Showing papers by "University of Rennes published in 2008"

Results of the Predictors of Response to CRT (PROSPECT) Trial

Abstract: Background— Data from single-center studies suggest that echocardiographic parameters of mechanical dyssynchrony may improve patient selection for cardiac resynchronization therapy (CRT). In a prospective, multicenter setting, the Predictors of Response to CRT (PROSPECT) study tested the performance of these parameters to predict CRT response. Methods and Results— Fifty-three centers in Europe, Hong Kong, and the United States enrolled 498 patients with standard CRT indications (New York Heart Association class III or IV heart failure, left ventricular ejection fraction ≤35%, QRS ≥130 ms, stable medical regimen). Twelve echocardiographic parameters of dyssynchrony, based on both conventional and tissue Doppler–based methods, were evaluated after site training in acquisition methods and blinded core laboratory analysis. Indicators of positive CRT response were improved clinical composite score and ≥15% reduction in left ventricular end-systolic volume at 6 months. Clinical composite score was improved in 6...

An Optimized Blockwise Nonlocal Means Denoising Filter for 3-D Magnetic Resonance Images

Abstract: A critical issue in image restoration is the problem of noise removal while keeping the integrity of relevant image information. Denoising is a crucial step to increase image quality and to improve the performance of all the tasks needed for quantitative imaging analysis. The method proposed in this paper is based on a 3-D optimized blockwise version of the nonlocal (NL)-means filter (Buades, , 2005). The NL-means filter uses the redundancy of information in the image under study to remove the noise. The performance of the NL-means filter has been already demonstrated for 2-D images, but reducing the computational burden is a critical aspect to extend the method to 3-D images. To overcome this problem, we propose improvements to reduce the computational complexity. These different improvements allow to drastically divide the computational time while preserving the performances of the NL-means filter. A fully automated and optimized version of the NL-means filter is then presented. Our contributions to the NL-means filter are: 1) an automatic tuning of the smoothing parameter; 2) a selection of the most relevant voxels; 3) a blockwise implementation; and 4) a parallelized computation. Quantitative validation was carried out on synthetic datasets generated with BrainWeb (Collins, , 1998). The results show that our optimized NL-means filter outperforms the classical implementation of the NL-means filter, as well as two other classical denoising methods [anisotropic diffusion (Perona and Malik, 1990)] and total variation minimization process (Rudin, , 1992) in terms of accuracy (measured by the peak signal-to-noise ratio) with low computation time. Finally, qualitative results on real data are presented.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.

Electrochemical reactivity in room-temperature ionic liquids.

Abstract: A review. Physicochem. properties of ionic liqs. are discussed. Chem. and electrochem. reactivity in ionic liqs. is described including electrode reactions, electrode reaction kinetics, electrosynthesis, etc.

Cyclical DNA methylation of a transcriptionally active promoter

Abstract: Processes that regulate gene transcription are directly under the influence of the genome organization. The epigenome contains additional information that is not brought by DNA sequence, and generates spatial and functional constraints that complement genetic instructions. DNA methylation on CpGs constitutes an epigenetic mark generally correlated with transcriptionally silent condensed chromatin. Replication of methylation patterns by DNA methyltransferases maintains genome stability through cell division. Here we present evidence of an unanticipated dynamic role for DNA methylation in gene regulation in human cells. Periodic, strand-specific methylation/demethylation occurs during transcriptional cycling of the pS2/TFF1 gene promoter on activation by oestrogens. DNA methyltransferases exhibit dual actions during these cycles, being involved in CpG methylation and active demethylation of 5mCpGs through deamination. Inhibition of this process precludes demethylation of the pS2 gene promoter and its subsequent transcriptional activation. Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement.

Transient cyclical methylation of promoter DNA

Abstract: Methylation of CpG dinucleotides is generally associated with epigenetic silencing of transcription and is maintained through cellular division. Multiple CpG sequences are rare in mammalian genomes, but frequently occur at the transcriptional start site of active genes, with most clusters of CpGs being hypomethylated. We reported previously that the proximal region of the trefoil factor 1 (TFF1, also known as pS2) and oestrogen receptor alpha (ERalpha) promoters could be partially methylated by treatment with deacetylase inhibitors, suggesting the possibility of dynamic changes in DNA methylation. Here we show that cyclical methylation and demethylation of CpG dinucleotides, with a periodicity of around 100 min, is characteristic for five selected promoters, including the oestrogen (E2)-responsive pS2 gene, in human cells. When the pS2 gene is actively transcribed, DNA methylation occurs after the cyclical occupancy of ERalpha and RNA polymerase II (polII). Moreover, we report conditions that provoke methylation cycling of the pS2 promoter in cell lines in which pS2 expression is quiescent and the proximal promoter is methylated. This coincides with a low-level re-expression of ERalpha and of pS2 transcripts.

