How useful is satellite positioning system (GPS) to track gait parameters? A review.

Over the last century, numerous techniques have been developed to analyze the movement of humans while walking and running. The combined use of kinematics and kinetics methods, mainly based on high speed video analysis and forceplate, have permitted a comprehensive description of locomotion process in terms of energetics and biomechanics. While the different phases of a single gait cycle are well understood, there is an increasing interest to know how the neuro-motor system controls gait form stride to stride. Indeed, it was observed that neurodegenerative diseases and aging could impact gait stability and gait parameters steadiness. From both clinical and fundamental research perspectives, there is therefore a need to develop techniques to accurately track gait parameters stride-by-stride over a long period with minimal constraints to patients. In this context, high accuracy satellite positioning can provide an alternative tool to monitor outdoor walking. Indeed, the high-end GPS receivers provide centimeter accuracy positioning with 5-20 Hz sampling rate: this allows the stride-by-stride assessment of a number of basic gait parameters--such as walking speed, step length and step frequency--that can be tracked over several thousand consecutive strides in free-living conditions. Furthermore, long-range correlations and fractal-like pattern was observed in those time series. As compared to other classical methods, GPS seems a promising technology in the field of gait variability analysis. However, relative high complexity and expensiveness--combined with a usability which requires further improvement--remain obstacles to the full development of the GPS technology in human applications.

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

MOTIVATION: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. Results: We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays.

Factors influencing the adoption of an innovation: an examination of the uptake of the Canadian Heart Health Kit (HHK)

BACKGROUND: There is an emerging knowledge base on the effectiveness of strategies to close the knowledge-practice gap. However, less is known about how attributes of an innovation and other contextual and situational factors facilitate and impede an innovation's adoption. The Healthy Heart Kit (HHK) is a risk management and patient education resource for the prevention of cardiovascular disease (CVD) and promotion of cardiovascular health. Although previous studies have demonstrated the HHK's content validity and practical utility, no published study has examined physicians' uptake of the HHK and factors that shape its adoption. OBJECTIVES: Conceptually informed by Rogers' Diffusion of Innovation theory, and Theory of Planned Behaviour, this study had two objectives: (1) to determine if specific attributes of the HHK as well as contextual and situational factors are associated with physicians' intention and actual usage of the HHK kit; and (2), to determine if any contextual and situational factors are associated with individual or environmental barriers that prevent the uptake of the HHK among those physicians who do not plan to use the kit. METHODS: A sample of 153 physicians who responded to an invitation letter sent to all family physicians in the province of Alberta, Canada were recruited for the study. Participating physicians were sent a HHK, and two months later a study questionnaire assessed primary factors on the physicians' clinical practice, attributes of the HHK (relative advantage, compatibility, complexity, trialability, observability), confidence and control using the HHK, barriers to use, and individual attributes. All measures were used in path analysis, employing a causal model based on Rogers' Diffusion of Innovations Theory and Theory of Planned Behaviour. RESULTS: 115 physicians (follow up rate of 75%) completed the questionnaire. Use of the HHK was associated with intention to use the HHK, relative advantage, and years of experience. Relative advantage and the observability of the HHK benefits were also significantly associated with physicians' intention to use the HHK. Physicians working in solo medical practices reported experiencing more individual and environmental barriers to using the HHK. CONCLUSION: The results of this study suggest that future information innovations must demonstrate an advantage over current resources and the research evidence supporting the innovation must be clearly visible. Findings also suggest that the innovation adoption process has a social element, and collegial interactions and discussions may facilitate that process. These results could be valuable for knowledge translation researchers and health promotion developers in future innovation adoption planning.

Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity.

Sarcomas are heterogeneous and aggressive mesenchymal tumors. Histological grading has so far been the best predictor for metastasis-free survival, but it has several limitations, such as moderate reproducibility and poor prognostic value for some histological types. To improve patient grading, we performed genomic and expression profiling in a training set of 183 sarcomas and established a prognostic gene expression signature, complexity index in sarcomas (CINSARC), composed of 67 genes related to mitosis and chromosome management. In a multivariate analysis, CINSARC predicts metastasis outcome in the training set and in an independent 127 sarcomas validation set. It is superior to the Fédération Francaise des Centres de Lutte Contre le Cancer grading system in determining metastatic outcome for sarcoma patients. Furthermore, it also predicts outcome for gastrointestinal stromal tumors (GISTs), breast carcinomas and lymphomas. Application of the signature will permit more selective use of adjuvant therapies for people with sarcomas, leading to decreased iatrogenic morbidity and improved outcomes for such individuals.

Predictors of developmental dyslexia in European orthographies with varying complexity.

