yes / Background Unilateral trans-tibial amputees have bilaterally reduced toe clearance, and an increased risk of foot contact, while crossing obstacles compared to the able-bodied. While the able-bodied tend to lead with a ‘preferred’ limb it is equivocal whether amputees prefer to lead with the intact or prosthetic limb. This study determined the effects of laterality, compared to side of amputation, on amputees' obstacle crossing performance. To help understand why laterality could affect performance we also assessed knee proprioception for both limbs. Methods Foot placement and toe clearance parameters were recorded while nine amputees crossed obstacles of varying heights leading with both their intact and prosthetic limbs. Joint-position sense was also assessed. Participants self-reported which limb was their preferred (dominant) limb. Findings There were no significant differences in foot placements or toe clearance variability across lead-limb conditions. There were no significant differences in toe clearance between intact and prosthetic lead-limbs (p = 0.28) but toe clearance was significantly higher when amputees led with their preferred compared to non-preferred limb (p = 0.025). There was no difference in joint-position sense between the intact and residual knees (p = 0.34) but joint-position sense tended to be more accurate for the preferred, compared to non-preferred limb (p = 0.08). Interpretation Findings suggest that, despite the mechanical constraints imposed by use of a prosthesis, laterality may be as important in lower-limb amputees as it is in the able bodied. This suggests that amputees should be encouraged to cross obstacles leading with their preferred limb. / Engineering and Physical Sciences Research Council

Wavelet intensity based algorithm developed previously at VirginiaTech has been furthered and paired with an SVM based classifier. The wavelet intensity algorithm acts as a feature extraction algorithm. The wavelet transform is an effective tool as it allows one to narrow down upon the transient, high frequency events and is able to tell their exact location in time. According to prior work done in the field of signal processing, the local regularities of a signal can be estimated using a Lipchitz exponent at each time step of the signal. The local Lipchitz exponent can then be used to generate the wavelet intensity factor values. For each vertical acceleration value, corresponding to a specific location on the track, we now have a corresponding intensity factor. The intensity factor corresponds to break-no break information and can now be used as a feature to classify the vertical acceleration as a fault or no fault. Support Vector Machines (SVM) is used for this binary classification task. SVM is chosen as it is a well-studied topic with efficient implementations available. SVM instead of hard threshold of the data is expected to do a better job of classification without increasing the complexity of the system appreciably. / Master of Science

Yes / Trips over obstacles are one of the main causes of falling in older adults, with vision playing an important role in successful obstacle negotiation. We determined whether a horizontal-vertical illusion, superimposed onto low-height obstacles to create a perceived increase in obstacle height, increased foot clearances during obstacle negotiation thus reducing the likelihood of tripping. Eleven adults (mean ± 1 SD: age 27.3 ± 5.1 years) negotiated obstacles of varying heights (3, 5, 7 cm) with four different appearance conditions; two were obstacles with a horizontal-vertical illusion (vertical stripes of different thickness) superimposed on the front, one was a plain obstacle and the fourth a plain obstacle with a horizontal black line painted on the top edge. Foot clearance parameters were compared across conditions. Both illusions led to a significant increase in foot clearance when crossing the obstacle, compared to the plain condition, irrespective of obstacle height. Superimposing a horizontal-vertical illusion onto low-height obstacles can increase foot clearance, and its use on the floor section of a double-glazing door frame for example may reduce the incidence of tripping in the home.

