Intraobserver and interobserver variability of ascending aorta diameter as assessed with ECG-gated MDCT: automatic versus manual measurements

Purpose: Recently morphometric measurements of the ascending aorta have been done with ECG-gated MDCT to help the development of future endovascular therapies (TCT) [1]. However, the variability of these measurements remains unknown. It will be interesting to know the impact of CAD (computer aided diagnosis) with automated segmentation of the vessel and automatic measurements of diameter on the management of ascending aorta aneurysms. Methods and Materials: Thirty patients referred for ECG-gated CT thoracic angiography (64-row CT scanner) were evaluated. Measurements of the maximum and minimum ascending aorta diameters were obtained automatically with a commercially available CAD and semi-manually by two observers separately. The CAD algorithms segment the iv-enhanced lumen of the ascending aorta into perpendicular planes along the centreline. The CAD then determines the largest and the smallest diameters. Both observers repeated the automatic measurements and the semimanual measurements during a different session at least one month after the first measurements. The Bland and Altman method was used to study the inter/intraobserver variability. A Wilcoxon signed-rank test was also used to analyse differences between observers. Results: Interobserver variability for semi-manual measurements between the first and second observers was between 1.2 to 1.0 mm for maximal and minimal diameter, respectively. Intraobserver variability of each observer ranged from 0.8 to 1.2 mm, the lowest variability being produced by the more experienced observer. CAD variability could be as low as 0.3 mm, showing that it can perform better than human observers. However, when used in nonoptimal conditions (streak artefacts from contrast in the superior vena cava or weak lumen enhancement), CAD has a variability that can be as high as 0.9 mm, reaching variability of semi-manual measurements. Furthermore, there were significant differences between both observers for maximal and minimal diameter measurements (p<0.001). There was also a significant difference between the first observer and CAD for maximal diameter measurements with the former underestimating the diameter compared to the latter (p<0.001). As for minimal diameters, they were higher when measured by the second observer than when measured by CAD (p<0.001). Neither the difference of mean minimal diameter between the first observer and CAD nor the difference of mean maximal diameter between the second observer and CAD was significant (p=0.20 and 0.06, respectively). Conclusion: CAD algorithms can lessen the variability of diameter measurements in the follow-up of ascending aorta aneurysms. Nevertheless, in non-optimal conditions, it may be necessary to correct manually the measurements. Improvements of the algorithms will help to avoid such a situation.

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA-DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.

The metaphysics of quantum gravity : a causal approach

The dissertation investigates some relevant metaphysical issues arising in the context of spacetime theories. In particular, the inquiry focuses on general relativity and canonical quantum gravity. A formal definition of spacetime theory is proposed and, against this framework, an analysis of the notions of general covariance, symmetry and background independence is performed. It is argued that many conceptual issues in general relativity and canonical quantum gravity derive from putting excessive emphasis on general covariance as an ontological prin-ciple. An original metaphysical position grounded in scientific essential- ism and causal realism (weak essentialism) is developed and defended. It is argued that, in the context of general relativity, weak essentialism supports spacetime substantivalism. It is also shown that weak essentialism escapes arguments from metaphysical underdetermination by positing a particular kind of causation, dubbed geometric. The proposed interpretive framework is then applied to Bohmian mechanics, pointing out that weak essentialism nicely fits into this theory. In the end, a possible Bohmian implementation of loop quantum gravity is considered, and such a Bohmian approach is interpreted in a geometric causal fashion. Under this interpretation, Bohmian loop quantum gravity straightforwardly commits us to an ontology of elementary extensions of space whose evolution is described by a non-local law. The causal mechanism underlying this evolution clarifies many conceptual issues related to the emergence of classical spacetime from the quantum regime. Although there is as yet no fully worked out physical theory of quantum gravity, it is argued that the proposed approach sets up a standard that proposals for a serious ontology in this field should meet.

Epidemiology of small intestinal atresia in Europe: a register-based study.

