Aggregation under a forced convective flow

Morphological transitions are analyzed for a radial multiparticle diffusion-limited aggregation process grown under a convective drift. The introduction of a tangential flow changes the morphology of the diffusion-limited structure, into multiarm structures, inclined opposite to the flow, whose limit consists of single arms, when decreasing density. The case of shear flow is also considered. The anisotropy of the patterns is characterized in terms of a tangential correlation function based analysis. Comparison between the simulation results and preliminary experimental results has been done.

The role of reputation, punishment and their interplay in human cooperation

The problem of how cooperation can evolve between individuals or entities with conflicting interests is central to biology as many of the major evolutionary transitions, from the first replicating molecules to human societies, have required solving this problem. There are many routes to cooperation but humans seem to be distinct from other species as they have more complex and diverse mechanisms, often due to their higher cognitive skills, allowing them to reap the benefits from living in groups. Among those mechanisms, the use of reputation or past experience with others as well as sanctioning mechanisms both seem to be of major importance. They have often been considered separately but the interaction between the two might provide new insights as to how punishment could have appeared as a means to enforce cooperation in early humans. In this thesis, I firstly use theoretical approaches from evolutionary game theory to investigate the evolution of punishment and cooperation through a reputation system based on punitive actions, and compare the efficacy of this system, in terms of cooperation achieved, with one based on cooperative actions. On the other hand, I use empirical approaches from economics to test, in real life, predictions from theoretical models but also to explore further conditions such as environmental variation, constrained memory, or even the scale of competition between individuals. Both approaches have allowed contributing to the understanding of how these factors affect reputation and punishment use, and ultimately how cooperation is achieved.

Development and validation of a gas chromatography-negative chemical ionization tandem mass spectrometry method for the determination of ethyl glucuronide in hair and its application to forensic toxicology.

Ethyl glucuronide (EtG) is a minor and direct metabolite of ethanol. EtG is incorporated into the growing hair allowing retrospective investigation of chronic alcohol abuse. In this study, we report the development and the validation of a method using gas chromatography-negative chemical ionization tandem mass spectrometry (GC-NCI-MS/MS) for the quantification of EtG in hair. EtG was extracted from about 30 mg of hair by aqueous incubation and purified by solid-phase extraction (SPE) using mixed mode extraction cartridges followed by derivation with perfluoropentanoic anhydride (PFPA). The analysis was performed in the selected reaction monitoring (SRM) mode using the transitions m/z 347-->163 (for the quantification) and m/z 347-->119 (for the identification) for EtG, and m/z 352-->163 for EtG-d(5) used as internal standard. For validation, we prepared quality controls (QC) using hair samples taken post mortem from 2 subjects with a known history of alcoholism. These samples were confirmed by a proficiency test with 7 participating laboratories. The assay linearity of EtG was confirmed over the range from 8.4 to 259.4 pg/mg hair, with a coefficient of determination (r(2)) above 0.999. The limit of detection (LOD) was estimated with 3.0 pg/mg. The lower limit of quantification (LLOQ) of the method was fixed at 8.4 pg/mg. Repeatability and intermediate precision (relative standard deviation, RSD%), tested at 4 QC levels, were less than 13.2%. The analytical method was applied to several hair samples obtained from autopsy cases with a history of alcoholism and/or lesions caused by alcohol. EtG concentrations in hair ranged from 60 to 820 pg/mg hair.

Dextramers: new generation of fluorescent MHC class I/peptide multimers for visualization of antigen-specific CD8+ T cells.

Direct identification as well as isolation of antigen-specific T cells became possible since the development of "tetramers" based on avidin-fluorochrome conjugates associated with mono-biotinylated class I MHC-peptide monomeric complexes. In principle, a series of distinct class I MHC-peptide tetramers, each labelled with a different fluorochrome, would allow to simultaneously enumerate as many unique antigen-specific CD8(+) T cells. Practically, however, only phycoerythrin and allophycocyanin conjugated tetramers have been generally available, imposing serious constraints for multiple labeling. To overcome this limitation, we have developed dextramers which are multimers based on a dextran backbone bearing multiple fluorescein and streptavidin moieties. Here we demonstrate the functionality and optimization of these new probes on human CD8(+) T cell clones with four independent antigen specificities. Their applications to the analysis of relatively low frequency antigen-specific T cells in peripheral blood, as well as their use in fluorescence microscopy, are demonstrated. The data show that dextramers produce a stronger signal than their fluoresceinated tetramer counterparts. Thus, these could become the reagents of choice as the antigen-specific T cell labeling transitions from basic research to clinical application.

Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.

