands systèmes de circulation d'eau souterraine dans une région de montagnes, une étude complète a été fait en Suisse italienne, basée sur deux grandes infrastructures actuellement en construction: (i) Le tunnel ferroviaire de base du Monte Ceneri (Tessin) et (ii) le tunnel routière de San Fedele (Roveredo, Grisons). L'approche choisie dans cette étude est la combinaison de variations temporelles et spatiales des mesures géochimiques et géophysiques. Environs 60 localités situées à la surface ainsi que dans les tunnels soujacents ont été suiviès du point de vue temporel et spatial pendant plus de un an. Dans un premier temps le projet se focalisait sur la collecte de données hydrochimiques et structurales. Un certain nombre de sources, sélectionnées dans les environs des infrastructures étudiées ont été suivies pour le débit, la conductivité électrique, le pH et la température. De l'eau (sources, infiltration d'eau de tunnel et pluie) a été échantillonnés pour des analyses isotopiques; ce sont surtout les isotopes stables (δ2Η, δ180) qui peuvent indiquer l'origine d'une eaux, à cause de la dépendance d'effets spatiaux (altitude de recharge, topographie etc.) ainsi que temporels (saisonaux) sur les précipitations météoriques , qui de suite influencent ainsi la composition isotopique de l'eau souterraine. Les infiltrations d'eau dans les tunnels dans les parties accessibles ont également été échantillonnées et si possible suivies au cours du temps. La concentration de gaz nobles et leurs rapports isotopiques ont également été utilisées pour quelques localités pour mieux comprendre l'origine et la circulation de l'eau souterraine. En plus, des campagnes de mesures de la résistivité électrique et électromagnétique de type VLF ont été menées afin d'identifier des zone de fractures ou d'altération qui pourraient interférer avec les tunnels en profondeur pendant la construction. Le but principal de cette étude était de démontrer que ces données hydrogéologiques et géophysiques peuvent être utilisées avec succès pour développer des modèles hydrogéologiques conceptionels de tunnels. Les résultats principaux de ce travail sont : i) d'avoir testé avec succès l'application de méthodes de la tomographie électrique et des campagnes de mesures électromagnétiques de type VLF afin de trouver des zones riches en eau pendant l'excavation d'un tunnel ; ii) d'avoir prouvé l'utilité des gaz nobles, des analyses ioniques et d'isotopes stables pour déterminer l'origine de l'eau infiltrée (de la pluie par le haut ou ascendant de l'eau remontant des profondeurs) et leur flux et pour déterminer la position de failles ; et iii) d'avoir testé d'une manière convainquant l'application combinée de méthodes géochimiques et géophysiques pour juger et prédire la vulnérabilité de sources lors de la construction de tunnels. - L'interazione dei tunnel con il circuito idrico sotterraneo costituisce un problema sia dal punto di vista ambientale che ingegneristico. Lo scavo di un tunnel puô infatti causare abbassamenti dei livelli piezometrici, inoltre le venute d'acqua in galleria sono un notevole problema sia in fase costruttiva che di esercizio. Nel caso di acquiferi in materiale sciolto, l'influenza dello scavo di un tunnel sul circuito idrico sotterraneo, in genere, puô essere adeguatamente predetta attraverso l'applicazione di soluzioni analitiche; al contrario un approccio di questo tipo appare inadeguato nel caso di scavo in roccia. Per gli ammassi rocciosi fratturati sono piuttosto preferibili soluzioni numeriche e, a tal proposito, sono stati proposti diversi approcci concettuali; nella fattispecie l'ammasso roccioso puô essere modellato come un mezzo discreto ο continuo équivalente. Tuttavia, una corretta applicazione di qualsiasi modello numerico richiede necessariamente indagini preliminari sul comportamento del sistema idrico sotterraneo basate su dati idrogeochimici e geologico strutturali. Per approfondire il tema dell'idrogeologia in ammassi rocciosi fratturati tipici di ambienti montani, è stato condotto uno studio multidisciplinare nel sud della Svizzera sfruttando come casi studio due infrastrutture attualmente in costruzione: (i) il tunnel di base del Monte Ceneri (canton Ticino) e (ii) il tunnel autostradale di San Fedele (Roveredo, canton Grigioni). L'approccio di studio scelto ha cercato di integrare misure idrogeochimiche sulla qualité e quantité delle acque e indagini geofisiche. Nella fattispecie sono state campionate le acque in circa 60 punti spazialmente distribuiti sia in superficie che in sotterraneo; laddove possibile il monitoraggio si è temporalmente prolungato per più di un anno. In una prima fase, il progetto di ricerca si è concentrato sull'acquisizione dati. Diverse sorgenti, selezionate nelle aree di possibile influenza attorno allé infrastrutture esaminate, sono state monitorate per quel che concerne i parametri fisico-chimici: portata, conduttività elettrica, pH e temperatura. Campioni d'acqua sono stati prelevati mensilmente su sorgenti, venute d'acqua e precipitazioni, per analisi isotopiche; nella fattispecie, la composizione in isotopi stabili (δ2Η, δ180) tende a riflettere l'origine delle acque, in quanto, variazioni sia spaziali (altitudine di ricarica, topografia, etc.) che temporali (variazioni stagionali) della composizione isotopica delle precipitazioni influenzano anche le acque sotterranee. Laddove possibile, sono state campionate le venute d'acqua in galleria sia puntualmente che al variare del tempo. Le concentrazioni dei gas nobili disciolti nell'acqua e i loro rapporti isotopici sono stati altresi utilizzati in alcuni casi specifici per meglio spiegare l'origine delle acque e le tipologie di circuiti idrici sotterranei. Inoltre, diverse indagini geofisiche di resistività