Background:  The relationship between phoneme awareness, rapid automatized naming (RAN), verbal short-term/working memory (ST/WM) and diagnostic category is investigated in control and dyslexic children, and the extent to which this depends on orthographic complexity. Methods:  General cognitive, phonological and literacy skills were tested in 1,138 control and 1,114 dyslexic children speaking six different languages spanning a large range of orthographic complexity (Finnish, Hungarian, German, Dutch, French, English). Results:  Phoneme deletion and RAN were strong concurrent predictors of developmental dyslexia, while verbal ST/WM and general verbal abilities played a comparatively minor role. In logistic regression models, more participants were classified correctly when orthography was more complex. The impact of phoneme deletion and RAN-digits was stronger in complex than in less complex orthographies. Conclusions:  Findings are largely consistent with the literature on predictors of dyslexia and literacy skills, while uniquely demonstrating how orthographic complexity exacerbates some symptoms of dyslexia.

Care complexity, mood, and quality of life in liver pre-transplant patients.

RATIONALE: This study was intended to document the frequency of care complexity in liver transplant candidates, and its association with mood disturbance and poor health-related quality of life (HRQoL). METHODS: Consecutive patients fulfilling inclusion criteria, recruited in three European hospitals, were assessed with INTERMED, a reliable and valid method for the early assessment of bio-psychosocial health risks and needs. Blind to the results, they were also assessed with the Hospital Anxiety and Depression Scale (HADS). HRQoL was documented with the EuroQol and the SF36. Statistical analysis included multivariate and multilevel techniques. RESULTS: Among patients fulfilling inclusion criteria, 60 patients (75.9%) completed the protocol and 38.3% of them were identified as "complex" by INTERMED, but significant between-center differences were found. In support of the working hypothesis, INTERMED scores were significantly associated with all measures of both the SF36 and the EuroQol, and also with the HADS. A one point increase in the INTERMED score results in a reduction in 0.93 points in EuroQol and a 20% increase in HADS score. CONCLUSIONS: INTERMED-measured case complexity is frequent in liver transplant candidates but varies widely between centers. The use of this method captures in one instrument multiple domains of patient status, including mood disturbances and reduced HRQoL.

Simulations in evolution. II. Relative fitness and the propagation of mutants.

In Neo-Darwinism, variation and natural selection are the two evolutionary mechanisms which propel biological evolution. Our previous article presented a histogram model [1] consisting in populations of individuals whose number changed under the influence of variation and/or fitness, the total population remaining constant. Individuals are classified into bins, and the content of each bin is calculated generation after generation by an Excel spreadsheet. Here, we apply the histogram model to a stable population with fitness F(1)=1.00 in which one or two fitter mutants emerge. In a first scenario, a single mutant emerged in the population whose fitness was greater than 1.00. The simulations ended when the original population was reduced to a single individual. The histogram model was validated by excellent agreement between its predictions and those of a classical continuous function (Eqn. 1) which predicts the number of generations needed for a favorable mutation to spread throughout a population. But in contrast to Eqn. 1, our histogram model is adaptable to more complex scenarios, as demonstrated here. In the second and third scenarios, the original population was present at time zero together with two mutants which differed from the original population by two higher and distinct fitness values. In the fourth scenario, the large original population was present at time zero together with one fitter mutant. After a number of generations, when the mutant offspring had multiplied, a second mutant was introduced whose fitness was even greater. The histogram model also allows Shannon entropy (SE) to be monitored continuously as the information content of the total population decreases or increases. The results of these simulations illustrate, in a graphically didactic manner, the influence of natural selection, operating through relative fitness, in the emergence and dominance of a fitter mutant.

Dire le futur au Moyen Age : du prologue au récit : du Chevalier au Lion de Chrétien de Troyes au Chevalier au Lion de Pierre Sala

