Showing papers by "University of Bordeaux published in 2001"

Dendritic Catalysts and Dendrimers in Catalysis

Abstract: 2. Thiol Oxidation to Disulfides 3007 3. Epoxidation of Alkenes 3007 4. Oxidation of Bromide 3008 5. Oxidation of Mercaptoethanol by Dioxygen 3008 V. Particle−Dendrimer Assemblies 3008 1. Hydrogenation 3008 2. Heck Reaction 3010 3. Anodic Oxidation of Ethanol 3010 VI. Redox Catalysis 3010 1. Anodic Oxygen Reduction 3010 2. Cathodic Reduction of CO2 to CO 3010 3. Ferrocenes as Redox Mediators for Glucose Oxidation 3010

Conformational change of proteins arising from normal mode calculations

Abstract: A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.

Organic photochromism (IUPAC Technical Report)

Abstract: This technical report is a general introduction to organic photo- chromism. The definition of photochromism (PC) is given together with that of words with the ending "chromism", such as thermo-, electro-, piezo-, and tri- bochromism. Important concepts such as two-photon, gated, dual-mode PC and chirochromism are illustrated. The concept of fatigue (chemical degradation) and the determination of the main photochromic parameters (number of cycles, cyclability, half-life), and the spectrokinetic and mechanistic aspects are dis- cussed. The main families of PC (organic compounds and biological receptors) are illustrated with chemical formulae, and the different types of reactions involved in the photochromic processes (pericyclic reactions, E/Z isomerization, group transfer, etc.) are listed. Some examples of applications to "optical power limiting" substances, photoresponsive materials, and photoswitchable biomate- rials are considered.

Supramolecular Materials via Block Copolymer Self-Assembly

Abstract: This review discusses the potential of block copolymer type macromolecular building blocks for the preparation of self-assembled materials. Three different classes of block copolymer type architectures will be distinguished: i) coil-coil diblock copolymers, ii) rod-coil diblock copolymers, and iii) rod-coil diblock oligomers. The basic principles that underlie the self-assembly of each of these different building blocks will be discussed. These theoretical considerations are complemented with examples from recent literature that illustrate the potential of the different type of block copolymers to prepare (functional) supramolecular materials. Finally, several strategies will be presented that could allow the preparation of stimuli-sensitive self-assembled materials, i.e., materials whose properties can be reversibly manipulated under the action of appropriate external stimuli.

Applications of B-splines in atomic and molecular physics

Abstract: One of the most significant developments in computational atomic and molecular physics in recent years has been the introduction of B-spline basis sets in calculations of atomic and molecular structure and dynamics. B-splines were introduced in applied mathematics more than 50 years ago, but it has been in the 1990s, with the advent of powerful computers, that the number of applications has grown exponentially. In this review we present the main properties of B-splines and discuss why they are useful to solve different problems in atomic and molecular physics. We provide an extensive reference list of theoretical works that have made use of B-spline basis sets up to 2000. Among these, we have focused on those applications that have led to the discovery of new interesting phenomena and pointed out the reasons behind the success of the approach.

Diverging Trends Between Heterozygosity and Allelic Richness During Postglacial Colonization in the European Beech

Abstract: Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity parameters, such as bottlenecks due to long-distance founding events, selection during population establishment, and increased gene flow at low population densities.

Photodimerization of anthracenes in fluid solutions: (part 2) mechanistic aspects of the photocycloaddition and of the photochemical and thermal cleavage

Abstract: One of the classics in photochemistry, the photodimerization of anthracenes can be considered as a paradigm of the photocycloaddition of non saturated hydrocarbons. The historical steps of the mechanistic studies are reviewed: based on fluorescence quenching, cyclization quantum yields measurement, the influence of dioxygen and solvents, they support a singlet state pathway; the dimerization rate constants are found to be generally high for reactions occurring within a few nanoseconds unless they are slowed down or inhibited by steric strain. In several cases, excimers have been demonstrated to be intermediates and it is shown that excimer fluorescence and cyclization are competitive processes. Another intermediate known as pericyclic minimum (or conical intersection) is postulated to form a sort of floppy cycloadduct where the reacting centres are at mutual distances shorter than in excimers and longer than in dimers. For intermolecular dimerizations, the triplet state is also reactive but through triplet–triplet annihilation in dilute solutions. Intramolecular photocycloadditions have also been carefully examined, for the role of multiple excimer formation, regioselectivity (9,10∶1′,4′ and 9,10∶1′,2′ cyclization) and solvent polarity. The triplet state reactivity is shown to lead to 4π + 2π or 4π + 4π cycloadducts, depending on geometric factors. In the latter case when intersystem crossing is favoured by the substituents, cyclization quantum yields as high as 0.65–0.72 have been observed. Photodissociation quantum yields are generally high and the reactions are partly adiabatic, leading to excimer and monomer fluorescence, but the major part follows another pathway not fully elucidated by flash photolysis. Thermodynamic and kinetic parameters for the thermal cleavage are given; they reveal a large gamut of stability for the photocycloadducts.

