Architectural features of bacterial genomes and their applications

Résumé -Caractéristiques architecturales des génomes bactériens et leurs applications Les bactéries possèdent généralement un seul chromosome circulaire. A chaque génération, ce chromosome est répliqué bidirectionnellement, par deux complexes enzymatiques de réplication se déplaçant en sens opposé depuis l'origine de réplication jusqu'au terminus, situé à l'opposé. Ce mode de réplication régit l'architecture du chromosome -l'orientation des gènes par rapport à la réplication, notamment - et est en grande partie à l'origine des pressions qui provoquent la variation de la composition en nucléotides du génome, hors des contraintes liées à la structure et à la fonction des protéines codées sur le chromosome. Le but de cette thèse est de contribuer à quantifier les effets de la réplication sur l'architecture chromosomique, en s'intéressant notamment aux gènes des ARN ribosomiques, cruciaux pour la bactérie. D'un autre côté, cette architecture est spécifique à l'espèce et donne ainsi une «identité génomique » aux gènes. Il est démontré ici qu'il est possible d'utiliser des marqueurs «naïfs » de cette identité pour détecter, notamment dans le génome du staphylocoque doré, des îlots de pathogénicité, qui concentrent un grand nombre de facteurs de virulence de la bactérie. Ces îlots de pathogénicité sont mobiles, et peuvent passer d'une bactérie à une autre, mais conservent durant un certain temps l'identité génomique de leur hôte précédent, ce qui permet de les reconnaître dans leur nouvel hôte. Ces méthodes simples, rapides et fiables seront de la plus haute importance lorsque le séquençage des génomes entiers sera rapide et disponible à très faible coût. Il sera alors possible d'analyser instantanément les déterminants pathogéniques et de résistance aux antibiotiques des agents pathogènes. Summary The bacterial genome is a highly organized structure, which may be referred to as the genome architecture, and is mainly directed by DNA replication. This thesis provides significant insights in the comprehension of the forces that shape bacterial chromosomes, different in each genome and contributing to confer them an identity. First, it shows the importance of the replication in directing the orientation of prokaryotic ribosomal RNAs, and how it shapes their nucleotide composition in a tax on-specific manner. Second, it highlights the pressure acting on the orientation of the genes in general, a majority of which are transcribed in the same direction as replication. Consequently, apparent infra-arm genome rearrangements, involving an exchange of the leading/lagging strands and shown to reduce growth rate, are very likely artifacts due to an incorrect contig assembly. Third, it shows that this genomic identity can be used to detect foreign parts in genomes, by establishing this identity for a given host and identifying the regions that deviate from it. This property is notably illustrated with Staphylococcus aureus: known pathogenicity islands and phages, and putative ancient pathogenicity islands concentrating many known pathogenicity-related genes are highlighted; the analysis also detects, incidentally, proteins responsible for the adhesion of S. aureus to the hosts' cells. In conclusion, the study of nucleotide composition of bacterial genomes provides the opportunity to better understand the genome-level pressures that shape DNA sequences, and to identify genes and regions potentially related to pathogenicity with fast, simple and reliable methods. This will be of crucial importance when whole-genome sequencing will be a rapid, inexpensive and routine tool.

Falls efficacy predicts functional status on month after discharge in elderly patients undergoing post-accute rehabilitation

