Metric field construction for anisotropic mesh adaptation with application to blood flow simulations.

The goal of this paper is to generate an anisotropic metric field suitable for cardiovascular geometries before a fluid simulation. Starting from a curvature map, an initial surface metric field is computed. This metric is used for anisotropic surface mesh adaptation and consecutively extended inside the volume in a frontal manner. The algorithm is based on the method proposed by Alauzet but replaces the metric intersection steps by an original metric 'blending'. This allows for a graded anisotropic volume mesh with a refinement layer close to the walls. The benefits of the resulting mesh are multiple: a reduced number of degrees of freedom, a priori refinement in areas with strong gradients of velocity and automatically increased resolution in regions with high surface curvature. The primal application of this method is in the domain of cardiovascular flows. Flow fields and derived quantities (wall shear stress) through a model bypass around a stenosed artery obtained on an adapted and standard isotropic mesh are compared. In addition, the mesh generation method is tested on a more complex patient-specific geometry. Values of computed wall shear stress are shown to be close to values obtained on anisotropic Hessian-adapted mesh, demonstrating the computational efficiency of the approach in comparison with adaptation based on error indicators derived from flow field.

Cardiovascular and lung mesh generation based on centerlines.

We present a fully automatic procedure for the mesh generation of tubular geometries such as blood vessels or airways. The procedure is implemented in the open-source Gmsh software and relies on a centerline description of the input geometry. The presented method can generate different type of meshes: isotropic tetrahedral meshes, anisotropic tetrahedral meshes, and mixed hexahedral/tetrahedral meshes. Additionally, a multiple layered arterial wall can be generated with a variable thickness. All the generated meshes rely on a mesh size field and a mesh metric that is based on centerline descriptions, namely the distance to the centerlines and a local reference system based on the tangent and the normal directions to the centerlines. Different examples show that the proposed method is very efficient and robust and leads to high quality computational meshes.

Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes.

OBJECTIVES: Rapid diagnosis and appropriate empirical antimicrobial therapy before the availability of conventional microbiological results is of pivotal importance for the clinical outcome of ventilator-associated pneumonia (VAP). We evaluated the VAPChip, a novel, closed cartridge molecular tool aiming to identify directly from clinical samples and within a working day the principal bacteria causative of VAP as well as clinically relevant ß-lactam resistance genes. METHODS: The Real-time Array PCR for Infectious Diseases (RAP-ID) is a novel technology that combines multiplex PCR with real-time microarray detection. The VAPChip is a closed cartridge kit adapted to the RAP-ID instrument that targets 13 key respiratory pathogens causative of VAP and 24 relevant antimicrobial resistance genes that mediate resistance to ß-lactam agents, including extended-spectrum cephalosporins and carbapenems. Analytical validation of the VAPChip was carried out blindly on a collection of 292 genotypically characterized bacterial reference and clinical isolates, including 225 isolates selected on the basis of their species identification and antimicrobial resistance profiles and 67 bacterial isolates belonging to the oropharyngeal flora not targeted by the array. RESULTS: The limit of detection of the assay lies between 10 and 100 genome copies/PCR and the dynamic range is five orders of magnitude permitting at least semi-quantitative reporting of the results. Sensitivity, specificity and negative and positive predictive values ranged from 95.8% to 100% for species identification and detection of resistance genes. CONCLUSIONS: VAPChip is a novel diagnostic tool able to identify resistant bacterial isolates by RAP-ID technology. The results of this analytical validation have to be confirmed on clinical specimens.

Design, recruitment, logistics, and data management of the GEHA (Genetics of Healthy Ageing) project.

In 2004, the integrated European project GEHA (Genetics of Healthy Ageing) was initiated with the aim of identifying genes involved in healthy ageing and longevity. The first step in the project was the recruitment of more than 2500 pairs of siblings aged 90 years or more together with one younger control person from 15 areas in 11 European countries through a coordinated and standardised effort. A biological sample, preferably a blood sample, was collected from each participant, and basic physical and cognitive measures were obtained together with information about health, life style, and family composition. From 2004 to 2008 a total of 2535 families comprising 5319 nonagenarian siblings were identified and included in the project. In addition, 2548 younger control persons aged 50-75 years were recruited. A total of 2249 complete trios with blood samples from at least two old siblings and the younger control were formed and are available for genetic analyses (e.g. linkage studies and genome-wide association studies). Mortality follow-up improves the possibility of identifying families with the most extreme longevity phenotypes. With a mean follow-up time of 3.7 years the number of families with all participating siblings aged 95 years or more has increased by a factor of 5 to 750 families compared to when interviews were conducted. Thus, the GEHA project represents a unique source in the search for genes related to healthy ageing and longevity.