Dinoflagellate cyst assemblages as tracers of sea‐surface conditions in the northern North Atlantic, Arctic and sub‐Arctic seas: the new ‘n = 677’ data base and its application for quantitative palaeoceanographic reconstruction

Abstract: The distribution of dinoflagellate cyst (dinocyst) assemblages in surface sediment samples from 677 sites of the northern North Atlantic, Arctic and sub-Arctic seas is discussed with emphasis on the relationships with sea-surface parameters, including sea-ice cover, salinity and temperature of the coldest and warmest months. Difficulties in developing a circum-Arctic data base include the morphological variation within taxa (e.g. Operculodinium centrocarpum, Islandinium? cezare and Polykrikos sp.), which probably relate to phenotypic adaptations to cold and/or low salinity environments. Sparse hydrographical data, together with large interannual variations of temperature and salinity in surface waters of Arctic seas constitute additional limitations. Nevertheless, the use of the best-analogue technique with this new dinocyst data base including 677 samples permits quantitative reconstruction of sea-surface conditions at the scale of the northern North Atlantic and the Arctic domain. The error of prediction calculated from modern assemblages is ±1.3 ° Ca nd±1.8 °C for the temperature of February and August, respectively, ±1.8 for the salinity, and ±1.5 months yr −1 for the sea-ice cover. Application to late Quaternary sequences from the western and eastern subpolar North Atlantic (Labrador Sea and Barents Sea) provide reconstructions compatible with those obtained using the previous dinocyst data base (n = 371), which mainly included modern data from the northern North Atlantic. Copyright  2001 John Wiley & Sons, Ltd. Journal of Quaternary Science

Accelerated Life Models: Modeling and Statistical Analysis

Abstract: Failure Time Distributions Introduction Parametric Classes of Failure Time Distributions Accelerated Life Models Introduction Generalized Sedyakin's Model Accelerated Failure Time Model Proportional Hazards Model Generalized Proportional Hazards Models Generalized Additive and Additive-Multiplicative Hazards Models Changing Shape and Scale Models Generalizations Models Including Switch-Up and Cycling Effects Heredity Hypothesis Summary Accelerated Degradation Models Introduction Degradation Models Modeling the Influence of Explanatory Variables on Degradation Modeling the Traumatic Event Process Maximum Likelihood Estimation for FTR Data Censored Failure Time Data Parametric Likelihood Function for Right Censored FTR Data Score Function Asymptotic Properties of the Maximum Likelihood Estimators Approximate Confidence Intervals Some Remarks on Semi-Parametric Estimation AFT Model: Parametric FTR and ALT Data Analysis Parametrization of the AFT Model Interpretation of the Regression Coefficients FTR Data Analysis: Scale-Shape Families of Distributions FTR Data Analysis: Generalized Weibull Distribution FTR Data Analysis: Exponential Distribution Plans of Experiments in Accelerated Life Testing Parametric Estimation in ALT Under the AFT Model AFT Models: Semi-Parametric FTR and AFT Data Analysis FTR Data Analysis Semi-Parametric Estimation in ALT PH Model: Semi-Parametric FTR Data Analysis Introduction Parametrization of the PH Model Interpretation of the Regression Coefficients Semi-Parametric FTR Data Analysis for the PH Model GPH Models: FTR Analysis Introduction Semi-Parametric FTR Data Analysis for the GPH1 Models Semi-Parametric FTR Data Analysis: Intersecting Hazards Changing Scale and Shape Model Parametric FTR Data Analysis Semi-Parametric FTR Data Analysis Semi-Parametric Estimation in ALT GAH and GAMH Model: Semi-Parametric FTR and ALT Data Analysis GAH Model GAMH Model AAR Model PPAR Model Estimation When a Process of Production in Unstable Application of the AFT Model Application of the GPH1 Model Goodness-of-Fit for Accelerated Life Models Goodness-of-Fit for the GS Model Goodness-of-Fit for the Model with Absence of Memory Goodness-of-Fit for the AFT Model Goodness-of-Fit for the PH Model Goodness-of-Fit for the GPH Models Goodness-of-Fit for the Parametric Regression Models Estimation in Degradation Models with Explanatory Variables Introduction Linear Path Models Gamma and Shock Processes Some Results from Stochastic Process Theory Stochastic Process. Filtration Counting Process Stochastic Integral Conditional Expectation Martingale Predictable Process and Doob-Meyer Decomposition Predictable Variation and Predictable Covariation Stochastic Integrals with Respect to Martingales Localization Stochastic Integrals with Respect to Martingales (continuation) Weak Convergence Central Limit Theorem for Martingales Non-Parametric Estimators of the Cumulative Hazard and the Survival Function Product-Integral Delta Method References