Enhanced two-photon absorption of organic chromophores: theoretical and experimental assessments ∗∗

Abstract: Functional organic materials with enhanced two-photon absorption lead to new technologies in the fields of chemistry, biology, and photonics. In this article we review experimental and theoretical methodologies allowing detailed investigation and analysis of two-photon absorption properties of organic chromophores. This includes femtosecond two-photon excited fluorescence experimental setups and quantum-chemical methodologies based on time-dependent density functional theory. We thoroughly analyze physical phenomena and trends leading to large twophoton absorption responses of a few series of model chromophores focusing on the effects of symmetric and asymmetric donor/acceptor substitution and branching.

Connectivity measures: a review

Abstract: One of the central problems in contemporary ecology and conservation biology is the drastic change of landscapes induced by anthropogenic activities, resulting in habitat loss and fragmentation. For many wild living species, local extinctions of fragmented populations are common and recolonization is critical for regional survival. Successful recolonization depends on the availability of dispersing individuals and the degree of landscape connectivity. The obvious implications of landscape connectivity for conservation biology have led to a proliferation of connectivity measures. However, general relationships between landscape connectivity and landscape structure are lacking, and so are the relationships between different connectivity metrics. Consequently, there is a need to develop landscape metrics that more accurately characterize the landscape with an emphasis on the underlying processes. Here we review various definitions of landscape connectivity, explain their mathematical connotations, and make some unifying conclusions and suggestions for future research.

Catecholamines and the effects of exercise, training and gender.

Abstract: Stress hormones, adrenaline (epinephrine) and noradrenaline (norepinephrine), are responsible for many adaptations both at rest and during exercise. Since their discovery, thousands of studies have focused on these two catecholamines and their importance in many adaptive processes to different stressors such as exercise, hypoglycaemia, hypoxia and heat exposure, and these studies are now well acknowledged. In fact, since adrenaline and noradrenaline are the main hormones whose concentrations increase markedly during exercise, many researchers have worked on the effect of exercise on these amines and reported 1.5 to >20 times basal concentrations depending on exercise characteristics (e.g. duration and intensity). Similarly, several studies have shown that adrenaline and noradrenaline are involved in cardiovascular and respiratory adjustments and in substrate mobilization and utilization. Thus, many studies have focused on physical training and gender effects on catecholamine response to exercise in an effort to verify if significant differences in catecholamine responses to exercise could be partly responsible for the different performances observed between trained and untrained subjects and/or men and women. In fact, previous studies conducted in men have used different types of exercise to compare trained and untrained subjects in response to exercise at the same absolute or relative intensity. Their results were conflicting for a while. As research progressed, parameters such as age, nutritional and emotional state have been found to influence catecholamine concentrations. As a result, most of the recent studies have taken into account all these parameters. Those studies also used very well trained subjects and/or more intense exercise, which is known to have a greater effect on catecholamine response so that differences between trained and untrained subjects are more likely to appear. Most findings then reported a higher adrenaline response to exercise in endurance-trained compared with untrained subjects in response to intense exercise at the same relative intensity as all-out exercise. This phenomenon is referred to as the 'sports adrenal medulla'. This higher capacity to secrete adrenaline was observed both in response to physical exercise and to other stimuli such as hypoglycaemia and hypoxia. For some authors, this phenomenon can partly explain the higher physical performance observed in trained compared with untrained subjects. More recently, these findings have also been reported in anaerobic-trained subjects in response to supramaximal exercise. In women, studies remain scarce; the results are more conflicting than in men and the physical training type (aerobic or anaerobic) effects on catecholamine response remain to be specified. Conversely, the works undertaken in animals are more unanimous and suggest that physical training can increase the capacity to secrete adrenaline via an increase of the adrenal gland volume and adrenaline content.

In search of a real definition of the biological invasion phenomenon itself

Abstract: The many qualifying terms attributed to invasive species reveal the lack of precision surrounding the notion of biological invasion itself. In spite of several proposed definitions, some basic disagreements persist concerning characterization of the phenomenon. These primarily arise from the lack of pertinence of both of the main current criteria—the geographic (or biogeographic) criterion and the impact criterion—to what is really intended by “invasion.” Faced with this situation, it seems preferable to adopt an ontological approach allowing a return to the basic principles of the elaboration of a definition. Starting with the nature of the phenomenon itself (i.e., its essence), we try to elucidate the notion of biological invasion and we suggest a general definition compatible with most of the ideas already expressed.

