Showing papers by "University of Paris published in 2005"

Computing communities in large networks using random walks

Abstract: Dense subgraphs of sparse graphs (communities), which appear in most real-world complex networks, play an important role in many contexts. Computing them however is generally expensive. We propose here a measure of similarities between vertices based on random walks which has several important advantages: it captures well the community structure in a network, it can be computed efficiently, it works at various scales, and it can be used in an agglomerative algorithm to compute efficiently the community structure of a network. We propose such an algorithm which runs in time O(mn2) and space O(n2) in the worst case, and in time O(n2log n) and space O(n2) in most real-world cases (n and m are respectively the number of vertices and edges in the input graph).

Oxidant and antioxidant signalling in plants: a re-evaluation of the concept of oxidative stress in a physiological context

Abstract: While the chemical nature of reactive oxygen species (ROS) dictates that they are potentially harmful to cells, recent genetic evidence suggests that in planta purely physicochemical damage may be much more limited than previously thought. The most potentially deleterious effect of ROS under most conditions is that at high concentrations they trigger genetically programmed cell suicide events. Moreover, because plants use ROS as second messengers in signal transduction cascades in processes as diverse as mitosis, tropisms and cell death, their accumulation is crucial to plant development as well as defence. Direct ROS signal transduction will ensue only if ROS escape destruction by antioxidants or are otherwise consumed in a ROS cascade. Thus, the major low molecular weight antioxidants determine the specificity of the signal. They are also themselves signal-transducing molecules that can either signal independently or further transmit ROS signals. The moment has come to re-evaluate the concept of oxidative stress. In contrast to this pejorative or negative term, implying a state to be avoided, we propose that the syndrome would be more usefully described as 'oxidative signalling', that is, an important and critical function associated with the mechanisms by which plant cells sense the environment and make appropriate adjustments to gene expression, metabolism and physiology.

Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms

Abstract: This paper examine the Euler-Lagrange equations for the solution of the large deformation diffeomorphic metric mapping problem studied in Dupuis et al. (1998) and Trouve (1995) in which two images I 0, I 1 are given and connected via the diffeomorphic change of coordinates I 0???1=I 1 where ?=?1 is the end point at t= 1 of curve ? t , t?[0, 1] satisfying .? t =v t (? t ), t? [0,1] with ?0=id. The variational problem takes the form $$\mathop {\arg {\text{m}}in}\limits_{\upsilon :\dot \phi _t = \upsilon _t \left( {\dot \phi } \right)} \left( {\int_0^1 {\left\| {\upsilon _t } \right\|} ^2 {\text{d}}t + \left\| {I_0 \circ \phi _1^{ - 1} - I_1 } \right\|_{L^2 }^2 } \right),$$ where ?v t? V is an appropriate Sobolev norm on the velocity field v t(·), and the second term enforces matching of the images with ?·?L 2 representing the squared-error norm. In this paper we derive the Euler-Lagrange equations characterizing the minimizing vector fields v t, t?[0, 1] assuming sufficient smoothness of the norm to guarantee existence of solutions in the space of diffeomorphisms. We describe the implementation of the Euler equations using semi-lagrangian method of computing particle flows and show the solutions for various examples. As well, we compute the metric distance on several anatomical configurations as measured by ?0 1?v t? V dt on the geodesic shortest paths.

Musculoskeletal ultrasound including definitions for ultrasonographic pathology

Abstract: Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis.

Definition of organ involvement and treatment response in immunoglobulin light chain amyloidosis (AL): A consensus opinion from the 10th International Symposium on Amyloid and Amyloidosis

Abstract: We undertook this study to develop uniformly accepted criteria for the definition of organ involvement and response for patients on treatment protocols for immunoglobulin light-chain amyloidosis (AL). A consensus panel was convened comprising 13 specialists actively involved in the treatment of patients with amyloidosis. Institutional criteria were submitted from each, and a consensus was developed defining each organ involved and the criteria for response. Specific criteria have been developed with agreed on definitions of organ and hematologic response as a result of discussions at the 10th International Symposium on Amyloid and Amyloidosis held in Tours, France, April 2004. These criteria now form the working definition of involvement and response for the purposes of future data collection and reporting. We report criteria that centers can now use to define organ involvement and uniform response criteria for reporting outcomes in patients with light-chain AL.

CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies.