The timing of the last deglaciation in North Atlantic climate records

Abstract: To determine the mechanisms governing the last deglaciation and the sequence of events that lead to deglaciation, it is important to obtain a temporal framework that applies to both continental and marine climate records. Radiocarbon dating has been widely used to derive calendar dates for marine sediments, but it rests on the assumption that the ‘apparent age’ of surface water (the age of surface water relative to the atmosphere) has remained constant over time1,2. Here we present new evidence for variation in the apparent age of surface water (or reservoir age) in the North Atlantic ocean north of 40° N over the past 20,000 years. In two cores we found apparent surface-water ages to be larger than those of today by 1,230 ± 600 and 1,940 ± 750 years at the end of the Heinrich 1 surge event (15,000 years BP) and by 820 ± 430 to 1,010 ± 340 years at the end of the Younger Dryas cold episode. During the warm Bolling–Allerod period, between these two periods of large reservoir ages, apparent surface-water ages were comparable to present values. Our results allow us to reconcile the chronologies from ice cores and the North Atlantic marine records over the entire deglaciation period. Moreover, the data imply that marine carbon dates from the North Atlantic north of 40° N will need to be corrected for these highly variable effects.

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis.

Abstract: Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name, mycoplasmas) and responsible for murine respiratory diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome with a G + C content of 26.6 mol%, i.e. the lowest reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative coding sequences (CDSs) covering 91.4% of its length and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of hypothetical proteins, leaving 204 CDSs without significant database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The replication origin oriC was localized by sequence analysis and by using the G + C skew method. Sequence polymorphisms within stretches of repeated nucleotides generate phase-variable protein antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in major M.pulmonis surface antigens. Furthermore, a hemolysin, secreted nucleases and a glyco-protease are predicted virulence factors. Surprisingly, several of the genes previously reported to be essential for a self-replicating minimal cell are missing in the M.pulmonis genome although this one is larger than the other mycoplasma genomes fully sequenced until now.

The Teaching and Learning of Decision Making in Team Sports

Abstract: In team sports, playing well means choosing the right course of action at the right moment and performing that course of action efficiently and consistently throughout the match. Research on decision making in sports indicates that although experts make more accurate decisions based on earlier occurring information, they tend to have speed, rather than accuracy, context-specific advantage in decision making. In light of the key notion of configuration of play, elements underlying its perception and interpretation and the ensuing anticipation and decision making are discussed. In connection with teachinglearning settings, observation and verbalization are presented as key strategies for eliciting critical thinking and the development of strategic and tactical knowledge. Finally, the authors present a dynamic model exploiting (a) action settings. (b) observation settings, and (c) debate-of-idea settings for the ultimate goal of conshucting strategic and tactical knowledge in team sports.

Covalent modification of iron surfaces by electrochemical reduction of aryldiazonium salts.

Abstract: Electrochemical reduction of aryldiazonium salts (in acetonitrile or acidic aqueous medium) on an iron or mild steel surface permits the strong bonding (which resists an ultrasonic cleaning) of aryl groups on these surfaces. Attachment of aryl groups was demonstrated by the combined used of electrochemistry, infrared spectroscopy and polarization modulation infrared reflection spectroscopy (PMIRRAS), Rutherford backscattering, X-ray photoelectron spectroscopy, and capacity measurements. The substituents of aryl groups, which can be widely varied, include NO2, I, COOH, and long alkyl chains. It is shown that the attachment of the aryl groups is to an iron and not to an oxygen atom and that the bond is covalent.