Does Urbanization Filter Birds on the Basis of Their Biological Traits

Abstract: Urbanization leads to the biotic homogenization of global avifauna. We hypothesized that urbanization acts as a filter on species traits and, therefore, that urban passerines share biological traits explaining their capacity to tolerate urban constraints. We investigated 18 biological traits of passerines related to their general biology, distribution, breeding, and morphometry. In a regional analysis conducted on passerine data from one Swiss and 11 French cities (regional analysis), we identified urban adapters (tolerant species) and urban avoiders (intolerant species), and compared their traits. In a local analysis conducted on passerine data of 13 woodlands located along a short rural-urban gradient, we identified groups of species associated with particular vegetation structures within or particular landscape structures around woodlands. We associated each of these species groups with a tolerance level to urbanization and compared their traits. Regional analysis revealed that urban adapters ...

Quadratic BSDEs with convex generators and unbounded terminal conditions

Abstract: In Briand and Hu (Probab Theory Relat Fields 136(4):604–618, 2006), the authors proved an existence result for BSDEs with quadratic generators with respect to the variable z and with unbounded terminal conditions. However, no uniqueness result was stated in that work. The main goal of this paper is to fill this gap. In order to obtain a comparison theorem for this kind of BSDEs, we assume that the generator is convex with respect to the variable z. Under this assumption of convexity, we are also able to prove a stability result in the spirit of the a priori estimates stated in Karoui et al. (Math Finance 7(1):1–71, 1997). With these tools in hands, we can derive the nonlinear Feynman–Kac formula in this context.

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.

Abstract: Background The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group.

Treatment of Churg-Strauss syndrome without poor-prognosis factors: a multicenter, prospective, randomized, open-label study of seventy-two patients.

Abstract: OBJECTIVE: To assess the efficacy of systemic corticosteroids (CS) alone as first-line treatment in patients with Churg-Strauss syndrome (CSS) without poor-prognosis factors, as defined by the Five-Factors Score (FFS), and to compare the efficacy and safety of oral azathioprine (AZA) versus intravenous pulse cyclophosphamide (CYC) as adjuvant immunosuppressive therapy for treatment failure or relapse. METHODS: This multicenter, prospective, randomized, open-label therapeutic trial included 72 patients with newly diagnosed CSS (FFS of 0) treated with CS alone. At treatment failure or relapse, patients were randomized to receive 6 months of oral AZA or 6 pulses of CYC. Analyses were performed according to an intent-to-treat strategy. RESULTS: The mean +/- SD followup was 56.2 +/- 31.7 months. Among the 72 patients studied, 93% achieved remission with CS therapy alone, and 35% relapsed, mainly during the first year of treatment. Among the 19 patients randomized to additional immunosuppression because of treatment failure or relapse, 5 of 10 receiving AZA and 7 of 9 receiving pulse CYC achieved remission, but the difference was not statistically significant. Survival rates in all patients at 1 and 5 years were 100% and 97%, respectively. At the end of followup, 79% of the patients whose disease was in remission required low-dose CS therapy, mainly to control respiratory disease. CS-related adverse events were observed in 31% of the 72 patients. CONCLUSION: In CSS patients with an FFS of 0, survival was excellent, confirming the predictive value of the FFS in this disease. First-line therapy with CS achieved remission in most patients, but relapses were common, and one-third of them required additional immunosuppressive therapy. AZA or pulse CYC was fairly effective in treating CS-resistant disease or major relapses. Over the long term, most patients continued to take oral CS, which might explain the high rate of CS-related adverse events.

Rician Noise Removal by Non-Local Means Filtering for Low Signal-to-Noise Ratio MRI: Applications to DT-MRI

Abstract: Diffusion-Weighted MRI (DW-MRI) is subject to random noise yielding measures that are different from their real values, and thus biasing the subsequently estimated tensors The Non-Local Means (NLMeans) filter has recently been proposed to denoise MRI with high signal-to-noise ratio (SNR) This filter has been shown to allow the best restoration of image intensities for the estimation of diffusion tensors (DT) compared to state-of-the-art methods However, for DW-MR images with high b-values (and thus low SNR), the noise, which is strictly Rician-distributed, can no longer be approximated as additive white Gaussian, as implicitly assumed in the classical formulation of the NLMeans High b-values are typically used in high angular resolution diffusion imaging (HARDI) or q-space imaging (QSI), for which an optimal restoration is critical In this paper, we propose to adapt the NLMeans filter to Rician noise corrupted data Validation is performed on synthetic data and on real data for both conventional MR images and DT images Our adaptation outperforms the original NLMeans filter in terms of peak-signal-to-noise ratio (PSNR) for DW-MRI