Abstract: The remarkable repetitive elements called CRISPRs (clustered regularly interspaced short palindromic repeats) consist of repeats interspaced with non-repetitive elements or 'spacers' CRISPRs are present in both archaea and bacteria, in association with genes involved in DNA recombination and repair In the Yersinia pestis genome, three such elements are found at three distinct loci, one of them being highly polymorphic The authors have sequenced a total of 109 alleles of the three Y pestis CRISPRs and they describe 29 new spacers, most being specific to one isolate In nine strains of Yersinia pseudotuberculosis, 132 spacers were found, of which only three are common to Y pestis isolates In Y pestis of the Orientalis biovar investigated in detail here, deletion of motifs is observed but it appears that addition of new motifs to a common ancestral element is the most frequent event This takes place at the three different loci, although at a higher rate in one of the loci, and the addition of new motifs is polarized Interestingly, the most recently acquired spacers were found to have a homologue at another locus in the genome, the majority of these inside an inactive prophage This is believed to be the first time that the origin of the spacers in CRISPR elements has been explained The CRISPR structure provides a new and robust identification tool

Reduction of macrophage infiltration and chemoattractant gene expression changes in white adipose tissue of morbidly obese subjects after surgery-induced weight loss.

Abstract: In human obesity, the stroma vascular fraction (SVF) of white adipose tissue (WAT) is enriched in macrophages. These cells may contribute to low-grade inflammation and to its metabolic complications. Little is known about the effect of weight loss on macrophages and genes involved in macrophage attraction. We examined subcutaneous WAT (scWAT) of 7 lean and 17 morbidly obese subjects before and 3 months after bypass surgery. Immunomorphological changes of the number of scWAT-infiltrating macrophages were evaluated, along with concomitant changes in expression of SVF-overexpressed genes. The number of scWAT-infiltrating macrophages before surgery was higher in obese than in lean subjects (HAM56+/CD68+; 22.6 +/- 4.3 vs. 1.4 +/- 0.6%, P < 0.001). Typical "crowns" of macrophages were observed around adipocytes. Drastic weight loss resulted in a significant decrease in macrophage number (-11.63 +/- 2.3%, P < 0.001), and remaining macrophages stained positive for the anti-inflammatory protein interleukin 10. Genes involved in macrophage attraction (monocyte chemotactic protein [MCP]-1, plasminogen activator urokinase receptor [PLAUR], and colony-stimulating factor [CSF]-3) and hypoxia (hypoxia-inducible factor-1alpha [HIF-1alpha]), expression of which increases in obesity and decreases after surgery, were predominantly expressed in the SVF. We show that improvement of the inflammatory profile after weight loss is related to a reduced number of macrophages in scWAT. MCP-1, PLAUR, CSF-3, and HIF-1alpha may play roles in the attraction of macrophages in scWAT.

The DNA sequence of the human X chromosome

Abstract: The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

SAPS 3—From evaluation of the patient to evaluation of the intensive care unit. Part 2: Development of a prognostic model for hospital mortality at ICU admission

Abstract: Objective To develop a model to assess severity of illness and predict vital status at hospital discharge based on ICU admission data.

Bilateral deep brain stimulation in Parkinson's disease: a multicentre study with 4 years follow-up

Abstract: Deep brain stimulation (DBS) is associated with significant improvement of motor complications in patients with severe Parkinson's disease after some 6-12 months of treatment. Long-term results in a large number of patients have been reported only from a single study centre. We report 69 Parkinson's disease patients treated with bilateral DBS of the subthalamic nucleus (STN, n = 49) or globus pallidus internus (GPi, n = 20) included in a multicentre study. Patients were assessed preoperatively and at 1 year and 3-4 years after surgery. The primary outcome measure was the change in the 'off' medication score of the Unified Parkinson's Disease Rating Scale motor part (UPDRS-III) at 3-4 years. Stimulation of the STN or GPi induced a significant improvement (50 and 39%; P < 0.0001) of the 'off' medication UPDRS-III score at 3-4 years with respect to baseline. Stimulation improved cardinal features and activities of daily living (ADL) (P < 0.0001 and P < 0.02 for STN and GPi, respectively) and prolonged the 'on' time spent with good mobility without dyskinesias (P < 0.00001). Daily dosage of levodopa was significantly reduced (35%) in the STN-treated group only (P < 0.001). Comparison of the improvement induced by stimulation at 1 year with 3-4 years showed a significant worsening in the 'on' medication motor states of the UPDRS-III, ADL and gait in both STN and GPi groups, and speech and postural stability in the STN-treated group. Adverse events (AEs) included cognitive decline, speech difficulty, instability, gait disorders and depression. These were more common in patients treated with DBS of the STN. No patient abandoned treatment as a result of these side effects. This experience, which represents the first multicentre study assessing the long-term efficacy of either STN or GPi stimulation, shows a significant and substantial clinically important therapeutic benefit for at least 3-4 years in a large cohort of patients with severe Parkinson's disease.