Objective: To investigate the relationship between falls efficacy at admission and functional status reported one month after discharge from post-acute rehabilitation in a cohort of elderly patients. Methods: Participants were elderly patients admitted to postacute rehabilitation in an academic geriatric facility. Data on demographics and affective status were collected upon admission; functional status and gait speed were measured at admission and at discharge; self-reported functional status and history of falls since discharge were collected one month after discharge (follow-up). Falls efficacy was measured using the Fall Efficacy Scale, that assesses confidence in performing 12 activities of daily living without falling (range 0 to 100, higher score indicating higher confidence). Patients were classified using the median FES score at baseline (95) as cut-off to divide the population into "confident" and "fearful" groups. Results: Participants' (N=180, mean age 81.3±7.1 years, 75.6% women) mean FES score was 92.3±8.7 at baseline (range 60-100). Basic ADL score averaged 3.5±1.6 at baseline, 4.7±1.3 at discharge, and 5.5±0.7 at follow-up (self-reported). Baseline FES score was positively correlated with basic ADL at follow-up (rho=0.35, p<.001). At follow-up, 58.7% of the patients were fully independent in basic ADL, this proportion being significantly higher in confident than fearful patients (70.7% vs 42.4%, p<.001). Compared to confident patients, those fearful had significantly lower odds (OR 0.3, 95%CI 0.2-0.6, p<.001) to report full independence at follow-up. This relationship remained (adjOR = 0.4, 95%CI 0.2-0.8, p=.01) after controlling for demographics, baseline gait speed, depressive symptoms, functional status at discharge, and history of falls since discharge. Conclusion: In this cohort of older rehab patients, poor falls efficacy at admission was associated with lower function reported one month after discharge even after controlling for initial mobility performance and functional status at discharge. Further studies should determine whether interventions aiming at falls efficacy improvement will also result in improved function in fearful subjects undergoing rehabilitation.

Improvement of rehabilitation possibilities with the MotionMaker (TM)

"MotionMaker (TM)" is a stationary programmable test and training system for the lower limbs developed at the 'Ecole Polytechnique Federale de Lausanne' with the 'Fondation Suisse pour les Cybertheses'.. The system is composed of two robotic orthoses comprising motors and sensors, and a control unit managing the trans-cutaneous electrical muscle stimulation with real-time regulation. The control of the Functional Electrical Stimulation (FES) induced muscle force necessary to mimic natural exercise is ensured by the control unit which receives a continuous input from the position and force sensors mounted on the robot. First results with control subjects showed the feasibility of creating movements by such closed-loop controlled FES induced muscle contractions. To make exercising with the MotionMaker (TM) safe for clinical trials with Spinal Cord Injured (SCI) volunteers, several original safety features have been introduced. The MotionMaker (TM) is able to identify and manage the occurrence of spasms. Fatigue can also be detected and overfatigue during exercise prevented.

Development of Evaluation, Rehabilitation, and Strengthening Concepts for Low Volume Bridges, Phase I Progress Report, HR-323, 1990

The primary objective of this project is to develop a design manual that would aid the county or municipal engineer in making structurally sound bridge strengthening or replacement decisions. The contents of this progress report are related only to Phase I of the study and deal primarily with defining the extent of the bridge problem in Iowa. In addition, the types of bridges to which the manual should be directed have been defined.

Evaluating spine micro-architectural texture (via TBS) discriminates major osteoporotic fractures from controls both as well as and independent of site matched BMD: the Eastern European TBS study.