Design and validation of a low density array (Nosochip) for the detection and identification of the main pathogenic bacteria and fungi responsible for nosocomial pneumonia.

The aim of this study was to be able to amplify and to detect on one array 27 different etiologic agents found in nosocomial pneumonia, some being phylogenetically closely related and others very distant. The assay is based on the use of consensus primers combined with the identification of the resulting amplicons by hybridization on specific capture probes present on an array. Three genes were necessary in order to cover the different pathogens. We took a redundancy of at least two positive spots to confirm the identity of each species. Each probe was present in triplicate on the array. The detection limit was between 10 and 1,000 DNA copies in the assay depending on the bacteria and the probe. The assay was also specific when tested both on reference collection strains corresponding to the 27 species of interest and on 57 other bacterial species of the normal human flora. Accuracy of the assay was assessed on 200 clinical isolates and some polymorphisms were indeed observed for 5 species. Effectiveness of the assay was preliminarily validated on 25 endotracheal aspirates and sputum samples, and the results were in accordance either with the cell culture or with the sequencing. Polybacterial infections were well detected in three samples. The results show that a combination of appropriate polymerase chain reaction (PCR) and redundancy of signals on the array allows specific screening of bacteria belonging to different species and genus and even fungi. The results open the way for a possible molecular detection of bacteria in the clinical diagnostic setting.

Comparative clinical and transcriptomal profiles of breast cancer between French and South Mediterranean patients show minor but significative biological differences.

BACKGROUND: In Western countries, breast cancer incidence and mortality are higher than in Mediterranean countries. These differences have been ascribed to environmental factors but also to late-stage diagnostic and biological specific characteristics. PATIENTS AND METHODS: Between September 2002 and September 2005, we collected clinical data by phone counselling 180 French and Mediterranean breast cancer patients and performed microarray experiments. RESULTS: Characteristics of breast cancer in patients from Lebanon, Tunisia and Morocco were more aggressive (more SBR grade III and positive node invasion) and patients were 10 years younger at diagnosis. Sixteen differentially expressed genes such as MMP9, VEGF, PHB1, BRCA1, TFAP2C, GJA1 and TFF1 were also found. Additionally, an up-regulation of cytokeratins KRT8 and KRT18 may indicate a luminal B subtype in "South" (Lebanon, Tunisia and Morocco) tumors while "North" (France) tumors may more frequently be luminal A type. CONCLUSION: This study allowed the identification of specific clinical and transcriptomic parameters in patients from South Mediterranean countries.

DNA microarray to detect and identify trichothecene- and moniliformin-producing Fusarium species.

AIMS: To develop a DNA microarray for easy and fast detection of trichothecene- and moniliformin-producing Fusarium species. METHOD AND RESULTS: A DNA microarray was developed for detection and identification of 14 trichothecene- and moniliformin-producing species of the fungal genus Fusarium. The array could also differentiate between four species groups. Capture probes were designed based on recent phylogenetic analyses of translation elongation factor-1 alpha (TEF-1alpha) sequences. Particular emphasis was put on designing capture probes corresponding to groups or species with particular mycotoxigenic synthetic abilities. A consensus PCR amplification of a part of the TEF-1alpha is followed by hybridization to the Fusarium chip and the results are visualized by a colorimetric Silverquant detection method. We validated the Fusarium chip against five naturally infected cereal samples for which we also have morphological and chemical data. The limit of detection was estimated to be less than 16 copies of genomic DNA in spiked commercial wheat flour. CONCLUSIONS: The current Fusarium chip proved to be a highly sensitive and fast microarray for detection and identification of Fusarium species. We postulate that the method also has potential for (semi-)quantification. SIGNIFICANCE AND IMPACT OF THE STUDY: The Fusarium chip may prove to be a very valuable tool for screening of cereal samples in the food and feed production chain, and may facilitate detection of new or introduced Fusarium spp.

Electrical detection of DNA hybridization: three extraction techniques based on interdigitated Al/Al2O3 capacitors.