No / The purpose of this article is to determine the relative importance to adaptive locomotion of peripheral visual cues provided by different parts of the visual field. Twelve subjects completed obstacle crossing trials while wearing goggles that provided four visual conditions: upper visual field occlusion, lower visual field occlusion (LO), circumferential peripheral visual field occlusion (CPO), and full vision. The obstacle was either positioned as a lone structure or within a doorframe. Given that subjects completed the task safely without cues from the lower or peripheral visual field, this suggests that subjects used exteroceptive information provided in a feed-forward manner under these conditions. LO and CPO led to increased foot placement distance from the obstacle and to increased toe clearance over the obstacle with a reduced crossing-walking velocity. The increased variability of dependent measures under LO and CPO suggests that exproprioceptive information from the peripheral visual field is generally used to provide online control of lower limbs. The presence of the doorframe facilitated lead-foot placement under LO by providing exproprioceptive cues in the upper visual field. However, under CPO conditions, the doorframe led to a further reduction in crossing velocity and increase in trail-foot horizontal distance and lead-toe clearance, which may have been because of concerns about hitting the doorframe with the head and/or upper body. Our findings suggest that exteroceptive cues are provided by the central visual field and are used in a feed-forward manner to plan the gait adaptations required to safely negotiate an obstacle, whereas exproprioceptive information is provided by the peripheral visual field and used online to “fine tune” adaptive gait. The loss of the upper and lower peripheral visual fields together had a greater effect on adaptive gait compared with the loss of the lower visual field alone, likely because of the absence of lamellar flow visual cues used to control egomotion.

L’agriculture moderne doit assurer notre sécurité alimentaire dans le contexte d’un changement climatique qui entraîne une baisse des rendements. Une meilleure compréhension des facteurs contrôlant la recombinaison méiotique ouvrirait la voie à la modification du nombre et de la répartition des crossing-overs, ce qui permettrait une localisation plus précise des facteurs génétiques contrôlant les caractères d’intérêt agronomique et faciliterait le pyramidage d’allèles favorables au sein d’un même génotype élite. Pendant ma thèse, j’ai développé une méthode de mesure à haut débit de la recombinaison chez la levure Saccharomyces cerevisiae pour étudier la diversité de la recombinaison et de l’interférence au sein d’une collection de 24 souches représentatives de la diversité de l’espèce ainsi qu’au sein d’un dispositif di-allèle à cinq parents. Les résultats montrent un nombre moyen de crossing-overs par méiose compris entre 24 et 61, ce qui est plus élevé que chez la majorité des autres espèces. Plus particulièrement, les profils de recombinaison diffèrent entre souches, atteignant un écart d’un facteur 9 dans certaines régions. Les souches originaires d’habitats peu stables n’ont cependant pas un niveau de recombinaison plus élevé que les souches originaires d’environnements stables. En outre, la plupart des souches montrent de l’interférence dont la force est corrélée positivement avec le niveau de recombinaison. L’étude de la relation entre niveau de recombinaison et similarité de séquence entre homologues, à différentes échelles locales ou globales, indique que la recombinaison est contrôlée à la fois par des éléments cis et des facteurs trans. Par ailleurs, l’hétérozygotie chez les hybrides a un effet négatif sur le niveau de recombinaison, mais les homozygotes ont aussi un niveau de recombinaison réduit par un effet de dépression de consanguinité. Ce travail permettra maintenant d’étudier la réponse de la recombinaison à la sélection et de détecter les QTL de nombre de crossing-overs, afin d’identifier des gènes qui contrôlent la recombinaison. / Modern agriculture must ensure food security in a context of climate change that will lower yields. A better understanding of the factors controlling meiotic recombination could pave the way to modifying the number and distribution of crossing-over, which would allow a more precise localization of genetic factors controlling agronomic traits, and facilitate gene pyramiding in selection programs. During my thesis, I developed a method for high-throughput measurement of recombination rates in the yeast Saccharomyces cerevisiae. This allowed me to study the diversity of recombination and interference in a collection of 24 strains representing most of the diversity of the species, as well as within a five-parent di-allele design. The results show an average number of crossovers per meiosis ranging between 24 and 61, higher than in the majority of other species. Furthermore, recombination patterns differ between strains, and ratios of local recombination rates show 9-fold differences in some regions. Strains from unstable habitats, however, do not have a higher level of recombination than those from stable environments. In addition, most strains show interference whose strength is positively correlated with the level of recombination. The study of the relationship between recombination rate and sequence similarity between homologs at different scales (from local to global) indicates that recombination is controlled by both cis elements and trans factors. Lastly, heterozygosity in hybrids has a negative effect on crossing-over, but homozygotes also have a reduced level of recombination due to inbreeding depression. This work will now be used to study the response of recombination to selection and to detect QTL of crossover number in order to identify genes controlling recombination.