The abundances of constituents of Titan's atmosphere from the GCMS instrument on the Huygens probe

Abstract: Saturn's largest moon, Titan, remains an enigma, explored only by remote sensing from Earth, and by the Voyager and Cassini spacecraft. The most puzzling aspects include the origin of the molecular nitrogen and methane in its atmosphere, and the mechanism(s) by which methane is maintained in the face of rapid destruction by photolysis. The Huygens probe, launched from the Cassini spacecraft, has made the first direct observations of the satellite's surface and lower atmosphere. Here we report direct atmospheric measurements from the Gas Chromatograph Mass Spectrometer (GCMS), including altitude profiles of the constituents, isotopic ratios and trace species (including organic compounds). The primary constituents were confirmed to be nitrogen and methane. Noble gases other than argon were not detected. The argon includes primordial 36Ar, and the radiogenic isotope 40Ar, providing an important constraint on the outgassing history of Titan. Trace organic species, including cyanogen and ethane, were found in surface measurements.

Heart-rate profile during exercise as a predictor of sudden death.

Abstract: background Changes in heart rate during exercise and recovery from exercise are mediated by the balance between sympathetic and vagal activity. Since alterations in the neural control of cardiac function contribute to the risk of sudden death, we tested the hypothesis that among apparently healthy persons, sudden death is more likely to occur in the presence of abnormal heart-rate profiles during exercise and recovery. methods A total of 5713 asymptomatic working men (between the ages of 42 and 53 years), none of whom had clinically detectable cardiovascular disease, underwent standardized graded exercise testing between 1967 and 1972. We examined data on the subjects’ resting heart rates, the increase in rate from the resting level to the peak exercise level, and the decrease in rate from the peak exercise level to the level one minute after the termination of exercise. results During a 23-year follow-up period, 81 subjects died suddenly. The risk of sudden death from myocardial infarction was increased in subjects with a resting heart rate that was more than 75 beats per minute (relative risk, 3.92; 95 percent confidence interval, 1.91 to 8.00); in subjects with an increase in heart rate during exercise that was less than 89 beats per minute (relative risk, 6.18; 95 percent confidence interval, 2.37 to 16.11); and in subjects with a decrease in heart rate of less than 25 beats per minute after the termination of exercise (relative risk, 2.20; 95 percent confidence interval, 1.02 to 4.74). After adjustment for potential confounding variables, these three factors remained strongly associated with an increased risk of sudden death, with a moderate but significantly increased risk of death from any cause but not of nonsudden death from myocardial infarction. conclusions The heart-rate profile during exercise and recovery is a predictor of sudden death.

Notch signals control the fate of immature progenitor cells in the intestine

Abstract: The Notch signalling pathway plays a crucial role in specifying cellular fates in metazoan development by regulating communication between adjacent cells. Correlative studies suggested an involvement of Notch in intestinal development. Here, by modulating Notch activity in the mouse intestine, we directly implicate Notch signals in intestinal cell lineage specification. We also show that Notch activation is capable of amplifying the intestinal progenitor pool while inhibiting cell differentiation. We conclude that Notch activity is required for the maintenance of proliferating crypt cells in the intestinal epithelium.

Convergence history across Zagros (Iran): constraints from collisional and earlier deformation

Abstract: The Zagros orogen provides a unique opportunity within the Alpine system to evaluate the interplay between a young Tertiary collision and earlier subduction/obduction processes. Within the Crush zone and the Sanandaj–Sirjan (internal) zone separating the Zagros Fold belt from Central Iran, we document several major tectonic events taking place at the end of the Cretaceous, of the Eocene and from the Mio–Pliocene onwards (ca. <20–15 Ma). Contrary to recent interpretations, our data (cross-sections and description of the overall deformation style) strongly suggest that the Main Zagros Thrust (MZT) is deeply rooted, possibly to Moho depths, and that the suture zone effectively runs along the MZT. Field observations show that the final resorption of the oceanic domain took place slightly after 35 Ma and that collision must have started before ca. 23–25 Ma in northern Zagros. The shortening rate across the Crush zone since the Mid-Miocene (20–15 Ma) is estimated at a minimum 3–4 mm/year. Shear movements in the Crush zone during the Eocene–Oligocene period and extensional/strike-slip movements in the internal zones during the late Cretaceous point to an oblique setting early in the convergence history. A geotectonic scenario for convergence from the time of obduction to the present is finally proposed.