The Caulobacter DNA methyltransferase CcrM is one of five master cell-cycle regulators. CcrM is transiently present near the end of DNA replication when it rapidly methylates the adenine in hemimethylated GANTC sequences. The timing of transcription of two master regulator genes and two cell division genes is controlled by the methylation state of GANTC sites in their promoters. To explore the global extent of this regulatory mechanism, we determined the methylation state of the entire chromosome at every base pair at five time points in the cell cycle using single-molecule, real-time sequencing. The methylation state of 4,515 GANTC sites, preferentially positioned in intergenic regions, changed progressively from full to hemimethylation as the replication forks advanced. However, 27 GANTC sites remained unmethylated throughout the cell cycle, suggesting that these protected sites could participate in epigenetic regulatory functions. An analysis of the time of activation of every cell-cycle regulatory transcription start site, coupled to both the position of a GANTC site in their promoter regions and the time in the cell cycle when the GANTC site transitions from full to hemimethylation, allowed the identification of 59 genes as candidates for epigenetic regulation. In addition, we identified two previously unidentified N(6)-methyladenine motifs and showed that they maintained a constant methylation state throughout the cell cycle. The cognate methyltransferase was identified for one of these motifs as well as for one of two 5-methylcytosine motifs.

Spatial and temporal regulation of " cdc16p " in the fission yeast " Schizosaccharomyces pombe "

Abstract: The fission yeast Schizosaccharomyces pombe has proven to be an excellent model system for the study of eukaryotic cell cycle control. S. pombe cells are rod-shaped and grow mainly by elongation at their tips. They divide by the means of a centrallyplaced division septum which provides two daughter cells of equal size. S. pombe cytokinesis begins at mitotic entry, when the division site is defined by formation of the contractile acto-myosin ring (CAR). Formation of the division septum is triggered at the end of mitosis by the spindle pole body (SPB) associated septation initiation network (SIN) proteins. SIN signalling requires activation of the GTPase spg1p, whose nucleotide status is regulated by the bipartite GAP byr4pcdc16p. Removal of cdc16p from the SPB during early mitosis is thought to allow priming of the SIN by association of cdc7p with both SPBs. During anaphase cdc7p is retained on the new SPB, which also recruits the kinase sid1 p and cdc14p, while the old SP8 reassembles the byr4-cdc16p GAP and is presumed not to signal; SPB asymmetry persists throughout anaphase. The trigger for inactivation of SIN signalling at the new SPB is unknown. This study has concentrated upon cdc16p. We have undertaken the analysis of the localisation of cdc16p using time-lapse microscopy. We have observed that the localisation of cdc16p is regulated at different transitions. We have shown that cdc16p is removed from the SPB prior to the onset of spindle formation and that it reappears asymmetrically at the beginning of anaphase B. We have also demonstrated that the resetting of the SIN at the new SPB is linked to completion of CAR contraction and septum formation. We propose the existence of a mechanism that monitors cytokinesis and that couples the activity of the SI N with the presence of the CAR. During the biochemical characterization of cdc16p, We have found that it is an unstable protein and that it is subjected to polyubiquitination by the SCF and proteasomal degradation. Together, these observations help to shed new light upon the mechanisms by which cytokinesis is regulated in S. pombe. R��sum��: La levure Schizosaccharomyces pombe est un excellent organisme mod��le pour l'��tude du cycle cellulaire eucaryote. Les cellules S. pombe ont la forme de b��tonnets et croissent par l'allongement de leurs extr��mit��s. Elles se divisent en formant, en leur milieu une paroi cellulaire, appel�� septum, permettant ainsi l'obtention de deux cellules filles de m��me taille. Chez S. pombe, la cytokin��se commence en d��but de mitose lorsque le site de division est d��termin�� par la formation d'un anneau d'acto-myosine. Le septum, lui, est form�� uniquement en fin de mitose par la contraction de l'anneau d'actomyosine. Cette contraction est sous le contr��le d'un r��seau de signalisation cellulaire appel�� le ��r��seau d'initiation de synth��se du septum �� ou �� septation initiation network �� (SIN), qui se situe sur les p��les du fuseau mitotique. L'activation du SIN d��pend d'une GTPase appel�� spg1p dont le statut nucl��otidique d��pend des prot��ines cdcl��p et byr4p qui forment un complexe qui favorise l'hydrolyse du GTP en GDP. En d��but de mitose, cdc16p ne se situe plus sur les poles du fuseau mitotique. La GTPase spg1p se retrouve donc principalement sous sa forme coupl��e au GTP, ce qu�� va permettre son interaction avec la kinase cdc7p. Cette prot��ine ainsi que deux autres kinases sid2p (avec mob1p) et sid1p (avec cdc14p) permettent la transmission du signal d'initiation de la contraction de l'anneau d'acto-myosine en fin d'anaphase. Pendant l'anaphase, cdc7p, sid1 p et cdc14p localisent sur un des deux p��les du fuseau mitotique. Il en est de m��me pour cdc1p et by14p et le p��le contenant cdc16p et byr4p est toujours diff��rent de celui ou les r��gulateurs positifs du SIN se situent. En fin de cytokin��se, cdc16 et byr4p se retrouvent �� nouveau sur chaque p��le des deux cellules filles. Dans cette ��tude, nous nous sommes concentr��s sur l'analyse de la localisation de cdc16p pendant la mitose en utilisant une technique de microscopie en temps r��el. Nous avons ��t�� en mesure de d��terminer que le d��part de cdc16p du pole s'effectue juste avant la formation du fuseau mitotique. Nous avons aussi d��couvert que la localisation asym��trique des composants du SIN d��pend fortement de l'entr��e en anaphase B. Finalement, Nous avons montr�� que distribution asym��trique des composants du SIN sur les p��les du fuseau mitotique d��pendait aussi fortement de !a pr��sence de l'anneau d'acto-myosine. Ceci nous permet donc de proposer l'existence d'un m��canisme cellulaire qui permet de s'assurer que la cytokin��se est achev��e avant de diminuer la signalisation du SIN. Par ailleurs, des ��tudes biochimiques nous ont permis de montrer que cdc16p est d��grad�� par le proteosome. Ces travaux ont permis la d��couverte de nouveaux modes de r��gulation du SIN.

