Showing papers by "University of Paris published in 2003"

LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1.

Abstract: We have previously shown correction of X-linked severe combined immunodeficiency [SCID-X1, also known as gamma chain (gamma(c)) deficiency] in 9 out of 10 patients by retrovirus-mediated gamma(c) gene transfer into autologous CD34 bone marrow cells. However, almost 3 years after gene therapy, uncontrolled exponential clonal proliferation of mature T cells (with gammadelta+ or alphabeta+ T cell receptors) has occurred in the two youngest patients. Both patients' clones showed retrovirus vector integration in proximity to the LMO2 proto-oncogene promoter, leading to aberrant transcription and expression of LMO2. Thus, retrovirus vector insertion can trigger deregulated premalignant cell proliferation with unexpected frequency, most likely driven by retrovirus enhancer activity on the LMO2 gene promoter.

Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia

Abstract: Background Imatinib, a selective inhibitor of the BCR-ABL tyrosine kinase, produces high response rates in patients with chronic-phase chronic myeloid leukemia (CML) who have had no response to interferon alfa. We compared the efficacy of imatinib with that of interferon alfa combined with low-dose cytarabine in newly diagnosed chronic-phase CML. Methods We randomly assigned 1106 patients to receive imatinib (553 patients) or interferon alfa plus low-dose cytarabine (553 patients). Crossover to the alternative group was allowed if stringent criteria defining treatment failure or intolerance were met. Patients were evaluated for hematologic and cytogenetic responses, toxic effects, and rates of progression. Results After a median follow-up of 19 months, the estimated rate of a major cytogenetic response (0 to 35 percent of cells in metaphase positive for the Philadelphia chromosome) at 18 months was 87.1 percent (95 percent confidence interval, 84.1 to 90.0) in the imatinib group and 34.7 percent (95 perce...

Semilinear Schrodinger Equations

Abstract: Preliminaries The linear Schrodinger equation The Cauchy problem in a general domain The local Cauchy problem Regularity and the smoothing effect Global existence and finite-time blowup Asymptotic behavior in the repulsive case Stability of bound states in the attractive case Further results Bibliography.

A Serious Adverse Event after Successful Gene Therapy for X-Linked Severe Combined Immunodeficiency

Abstract: To the Editor: We recently reported (April 18 issue)1 the sustained correction of X-linked severe combined immunodeficiency disease by ex vivo, retrovirally mediated transfer of the γc gene into CD34+ cells in four of five patients with the disease. These results have since been confirmed in four additional patients with typical X-linked severe combined immunodeficiency. Of the first four successfully treated patients, three continue to do well up to 3.6 years after gene therapy, whereas a serious adverse event occurred in the fourth patient. At a routine checkup 30 months after gene therapy, lymphocytosis consisting of a monoclonal population . . .

Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism.

Abstract: Many studies have supported a genetic etiology for autism. Here we report mutations in two X-linked genes encoding neuroligins NLGN3 and NLGN4 in siblings with autism-spectrum disorders. These mutations affect cell-adhesion molecules localized at the synapse and suggest that a defect of synaptogenesis may predispose to autism.

Technology probes: inspiring design for and with families

Abstract: We describe a new method for use in the process of co-designing technologies with users called technology probes. Technology probes are simple, flexible, adaptable technologies with three interdisciplinary goals: the social science goal of understanding the needs and desires of users in a real-world setting, the engineering goal of field-testing the technology, and the design goal of inspiring users and researchers to think about new technologies. We present the results of designing and deploying two technology probes, the messageProbe and the videoProbe, with diverse families in France, Sweden, and the U.S. We conclude with our plans for creating new technologies for and with families based on our experiences.

Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria

Abstract: Chloroplasts and mitochondria are the powerhouses of photosynthetic cells. The oxidation-reduction (redox) cascades of the photosynthetic and respiratory electron transport chains not only provide the driving forces for metabolism but also generate redox signals, which participate in and regulate every aspect of plant biology from gene expression and translation to enzyme chemistry. Plastoquinone, thioredoxin and reactive oxygen have all been shown to have signalling functions. Moreover, the intrinsic involvement of molecular oxygen in electron transport processes with the inherent generation of superoxide, hydrogen peroxide and singlet oxygen provides a repertoire of additional extremely powerful signals. Accumulating evidence implicates the major redox buffers of plant cells, ascorbate and glutathione, in redox signal transduction. The network of redox signals from energy-generating organelles orchestrates metabolism to adjust energy production to utilization, interfacing with hormone signalling to respond to environmental change at every stage of plant development.