Diagnosis and classification of myelodysplastic syndrome: International Working Group on Morphology of myelodysplastic syndrome (IWGM-MDS) consensus proposals for the definition and enumeration of myeloblasts and ring sideroblasts

Abstract: The classification of myelodysplastic syndromes is based on the morphological criteria proposed by the French-American-British (FAB) and World Health Organization (WHO) groups. Accurate enumeration of blast cells, although essential for diagnosis of myelodysplastic syndrome and for assignment to prognostic groups, is often difficult, due to imprecise criteria for the morphological definition of blasts and promyelocytes. An International Working Group on Morphology of Myelodysplastic Syndrome (IWGM-MDS) of hematopathologists and hematologists expert in the field of myelodysplastic syndrome reviewed the morphological features of bone marrows from all subtypes of myelodysplastic syndrome and agreed on a set of recommendations, including recommendations for the definition and enumeration of blast cells and ring sideroblasts. It is recommended that (1) agranular or granular blast cells be defined (replacing the previous type I, II and III blasts), (2) dysplastic promyelocytes be distinguished from cytologically normal promyelocytes and from granular blast cells, (3) sufficient cells be counted to give a precise blast percentage, particularly at thresholds that are important for diagnosis or prognosis and (4) ring sideroblasts be defined as erythroblasts in which there are a minimum of 5 siderotic granules covering at least a third of the nuclear circumference. Clear definitions and a differential count of a sufficient number of cells is likely to improve precision in the diagnosis and classification of myelodysplastic syndrome. Recommendations should be applied in the context of the WHO classification.

FTIR spectroscopy can be used as a screening tool for organic matter quality in regenerating cutover peatlands

Abstract: Vegetational changes during the restoration of cutover peatlands leave a legacy in terms of the organic matter quality of the newly formed peat. Current efforts to restore peatlands at a large scale therefore require low cost and high throughput techniques to monitor the evolution of organic matter. In this study, we assessed the merits of using Fourier transform infrared (FTIR) spectra to predict the organic matter composition in peat samples at various stages of peatland regeneration from five European countries. Using predictive partial least squares (PLS) analyses, we were able to reconstruct peat C:N ratio and carbohydrate signatures with reasonable accuracy, but not the micromorphological composition of vegetation remains. Despite utilising different size fractions, both carbohydrate (

Current features of infective endocarditis in elderly patients: results of the International Collaboration on Endocarditis Prospective Cohort Study

Abstract: Results: Elderly patients reported more frequently a hospitalization or an invasive procedure before IE onset. Diabetes mellitus and genitourinary and gastrointestinal cancer were the major predisposing conditions. Blood culture yield was higher among elderly patients with IE. The leading causative organism was Staphylococcus aureus, with a higher rate of methicillin resistance.Streptococcusbovis and enterococci were also significantly more prevalent. The clinical presentation of elderly patients with IE was remarkable for lower rates of embolism, immune-mediated phenomena, or septic complications. At both echocardiography and surgery, fewer vegetations and more abscesses were found, and the gain in the diagnostic yield of transesophageal echocardiography was significantly larger. Significantly fewer elderly patients underwent cardiac surgery (38.9% vs 53.5%; P.001). Elderly patients with IE showed a higher rate of in-hospital death (24.9% vs 12.8%; P.001), and age older than 65 years was an independent predictor of mortality. Conclusions: In this large prospective study, increasing age emerges as a major determinant of the clinical characteristics of IE. Lower rates of surgical treatment and high mortality are the most prominent features of elderly patients with IE. Efforts should be made to prevent health care–associated acquisition and improve outcomes in this major subgroup of patients with IE.

EB1 regulates microtubule dynamics and tubulin sheet closure in vitro.

Abstract: End binding 1 (EB1) is a plus-end-tracking protein (+TIP) that localizes to microtubule plus ends where it modulates their dynamics and interactions with intracellular organelles. Although the regulating activity of EB1 on microtubule dynamics has been studied in cells and purified systems, the molecular mechanisms involved in its specific activity are still unclear. Here, we describe how EB1 regulates the dynamics and structure of microtubules assembled from pure tubulin. We found that EB1 stimulates spontaneous nucleation and growth of microtubules, and promotes both catastrophes (transitions from growth to shrinkage) and rescues (reverse events). Electron cryomicroscopy showed that EB1 induces the initial formation of tubulin sheets, which rapidly close into the common 13-protofilament-microtubule architecture. Our results suggest that EB1 favours the lateral association of free tubulin at microtubule-sheet edges, thereby stimulating nucleation, sheet growth and closure. The reduction of sheet length at microtubule growing-ends together with the elimination of stressed microtubule lattices may account for catastrophes. Conversely, occasional binding of EB1 to the microtubule lattice may induce rescues.