elettrica ed elettromagnetiche a bassissima frequenza (VLF) sono state condotte al fine di individuare le acque sotterranee circolanti attraverso fratture dell'ammasso roccioso. Principale obiettivo di questo lavoro è stato dimostrare come misure idrogeochimiche ed indagini geofisiche possano essere integrate alio scopo di sviluppare opportuni modelli idrogeologici concettuali utili per lo scavo di opere sotterranee. I principali risultati ottenuti al termine di questa ricerca sono stati: (i) aver testato con successo indagini geofisiche (ERT e VLF-EM) per l'individuazione di acque sotterranee circolanti attraverso fratture dell'ammasso roccioso e che possano essere causa di venute d'acqua in galleria durante lo scavo di tunnel; (ii) aver provato l'utilità di analisi su gas nobili, ioni maggiori e isotopi stabili per l'individuazione di faglie e per comprendere l'origine delle acque sotterranee (acque di recente infiltrazione ο provenienti da circolazioni profonde); (iii) aver testato in maniera convincente l'integrazione delle indagini geofisiche e di misure geochimiche per la valutazione della vulnérabilité delle sorgenti durante lo scavo di nuovi tunnel. - "La NLFA (Nouvelle Ligne Ferroviaire à travers les Alpes) axe du Saint-Gothard est le plus important projet de construction de Suisse. En bâtissant la nouvelle ligne du Saint-Gothard, la Suisse réalise un des plus grands projets de protection de l'environnement d'Europe". Cette phrase, qu'on lit comme présentation du projet Alptransit est particulièrement éloquente pour expliquer l'utilité des nouvelles lignes ferroviaires transeuropéens pour le développement durable. Toutefois, comme toutes grandes infrastructures, la construction de nouveaux tunnels ont des impacts inévitables sur l'environnement. En particulier, le possible drainage des eaux souterraines réalisées par le tunnel peut provoquer un abaissement du niveau des nappes piézométriques. De plus, l'écoulement de l'eau à l'intérieur du tunnel, conduit souvent à des problèmes d'ingénierie. Par exemple, d'importantes infiltrations d'eau dans le tunnel peuvent compliquer les phases d'excavation, provoquant un retard dans l'avancement et dans le pire des cas, peuvent mettre en danger la sécurité des travailleurs. Enfin, l'infiltration d'eau peut être un gros problème pendant le fonctionnement du tunnel. Du point de vue de la science, avoir accès à des infrastructures souterraines représente une occasion unique d'obtenir des informations géologiques en profondeur et pour échantillonner des eaux autrement inaccessibles. Dans ce travail, nous avons utilisé une approche pluridisciplinaire qui intègre des mesures d'étude hydrogéochimiques effectués sur les eaux de surface et des investigations géophysiques indirects, tels que la tomographic de résistivité électrique (TRE) et les mesures électromagnétiques de type VLF. L'étude complète a été fait en Suisse italienne, basée sur deux grandes infrastructures actuellement en construction, qui sont le tunnel ferroviaire de base du Monte Ceneri, une partie du susmentionné projet Alptransit, situé entièrement dans le canton Tessin, et le tunnel routière de San Fedele, situé a Roveredo dans le canton des Grisons. Le principal objectif était de montrer comment il était possible d'intégrer les deux approches, géophysiques et géochimiques, afin de répondre à la question de ce que pourraient être les effets possibles dû au drainage causés par les travaux souterrains. L'accès aux galeries ci-dessus a permis une validation adéquate des enquêtes menées confirmant, dans chaque cas, les hypothèses proposées. A cette fin, nous avons fait environ 50 profils géophysiques (28 imageries électrique bidimensionnels et 23 électromagnétiques) dans les zones de possible influence par le tunnel, dans le but d'identifier les fractures et les discontinuités dans lesquelles l'eau souterraine peut circuler. De plus, des eaux ont été échantillonnés dans 60 localités situées la surface ainsi que dans les tunnels subjacents, le suivi mensuelle a duré plus d'un an. Nous avons mesurés tous les principaux paramètres physiques et chimiques: débit, conductivité électrique, pH et température. De plus, des échantillons d'eaux ont été prélevés pour l'analyse mensuelle des isotopes stables de l'hydrogène et de l'oxygène (δ2Η, δ180). Avec ces analyses, ainsi que par la mesure des concentrations des gaz rares dissous dans les eaux et de leurs rapports isotopiques que nous avons effectués dans certains cas spécifiques, il était possible d'expliquer l'origine des différents eaux souterraines, les divers modes de recharge des nappes souterraines, la présence de possible phénomènes de mélange et, en général, de mieux expliquer les circulations d'eaux dans le sous-sol. Le travail, même en constituant qu'une réponse partielle à une question très complexe, a permis d'atteindre certains importants objectifs. D'abord, nous avons testé avec succès l'applicabilité des méthodes géophysiques indirectes (TRE et électromagnétiques de type VLF) pour prédire la présence d'eaux souterraines dans le sous-sol des massifs rocheux. De plus, nous avons démontré l'utilité de l'analyse des gaz rares, des isotopes stables et de l'analyses des ions majeurs pour la détection de failles et pour comprendre l'origine des eaux souterraines (eau de pluie par le haut ou eau remontant des profondeurs). En conclusion, avec cette recherche, on a montré que l'intégration des ces informations (géophysiques et géochimiques) permet le développement de modèles conceptuels appropriés, qui permettant d'expliquer comment l'eau souterraine circule. Ces modèles permettent de prévoir les infiltrations d'eau dans les tunnels et de prédire la vulnérabilité de sources et des autres ressources en eau lors de construction de tunnels.