Dans un contexte de vieillissement démographique et de mutation des modes de déplacements urbains majorant la place du piéton, ce travail de thèse vise à mieux comprendre les caractéristiques comportementales et biomécaniques de la traversée de rue des piétons âgés. La méthodologie est essentiellement expérimentale. Si quelques données ont été recueillies en laboratoire ou en environnement naturel, l'étude principale a été conduite dans un simulateur immersif de réalité projetée, outil dénommé Simulateur de Rues pour Piétons (SRP). La hauteur de trottoir est modulable. Le dispositif intègre différents outils de mesures, tels des plates-formes de force et un système d'analyse gestuelle en trois dimensions. Hors simulateur, la comparaison des temps de traversée réelle et estimée, sur un champ de marche, révèle l'occurrence d'un risque de sous-estimation a priori du temps nécessaire chez certains seniors. L'expérience en simulateur confirme l'importance de la modulation exercée par le vieillissement sur la perception du temps en tant que déterminant des estimations a posteriori des temps de traversées quantifiées via la sensation de mise en danger. En simulateur, les seniors adoptent un comportement sécuritaire, requérant des intervalles temporels plus longs pour décider d'initier une traversée. Dans des conditions de trafic favorables, ils marchent plus rapidement que les jeunes. Leurs marges de sécurité sont plus grandes. L'approche biomécanique, révèle des différences intergroupes, dont certaines sont potentiellement à risque (ex. la flexion plantaire) alors que d’autres (ex. les rotations exploratoires) participent à l’adaptation. / In the framework of population ageing and increased importance attached to walking in urban cities, the aim of this PhD work is to better understand behavioral and biomechanical characteristics of older pedestrian road crossing. We mostly used the experimental method. Some data were collected in laboratory or natural environment, but the main study was performed in an immersive road crossing simulator with projected reality: the Simulator of Road for Pedestrians (SRP). The curb height was adjustable. The device integrated various biomechanical measurement tools such as force plates and 3D-gait analysis systems. The real and the imagined crossing times were compared in a task performed outside the simulator. It reveals that some seniors underestimated their crossing time. The experiment within the simulator confirmed the relevance of the age-related modulation of the crossing time perception, which was indirectly estimated by the feeling of endangerment. Inside the simulator, the road crossing behavior of the elderly participants was safe, requiring longer temporal intervals for deciding to initiate the crossing. In favorable traffic gap conditions, they walked more quickly than the younger participants and their safety margins were larger. The biomechanical approach revealed intergroup differences, some of which inducing potential risks (e.g., plantar flexion) while others (e.g., exploratory rotations) participated in the coping.

Många gående skadas eller dör i trafiken varje år. En stor del av olyckorna inträffarvid övergångsställen, flest olyckor sker vid obevakade övergångsställen. Nollvisionenär ett långsiktigt mål att ingen människa ska behöva skadas eller dö itrafiken. Somett ytterligare steg mot  nollvisionen infördes år 2000 den så kallade”Zebralagen”, en lag som innebär att fordonsförare har väjningsplikt gentemotgående. Eftersom denna lag är aktuell i samhällsdebatten har vi valt attstudera hur lagen efterlevs i praktiken detta genom att observera fyra olikatyper av övergångsställen vid sammanlagt 14 olika tillfällen och olika tider pådygnet (vardagar mellan 6-20). För att kunna jämföra observationerna medförares och fotgängares påstådda agerande har även 100 stycken enkäter delatsut och sammanställts. Utifrån dessa studier och sammanställningar har vi kommitfram till resultatet att människor upplever sig själva vara betydligt meruppmärksam och skötsamma i trafiken än vad de egentligen är och även attutformningen på övergångsstället har stor påverkan på fordonsförarna men ingenalls på fotgängarna. / Many people walking in traffic gets injured or killed in traffic each year. The place where this occurs mostly is on zebra crossings, the ones that have no surveillance are the ones where the accidents are most common. A vision zero has been establish to create a long term goal to make sure that no persons gets injured or killed in traffic. To enhance vision zero has a “zebra law” been instate year 2000, the law states that cars needs to give way for people walking. This law has been discussed in media and that is why we want to do this research about it. We did the research through observation at four different zebra crossings during 14 different times and different times of the day, all between 6 am and 8 pm. To get the people who is walking and the drivers opinions about their experiences in traffic was a survey answered by 100 participants and then analysed conducted and analysed with 100 participants. The results shows that people believe that they are more observant in traffic then what the observations has shown is true. The design of the zebra crossings did also play a role in how observant the drivers were but did not have the same effect on the people walking.