BACKGROUND: The epidemiology of congenital small intestinal atresia (SIA) has not been well studied. This study describes the presence of additional anomalies, pregnancy outcomes, total prevalence and association with maternal age in SIA cases in Europe. METHODS: Cases of SIA delivered during January 1990 to December 2006 notified to 20 EUROCAT registers formed the population-based case series. Prevalence over time was estimated using multilevel Poisson regression, and heterogeneity between registers was evaluated from the random component of the intercept. RESULTS: In total 1133 SIA cases were reported among 5126, 164 registered births. Of 1044 singleton cases, 215 (20.6%) cases were associated with a chromosomal anomaly. Of 829 singleton SIA cases with normal karyotype, 221 (26.7%) were associated with other structural anomalies. Considering cases with normal karyotype, the total prevalence per 10 000 births was 1.6 (95% CI 1.5 to 1.7) for SIA, 0.9 (95% CI 0.8 to 1.0) for duodenal atresia and 0.7 (95% CI 0.7 to 0.8) for jejunoileal atresia (JIA). There was no significant trend in SIA, duodenal atresia or JIA prevalence over time (RR=1.0, 95% credible interval (CrI): 1.0 to 1.0 for each), but SIA and duodenal atresia prevalence varied by geographical location (p=0.03 and p=0.04, respectively). There was weak evidence of an increased risk of SIA in mothers aged less than 20 years compared with mothers aged 20 to 29 years (RR=1.3, 95% CrI: 1.0 to 1.8). CONCLUSION: This study found no evidence of a temporal trend in the prevalence of SIA, duodenal atresia or JIA, although SIA and duodenal atresia prevalence varied significantly between registers.

Hierarchy of Notch-Delta interactions promoting T cell lineage commitment and maturation.

Notch1 (N1) receptor signaling is essential and sufficient for T cell development, and recently developed in vitro culture systems point to members of the Delta family as being the physiological N1 ligands. We explored the ability of Delta1 (DL1) and DL4 to induce T cell lineage commitment and/or maturation in vitro and in vivo from bone marrow (BM) precursors conditionally gene targeted for N1 and/or N2. In vitro DL1 can trigger T cell lineage commitment via either N1 or N2. N1- or N2-mediated T cell lineage commitment can also occur in the spleen after short-term BM transplantation. However, N2-DL1-mediated signaling does not allow further T cell maturation beyond the CD25(+) stage due to a lack of T cell receptor beta expression. In contrast to DL1, DL4 induces and supports T cell commitment and maturation in vitro and in vivo exclusively via specific interaction with N1. Moreover, comparative binding studies show preferential interaction of DL4 with N1, whereas binding of DL1 to N1 is weak. Interestingly, preferential N1-DL4 binding reflects reduced dependence of this interaction on Lunatic fringe, a glycosyl transferase that generally enhances the avidity of Notch receptors for Delta ligands. Collectively, our results establish a hierarchy of Notch-Delta interactions in which N1-DL4 exhibits the greatest capacity to induce and support T cell development.

CD8 beta increases CD8 coreceptor function and participation in TCR-ligand binding.

To study the role of CD8 beta in T cell function, we derived a CD8 alpha/beta-(CD8-/-) T cell hybridoma of the H-2Kd-restricted N9 cytotoxic T lymphocyte clone specific for a photoreactive derivative of the Plasmodium berghei circumsporozoite peptide PbCS 252-260. This hybridoma was transfected either with CD8 alpha alone or together with CD8 beta. All three hybridomas released interleukin 2 upon incubation with L cells expressing Kd-peptide derivative complexes, though CD8 alpha/beta cells did so more efficiently than CD8 alpha/alpha and especially CD8-/- cells. More strikingly, only CD8 alpha/beta cells were able to recognize a weak agonist peptide derivative variant. This recognition was abolished by Fab' fragments of the anti-Kd alpha 3 monoclonal antibody SF1-1.1.1 or substitution of Kd D-227 with K, both conditions known to impair CD8 coreceptor function. T cell receptor (TCR) photoaffinity labeling indicated that TCR-ligand binding on CD8 alpha/beta cells was approximately 5- and 20-fold more avid than on CD8 alpha/a and CD8-/- cells, respectively. SF1-1.1.1 Fab' or Kd mutation D227K reduced the TCR photoaffinity labeling on CD8 alpha/beta cells to approximately the same low levels observed on CD8-/- cells. These results indicate that CD8 alpha/beta is a more efficient coreceptor than CD8alpha/alpha, because it more avidly strengthens TCR-ligand binding.