Reconstruction of the recent history of a large deep prealpine lake (Lake Bourget, France) using subfossil chironomids, diatoms, and organic matter analysis: towards the definition of a lake-specific reference state

This paper presents the recent history of a large prealpine lake (Lake Bourget) using chironomids, diatoms and organic matter analysis, and deals with the ability of paleolimnological approach to define an ecological reference state for the lake in the sense of the European Framework Directive. The study at low resolution of subfossil chironomids in a 4-m-long core shows the remarkable stability over the last 2.5 kyrs of the profundal community dominated by a Micropsectra-association until the beginning of the twentieth century, when oxyphilous taxa disappeared. Focusing on this key recent period, a high resolution and multiproxy study of two short cores reveals a progressive evolution of the lake's ecological state. Until AD 1880, Lake Bourget showed low organic matter content in the deep sediments (TOC less than 1%) and a well-oxygenated hypolimnion that allowed the development of a profundal oxyphilous chironomid fauna (Micropsectra-association). Diatom communities were characteristic of oligotrophic conditions. Around AD 1880, a slight increase in the TOC was the first sign of changes in lake conditions. This was followed by a first limited decline in oligotrophic diatom taxa and the disappearance of two oxyphilous chironomid taxa at the beginning of the twentieth century. The 1940s were a major turning point in recent lake history. Diatom assemblages and accumulation of well preserved planktonic organic matter in the sediment provide evidence of strong eutrophication. The absence of profundal chironomid communities reveals permanent hypolimnetic anoxia. From AD 1995 to 2006, the diatom assemblages suggest a reduction in nutrients, and a return to mesotrophic conditions, a result of improved wastewater management. However, no change in hypolimnion benthic conditions has been shown by either the organic matter or the subfossil chironomid profundal community. Our results emphasize the relevance of the paleolimnological approach for the assessment of reference conditions for modern lakes. Before AD 1900, the profundal Micropsectra-association and the Cyclotella dominated diatom community can be considered as the Lake Bourget reference community, which reflects the reference ecological state of the lake.