S'inscrivant dans le domaine de l'analyse des relations temporelles dans les textes, la présente étude est consacrée à la notion du futur définie en tant qu'anticipation sur les événements à venir dans le récit. Ainsi, la recherche en question se propose de mettre en lumière les différents mécanismes d'anticipation propres aux récits d'aventures au Moyen Âge. Recourant aux moyens heuristiques existants (les bases de la théorie de la réception telle qu'elle est représentée dans les travaux de Jauss, Eco et Greimas), cette thèse se concentre sur l'étude du prologue de l'oeuvre littéraire dont elle élabore une grille de lecture particulière qui tient compte de la complexité de la notion du futur envisagée aux plans grammatical (formes verbales du futur), rhétorique (la figure de la prolepse) et littéraire (les scénarios et les isotopies). La démarche de la lecture détaillée du prologue adoptée au cours de ce travail s'applique d'abord au Chevalier au Lion de Chrétien de Troyes, texte fondateur du corpus, qui constitue, pour parler avec Philippe Walter, un vrai « drame du temps ». L'étude des mécanismes d'anticipation mis en place dans le prologue se prolonge ensuite dans les chapitres consacrés à Claris et Laris et au Chevalier au Lion de Pierre Sala, deux réécritures du célèbre roman du maître champenois. Datant, respectivement, du XIIIe et du début du XVIe siècle, ces oeuvres permettent de saisir le chemin parcouru par le futur dans son aspect thématique et diachronique, ce qui est particulièrement propice au repérage des critères qui influencent l'attente du lecteur par rapport aux événements à venir au fil des siècles. Ainsi, à côté des moyens d'expression « standards » du futur (scénarios intertextuels et isotopies), la présente recherche fait apparaître d'autres facteurs qui influencent l'anticipation, notamment le procédé de la disputatio, le recours à la satire, la démarche de l'engagement indirect et l'opposition vers/prose. La seconde partie de la thèse qui traite, d'un côté, des récits consacrés à la fée Mélusine de Jean d'Arras et de Coudrette, du Livre du Cuer d'amours espris de René d'Anjou de l'autre, sert à vérifier dans quelle mesure la démarche choisie s'applique à des oeuvres du Moyen Âge tardif qui combinent des éléments empruntés à la tradition antérieure avec des éléments d'autre provenance. L'analyse de Mélusine et du Livre du Cuer conduit à ajouter deux facteurs supplémentaires qui influencent l'attente du lecteur, à savoir la démarche de l'engagement partiel et le recours au genre judiciaire. Cette étude démontre que le traitement du futur est d'un enjeu capital pour lire les textes du Moyen Âge, car il permet au lecteur, dès le prologue, de reconnaître la fin vers laquelle tend le récit et de faire par là- même une lecture enrichie, supérieure à d'autres. Telling the Future in the Middle Ages : from the Prologue to the Narrative. From Chrétien de Troyes ' Chevalier au Lion to Pierre Sala 's Chevalier au Lion. Part of the analyses of the time based relations within the texts, the present study deals with the notion of future characterized as an anticipation of the events to come in the narrative. Therefore, the purpose of this research is to bring to light the various mechanisms of anticipation peculiar to the narratives of adventures in the Middle Ages. Making the use of the existing heuristic instruments (the bases of the theory of the reception as it presents itself in the works by Jauss, Eco and Greimas), this thesis is dedicated to the study of the prologue of the work of fiction by means of a particular key for reading which takes into account the complexity of the notion of future with regard to its grammatical side (future tenses), to its rhetorical side (prolepse) and to its literary side (scenario and isotopy). First of all, the close reading of the prologue used in this work is applied to Chrétien de Troyes's Chevalier au Lion (Lion Knight), the founding text of our literary corpus, which represents, according to Philippe Walter, the real « drama of Time ». Then, the study of the mechanisms of anticipation in the prologue is carried over to the chapters devoted to Claris et Laris and to Pierre Sala's Chevalier au Lion, two romances that rewrite Chrétien de Troyes' famous work. Written, respectively, in the XIIIth and in the beginning of the XVI century, these romances enable the reader to ascertain the changes in the manner of telling the future from the thematic and diachronic point of view : this is particularly convenient to the identification of the criteria which influence the reader's expectations relative to the future events in the course of the centuries. Therefore, next to the « standard » means of expression of future (intertextual scenario and isotopy), the present study reveals other factors which influence the anticipation, in particular the method of the disputatio, the use of the satire, the approach of the indirect commitment and the verse/prose opposition. The second part of the thesis which deals with the narratives concerning the fairy Melusine written by Jean d'Arras and by Coudrette on one hand, with René d'Anjou's Livre du Cuer d'amours espris on the other hand, is used to verify to what extent the chosen approach applies to the works of fiction of the Late Middle Ages that combine the elements from the previous tradition with the elements of other origin. The analysis of Melusine's romances and of the Livre du Cuer brings us to add two new factors which influence the reader's expectations : the approach of the partial commitment, and the use of the legal discourse. This study demonstrates that the manner of telling the future is of the utmost importance to read the texts of the Middle Ages, because it enables the reader to know the end of the story from the very beginning, from the prologue, thus leading to a richer and superior reading.

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.

Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Growth decrease in Alpine whitefish: investigating the relative contribution of fishing induced selection and environmental change and its implication for conservation measures