Everolimus for the prevention of allograft rejection and vasculopathy in cardiac-transplant recipients.

Abstract: Background Everolimus, a novel proliferation inhibitor and immunosuppressive agent, may suppress cardiac-allograft vasculopathy. We conducted a randomized, double-blind, clinical trial comparing everolimus with azathioprine in recipients of a first heart transplant. Methods A total of 634 patients were randomly assigned to receive 1.5 mg of everolimus per day (209 patients), 3.0 mg of everolimus per day (211 patients), or 1.0 to 3.0 mg of azathioprine per kilogram of body weight per day (214 patients), in combination with cyclosporine, corticosteroids, and statins. The primary efficacy end point was a composite of death, graft loss or retransplantation, loss to follow-up, biopsy-proved acute rejection of grade 3A, or rejection with hemodynamic compromise. Results At six months, the percentage of patients who had reached the primary efficacy end point was significantly smaller in the group given 3.0 mg of everolimus (27.0 percent, P<0.001) and the group given 1.5 mg of everolimus (36.4 percent, P=0.03) tha...

Quantum random-walk search algorithm

Abstract: Quantum random walks on graphs have been shown to display many interesting properties, including exponentially fast hitting times when compared with their classical counterparts. However, it is still unclear how to use these novel properties to gain an algorithmic speedup over classical algorithms. In this paper, we present a quantum search algorithm based on the quantum random-walk architecture that provides such a speedup. It will be shown that this algorithm performs an oracle search on a database of N items with $O(\sqrt{N})$ calls to the oracle, yielding a speedup similar to other quantum search algorithms. It appears that the quantum random-walk formulation has considerable flexibility, presenting interesting opportunities for development of other, possibly novel quantum algorithms.

Automatic Sequences: Theory, Applications, Generalizations

Abstract: Preface 1. Stringology 2. Number theory and algebra 3. Numeration systems 4. Finite automata and other models of computation 5. Automatic sequences 6. Uniform morphisms and automatic sequences 7. Morphic sequences 8. Frequency of letters 9. Characteristic words 10. Subwords 11. Cobham's theorem 12. Formal power series 13. Automatic real numbers 14. Multidimensional automatic sequences 15. Automaticity 16. k-regular sequences 17. Physics Appendix. Hints, references and solutions for selected exercises Bibliography Index.

A global simulation of tropospheric ozone and related tracers: Description and evaluation of MOZART, version 2

Abstract: [1] We have developed a global three-dimensional chemical transport model called Model of Ozone and Related Chemical Tracers (MOZART), version 2. This model, which will be made available to the community, is built on the framework of the National Center for Atmospheric Research (NCAR) Model of Atmospheric Transport and Chemistry (MATCH) and can easily be driven with various meteorological inputs and model resolutions. In this work, we describe the standard configuration of the model, in which the model is driven by meteorological inputs every 3 hours from the middle atmosphere version of the NCAR Community Climate Model (MACCM3) and uses a 20-min time step and a horizontal resolution of 2.8° latitude × 2.8° longitude with 34 vertical levels extending up to approximately 40 km. The model includes a detailed chemistry scheme for tropospheric ozone, nitrogen oxides, and hydrocarbon chemistry, with 63 chemical species. Tracer advection is performed using a flux-form semi-Lagrangian scheme with a pressure fixer. Subgrid-scale convective and boundary layer parameterizations are included in the model. Surface emissions include sources from fossil fuel combustion, biofuel and biomass burning, biogenic and soil emissions, and oceanic emissions. Parameterizations of dry and wet deposition are included. Stratospheric concentrations of several long-lived species (including ozone) are constrained by relaxation toward climatological values. The distribution of tropospheric ozone is well simulated in the model, including seasonality and horizontal and vertical gradients. However, the model tends to overestimate ozone near the tropopause at high northern latitudes. Concentrations of nitrogen oxides (NOx) and nitric acid (HNO3) agree well with observed values, but peroxyacetylnitrate (PAN) is overestimated by the model in the upper troposphere at several locations. Carbon monoxide (CO) is simulated well at most locations, but the seasonal cycle is underestimated at some sites in the Northern Hemisphere. We find that in situ photochemical production and loss dominate the tropospheric ozone budget, over input from the stratosphere and dry deposition. Approximately 75% of the tropospheric production and loss of ozone occurs within the tropics, with large net production in the tropical upper troposphere. Tropospheric production and loss of ozone are three to four times greater in the northern extratropics than the southern extratropics. The global sources of CO consist of photochemical production (55%) and direct emissions (45%). The tropics dominate the chemistry of CO, accounting for about 75% of the tropospheric production and loss. The global budgets of tropospheric ozone and CO are generally consistent with the range found in recent studies. The lifetime of methane (9.5 years) and methylchloroform (5.7 years) versus oxidation by tropospheric hydroxyl radical (OH), two useful measures of the global abundance of OH, agree well with recent estimates. Concentrations of nonmethane hydrocarbons and oxygenated intermediates (carbonyls and peroxides) generally agree well with observations.