The aim of the study was to assess the clinical performance of the model combining areal bone mineral density (aBMD) at spine and microarchitecural texture (TBS) for the detection of the osteoporotic fracture. The Eastern European Study is a multicenter study (Serbia, Bulgaria, Romania and Ukraine) evaluating the role of TBS in routine clinical practice as a complement to aBMD. All scans were acquired on Hologic Discovery and GE Prodigy densitometers in a routine clinical manner. The additional clinical values of aBMD and TBS were analyzed using a two steps classification tree approach (aBMD followed by TBS tertiles) for all type of osteoporotic fracture (All-OP Fx). Sensitivity, specificity and accuracy of fracture detection as well as the Net Reclassification Index (NRI) were calculated. This study involves 1031 women subjects aged 45 and older recruited in east European countries. Clinical centers were cross-calibrated in terms of BMD and TBS. As expected, areal BMD (aBMD) at spine and TBS were only moderately correlated (r (2) = 0.19). Prevalence rate for All-OP Fx was 26 %. Subjects with fracture have significant lower TBS and aBMD than subjects without fracture (p < 0.01). TBS remains associated with the fracture even after adjustment for age and aBMD with an OR of 1.27 [1.07-1.51]. When using aBMD T-score of -2.5 and the lowest TBS tertile thresholds, both BMD and TBS were similar in terms of sensitivity (35 vs. 39 %), specificity (78 vs. 80 %) and accuracy (64 vs. 66 %). aBMD and TBS combination, induced a significant improvement in sensitivity (+28 %) and accuracy (+17 %) compared to aBMD alone whereas a moderate improvement was observed in terms of specificity (+9 %). The overall combination gain was 36 % as expressed using the NRI. aBMD and TBS combination decrease significantly the number of subjects needed to diagnose from 7 for aBMD alone to 2. In a multi-centre Eastern European cohort, we have shown that the use of TBS in addition to the aBMD permit to reclassified correctly more than one-third of the overall subjects. Furthermore, the number of subjects needed to diagnose fell to 2 subjects. Economical studies have to be performed to evaluate the gain induced by the use of TBS for the healthcare system.

Closed loop electrical muscle stimulation in spinal cord injured rehabilitation

The effect of motor training using closed loop controlled Functional Electrical Stimulation (FES) on motor performance was studied in 5 spinal cord injured (SCI) volunteers. The subjects trained 2 to 3 times a week during 2 months on a newly developed rehabilitation robot (MotionMaker?). The FES induced muscle force could be adequately adjusted throughout the programmed exercises by the way of a closed loop control of the stimulation currents. The software of the MotionMaker? allowed spasms to be detected accurately and managed in a way to prevent any harm to the SCI persons. Subjects with incomplete SCI reported an increased proprioceptive awareness for motion and were able to achieve a better voluntary activation of their leg muscles during controlled FES. At the end of the training, the voluntary force of the 4 incomplete SCI patients was found increased by 388% on their most affected leg and by 193% on the other leg. Active mobilisation with controlled FES seems to be effective in improving motor function in SCI persons by increasing the sensory input to neuronal circuits involved in motor control as well as by increasing muscle strength.

Ornementation et discours architectural de la "villa" gallo-romaine d'Orbe-Boscéaz : l'apport des peintures