La pression exercée par les activités humaines menace pratiquement tous les écosystèmes aquatiques du globe. Ainsi, sous l'effet de divers facteurs tels que la pollution, le réchauffement climatique ou encore la pêche industrielle, de nombreuses populations de poissons ont vu leurs effectifs chuter et divers changements morphologiques ont été observés. Dans cette étude, nous nous sommes intéressés à une menace particulière: la sélection induite par la pêche sur la croissance des poissons. En effet, la génétique des populations prédit que la soustraction régulière des individus les plus gros peut entraîner des modifications rapides de certains traits physiques comme la croissance individuelle. Cela a par ailleurs été observé dans de nombreuses populations marines ou lacustres, dont les populations de féras, bondelles et autres corégones des lacs suisses. Toutefois, malgré un nombre croissant d'études décrivant ce phénomène, peu de plans de gestion en tiennent compte, car l'importance des effets génétiques liés à la pêche est le plus souvent négligée par rapport à l'impact des changements environnementaux. Le but premier de cette étude a donc été de quantifier l'importance des facteurs génétiques et environnementaux. Dans le premier chapitre, nous avons étudié la population de palée du lac de Joux (Coregonus palaea). Nous avons déterminé les différentiels de sélection dus à la pêche, c'est-à-dire l'intensité de la sélection sur le taux de croissance, ainsi que les changements nets de croissance au cours du temps. Nous avons observé une baisse marquée de croissance et un différentiel de sélection important indiquant qu'au moins 30% de la diminution de croissance observée était due à la pression de sélection induite par la pêche. Dans le deuxième chapitre, nous avons effectué les mêmes analyses sur deux espèces proches du lac de Brienz (C. albellus et C. fatioi) et avons observé des effets similaires dont l'intensité était spécifique à chaque espèce. Dans le troisième chapitre, nous avons analysé deux autres espèces : C. palaea et C. confusus du lac de Bienne, et avons constaté que le lien entre la pression de sélection et la diminution de croissance était influencé par des facteurs environnementaux. Finalement, dans le dernier chapitre, nous avons étudié les effets potentiels de différentes modifications de la taille des mailles des filets utilisés pour la pêche à l'aide de modèles mathématiques. Nous concluons que la pêche a un effet génétique non négligeable (et donc peu réversible) sur la croissance individuelle dans les populations observée, que cet effet est lié à la compétition pour la nourriture et à la qualité de l'environnement, et que certaines modifications simples de la taille des mailles des filets de pêche pourraient nettement diminuer l'effet de sélection et ainsi ralentir, voir même renverser la diminution de croissance observée.

Effect of a governmentally-led physical activity program on motor skills in young children attending child care centers: a cluster randomized controlled trial.

OBJECTIVE: To assess the effect of a governmentally-led center based child care physical activity program (Youp'la Bouge) on child motor skills.Patients and methods: We conducted a single blinded cluster randomized controlled trial in 58 Swiss child care centers. Centers were randomly selected and 1:1 assigned to a control or intervention group. The intervention lasted from September 2009 to June 2010 and included training of the educators, adaptation of the child care built environment, parental involvement and daily physical activity. Motor skill was the primary outcome and body mass index (BMI), physical activity and quality of life secondary outcomes. The intervention implementation was also assessed. RESULTS: At baseline, 648 children present on the motor test day were included (age 3.3 +/- 0.6, BMI 16.3 +/- 1.3 kg/m2, 13.2% overweight, 49% girls) and 313 received the intervention. Relative to children in the control group (n = 201), children in the intervention group (n = 187) showed no significant increase in motor skills (delta of mean change (95% confidence interval: -0.2 (-0.8 to 0.3), p = 0.43) or in any of the secondary outcomes. Not all child care centers implemented all the intervention components. Within the intervention group, several predictors were positively associated with trial outcomes: 1) free-access to a movement space and parental information session for motor skills 2) highly motivated and trained educators for BMI 3) free-access to a movement space and purchase of mobile equipment for physical activity (all p < 0.05). CONCLUSION: This "real-life" physical activity program in child care centers confirms the complexity of implementing an intervention outside a study setting and identified potentially relevant predictors that could improve future programs.Trial registration: Trial registration number: clinical trials.gov NCT00967460 http://clinicaltrials.gov/ct2/show/NCT00967460.

Origin and expansion of the allotetraploid Aegilops geniculata, a wild relative of wheat.

*This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species. *We combined chloroplast DNA (cpDNA) sequencing, analysed using statistical parsimony network, with nonhierarchical K-means clustering of amplified fragment length polymorphism (AFLP) genotyping, to unravel patterns of genetic structure across the native range of Ae. geniculata. The AFLP dataset was further explored by measurement of the regional genetic diversity and the detection of isolation by distance patterns. *Both cpDNA and AFLP suggest an eastern Mediterranean origin of Ae. geniculata. Two lineages have spread independently over northern and southern Mediterranean areas. Northern populations show low genetic diversity but strong phylogeographical structure among the main peninsulas, indicating a major influence of glacial cycles. By contrast, low genetic structuring and a high genetic diversity are detected in southern Mediterranean populations. Finally, we highlight human-mediated dispersal resulting in substantial introgression between resident and migrant populations. *We have shown that the evolutionary trajectories of ruderal plants can be similar to those of wild species, but are interfered by human activities, promoting range expansions through increased long-distance dispersal and the creation of suitable habitats.