Based on interdigitated aluminum electrodes covered with Al(2)O(3) and silver precipitation via biotin-antibody coupled gold nano-labels as signal enhancement, three complementary electrical methods were used and compared to detect the hybridization of target DNA for concentrations down to the 50 pM of a PCR product from cytochrome P450 2b2 gene. Human hepatic cytochrome P450 (CYP) enzymes participate in detoxification metabolism of xenobiotics. Therefore, determination of mutational status of P450 gene in a patient could have a significant impact on the choice of a medical treatment. Our three electrical extraction procedures are performed on the same interdigitated capacitive sensor lying on a passivated silicon substrate and consist in the measurement of respectively the low-frequency inter-electrodes capacitance, the high-frequency self-resonance frequency, and the equivalent MOS capacitance between the short-circuited electrodes and the backside metallization of the silicon substrate. This study is the first of its kind as it opens the way for correlation studies and noise reduction techniques based on multiple electrical measurements of the same DNA hybridization event with a single sensor.

CTLA-4 interacts with STAT5 and inhibits STAT5-mediated transcription.

Cytotoxic T-lymphocyte antigen-4 (CTLA-4; CD152) is a member of the immunoglobulin gene superfamily with strong homology to the receptor CD28 with which it shares the ligands CD80 and CD86. Unlike CD28, a potent costimulator of T-cell responses, CTLA-4 is transiently expressed on the cell surface of activated T cells and appears to operate predominantly as a negative regulator of T-cell proliferation. Signal transduction mechanisms utilized by CTLA-4 remain unclear although several mechanisms have been implicated. In this study, we show that the cytoplasmic domain of CTLA-4, but not of CD28, binds to STAT5 in yeast two-hybrid assay and in coimmunoprecipitation assays. Mutations of Tyr165 and Tyr182 in CTLA-4 did not abrogate the interaction of STAT5 with CTLA-4. Finally, the overexpression of CTLA-4 in Jurkat T cells inhibits STAT-mediated activation of STAT5 responsive elements. These results suggest that CTLA-4 and STAT5 interact in T cells and that this interaction is important for CTLA-4 signalling.

Identification of potential anti-photoageing algal compounds using an in-vitro model of photoageing.

Stress-induced premature senescence (SIPS) has been proposed as an in-vitro model for testing the long-term effects of stressful events and to find molecules/natural extracts that protect against such stress. Premature senescence of human skin diploid fibroblasts (HDFs) can be induced by repeated subcytotoxic exposure to UVB, with the appearance of so-called biomarkers of senescence such as growth arrest, senescence-associated beta-galactosidase activity, senescence-associated gene over-expression and the common 4977-bp mitochondrial DNA deletion. This model of UVB-induced premature senescence has been acknowledged as a robust in-vitro model in photoageing research. In this study, the potential anti-photoageing effects of a series of algal extracts were tested. The appearance of the biomarkers of UVB-induced premature senescence of HDFs was studied with or without algal extracts. One algal extract was shown to be particularly protective against UVB-induced SIPS. The results obtained here reinforce the notion that UVB-induced premature senescence of HDFs can be used to screen potential anti-photoageing compounds.

Hypothalamic stimulation in chronic cluster headache: a pilot study of efficacy and mode of action.

We enrolled six patients suffering from refractory chronic cluster headache in a pilot trial of neurostimulation of the ipsilateral ventroposterior hypothalamus using the stereotactic coordinates published previously. After the varying durations needed to determine optimal stimulation parameters and a mean follow-up of 14.5 months, the clinical outcome is excellent in three patients (two are pain-free; one has fewer than three attacks per month), but unsatisfactory in one patient, who only has had transient remissions. Mean voltage is 3.28 V, diplopia being the major factor limiting its increase. When the stimulator was switched off in one pain-free patient, attacks resumed after 3 months until it was turned on again. In one patient the implantation procedure had to be interrupted because of a panic attack with autonomic disturbances. Another patient died from an intracerebral haemorrhage that developed along the lead tract several hours after surgery; there were no other vascular changes on post-mortem examination. After 1 month, the hypothalamic stimulation induced resistance against the attack-triggering agent nitroglycerin and tended to increase pain thresholds at extracephalic, but not at cephalic, sites. It had no detectable effect on neurohypophyseal hormones or melatonin excretion. We conclude that hypothalamic stimulation has remarkable efficacy in most, but not all, patients with treatment-resistant chronic cluster headache. Its efficacy is not due to a simple analgesic effect or to hormonal changes. Intracerebral haemorrhage cannot be neglected in the risk evaluation of the procedure. Whether it might be more prevalent than in deep-brain stimulation for movement disorders remains to be determined.

Comparison of DNA detection methods using nanoparticles and silver enhancement.