On the fixed parameter complexity of graph enumeration problems definable in monadic second-order logic

Abstract: We discuss the parametrized complexity of counting and evaluation problems on graphs where the range of counting is denable in monadic second-order logic (MSOL). We show that for bounded tree-width these problems are solvable in polynomial time. The same holds for bounded clique width in the cases, where the decomposition, which establishes the bound on the clique-width, can be computed in polynomial time and for problems expressible by monadic second-order formulas without edge set quantication. Such quantications are allowed in the case of graphs with bounded tree-width. As applications we discuss in detail how this aects the parametrized complexity of the permanent and the hamiltonian of a matrix, and more generally, various generating functions of MSOL denable graph properties. Finally, our results are also applicable to SAT and ]SAT. ? 2001 Elsevier Science B.V. All rights reserved.

Selective trapping of organochlorine compounds in mountain lakes of temperate areas.

Abstract: The study of fish concentrations and sediment inventories in 19 European high mountain lakes (40-67 degrees N) shows that a fraction of organochlorine compounds (OCs), the less volatile compounds (LVC; subcooled liquid vapor pressure < or = 10(-2.5) Pa), are trapped in the higher locations. This general trend is not significantly influenced by possible local sources. Compound distribution is related to average air temperatures. The phase-change pseudoenthalpies calculated from the sediment inventories closely match the summed theoretical volatilization and dissolution enthalpies. This fractionation effect is responsible for the accumulation of high concentrations of the LVC, the more persistent and toxic according to literature data, in organisms inhabiting sites far from the locations of synthesis or use.

Inversely graded turbidite sequences in the deep Mediterranean: a record of deposits from flood-generated turbidity currents?

Abstract: Turbidity currents generated during floods of small and medium rivers have been demonstrated to be an important process of sediment transport from continent to abyss. They produce fine-grained turbidite deposits. No deposit related to these flood-related turbidity currents has yet been described in the deep sea. In this paper, we present some unusual sandy to muddy turbidite beds cored in the Var turbidite system (NW Mediterranean). They show a coarsening-upward basal unit capped with a classical fining-upward unit which are related to the periods of increasing and decreasing discharge at the river mouth, respectively. The two units are separated by a contact which can be gradational to erosional. This intrabed contact is interpreted as resulting from erosion during peak flood conditions. This intrabed contact can be confused with classical basal contacts of turbidite beds. The frequency of hyperpycnal turbidite beds can be used to relate climatic changes inland to the deep-sea sedimentary record, as an increase corresponds to periods of enhanced flooding at the river mouth.

The influence of local and non-local forcing effects on the subtidal circulation of Patos Lagoon

Abstract: Some basic features concerning the subtidal circulation of Patos Lagoon were studied through time series analysis of wind, freshwater discharge, and water level records, as well as by means of experiments carried out with a 3D numerical model. The results indicate that during low to moderate river discharge the wind is the main forcing mechanism in time scales associated with meteorological fronts. The two types of wind action, local and non-local effects, are distinguished and their relative importance is evaluated. Salt water enters the system due to a combination of both remote and local wind effects that favors the development of a pressure gradient towards the lagoon during southwesterly winds. This situation is reversed when northeasterly winds dominate. In the inner parts of the lagoon, local wind plays the major role by inducing set up/set down oscillations. An upwind return flow is then developed under these conditions. During high flood periods, normally observed in late winter, the circulation is driven by freshwater discharge.

Mortality with Dementia: Results from a French Prospective Community-based Cohort

Abstract: Despite the magnitude of the problem, little is known about the duration of dementia. Survival and risk factors of mortality with dementia and the impact of dementia on the risk of death were investigated using the Personnes Agees Quid (PAQUID) prospective population-based cohort study between 1988 and 1998. Statistical models dealing with interval censoring were performed. Among 3,675 participants aged 65 years or older and initially nondemented, 2,923 have been followed up for 8 years. Of these, 281 persons with incident dementia were actively diagnosed. The mean age of onset of dementia was 82.3 years. In the total population, the relative risk of dying after developing dementia was estimated to be 1.82 (95% confidence interval (CI): 1.77, 2.68) when adjusted for sociodemographic variables and comorbidity. Deaths from cerebrovascular diseases and respiratory diseases were particularly increased among persons with dementia, compared with those without. The median survival time of the persons with dementia was estimated to be 4.5 years. Women with dementia had a longer survival than did men with dementia, particularly for Alzheimer-type dementia (relative risk = 0.47, 95% CI: 0.27, 0.83). Educational level was not significantly associated with survival in persons with dementia. These results provide further evidence of the malignancy of dementia, which will be a challenge for the 21st century.