Predictors of major bleeding in acute coronary syndromes: the Global Registry of Acute Coronary Events (GRACE)

Abstract: Aims There have been no large observational studies attempting to identify predictors of major bleeding in patients with acute coronary syndromes (ACS), particularly from a multinational perspective. The objective of our study was thus to develop a prediction rule for the identification of patients with ACS at higher risk of major bleeding. Methods and results Data from 24 045 patients from the Global Registry of Acute Coronary Events (GRACE) were analysed. Factors associated with major bleeding were identified using logistic regression analysis. Predictive models were developed for the overall patient population and for subgroups of patients with ST-segment elevation myocardial infarction (STEMI), non-ST-segment elevation myocardial infarction (NSTEMI) and unstable angina. The overall incidence of major bleeding was 3.9% (4.8% in patients with STEMI, 4.7% in patients with NSTEMI and 2.3% in patients with unstable angina). Advanced age, female sex, history of bleeding, and renal insufficiency were independently associated with a higher risk of bleeding ( P <0.01). The association remained after adjustment for hospital therapies and performance of invasive procedures. After adjustment for a variety of potential confounders, major bleeding was significantly associated with an increased risk of hospital death (adjusted odds ratio 1.64, 95% confidence interval 1.18, 2.28). Conclusions In routine clinical practice, major bleeding is a relatively frequent non-cardiac complication of contemporary therapy for ACS and it is associated with a poor hospital prognosis. Simple baseline demographic and clinical characteristics identify patients at increased risk of major bleeding.

Impaired response to interferon-alpha/beta and lethal viral disease in human STAT1 deficiency.

Abstract: The receptors for interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma activate components of the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, leading to the formation of at least two transcription factor complexes. STAT1 interacts with STAT2 and p48/IRF-9 to form the transcription factor IFN-stimulated gene factor 3 (ISGF3). STAT1 dimers form gamma-activated factor (GAF). ISGF3 is induced mainly by IFN-alpha/beta, and GAF by IFN-gamma, although both factors can be activated by both types of IFN. Individuals with mutations in either chain of the IFN-gamma receptor (IFN-gammaR) are susceptible to infection with mycobacteria. A heterozygous STAT1 mutation that impairs GAF but not ISGF3 activation has been found in other individuals with mycobacterial disease. No individuals with deleterious mutations in the IFN-alpha/beta signaling pathway have been described. We report here two unrelated infants homozygous with respect to mutated STAT1 alleles. Neither IFN-alpha/beta nor IFN-gamma activated STAT1-containing transcription factors. Like individuals with IFN-gammaR deficiency, both infants suffered from mycobacterial disease, but unlike individuals with IFN-gammaR deficiency, both died of viral disease. Viral multiplication was not inhibited by recombinant IFN-alpha/beta in cell lines from the two individuals. Inherited impairment of the STAT1-dependent response to human IFN-alpha/beta thus results in susceptibility to viral disease.

Recombinant human tumor necrosis factor receptor (etanercept) for treating ankylosing spondylitis: a randomized, controlled trial.

Abstract: Objective To determine the safety and efficacy of etanercept in a multicenter, randomized, placebo-controlled, double-blind trial of adults with moderate to severe active ankylosing spondylitis (AS). Methods Patients (n = 277) were treated with either etanercept 25 mg (n = 138) or placebo (n = 139) subcutaneously twice weekly for 24 weeks. The primary outcome measures were the percentages of patients achieving the Assessments in Ankylosing Spondylitis 20% response (ASAS20) at weeks 12 and 24. Other outcome measures included the percentage of patients achieving higher ASAS responses, and the safety of etanercept in patients with AS. All outcome measures were assessed at 2, 4, 8, 12, and 24 weeks. Results Treatment with etanercept resulted in dramatic improvement. The ASAS20 was achieved by 59% of patients in the etanercept group and by 28% of patients in the placebo group (P < 0.0001) at week 12, and by 57% and 22% of patients, respectively, at week 24 (P < 0.0001). All individual ASAS components, acute-phase reactant levels, and spinal mobility measures were also significantly improved. The safety profile of etanercept was similar to that reported in studies of patients with rheumatoid arthritis or psoriatic arthritis. The only adverse events that occurred significantly more often in the etanercept group were injection-site reactions, accidental injuries, and upper respiratory tract infections. Conclusion Etanercept is a highly effective and well tolerated treatment in patients with active AS.