We consider real zero-crossing analysis of the real/imaginary parts of the spectrum, namely, spectral zero-crossings (SZCs). The two major contributions are to show that: (i) SZCs provide enable temporal localization of transients; and (b) SZCs are suitable for modeling transient signals. We develop a spectral dual of Kedem’s result linking temporal zero-crossing rate (ZCR) to the spectral centroid. The key requirement is stationarity, which we achieve through random-phase modulations of the time-domain signal. Transient signals are not amenable to modelling in the time domain since they are bursts of energy localized in time and lack structure. We show that the spectrum of transient signals have a rich modulation structure, which leads to an amplitude-modulation – frequency-modulation (AM-FM) model of the spectrum. We generalize Kedem’s arc-cosine formula for lags greater than one. For the specific case of a sinusoid in white Gaussian noise, He and Kedem devised an iterative filtering algorithm, which leads to a contraction mapping. An autoregressive filter of order one is employed and the location of the pole is the parameter that is updated based on the filtered output. We use the higher-order property, which relates the autocorrelation to the expected ZCR of the filtered process, between lagged ZCR and higher-lag autocorrelation to develop an iterative higher-order autoregressive-filtering scheme, which stabilizes the ZCR and consequently provides robust estimates of the autocorrelation at higher lags. Next, we investigate ZC properties of critically sampled outputs of a maximally decimated M-channel power complementary analysis filterbank (PCAF) and derive the relationship between the ZCR of the input Gaussian process at lags that are integer multiples of M in terms of the subband ZCRs. Based on this result, we propose a robust autocorrelation estimator for a signal consisting of a sum of sinusoids of fixed amplitudes and uniformly distributed random phases. Robust subband ZCRs are obtained through iterative filtering and the subband variances are estimated using the method-of-moments estimator. We compare the performance of the proposed estimator with the sample auto-correlation estimate in terms of bias, variance, and mean-squared error, and show through simulations that the performance of the proposed estimator is better than the sample auto- correlation for medium to low SNR. We then consider the ZC statistics of the real/imaginary parts of the discrete Fourier spectrum. We introduce the notion of the spectral zero-crossing rate (SZCR) and show that, for transients, it gives information regarding the location of the transient. We also demonstrate the utility of SZCR to estimate interaural time delay between the left and right head-related impulse responses. The accuracy of interaural time delay plays a vital role in binaural synthesis and a comparison of the performance of the SZCR estimates with that of the cross-correlation estimates illustrate that spectral zeros alone contain enough information for accurately estimating interaural time delay. We provide a mathematical formalism for establishing the dual of the link between zero-crossing rate and spectral centroid. Specifically, we show that the expected SZCR of a stationary spectrum is a temporal centroid. For a deterministic sequence, we obtain the stationary spectrum by modulating the sequence with a random phase unit amplitude sequence and then computing the spectrum. The notion of a stationary spectrum is necessary for deriving counterparts of the results available in temporal zero-crossings literature. The robustness of location information embedded in SZCR is analyzed in presence of a second transient within the observation window, and also in the presence of additive white Gaussian noise. A spectral-domain iterative filtering scheme based on autoregressive filters is presented and improvement in the robustness of the location estimates is demonstrated. As an application, we consider epoch estimation in voiced speech signals and show that the location information is accurately estimated using spectral zeros than other techniques. The relationship between temporal centroid and SZCR also finds applications in frequency-domain linear prediction (FDLP), which is used in audio compression. The prediction coefficients are estimated by solving the Yule-Walker equations constructed from the spectral autocorrelation. We use the relationship between the spectral autocorrelation and temporal centroid to obtain the spectral autocorrelation directly by time-domain windowing without explicitly computing the spectrum. The proposed method leads to identical results as the standard FDLP method but with reduced computational load. We then develop a SZCs-based spectral-envelope and group-delay (SEGD) model, which finds applications in modelling of non-stationary signals such as Castanets. Taking into account the modulation structure and spectral continuity, local polynomial regression is performed to estimate the GD from the real spectral zeros. The SE is estimated based on the phase function computed from the estimated GD. Since the GD estimate is parametric, the degree of smoothness can be controlled directly. Simulation results based on synthetic transient signals are presented to analyze the noise-robustness of the SE-GD model. Applications to castanet modeling, transient compression, and estimation of the glottal closure instants in speech are shown.