Assessment of diesel exhaust particulate exposure and surface characteristics in association with levels of oxidative stress biomarkers

Exposure to PM10 and PM2.5 (particulate matter with aerodynamic diameter smaller than 10 μm and 2.5 μm, respectively) is associated with a range of adverse health effects, including cancer, pulmonary and cardiovascular diseases. Surface characteristics (chemical reactivity, surface area) are considered of prime importance to understand the mechanisms which lead to harmful effects. A hypothetical mechanism to explain these adverse effects is the ability of components (organics, metal ions) adsorbed on these particles to generate Reactive Oxygen Species (ROS), and thereby to cause oxidative stress in biological systems (Donaldson et al., 2003). ROS can attack almost any cellular structure, like DNA or cellular membrane, leading to the formation of a wide variety of degradation products which can be used as a biomarker of oxidative stress. The aim of the present research project is to test whether there is a correlation between the exposure to Diesel Exhaust Particulate (DEP) and the oxidative stress status. For that purpose, a survey has been conducted in real occupational situations where workers were exposed to DEP (bus depots). Different exposure variables have been considered: - particulate number, size distribution and surface area (SMPS); - particulate mass - PM2.5 and PM4 (gravimetry); - elemental and organic carbon (coulometry); - total adsorbed heavy metals - iron, copper, manganese (atomic adsorption); - surface functional groups present on aerosols (Knudsen flow reactor). Several biomarkers of oxidative stress (8-hydroxy-2'-deoxyguanosine and several aldehydes) have been determined either in urine or serum of volunteers. Results obtained during the sampling campaign in several bus depots indicated that the occupational exposure to particulates in these places was rather low (40-50 μg/m3 for PM4). Bimodal size distributions were generally observed (5 μm and <1 μm). Surface characteristics of PM4 varied strongly, depending on the bus depot. They were usually characterized by high carbonyl and low acidic sites content. Among the different biomarkers which have been analyzed within the framework of this study, mean urinary levels of 8-hydroxy-2'-deoxyguanosine increased significantly (p<0.05) during two consecutive days of exposure for non-smoker workers. On the other hand, no statistically significant differences were observed for serum levels of hexanal, nonanal and 4- hydroxy-nonenal (p>0.05). Biomarkers levels will be compared to exposure variables to gain a better understanding of the relation between the particulate characteristics and the formation of ROS by-products. This project is financed by the Swiss State Secretariat for Education and Research. It is conducted within the framework of the COST Action 633 "Particulate Matter - Properties Related to Health Effects".