Textual autocorrelation : formalism and illustrations

Abstract Textual autocorrelation is a broad and pervasive concept, referring to the similarity between nearby textual units: lexical repetitions along consecutive sentences, semantic association between neighbouring lexemes, persistence of discourse types (narrative, descriptive, dialogal...) and so on. Textual autocorrelation can also be negative, as illustrated by alternating phonological or morpho-syntactic categories, or the succession of word lengths. This contribution proposes a general Markov formalism for textual navigation, and inspired by spatial statistics. The formalism can express well-known constructs in textual data analysis, such as term-document matrices, references and hyperlinks navigation, (web) information retrieval, and in particular textual autocorrelation, as measured by Moran's I relatively to the exchange matrix associated to neighbourhoods of various possible types. Four case studies (word lengths alternation, lexical repulsion, parts of speech autocorrelation, and semantic autocorrelation) illustrate the theory. In particular, one observes a short-range repulsion between nouns together with a short-range attraction between verbs, both at the lexical and semantic levels. R��sum��: Le concept d'autocorr��lation textuelle, fort vaste, r��f��re �� la similarit�� entre unit��s textuelles voisines: r��p��titions lexicales entre phrases successives, association s��mantique entre lex��mes voisins, persistance du type de discours (narratif, descriptif, dialogal...) et ainsi de suite. L'autocorr��lation textuelle peut ��tre ��galement n��gative, comme l'illustrent l'alternance entre les cat��gories phonologiques ou morpho-syntaxiques, ou la succession des longueurs de mots. Cette contribution propose un formalisme markovien g��n��ral pour la navigation textuelle, inspir�� par la statistique spatiale. Le formalisme est capable d'exprimer des constructions bien connues en analyse des donn��es textuelles, telles que les matrices termes-documents, les r��f��rences et la navigation par hyperliens, la recherche documentaire sur internet, et, en particulier, l'autocor��lation textuelle, telle que mesur��e par le I de Moran relatif �� une matrice d'��change associ��e �� des voisinages de diff��rents types possibles. Quatre cas d'��tude illustrent la th��orie: alternance des longueurs de mots, r��pulsion lexicale, autocorr��lation des cat��gories morpho-syntaxiques et autocorr��lation s��mantique. On observe en particulier une r��pulsion �� courte port��e entre les noms, ainsi qu'une attraction �� courte port��e entre les verbes, tant au niveau lexical que s��mantique.