En génomique comparative, on considère classiquement trois forces déterminant l'évolution des séquences : la mutation, la sélection et la dérive génétique. Récemment, lors de l'étude de l'origine évolutive des variations de la composition en base des génomes, un quatrième agent a été identifié : la conversion génique biaisée (BGC). Le BGC est intimement lié à la recombinaison méiotique et semble présent chez la plupart des eucaryotes. Ce phénomène introduit une surreprésentation de certains allèles dans les produits méiotiques aboutissant à une augmentation de la fréquence de ces variants dans la population. Ce processus est capable de mimer et d'interférer avec la sélection naturelle. Il est donc important de le caractériser afin de pouvoir le distinguer efficacement de la sélection dans l'étude de l'adaptation à l'échelle moléculaire. C'est ce que nous nous attachons à faire dans le cadre de ce travail. Pour cela nous utilisons deux espèces modèles. Premièrement la levure Saccharomyces cerevisiae pour laquelle une carte de recombinaison haute résolution permettant l'analyse du processus de conversion, est disponible. L'étude approfondie de cette carte nous a permis de lever le voile sur les mécanismes moléculaires qui sous-tendent le BGC. Deuxièmement, grâce à des découvertes récentes sur la détermination des patrons de recombinaison via la protéine PRDM9 chez les mammifères, nous avons quantifié la dynamique et l'intensité de ce processus dans l'histoire évolutive récente de l'homme. Ces résultats nous ont permis de confirmer la place du BGC comme quatrième force d'évolution moléculaire, mais aussi de discuter de l'origine évolutive de ce phénomène / Usually, three main forces are considered when studying sequences evolution in comparative genomics : mutation, selection and genetic drift. Recently, a fourth process has been identified during the study of base composition landscapes in genomes : biased gene conversion (BGC). This phenomenon introduces an overrepresentation of certain alleles in meiosis products (gametes or spores) leading to an increase of the frequency of those variants in the population. Thus, it is able to mimic and interfere with natural selection. Hence, it is important to describe this phenomenon in order to be able to trustfully distinguish BGC and selection in the study of adaptation at the molecular scale. So, the main goal of this work is to analyze the molecular origin, the intensity and the dynamics of BGC. To do so, we use two model species. First, we use the yeast Saccharomyces cerevisiae because, for this specie, a high-resolution recombination map is available which allows a fine study of the conversion process. Analyzing this map led us to shed the light on the molecular mechanisms of BGC. Secondly, recent discoveries on the role of the PRDM9 protein in the determination of recombination landscapes in mammals allowed us to quantify the dynamics and intensity of BGC in the recent human history. Thanks to those two studies, we first confirmed that BGC is the fourth force of molecular evolution and we also provided hypotheses about the evolutionary origin of this process

La recombinaison homologue est un mécanisme de réparation de l’ADN extrêmement contrôlé et particulièrement chez les eucaryotes supérieurs. Dans les cellules méiotiques de ces derniers, où les cassures doubles brin de l’ADN sont programmées, les voies de crossing-over de la recombinaison homologue, qui génèrent de nouvelles combinaisons de gènes, sont restreintes. Dans les cellules somatiques, la recombinaison illégitime, qui assure majoritairement la réparation des cassures double brin de l’ADN, limite l’intégration ciblée du transgène par recombinaison homologue. Les entreprises de biotechnologie convoitent de maitriser la recombinaison homologue afin de contrôler d’une part le brassage