Optimisation de la cryo microscopie électronique pour les études des minicercles d'ADN

RESUME : Bien que les propriétés physiques de la structure de l'ADN aient été intensivement étudiées pendant plus de 50 ans il y a encore beaucoup de questions importantes qui attendent des réponses. Par exemple, qu'arrive-t-il à la structure de la double hélice d'ADN nue (sans protéines liées) lorsqu'elle est fortement courbée, de la même manière que dans les nucléosomes? Cet ADN nu est-il facilement plié (il reste dans le régime élastique) ou réduit-il la contrainte de flexion en formant des sites hyperflexibles «kinks» (il sort du régime élastique en cassant l'empilement des paires de bases à certains endroits) ? La microscopie électronique peut fournir une réponse à cette question par visualisation directe des minicercles d'ADN de la longueur d'un tour de nucléosome (environ 90 paires de bases). Pour que la réponse soit scientifiquement valide, on doit observer les molécules d'ADN lorsqu'elles sont en suspension dans la solution d'intérêt et sans que des colorations, produits chimiques ou fixatifs n'aient été ajoutés, étant donné que ceux-ci peuvent changer les propriétés de l'ADN. La technique de la cryo-microscopie électronique (cryo-EM) développée par le groupe de Jacques Dubochet au début des années 80, permet la visualisation directe des molécules d'ADN suspendues dans des couche minces vitrifiées de solutions aqueuses. Toutefois, le faible contraste qui caractérise la cryo-EM combinée avec la très petite taille des minicercles d'ADN rendent nécessaire l'optimisation de plusieurs étapes, aussi bien dans la préparation des échantillons que dans le processus d'acquisition d'images afin d'obtenir deux clichés stéréo qui permettent la reconstruction 3-D des minicercles d'ADN. Dans la première partie de ma thèse, je décris l'optimisation de certains paramètres pour la cryoEM et des processus d'acquisition d'image utilisant comme objets de test des plasmides et d'autres molécules d'ADN. Dans la deuxième partie, je .décris comment j'ai construit les minicercles d'ADN de 94 bp et comment j'ai introduit des modifications structurelles comme des coupures ou des lacunes. Dans la troisième partie, je décris l'analyse des reconstructions des rninicercles d'ADN. Cette analyse, appuyée par des tests biochimiques, indique fortement que des molécules d'ADN sont capables de former de petites molécules circulaires de 94 bp sans dépasser les limites d'élasticité, indiquant que les minicercles adoptent une forme circulaire régulière où la flexion est redistribuée le long la molécule. ABSTRACT : Although physical properties of DNA structure have been intensively studied for over 50 years there are still many important questions that need to be answered. For example, what happens to protein-free double-stranded DNA when it is strongly bent, as in DNA forming nucleosomes? Is such protein-free DNA smoothly bent (i.e. it remains within elastic limits of DNA rigidity) or does it release its bending stress by forming sharp kinks (i.e. it exits the elastic regime and breaks the stacking between neighbouring base-pairs in localized regions)? Electron microscopy can provide an answer to this question by directly visualizing DNA minicircles that have the size of nucleosome gyres (ca 90 bp). For the answer to be scientifically valid, one needs to observe DNA molecules while they are still suspended in the solution of interest and no staining chemicals or fixatives have been added since these can change the properties of the DNA. CryoEM techniques developed by Jacques Dubochet's group beginning in the 1980's permit direct visualization of DNA molecules suspended in cryo-vitrified layers of aqueous solutions. However, a relatively weak contrast of cryo-EM preparations combined with the very small size of the DNA minicircles made it necessary to optimize many of the steps and parameters of the cryo-EM specimen preparation and image acquisition processes in order to obtain stereo-pairs of images that permit the 3-D reconstruction of the observed DNA minicircles. In the first part of my thesis I describe the optimization of the cryo-EM preparation and the image acquisition processes using plasmid size DNA molecules as a test object. In the second part, I describe how I formed the 94 by DNA minicircles and how I introduced structural modifications like nicks or gaps. In the third part, I describe the cryo-EM analysis of the constructed DNA minicircles. That analysis, supported by biochemical tests, strongly indicates that DNA minicircles as small as 94 by remain within the elastic limits of DNA structure, i.e. the minicircles adopt a regular circular shape where bending is redistributed along the molecules.