An atypical haem in the cytochrome b 6 f complex

Abstract: Photosystems I and II (PSI and II) are reaction centres that capture light energy in order to drive oxygenic photosynthesis; however, they can only do so by interacting with the multisubunit cytochrome b(6)f complex. This complex receives electrons from PSII and passes them to PSI, pumping protons across the membrane and powering the Q-cycle. Unlike the mitochondrial and bacterial homologue cytochrome bc(1), cytochrome b(6)f can switch to a cyclic mode of electron transfer around PSI using an unknown pathway. Here we present the X-ray structure at 3.1 A of cytochrome b(6)f from the alga Chlamydomonas reinhardtii. The structure bears similarities to cytochrome bc(1) but also exhibits some unique features, such as binding chlorophyll, beta-carotene and an unexpected haem sharing a quinone site. This haem is atypical as it is covalently bound by one thioether linkage and has no axial amino acid ligand. This haem may be the missing link in oxygenic photosynthesis.

On the Cauchy Problem for the Generalized Korteweg-de Vries Equation

Abstract: We consider the local and global Cauchy problem for the generalized Korteweg-de Vries equation , with initial data in homogeneous and nonhomogeneous Besov spaces. This allows us to slightly extend ...

Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0

Abstract: The methods for treating experimental data in the isomorphous replacement and anomalous scattering methods of macromolecular phase determination have undergone considerable evolution since their inception 50 years ago. The successive formulations used are reviewed, from the most simplistic viewpoint to the most advanced, including the exploration of some blind alleys. A new treatment is proposed and demonstrated for the improved encoding and subsequent exploitation of phase information in the complex plane. It is concluded that there is still considerable scope for further improvements in the statistical analysis of phase information, which touch upon numerous fundamental issues related to data processing and experimental design.

Global protein function prediction from protein-protein interaction networks

Abstract: Determining protein function is one of the most challenging problems of the post-genomic era. The availability of entire genome sequences and of high-throughput capabilities to determine gene coexpression patterns has shifted the research focus from the study of single proteins or small complexes to that of the entire proteome 1 . In this context, the search for reliable methods for assigning protein function is of primary importance. There are various approaches available for deducing the function of proteins of unknown function using information derived from sequence similarity or clustering patterns of coregulated genes 2,3 , phylogenetic profiles 4 , protein-protein interactions (refs. 5‐8 and Samanta, M.P. and Liang, S., unpublished data), and protein complexes 9,10 . Here we propose the assignment of proteins to functional classes on the basis of their network of physical interactions as determined by minimizing the number of protein interactions among different functional categories. Function assignment is proteome-wide and is determined by the global connectivity pattern of the protein network. The approach results in multiple functional assignments, a consequence of the existence of multiple equivalent solutions. We apply the method to analyze the yeast Saccharomyces cerevisiae protein-protein interaction network 5 .

Mutations in INVS encoding inversin cause nephronophthisis type 2, linking renal cystic disease to the function of primary cilia and left-right axis determination.

Abstract: Nephronophthisis (NPHP), an autosomal recessive cystic kidney disease, leads to chronic renal failure in children. The genes mutated in NPHP1 and NPHP4 have been identified, and a gene locus associated with infantile nephronophthisis (NPHP2) was mapped. The kidney phenotype of NPHP2 combines clinical features of NPHP and polycystic kidney disease (PKD). Here, we identify inversin (INVS) as the gene mutated in NPHP2 with and without situs inversus. We show molecular interaction of inversin with nephrocystin, the product of the gene mutated in NPHP1 and interaction of nephrocystin with β-tubulin, a main component of primary cilia. We show that nephrocystin, inversin and β-tubulin colocalize to primary cilia of renal tubular cells. Furthermore, we produce a PKD-like renal cystic phenotype and randomization of heart looping by knockdown of invs expression in zebrafish. The interaction and colocalization in cilia of inversin, nephrocystin and β-tubulin connect pathogenetic aspects of NPHP to PKD, to primary cilia function and to left-right axis determination.