génomique qui a lieu pendant la méiose, et d’autre part l’intégration du transgène dans le génome. Cette étude a porté sur le développement d’outils afin d’atteindre ces deux objectifs. Afin d’augmenter le brassage du génome, ayant lieu pendant la méiose, une version du promoteur OsDmc1b, active dans les cellules méiotiques, a été caractérisée chez le maïs. Des plantes sur-exprimant le gène ZmSpo11.1, sous contrôle de ce promoteur, ont ainsi été développées afin d’obtenir des lignées potentiellement hyper-recombinantes. Si la surexpression de ZmSpo11.1 permet effectivement d’augmenter le taux de crossing-over, il pourra être utilisé par les sélectionneurs afin d’accélérer l’introgression d’allèles d’intérêt dans des variétés élites. Concernant la mise en place d’une technique de ciblage de gène, deux stratégies, reposant sur l’utilisation de la méganucléase I-SceI, ont été testées. La démarche a nécessité trois éléments : un locus cible contenant le site de coupure I-SceI, une matrice de réparation et la séquence codant I-SceI (ou I-SceI::GR). La première stratégie, consistant à retransformer les lignées présentant le locus cible avec la matrice de réparation et I-SceI, ne semble pas exploitable car aucun évènement de ciblage de gène n’a été mis en évidence. La seconde stratégie, reposant sur l’assemblage des trois éléments par croisement, est beaucoup plus prometteuse. Malgré la faible activité d’I-SceI::GR, des évènements de recombinaison homologue ont été observés dans les tissus foliaires de certaines plantes. Du cal embryogène, développé à partir de ces dernières, a permis de régénérer des plantes présentant des évènements de ciblage de gène. Ces travaux ouvrent de nouvelles perspectives dans l’élaboration contrôlée d’OGM. / Homologous recombination is a DNA repair mechanism highly regulated in higher eukaryotes. In their meiotic cells, where DNA double-stranded breaks are programmed, the crossing-over pathway of homologous recombination, which generates new gene combinations, is limited in activity and genomic distribution. In somatic cells, illegitimate recombination, which mainly ensures DNA double-strand repair, limits the targeted integration of transgenes by homologous recombination. Biotechnology companies aim to master homologous recombination to control on the one hand the genomic mixing that occurs during meiosis, and on other hand, the integration of transgenes into the genome. This study focuses on the development of tools to achieve these two objectives.To increase genome mixing occurring during meiosis, a version of the OsDmc1b promoter active in maize meiotic cells was isolated. Then, plants over-expressing the ZmSpo11.1 gene under control of this promoter have been developed to obtain potentially hyper-recombinant lines. If ZmSPO11.1 overexpression increases the crossing over rate, it can be used by breeders to accelerate the introgression of alleles of interest into elite varieties. For the establishment of a gene targeting technique, two strategies based on the use of the I-SceI meganuclease were tested. These approaches involved the use of three elements which are: a target locus containing the cleavage site of I-SceI, a repair template and the sequence encoding I-SceI (or ISceI::GR). The first strategy, consisting of the retransformation of target locus lines with the repair template and I-SceI, does not seem workable because no gene targeting events were isolated. The second strategy, based on the assembly of the three components by crossing, is more promising. Despite the low activity of I-SceI::GR, homologous recombination events were observed in leaf tissues of certain plants. Embryogenic callus, developed from these plants, permitted the regeneration of plants with gene targeting events. This work opens new perspectives in the development of controlled GMO production.