La présente thèse s'inscrit dans la continuité de la publication des fouilles menées de 1986 à 2002 sur le site de la villa gallo-romaine d'Orbe-Boscéaz/VD par l'Institut d'archéologie et des sciences de l'antiquité de l'Université de Lausanne (URBA I, à paraître dans les Cahiers d'archéologie romande). Elle constitue l'analyse approfondie du corpus des peintures murales fragmentaires -succinctement présentées dans URBA I - appartenant à la pars urbana qui succéda, entre 161 et 180 apr. J.-C, à un édifice plus petit du Ier s. de notre ère -dont les peintures sont publiées dans l'ouvrage sus-mentionné. N'ayant subi que de très rares modifications, cette pars urbana de caractère palatial forme un "ensemble clos" autorisant une analyse globale de la conception architecturale et décorative voulue par le bâtisseur ou son commanditaire. Le corpus pictural, composé d'un matériel assez ingrat remplissant quelque 600 cagettes de stockage, offre de ce fait l'intérêt d'une grande homogénéité chronologique et reflète la cohérence et l'unité de la décoration peinte d'origine. Le travail de discrimination et de remontage des ensembles a permet d'individualiser au moins 220 décors et revêtements muraux; l'ensemble des hypothèses de restitution des peintures donne ainsi une image minimale de l'environnement pictural de la pars urbana. Ce corpus pictural n'est toutefois que l'une des composantes du programme décoratif, aussi l'analyse de ses caractéristiques est-elle confrontée à celle des autres composantes ornementales (architecture, placages de marbres et surtout le remarquable ensemble des mosaïques qui fait la célébrité du site). La conjugaison des divers éléments et leur répartition au sein d'un plan bien connu et très symétrique orientent sur les choix décoratifs majeurs, et permettent sinon de reconstituer, tout au moins d'approcher la conception du programme architectural et décoratif voulu par le commanditaire ou son architecte; ce programme, comme fréquemment, reflète le statut du commanditaire, le met évidemment en scène et tient un discours sur la villa, adressé tant aux habitants qu'aux visiteurs. On trouvera dans le travail six chapitres formant l'essentiel de l'exploitation du corpus pictural urbigène. Le premier chapitre est introductif, et présente dans ses grandes lignes la pars urbana de Boscéaz comme cadre de référence. Il est suivi par un état des lieux des peintures murales retrouvées sur le site, abordant leur répartition, leur état de conservation et la méthodologie adoptée pour leur traitement comme leur étude (chapitre 2). Le chapitre 3 constitue l'étude technique des enduits peints. Il réunit toutes les observations que l'on peut faire sur les techniques de réalisation des peinture murales, de la préparation et la pose des mortiers de support aux tours de main des peintres pour le rendu d'un motif. Ce chapitre s'inscrit dans la perspective, appliquée à Boscéaz, d'études marquantes comme celles sur les techniques de préparation des parois (Allag /Barbet 1972, Barbet 1995) sur l'identification des pigments (PACT 17, 1985, Béarat 1997, Colloque de Fribourg 1997) et sur l'analyse des mortiers (Coutelas 2003). Suit le catalogue des peintures, basé sur une sélection de 3414 plaques remontées et fragments (chapitre 4) : il propose une description rigoureuse et systématique des motifs, ainsi que leur analyse stylistique qui apporte les éléments comparatifs permettant la compréhension du matériel, et justifiant son interprétation, voire sa restitution. Les décors y sont présentés par local de découverte; un paragraphe introductif réunit les données de fouille et des informations sur le local ou le prélèvement des enduits, et donne le nombre et la détermination des décors retrouvés. Chacun d'eux fait l'objet d'une notice regroupant: une détermination par le mortier de support (le tectorium); les observations techniques diverses; la description, la restitution le cas échéant, et l'analyse stylistique. Cette dernière privilégie les comparaisons locales, en Suisse d'abord puis dans les pays limitrophes de façon à mettre en évidence les liens plausibles entre certains sites et les éventuels indices d'une production régionale. La documentation graphique qui accompagne chaque décor dans le volume d'illustrations est constituée avant tout des planches photographiques des fragments à l'échelle 1:3, accompagnés le cas échéant de dessins au trait justifiant la lecture des motifs. Ceux-ci permettent la reconstitution idéale

Auxin-mediated plant architectural changes in response to shade and high temperature.

The remarkable plasticity of their architecture allows plants to adjust growth to the environment and to overcome adverse conditions. Two examples of environmental stresses that drastically affect shoot development are imminent shade and high temperature. Plants in crowded environments and plants in elevated ambient temperature display very similar phenotypic adaptations of elongated hypocotyls in seedlings and elevated and elongated leaves at later developmental stages. The comparable growth responses to shade and high temperature are partly regulated through shared signaling pathways, of which the phytohormone auxin and the phytochrome interacting factors (PIFs) are important components. During both shade- and temperature-induced elongation growth auxin biosynthesis and signaling are upregulated in a PIF-dependent manner. In this review we will discuss recent progress in our understanding of how auxin mediates architectural adaptations to shade and high temperature.

The INTERMED questionnaire for predicting return to work after a multidisciplinary rehabilitation program for chronic low back pain.