Impact of engineered nanomaterials on health : considerations for benefit-risk assessment

Nanotechnology encompasses the design, characterisation, production and application of materials and systems by controlling shape and size at the nanoscale (nanometres). Nanomaterials may differ from other materials because of their relatively large specific surface area, such that surface properties become particularly important. There has been rapid growth in investment in nanotechnology by both the public and private sectors worldwide. In the EU, nanotechnology is expected to become an important strategic contributor to achieving economic gain and societal and individual benefits. At the same time there is continuing scientific uncertainty and controversy about the safety of nanomaterials. It is important to ensure that timely policy development takes this into consideration. Uncertainty about safety may lead to polarised public debate and to business unwillingness to invest further. A clear regulatory framework to address potential health and environmental impacts, within the wider context of evaluating and communicating the benefit-risk balance, must be a core part of Europe's integrated efforts for nanotechnology innovation. While a number of studies have been carried out on the effect of environmental nanoparticles, e.g. from combustion processes, on human health, there is yet no generally acceptable paradigm for safety assessment of nanomaterials in consumer and other products. Therefore, a working group was established to consider issues for the possible impact of nanomaterials on human health focussing specifically on engineered nanomaterials. This represents the first joint initiative between EASAC and the Joint Research Centre of the European Commission. The working group was given the remit to describe the state of the art of benefits and potential risks, current methods for safety assessment, and to evaluate their relevance, identify knowledge gaps in studying the safety of current nanomaterials, and recommend on priorities for nanomaterial research and the regulatory framework. This report focuses on key principles and issues, cross-referencing other sources for detailed information, rather than attempting a comprehensive account of the science. The focus is on human health although environmental effects are also discussed when directly relevant to health

Validation of the spiritual distress assessment tool in older hospitalized patients.

ABSTRACT:¦BACKGROUND: The Spiritual Distress Assessment Tool (SDAT) is a 5-item instrument developed to assess unmet spiritual needs in hospitalized elderly patients and to determine the presence of spiritual distress. The objective of this study was to investigate the SDAT psychometric properties.¦METHODS: This cross-sectional study was performed in a Geriatric Rehabilitation Unit. Patients (N = 203), aged 65 years and over with Mini Mental State Exam score ≥ 20, were consecutively enrolled over a 6-month period. Data on health, functional, cognitive, affective and spiritual status were collected upon admission. Interviews using the SDAT (score from 0 to 15, higher scores indicating higher distress) were conducted by a trained chaplain. Factor analysis, measures of internal consistency (inter-item and item-to-total correlations, Cronbach α), and reliability (intra-rater and inter-rater) were performed. Criterion-related validity was assessed using the Functional Assessment of Chronic Illness Therapy-Spiritual well-being (FACIT-Sp) and the question "Are you at peace?" as criterion-standard. Concurrent and predictive validity were assessed using the Geriatric Depression Scale (GDS), occurrence of a family meeting, hospital length of stay (LOS) and destination at discharge.¦RESULTS: SDAT scores ranged from 1 to 11 (mean 5.6 ± 2.4). Overall, 65.0% (132/203) of the patients reported some spiritual distress on SDAT total score and 22.2% (45/203) reported at least one severe unmet spiritual need. A two-factor solution explained 60% of the variance. Inter-item correlations ranged from 0.11 to 0.41 (eight out of ten with P < 0.05). Item-to-total correlations ranged from 0.57 to 0.66 (all P < 0.001). Cronbach α was acceptable (0.60). Intra-rater and inter-rater reliabilities were high (Intraclass Correlation Coefficients ranging from 0.87 to 0.96). SDAT correlated significantly with the FACIT-Sp, "Are you at peace?", GDS (Rho -0.45, -0.33, and 0.43, respectively, all P < .001), and LOS (Rho 0.15, P = .03). Compared with patients showing no severely unmet spiritual need, patients with at least one severe unmet spiritual need had higher odds of occurrence of a family meeting (adjOR 4.7, 95%CI 1.4-16.3, P = .02) and were more often discharged to a nursing home (13.3% vs 3.8%; P = .027).¦CONCLUSIONS: SDAT has acceptable psychometrics properties and appears to be a valid and reliable instrument to assess spiritual distress in elderly hospitalized patients.

Preoperative nutritional screening by the specialist instead of the nutritional risk score might prevent excess nutrition: a multivariate analysis of nutritional risk factors.