Alternativas tecnológicas para la recuperación y valorización del nitrógeno presente en los residuos orgánicos

La conciencia de los problemas asociados a la gestión de los residuos orgánicos y el interés por las oportunidades de su recuperación y valorización han ido tomando importancia en los últimos años, tanto en el campo de las deyecciones ganaderas como en el sector de las aguas residuales. Consecuentemente, las combinaciones tecnológicas que permitan cerrar los ciclos de los nutrientes y la recuperación energética han adquirido mayor importancia en la investigación así como en las nuevas normativas sectoriales. En este contexto se sitúa el trabajo realizado durante el periodo becado (octubre 2010 - noviembre 2011). En una primera etapa de estudio bibliográfico se identificaron i) el aumento de la eficiencia en el uso del nitrógeno en la agricultura y en la ganadería, ii) la reutilización del nitrógeno en los mismos ecosistemas agrícolas y iii) el tratamiento de las deyecciones para redistribuir el nitrógeno a zonas con poca disponibilidad, como las tres direcciones principales hacia las cuales se está focalizando el interés del sector agrícola. Se puso en marcha una planta piloto de stripping y absorción para estudiar la posibilidad de recuperar y valorizar el amoniaco presente en los purines en forma de solución amoniacal para la industria de fertilizantes. Los resultados obtenidos evidenciaron el rol fundamental de las características iníciales del substrato en el rendimiento global del proceso. En particular, elevados contenidos en materia orgánica resultaron en bajas eficiencias y en elevadas contaminaciones del producto obtenido. Finalmente, considerando sus potenciales ventajas tanto en la gestión de los residuos ganaderos como de las aguas residuales y focalizándose en las perdidas de nitrógeno se estudió un sistema descentralizado de separación de orina instalado en un centro de investigación. Los resultados preliminares permitieron caracterizar los principales procesos que ocurren en el sistema e identificar las posibles líneas futuras de investigación.

Obésité en Suisse: percentiles d'indice de masse corporelle (IMC) d'une population d'enfants et d'adolescents nés en 1980 à Lausanne et écart avec les normes suisses (1955)

OBJECTIVES: The objective of this study is to calculate the percentiles of BMI of a cohort of 1,203 children and adolescents, representing the 95% of the pupils of the school, born in 1980 followed longitudinally between 5 and 16 years. We compare these percentiles with those of the first swiss study, calculated on a cohort born in 1954-1956. METHODS: The percentiles were calculated with the method of Cole, on the basis of weight and height measured during the controls by the school health service, at a non-periodic mean interval of 14 months. RESULTS: The gap between the BMI percentiles of the two cohorts is near zero for the third percentiles, weak but progressively growing with age up to two units of BMI for the 50th percentiles. For the percentiles 97 the difference, straight away present at five years, grows regularly up to 11 years, and remains thereafter for the girls at 4.3 units of BMI, while growing more up to 6.8 units of BMI at 15 years for the boys. The percentages of children and adolescents of the present study with overweight, in accordance with the thresholds of Cole, constant for the girls at 14%, increase for the five to 11.5 years old boys from 13.4% to 17.6% for the 11.5 to 16 years old. The percentage of obesity is 2.7% for the girls, and increase for the same categories for the boys from a percentage of 1.7% to 2.3% for the boys. CONCLUSIONS: The changes during this quarter of century are important, especially for the boys. We can postulate thereafter a very early change in the energy balance. A chronic increase of the food supply, linked or not with a decrease of the physical activity, would be an explanation.