OBJECTIVES: To evaluate the performance of the INTERMED questionnaire score, alone or combined with other criteria, in predicting return to work after a multidisciplinary rehabilitation program in patients with non-specific chronic low back pain. METHODS: The INTERMED questionnaire is a biopsychosocial assessment and clinical classification tool that separates heterogeneous populations into subgroups according to case complexity. We studied 88 patients with chronic low back pain who followed an intensive multidisciplinary rehabilitation program on an outpatient basis. Before the program, we recorded the INTERMED score, radiological abnormalities, subjective pain severity, and sick leave duration. Associations between these variables and return to full-time work within 3 months after the end of the program were evaluated using one-sided Fisher tests and univariate logistic regression followed by multivariate logistic regression. RESULTS: The univariate analysis showed a significant association between the INTERMED score and return to work (P<0.001; odds ratio, 0.90; 95% confidence interval, 0.86-0.96). In the multivariate analysis, prediction was best when the INTERMED score and sick leave duration were used in combination (P=0.03; odds ratio, 0.48; 95% confidence interval, 0.25-0.93). CONCLUSION: The INTERMED questionnaire is useful for evaluating patients with chronic low back pain. It could be used to improve the selection of patients for intensive multidisciplinary programs, thereby improving the quality of care, while reducing healthcare costs.

Screening fo osteoporosis in elderly patients admitted to post-acute rehabilitation.

Background: Screening for osteoporosis is important in older patients admitted to post-acute rehabilitation. However, DXA measurement is sometimes difficult to perform because of difficulties in positioning the patient and artefacts (osteoarthritis, prosthesis). The objectives were to determine the prevalence of unknown clinical osteoporosis in rehab patients and to determine new strategies for identifying clinical osteoporosis in this population. Method: Over a 9-months period, patients consecutively admitted to post-acute rehabilitation were included in th stdy. Patients with osteoporosis diagnosis, and those with terminal illness or severe physical limitations were excluded. Patients underwent Bone Mineral Density (BMD) by DXA and Vertebral Fracture Assessment (VFA). Clinical osteoporosis was defined as BMD ≤-2.5 SD at any site (lumbar spine, femoral neck, total hip or distal radius), ≥1 vertebral fracture, ≥1 hip fracture, or another fragility fracture and BMD ≤-2 SD. Results: Overall, 102 (17.0%) of the 600 patients admitted to rehab refused to participate in the study or were unable to consent. Among the 498 remaining patients, 99 (19.9%) were excluded because of already known diagnosis of osteoporosis, 101 (20.3%) were excluded because of terminal illness, severe physical limitations, and 45 (9.0%) because of inability to perform DXA during the stay (death, hospital transfer). Overall, 253 patients were assessed with DXA and VFA (166 women, mean age 83±7 years, mean BMI 27±6 kg/m2, and 87 men, mean age 82±6 yrs, mean BMI 27±5 kg/m2). Of these, 70% had history of fall during the last 6 months and 9.1% had hip fracture history. Prevalence of osteoporotic vertebral fracture was 36% in women and 32% in men. Overall, 152 (60.1%) patients had clinical osteoporosis (women: 67%; men: 46%) according to above criteria. Hip fracture history and vertebral fracture assessment identified correctly 105 (69.1%) of these 152 patients. Conclusion: A high prevalence of osteoporosis was observed in this population of rehab patients. Osteoporosis status should be systematically assessed in these patients at high fall risk, at least with careful history of hip fracture and an assessment for vertebral fractures with spine X-ray.

The Arcuated Lintel and the "Serlian Motif". Imperial Identity, Architectural and Symbolic Interactions in Ancient Rome

Essay on the origin, use and development of the arcuated lintel in ancient Rome and the configuration of the so– called ‘Serlian motif’. These architectural elements will be related to the architecture of prestige on its technical, functional, visual and symbolic sphere. Its depictions, in addition to buildings, can offer a rich repertory of images that speak about the relations between visual culture, religion and power. Furthermore, the analyzed motifs will become important elements of the Western cultural legacy for centuries. The analysis of these events will contribute to the comprehension of the role played by some resources of ancient Rome architecture of prestige and its success