DNA microarrays are an emerging technology for the parallel detection of DNA molecules. Fluorescent molecules are the current standard for a DNA array's optical readout but they possess some drawbacks including the stability of the dyes and the cost of the scanners. Therefore alternative labelling strategies are of considerable interests. One such strategy is the use of nanoparticles which offers several advantages in terms of stability and versatility of the detection mode. The authors present a review on the different ways DNA can be detected, mainly onto a solid support, using nanoparticle labels.

DNA microarrays as a tool in toxicogenomics.

Toxicogenomics is an emerging technology that defines the use of novel genomic techniques to investigate the adverse effects of xenobiotic on gene expression. Toxicogenomics is based on the fact that most of relevant toxicological effects of a compound affect directly or indirectly the gene expression. The most common methods to profile gene expression at the transcript level are Northern Blotting and the real-time PCR. While commonly used and well accepted, these techniques are now superseded by new technologies allowing the analysis of the expression for multiple genes simultaneously. DNA microarrays are now developed for simultaneous gene analysis but inherent to such multiple assays, their quantitative aspect and their relevance for toxicogenomics have been questioned. We will review here recent studies on their use for toxicogenomics and examine the possible future of such technology in complementation with the other toxicology methods.

Nasal dermoid cyst: diagnosis and management of five cases.

Five cases of nasal dermoid cyst are presented. Three out of five cases were settled during childhood. Three presented a mass with a hole on the external nose with recurrent local infections. One case was wrongly referred for a dacryocystitis. The first one was detected during an infection of the cerebral extension and frontal abscess was assessed by CT scan and MRI. Two patients had other associated congenital abnormalities: hypotrophy of the external ear in one case, multiples malformations in an other. Adequate exposure and cosmetic results are sometimes contradictory to define the best surgical approach. Dermoid cysts and sinuses must be completely removed to prevent recurrence. External rhinoplasty and bicoronal approach are the main procedures for removing these lesions.

Compact disc with both numeric and genomic information as DNA microarray platform.

The compact disc (CD) is an ideal toolfor reading, writing, and storing numeric information. It was used in this work as a support for constructing DNA microarrays suited for genomic analysis. The CD was divided into two functional areas: the external ring of the CD was used for multiparametric DNA analysis on arrays, and the inner portion was usedfor storing numeric information. Because polycarbonate and CD resins autofluoresce, a colorimetric method for DNA microarray detection was used that is well adaptedfor the fast detection necessary when using a CD reader. A double-sided CD reader was developed for the simultaneous analysis of both array and numeric data. The numeric data are engraved as pits in the CD tracks and result in the succession of 0/1, which results from the modulation of the laser reflection when one reads the edges of the pits. Another diffraction-based laser was placed above the CD for the detection of the DNA targets on the microarrays. Both readersfit easily in a PC tower. Both numeric and genomic information data were simultaneously acquired, and each array was reconstituted, analyzed, and processed for quantification by the appropriate software.

Role of the endothelium and blood stasis in the appearance of varicose veins.

Today, chronic venous insufficiency affects millions of people but the investigation of veins and of venous diseases is still very poor. Additionally, the mechanism of the occurrence of varicose veins is not understood. Blood stasis is often associated with these pathological situations and we propose that resulting ischemic conditions can trigger the endothelium to release inflammatory mediators and growth factors. On one hand, the inflammatory mediators will recruit and activate neutrophils, which then infiltrate the venous wall and damage components of the extracellular matrix. On the other hand, growth factors induce smooth muscle cell migration, proliferation and de-differentiation into the synthetic phenotype, all together leading to the formation of neointima. These processes, being repeated over time, would eventually lead to alterations of the venous wall as observed in varicose veins. Venotropic drugs are used to treat chronic venous insufficiency. They are able to increase venous tone and to decrease vein and capillary permeability but they are also able to protect the endothelial cells against ischemia. Indeed, they target complexes of the mitochondrial respiratory chain and maintain ATP production during hypoxia. Hence, the cells are resistant to ischemia and do not release inflammatory mediators and growth factors. These drugs should thus be able to prevent the alterations of the venous wall induced by blood stasis.

A low-density DNA microarray for analysis of markers in breast cancer.

Breast cancer remains a major cause of death in women from Western countries. In the near future, advances in both nucleic acids technology and tumor biology should be widely exploited to improve the diagnosis, prognosis, and outcome prediction of this disease. The DNA microarray, also called biochip, is a promising tool for performing massive, simultaneous, fast, and standardized analyses of multiple molecular markers in tumor samples. However, most currently available microarrays are expensive, which is mainly due to the amount (several thousands) of different DNA capture sequences that they carry. While these high-density microarrays are best suited for basic studies, their introduction into the clinical routine remains hypothetical. We describe here the principles of a low-density microarray, carrying only a few hundreds of capture sequences specific to markers whose importance in breast cancer is generally recognized or suggested by the current medical literature. We provide a list of about 250 of these markers. We also examine some potential difficulties (homologies between marker and/or variant sequences, size of sequences, etc.) associated with the production of such a low-cost microarray.