Routing in Trees

Abstract: This article focuses on routing messages along shortest paths in tree networks, using compact distributed data structures. We mainly prove that n-node trees support routing schemes with message headers, node addresses, and local memory space of size O(log n) bits, and such that every local routing decision is taken in constant time. This improves the best known routing scheme by a factor of O(log n) in term of both memory requirements and routing time. Our routing scheme requires headers and addresses of size slightly larger than log n, motivated by an inherent trade-off between address-size and memory space, i.e., any routing scheme with addresses on log n bits requires Ω(√n) bits of local memory-space. This shows that a little variation of the address size, e.g., by an additive O(log n) bits factor, has a significant impact on the local memory space.

Dopamine agonist-induced dyskinesias are correlated to both firing pattern and frequency alterations of pallidal neurones in the MPTP-treated monkey

Abstract: Despite the importance and frequency of levodopa-induced dyskinesias, little is known about their causal mechanisms. In this study, electrophysiological single-unit recordings of the neuronal activity of the globus pallidus internalis (GPi), the main basal ganglia output structure, and the globus pallidus externalis (GPe) were recorded continuously in both normal and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine treated subhuman primates before and after the administration of three dopamine agonists--apomorphine (a dopaminergic mixed agonist), SKF-38393 (a D1 partial agonist) and piribedil (a D2/D3 agonist)--at doses known to induce dyskinesias in the parkinsonian monkey. Changes in both the firing frequency and the firing pattern were analysed in relation to behavioural modifications. In both the normal and the parkinsonian monkey, the three agonists induced a decrease in the mean firing frequency of GPi neurones, although dyskinesias were induced only in the parkinsonian animals. In this situation, the improvement of parkinsonian motor abnormalities was correlated with the decrease in GPi firing frequency, whereas firing pattern changes were concomitant with the onset of dyskinesias. Moreover, firing frequency seemed to be decreased excessively during dyskinesias. The results indicate that the electrophysiological mechanism of dyskinesia involves an excessive decrease in GPi firing frequency and a modification of the firing pattern. However, the similarity between the induced decrease in firing frequency in normal and parkinsonian animals underlines the need for dopamine depletion in the induction of dyskinesias.

Microbiology. Cyanobacteria track water in desert soils.

Abstract: Cyanobacteria develop as large, cryptic populations in the topsoil of arid land, where plant cover is restricted, water is scarce and harsh microenvironmental conditions prevail. Here we show that some cyanobacteria can actively move in response to wetting or drying events by migrating to the soil surface or retreating to their refuge below. This ability to follow water, which to our knowledge has not been demonstrated before in microbes, may turn out to be important for microbial terrestrial populations in general.

Safety Considerations of DNA in Food

Abstract: Recombinant DNA techniques are capable of introducing genetic changes into food organisms that are more predictable than those introduced through conventional breeding techniques. This review discusses whether the consumption of DNA in approved novel foods and novel food ingredients derived from genetically modified organisms (GMOs) can be regarded as being as safe as the consumption of DNA in existing foods. It concludes that DNA from GMOs is equivalent to DNA from existing food organisms that has always been consumed with human diets. Any risks associated with the consumption of DNA will remain, irrespective of its origin, because the body handles all DNA in the same way. The breakdown of DNA during food processing and passage through the gastrointestinal tract reduces the likelihood that intact genes capable of encoding foreign proteins will be transferred to gut microflora. The review does not specifically address food safety issues arising from the consumption of viable genetically modified microorganisms but it shows that the likelihood of transfer and functional integration of DNA from ingested food by gut microflora and/or human cells is minimal. Information reviewed does not indicate any safety concerns associated with the ingestion of DNA per se from GMOs resulting from the use of currently available recombinant DNA techniques in the food chain.