BACKGROUND: The aim of the current study was to assess whether widely used nutritional parameters are correlated with the nutritional risk score (NRS-2002) to identify postoperative morbidity and to evaluate the role of nutritionists in nutritional assessment. METHODS: A randomized trial on preoperative nutritional interventions (NCT00512213) provided the study cohort of 152 patients at nutritional risk (NRS-2002 ≥3) with a comprehensive phenotyping including diverse nutritional parameters (n=17), elaborated by nutritional specialists, and potential demographic and surgical (n=5) confounders. Risk factors for overall, severe (Dindo-Clavien 3-5) and infectious complications were identified by univariate analysis; parameters with P<0.20 were then entered in a multiple logistic regression model. RESULTS: Final analysis included 140 patients with complete datasets. Of these, 61 patients (43.6%) were overweight, and 72 patients (51.4%) experienced at least one complication of any degree of severity. Univariate analysis identified a correlation between few (≤3) active co-morbidities (OR=4.94; 95% CI: 1.47-16.56, p=0.01) and overall complications. Patients screened as being malnourished by nutritional specialists presented less overall complications compared to the not malnourished (OR=0.47; 95% CI: 0.22-0.97, p=0.043). Severe postoperative complications occurred more often in patients with low lean body mass (OR=1.06; 95% CI: 1-1.12, p=0.028). Few (≤3) active co-morbidities (OR=8.8; 95% CI: 1.12-68.99, p=0.008) were related with postoperative infections. Patients screened as being malnourished by nutritional specialists presented less infectious complications (OR=0.28; 95% CI: 0.1-0.78), p=0.014) as compared to the not malnourished. Multivariate analysis identified few co-morbidities (OR=6.33; 95% CI: 1.75-22.84, p=0.005), low weight loss (OR=1.08; 95% CI: 1.02-1.14, p=0.006) and low hemoglobin concentration (OR=2.84; 95% CI: 1.22-6.59, p=0.021) as independent risk factors for overall postoperative complications. Compliance with nutritional supplements (OR=0.37; 95% CI: 0.14-0.97, p=0.041) and supplementation of malnourished patients as assessed by nutritional specialists (OR=0.24; 95% CI: 0.08-0.69, p=0.009) were independently associated with decreased infectious complications. CONCLUSIONS: Nutritional support based upon NRS-2002 screening might result in overnutrition, with potentially deleterious clinical consequences. We emphasize the importance of detailed assessment of the nutritional status by a dedicated specialist before deciding on early nutritional intervention for patients with an initial NRS-2002 score of ≥3.

Quantitative TCR:pMHC Dissociation Rate Assessment by NTAmers Reveals Antimelanoma T Cell Repertoires Enriched for High Functional Competence.

Experimental models demonstrated that therapeutic induction of CD8 T cell responses may offer protection against tumors or infectious diseases providing that T cells have sufficiently high TCR/CD8:pMHC avidity for efficient Ag recognition and consequently strong immune functions. However, comprehensive characterization of TCR/CD8:pMHC avidity in clinically relevant situations has remained elusive. In this study, using the novel NTA-His tag-containing multimer technology, we quantified the TCR:pMHC dissociation rates (koff) of tumor-specific vaccine-induced CD8 T cell clones (n = 139) derived from seven melanoma patients vaccinated with IFA, CpG, and the native/EAA or analog/ELA Melan-A(MART-1)(26-35) peptide, binding with low or high affinity to MHC, respectively. We observed substantial correlations between koff and Ca(2+) mobilization (p = 0.016) and target cell recognition (p < 0.0001), with the latter independently of the T cell differentiation state. Our strategy was successful in demonstrating that the type of peptide impacted on TCR/CD8:pMHC avidity, as tumor-reactive T cell clones derived from patients vaccinated with the low-affinity (native) peptide expressed slower koff rates than those derived from patients vaccinated with the high-affinity (analog) peptide (p < 0.0001). Furthermore, we observed that the low-affinity peptide promoted the selective differentiation of tumor-specific T cells bearing TCRs with high TCR/CD8:pMHC avidity (p < 0.0001). Altogether, TCR:pMHC interaction kinetics correlated strongly with T cell functions. Our study demonstrates the feasibility and usefulness of TCR/CD8:pMHC avidity assessment by NTA-His tag-containing multimers of naturally occurring polyclonal T cell responses, which represents a strong asset for the development of immunotherapy.