Desarrollo del nuevo karat Starter Kit

El proyecto se desarrolla en el marco de un convenio entre la UAB y la empresa UNIT4 en las oficinas de UNIT4 Ibérica en Barberà del Vallès. El objetivo del proyecto es crear una nueva herramienta, denominada karat Starter Kit Reloaded, que sirva de autoformación y demostración de la plataforma de desarrollo propia utilizada en la empresa (karat) reforzando los puntos débiles de la anterior y manteniendo los puntos fuertes de los que ya disponía.

Genetic and environmental components of phenotypic variation in immune response and body size of a colonial bird, Delichon urbica (the house martin).

Directional selection for parasite resistance is often intense in highly social host species. Using a partial cross-fostering experiment we studied environmental and genetic variation in immune response and morphology in a highly colonial bird species, the house martin (Delichon urbica). We manipulated intensity of infestation of house martin nests by the haematophagous parasitic house martin bug Oeciacus hirundinis either by spraying nests with a weak pesticide or by inoculating them with 50 bugs. Parasitism significantly affected tarsus length, T cell response, immunoglobulin and leucocyte concentrations. We found evidence of strong environmental effects on nestling body mass, body condition, wing length and tarsus length, and evidence of significant additive genetic variance for wing length and haematocrit. We found significant environmental variance, but no significant additive genetic variance in immune response parameters such as T cell response to the antigenic phytohemagglutinin, immunoglobulins, and relative and absolute numbers of leucocytes. Environmental variances were generally greater than additive genetic variances, and the low heritabilities of phenotypic traits were mainly a consequence of large environmental variances and small additive genetic variances. Hence, highly social bird species such as the house martin, which are subject to intense selection by parasites, have a limited scope for immediate microevolutionary response to selection because of low heritabilities, but also a limited scope for long-term response to selection because evolvability as indicated by small additive genetic coefficients of variation is weak.

Arthritis is linked to local and systemic activation of coagulation and fibrinolysis pathways.

BACKGROUND: Activation of coagulation and fibrinolysis play a role in the pathophysiology of experimental arthritis. Objective: To determine the extent of activation of the coagulation and fibrinolytic pathways in different joint diseases in humans and to ascertain the factors that may influence fibrin deposition within the joint. METHODS: Plasma from normal subjects (controls, n= 21) and plasma and synovial fluid samples from patients with rheumatoid arthritis (RA; n = 64), osteoarthritis (OA; n = 29), spondyloarthropathy (SpA; n = 22) and crystal arthritis (CA; n = 25) were analyzed for the levels of TF (tissue factor) and tissue factor pathway inhibitor (TFPI) activities, thrombin-antithrombin III (TAT) complexes, and F1 + 2 (thrombin fragment), fibrin d-dimer and thrombin-activated fibrinolysis inhibitor (TAFI) antigenic levels. The measurements were analyzed by pairwise correlation with each other as well as with standard parameters of inflammation [C-reactive protein (CRP), joint leukocyte count]. Inter-group comparisons were performed to look for disease-specific differences. RESULTS: Compared with healthy controls, patients with joint diseases had higher levels of TAT, F1 + 2 and d-dimers in their plasma. In the synovial fluid, TF activity, TAT, d-dimers, and TAFI were significantly higher in inflammatory arthritides than in OA. The levels were highest in RA patients. In the plasma, TF activity was correlated with TAT and d-dimer levels with CRP, TFPI, and TAT. In the synovial fluid, TF activity correlated with plasma CRP levels, synovial fluid leukocyte count, and synovial TAT and TAFI levels. In addition, synovial d-dimers correlated with CRP, and synovial TAFI levels were correlated with synovial F1 + 2 and TAT. CONCLUSIONS: Activation of the coagulation and fibrinolytic cascades in the joint and in the circulation is evident in both inflammatory and degenerative joint diseases. Within the joint, inflammatory mechanisms leading to TF-mediated activation of the coagulation pathway and subsequent fibrin deposition is the most likely explanation for the observed findings. In the plasma, the link between inflammation (CRP increase) and TF activation is weak, and a non-TF-mediated mechanism of coagulation activation could explain these findings. RA is characterized by significantly higher levels of TAT in the synovial fluid and plasma than other arthritides. Although fibrinolytic activity is linked to inflammation, the increased amounts of TAFI in the joint, particularly in RA, may explain why fibrin formation is so prominent in this condition compared with other joint diseases.