Requirements engineering paper classification and evaluation criteria: a proposal and a discussion

Abstract: In recent years, members of the steering committee of the IEEE Requirements Engineering (RE) Conference have discussed paper classification and evaluation criteria for RE papers. The immediate trigger for this discussion was our concern about differences in opinion that sometimes arise in program committees about the criteria to be used in evaluating papers. If program committee members do not all use the same criteria, or if they use criteria different from those used by authors, then papers might be rejected or accepted for the wrong reasons. Surely not all papers should be evaluated according to the same criteria. Some papers describe new techniques but do not report on empirical research; others describe new conceptual frameworks for investigating certain RE problems; others report on industrial experience with existing RE techniques. Other kinds of papers can also be easily recognized. All of these types of papers should be evaluated according to different criteria. But we are far from a consensus about what classes of paper we should distinguish, and what the criteria are for each of these classes.

SPlot: A Statistical tool to unfold data distributions

Abstract: The paper advocates the use of a statistical tool dedicated to the exploration of data samples populated by several sources of events. This new technique, called P lot s , is able to unfold the contributions of the different sources to the distribution of a data sample in a given variable. The P lot s tool applies in the context of a likelihood fit which is performed on the data sample to determine the yields of the various sources.

Atmospheric Chemistry Experiment (ACE): Mission overview.

Abstract: SCISAT-1, also known as the Atmospheric Chemistry Experiment (ACE), is a Canadian satellite mission for remote sensing of the Earth's atmosphere. It was launched into low Earth circular orbit (altitude 650 km, inclination 74°) on 12 Aug. 2003. The primary ACE instrument is a high spectral resolution (0.02 cm-1) Fourier Transform Spectrometer (FTS) operating from 2.2 to 13.3 μm (750-4400 cm-1). The satellite also features a dual spectrophotometer known as MAESTRO with wavelength coverage of 285-1030 nm and spectral resolution of 1-2 nm. A pair of filtered CMOS detector arrays records images of the Sun at 0.525 and 1.02 μm. Working primarily in solar occultation, the satellite provides altitude profile information (typically 10-100 km) for temperature, pressure, and the volume mixing ratios for several dozen molecules of atmospheric interest, as well as atmospheric extinction profiles over the latitudes 85°N to 85°S. This paper presents a mission overview and some of the first scientific results. Copyright 2005 by the American Geophysical Union.

Force mapping in epithelial cell migration

Abstract: We measure dynamic traction forces exerted by epithelial cells on a substrate. The force sensor is a high-density array of elastomeric microfabricated pillars that support the cells. Traction forces induced by cell migration are deduced from the measurement of the bending of these pillars and are correlated with actin localization by fluorescence microscopy. We use a multiple-particle tracking method to estimate the mechanical activity of cells in real time with a high-spatial resolution (down to 2 μm) imposed by the periodicity of the post array. For these experiments, we use differentiated Madin-Darby canine kidney (MDCK) epithelial cells. Our data provide definite information on mechanical forces exerted by a cellular assembly. The maximum intensity of the forces is localized on the edge of the epithelia. Hepatocyte growth factor promotes cell motility and induces strong scattering activity of MDCK cells. Thus, we compare forces generated by MDCK cells in subconfluent epithelia versus isolated cells after hepatocyte growth factor treatment. Maximal-traction stresses at the edge of a monolayer correspond to higher values than those measured for a single cell and may be due to a collective behavior.

Digital Image Correlation: From Displacement Measurement to Identification of Elastic Properties - A Review

Abstract: The current development of digital image correlation, whose displacement uncertainty is well below the pixel value, enables one to better characterise the behaviour of materials and the response of structures to external loads. A general presentation of the extraction of displacement fields from the knowledge of pictures taken at different instants of an experiment is given. Different strategies can be followed to achieve a sub-pixel uncertainty. From these measurements, new identification procedures are devised making use of full-field measures. A priori or a posteriori routes can be followed. They are illustrated on the analysis of a Brazilian test.