Social sensing for psychology: Automated interpersonal behavior assessment

In this article, we show how the use of state-of-the-art methods in computer science based on machine perception and learning allows the unobtrusive capture and automated analysis of interpersonal behavior in real time (social sensing). Given the high ecological validity of the behavioral sensing, the ease of behavioral-cue extraction for large groups over long observation periods in the field, the possibility of investigating completely new research questions, and the ability to provide people with immediate feedback on behavior, social sensing will fundamentally impact psychology.

Use of the nutritional risk score by surgeons and nutritionists.

BACKGROUND: The Nutritional Risk Score (NRS) is a validated tool to identify patients who should benefit of nutritional interventions. Nutritional screening however has not yet been widely adopted by surgeons. Furthermore, the question about reliability of nutritional assessment performed by surgeons is still unanswered. METHODS: Data was obtained from a recent randomised trial including 146 patients with an NRS ≥3 as assessed by the surgeons. Additional detailed nutritional assessment was performed for all patients by nutritional specialists and entered prospectively in a dedicated database. In this retrospective, surgeons' scoring of NRS and its components was compared to the assessment by nutritionists (considered as gold standard). RESULTS: Prospective NRS scores by surgeons and nutritionists were available for 141 patients (97%). Surgeons calculated a NRS of 7, 6, 5, 4 and 3 in 2, 8, 38, 21 and 72 patients respectively. Nutritionists calculated a NRS of 6, 5, 4, 3 and 2 in 8, 26, 47, 57, 3 patients, respectively. Surgeons' assessment was entirely correct in 56 patients (40%), while at least the final score was consistent in 63 patients (45%). Surgeons overrated the NRS in 21% of patients and underestimated the score in 29%. Evaluation of the nutritional status showed most of the discrepancies (54%). CONCLUSION: Surgeon's assessment of nutritional status is modest at best. Close collaboration with nutritional specialists should be recommended in order to avoid misdiagnosis and under-treatment of patients at nutritional risk.

A non-contrast self-navigated 3-dimensional MR technique for aortic root and vascular access route assessment in the context of transcatheter aortic valve replacement: proof of concept.

OBJECTIVES: Due to the high prevalence of renal failure in transcatheter aortic valve replacement (TAVR) candidates, a non-contrast MR technique is desirable for pre-procedural planning. We sought to evaluate the feasibility of a novel, non-contrast, free-breathing, self-navigated three-dimensional (SN3D) MR sequence for imaging the aorta from its root to the iliofemoral run-off in comparison to non-contrast two-dimensional-balanced steady-state free-precession (2D-bSSFP) imaging. METHODS: SN3D [field of view (FOV), 220-370 mm(3); slice thickness, 1.15 mm; repetition/echo time (TR/TE), 3.1/1.5 ms; and flip angle, 115°] and 2D-bSSFP acquisitions (FOV, 340 mm; slice thickness, 6 mm; TR/TE, 2.3/1.1 ms; flip angle, 77°) were performed in 10 healthy subjects (all male; mean age, 30.3 ± 4.3 yrs) using a 1.5-T MRI system. Aortic root measurements and qualitative image ratings (four-point Likert-scale) were compared. RESULTS: The mean effective aortic annulus diameter was similar for 2D-bSSFP and SN3D (26.7 ± 0.7 vs. 26.1 ± 0.9 mm, p = 0.23). The mean image quality of 2D-bSSFP (4; IQR 3-4) was rated slightly higher (p = 0.03) than SN3D (3; IQR 2-4). The mean total acquisition time for SN3D imaging was 12.8 ± 2.4 min. CONCLUSIONS: Our results suggest that a novel SN3D sequence allows rapid, free-breathing assessment of the aortic root and the aortoiliofemoral system without administration of contrast medium. KEY POINTS: • The prevalence of renal failure is high among TAVR candidates. • Non-contrast 3D MR angiography allows for TAVR procedure planning. • The self-navigated sequence provides a significantly reduced scanning time.