Additives and Protein-DNA Combinations Modulate the Humoral Immune Response Elicited by a Hepatitis C Virus Core-encoding Plasmid in Mice

Humoral and cellular immune responses are currently induced against hepatitis C virus (HCV) core following vaccination with core-encoding plasmids. However, the anti-core antibody response is frequently weak or transient. In this paper, we evaluated the effect of different additives and DNA-protein combinations on the anti-core antibody response. BALB/c mice were intramuscularly injected with an expression plasmid (pIDKCo), encoding a C-terminal truncated variant of the HCV core protein, alone or combined with CaCl2, PEG 6000, Freund's adjuvant, sonicated calf thymus DNA and a recombinant core protein (Co.120). Mixture of pIDKCo with PEG 6000 and Freund's adjuvant accelerated the development of the anti-core Ab response. Combination with PEG 6000 also induced a bias to IgG2a subclass predominance among anti-core antibodies. The kinetics, IgG2a/IgG1 ratio and epitope specificity of the anti-core antibody response elicited by Co.120 alone or combined with pIDKCo was different regarding that induced by the pIDKCo alone. Our data indicate that the antibody response induced following DNA immunization can be modified by formulation strategies.

Screening of some plants used in the Brazilian folk medicine for the treatment of infectious diseases

Extracts of 13 Brazilian medicinal plants were screened for their antimicrobial activity against bacteria and yeasts. Of these, 10 plant extracts showed varied levels of antibacterial activity. Piper regnellii presented a good activity against Staphylococus aureus and Bacillus subtilis, a moderate activity on Pseudomonas aeruginosa, and a weak activity against Escherichia coli. Punica granatum showed good activity on S. aureus and was inactive against the other standard strains. Eugenia uniflora presented moderate activity on both S. aureus and E. coli. Psidium guajava,Tanacetum vulgare, Arctium lappa, Mikania glomerata, Sambucus canadensis, Plantago major and Erythrina speciosa presented some degree of antibacterial activity. Spilanthes acmella, Lippia alba, and Achillea millefolium were considered inactive. Five of the plant extracts presented compounds with Rf values similar to the antibacterial compounds visible on bioautogram. Of these, three plants belong to the Asteraceae family. This may mean that the same compounds are responsible for the antibacterial activity in these plants. Anticandidal activity was detected in nine plant extracts (P. guajava, E. uniflora, P. granatum, A. lappa, T. vulgare, M. glomerata, L. alba, P. regnellii, and P. major). The results might explain the ethnobotanical use of the studied species for the treatment of various infectious diseases.

Epidemiological and immunological aspects of human visceral leishmaniasis on Margarita Island, Venezuela

Sixty-five patients were diagnosed with visceral leishmaniasis (VL) on Margarita Island in the decade from 1990 to1999; 86.2% were <= 3 years old. All were leishmanin-negative at diagnosis. Evaluation of 23 cured patients in 1999 revealed that 22/23 had converted to leishmanin-positive; five had persisting antibodies to rK39 antigen, with no clinical evidence of disease. Leishmanin tests were positive in 20.2% of 1,643 healthy individuals from 417 households in endemic areas. Of the positive reactors, 39.8% were identified in 35 (8.4%) of the households, 15 of which had an antecedent case of VL, a serologically positive dog or both. Weak serological activity to rK39 antigen was detected in 3 of 488 human sera from the endemic areas. The presence of micro-foci of intense peri-urban transmission and the apparent absence of other Trypanosomatidae causing human disease offer a unique opportunity for the study of reservoirs, alternative vectors and evaluation of control measures on the Island.