Compassion and Repression: The Moral Economy of Immigration Policies in France

Abstract: Immigration policies in Europe in the last three decades have become increasingly restrictive. During the 1990s, political asylum lost much of its legitimacy, as new criteria based on humanitarian claims became more common in appeals for immigration. Asylum seekers were increasingly identified as illegal immigrants and therefore candidates for expulsion, unless humanitarian reasons could be found to requalify them as victims deserving sympathy. This substitution of a right to asylum by an obligation in terms of charity leads to a reconsideration of Giorgio Agamben's separation of the humanitarian and the political, suggesting instead a humanitarianization of policies. Sangatte Center, often referred to as a transit camp, became a symbol of this ambiguous European treatment of the “misery of the world” and serves here as an analytical thread revealing the tensions between repression and compassion as well as the moral economy of contemporary biopolitics.

Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division

Abstract: In macroscopic organisms, aging is often obvious; in single-celled organisms, where there is the greatest potential to identify the molecular mechanisms involved, identifying and quantifying aging is harder. The primary results in this area have come from organisms that share the traits of a visibly asymmetric division and an identifiable juvenile phase. As reproductive aging must require a differential distribution of aged and young components between parent and offspring, it has been postulated that organisms without these traits do not age, thus exhibiting functional immortality. Through automated time-lapse microscopy, we followed repeated cycles of reproduction by individual cells of the model organism Escherichia coli, which reproduces without a juvenile phase and with an apparently symmetric division. We show that the cell that inherits the old pole exhibits a diminished growth rate, decreased offspring production, and an increased incidence of death. We conclude that the two supposedly identical cells produced during cell division are functionally asymmetric; the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring. These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.

Ex vivo generation of fully mature human red blood cells from hematopoietic stem cells.

Abstract: We describe here the large-scale ex vivo production of mature human red blood cells (RBCs) from hematopoietic stem cells of diverse origins. By mimicking the marrow microenvironment through the application of cytokines and coculture on stromal cells, we coupled substantial amplification of CD34(+) stem cells (up to 1.95 x 10(6)-fold) with 100% terminal differentiation into fully mature, functional RBCs. These cells survived in nonobese diabetic/severe combined immunodeficient mice, as do native RBCs. Our system for producing 'cultured RBCs' lends itself to a fundamental analysis of erythropoiesis and provides a simple in vitro model for studying important human viral or parasitic infections that target erythroid cells. Further development of large-scale production of cultured RBCs will have implications for gene therapy, blood transfusion and tropical medicine.

Polycarbazoles: 25 Years of Progress

Abstract: Summary: Carbazole-based oligomeric and polymeric materials have been studied for almost 25 years for their unique electrical, electrochemical and optical properties. Interestingly, carbazole units can be linked in two different ways leading to either poly(3,6-carbazole) or poly(2,7-carbazole) derivatives. While the former class seems to be very interesting for electrochemical and phosphorescence applications, the latter shows very promising optical properties in the visible range for light emitting diodes (LED). The major intrinsic difference between these two classes is the effective conjugation length: poly(2,7-carbazole) materials having the longer one, due to their poly(p-phenylene)-like structure. Using different synthetic strategies and substitution patterns, the physico-chemical properties of both classes can be fine-tuned, leading to high performance materials for a large number electronic applications. Chemical structures for poly(3,6-carbazole) and poly(2,7-carbazole) and the materials used as the starting points for their respective syntheses.

Antineutrophil Cytoplasmic Antibodies and the Churg–Strauss Syndrome

Abstract: Of 112 patients with a new diagnosis of the Churg–Strauss syndrome, 43 (38%) were positive for antineutrophil cytoplasmic antibody (ANCA). Positive ANCA status was associated with renal involvement...

Theory of classification : a survey of some recent advances

Abstract: The last few years have witnessed important new developments in the theory and practice of pattern classification. We intend to survey some of the main new ideas that have lead to these important recent developments. Resume. Durant ces dernieres annees, la theorie et la pratique de la reconnaissance des formes ont ´e marquees par des developpements originaux. Ce survol presente certaines des principales idees novatrices qui ont conduitces developpements importants.