CREB activation induced by mitochondrial dysfunction is a new signaling pathway that impairs cell proliferation.

We characterized a new signaling pathway leading to the activation of cAMP-responsive element-binding protein (CREB) in several cell lines affected by mitochondrial dysfunction. In vitro kinase assays, inhibitors of several kinase pathways and overexpression of a dominant-negative mutant for calcium/calmodulin kinase IV (CaMKIV), which blocks the activation of CREB, showed that CaMKIV is activated by a mitochondrial activity impairment. A high calcium concentration leading to the disruption of the protein interaction with protein phosphatase 2A explains CaMKIV activation in these conditions. Transcrip tionally active phosphorylated CREB was also found in a rho0 143B human osteosarcoma cell line and in a MERRF cybrid cell line mutated for tRNA(Lys) (A8344G). We also showed that phosphorylated CREB is involved in the proliferation defect induced by a mitochondrial dysfunction. Indeed, cell proliferation inhibition can be prevented by CaMKIV inhibition and CREB dominant-negative mutants. Finally, our data suggest that phosphorylated CREB recruits p53 tumor suppressor protein, modifies its transcriptional activity and increases the expression of p21(Waf1/Cip1), a p53-regulated cyclin-dependent kinase inhibitor.

Role of the endothelium and blood stasis in the development of varicose veins.

Today, chronic venous insufficiency affects millions of people but the investigation of veins and of venous diseases is still very poor. Additionally, the mechanism of the occurrence of varicose veins is not understood. Blood stasis is often associated with these pathological situations and we propose that resulting ischemic conditions can trigger the endothelium to release inflammatory mediators and growth factors. On one hand, the inflammatory mediators will recruit and activate neutrophils, which then infiltrate the venous wall and damage components of the extracellular matrix. On the other hand, growth factors induce smooth muscle cell migration, proliferation and de-differentiation into the synthetic phenotype, all together leading to the formation of neointima. These processes, being repeated over time, would eventually lead to alterations of the venous wall as observed in varicose veins. Venotropic drugs are used to treat chronic venous insufficiency. They are able to increase venous tone and to decrease vein and capillary permeability but they are also able to protect the endothelial cells against ischemia. Indeed, they target complexes of the mitochondrial respiratory chain and maintain ATP production during hypoxia. Hence, the cells are resistant to ischemia and do not release inflammatory mediators and growth factors. These drugs should thus be able to prevent the alterations of the venous wall induced by blood stasis.

Hypoxia-induced increase in intracellular calcium concentration in endothelial cells: role of the Na(+)-glucose cotransporter.

Hypoxia is a common denominator of many vascular disorders, especially those associated with ischemia. To study the effect of oxygen depletion on endothelium, we developed an in vitro model of hypoxia on human umbilical vein endothelial cells (HUVEC). Hypoxia strongly activates HUVEC, which then synthesize large amounts of prostaglandins and platelet-activating factor. The first step of this activation is a decrease in ATP content of the cells, followed by an increase in the cytosolic calcium concentration ([Ca(2+)](i)) which then activates the phospholipase A(2) (PLA(2)). The link between the decrease in ATP and the increase in [Ca(2+)](i) was not known and is investigated in this work. We first showed that the presence of extracellular Na(+) was necessary to observe the hypoxia-induced increase in [Ca(2+)](i) and the activation of PLA(2). This increase was not due to the release of Ca(2+) from intracellular stores, since thapsigargin did not inhibit this process. The Na(+)/Ca(2+) exchanger was involved since dichlorobenzamil inhibited the [Ca(2+)](i) and the PLA(2) activation. The glycolysis was activated, but the intracellular pH (pH(i)) in hypoxic cells did not differ from control cells. Finally, the hypoxia-induced increase in [Ca(2+)](i) and PLA(2) activation were inhibited by phlorizin, an inhibitor of the Na(+)-glucose cotransport. The proposed biochemical mechanism occurring under hypoxia is the following: glycolysis is first activated due to a requirement for ATP, leading to an influx of Na(+) through the activated Na(+)-glucose cotransport followed by the activation of the Na(+)/Ca(2+) exchanger, resulting in a net influx of Ca(2+).