La construcci��n narrativa de la identidad en un contexto educativo intercultural = The narrative construction of identity in a intercultural educative setting

En este trabajo se expone e ilustra un modelo te��rico para entender las funciones de la identidad, as�� como los mecanismospsicosociales asociados a su construcci��n: ���Modelo Evolutivo y Funcional de la Identidad Mediada��� (MEBIM). La identidad, mediada narrativamente, cumple una funci��n personal orientada a la direcci��n de la propia vida, as�� como una funci��n sociocultural vinculada a la b��squeda de reconocimiento de los derechos de los grupos sociales a los que uno se siente apegado. Se ilustran los factores asociados a la construcci��n de la identidad personal (s�� mismos posibles, transiciones vitales, v��nculo afectivo) y sociocultural (acci��n-transformaci��n e identificaci��n simb��lica) a partir de 12 historias de vida realizadas con mestizos e ind��genasde la Universidad Intercultural de Chiapas (M��xico). Se sugiere que en contextos educativos formales, como la escuela o la Universidad, se deben propiciar narrativas personales y socioculturales con el objetivo de optimizar la identidad en un mundo a la vez globalizado y plural

Matching stages of heavy-ion collision models

Heavy-ion reactions and other collective dynamical processes are frequently described by different theoretical approaches for the different stages of the process, like initial equilibration stage, intermediate locally equilibrated fluid dynamical stage, and final freeze-out stage. For the last stage, the best known is the Cooper-Frye description used to generate the phase space distribution of emitted, noninteracting particles from a fluid dynamical expansion or explosion, assuming a final ideal gas distribution, or (less frequently) an out-of-equilibrium distribution. In this work we do not want to replace the Cooper-Frye description, but rather clarify the ways of using it and how to choose the parameters of the distribution and, eventually, how to choose the form of the phase space distribution used in the Cooper-Frye formula. Moreover, the Cooper-Frye formula is used in connection with the freeze-out problem, while the discussion of transition between different stages of the collision is applicable to other transitions also. More recently, hadronization and molecular dynamics models have been matched to the end of a fluid dynamical stage to describe hadronization and freeze-out. The stages of the model description can be matched to each other on space-time hypersurfaces (just like through the frequently used freeze-out hypersurface). This work presents a generalized description of how to match the stages of the description of a reaction to each other, extending the methodology used at freeze-out, in simple covariant form which is easily applicable in its simplest version for most applications.

Controlling anomalous stresses in soft field-responsive systems

We report a phenomenon occurring in field-responsive suspensions: shear-induced anomalous stresses. Competition between a rotating field and a shear flow originates a multiplicity of anomalous stress behaviors in suspensions of bound dimers constituted by induced dipoles. The great variety of stress regimes includes nonmonotonic behaviors, multiresonances, negative viscosity effect, and blockades. The reversibility of the transitions between the different regimes and the self-similarity of the stresses make this phenomenon controllable and therefore applicable to modify macroscopic properties of soft condensed matter phases.

Brittle to ductile transition in a fiber bundle with strong heterogeneity

We analyze the failure process of a two-component system with widely different fracture strength in the framework of a fiber bundle model with localized load sharing. A fraction 0��������1 of the bundle is strong and it is represented by unbreakable fibers, while fibers of the weak component have randomly distributed failure strength. Computer simulations revealed that there exists a critical composition ��c which separates two qualitatively different behaviors: Below the critical point, the failure of the bundle is brittle, characterized by an abrupt damage growth within the breakable part of the system. Above ��c, however, the macroscopic response becomes ductile, providing stability during the entire breaking process. The transition occurs at an astonishingly low fraction of strong fibers which can have importance for applications. We show that in the ductile phase, the size distribution of breaking bursts has a power law functional form with an exponent ��=2 followed by an exponential cutoff. In the brittle phase, the power law also prevails but with a higher exponent ��=92. The transition between the two phases shows analogies to continuous phase transitions. Analyzing the microstructure of the damage, it was found that at the beginning of the fracture process cracks nucleate randomly, while later on growth and coalescence of cracks dominate, which give rise to power law distributed crack sizes.

Avian haemosporidian persistence and co-infection in great tits at the individual level.

BACKGROUND: Many studies have tracked the distribution and persistence of avian haemosporidian communities across space and time at the population level, but few studies have investigated these aspects of infection at the individual level over time. Important aspects of parasite infection at the individual level can be missed if only trends at the population level are studied. This study aimed to determine how persistent Haemosporida are in great tit individuals recaptured over several years, whether parasitaemia differed by parasite lineage (mitochondrial cytochrome b haplotype) and how co-infection (i.e. concurrent infection with multiple genera of parasites) affects parasitaemia and body mass. METHODS: Parasite prevalence was determined by polymerase chain reaction (PCR), quantitative PCR were used to assess parasitaemia and sequencing was employed to determine the identity of the lineages using the MalAvi database. RESULTS: Haemosporidian prevalence was high over sampled years with 98% of 55 recaptured individuals showing infection in at least one year of capture. Eighty-two percent of all positive individuals suffered co-infection, with an overall haemosporidian lineage diversity of seventeen. Plasmodium and Haemoproteus parasites were found to be highly persistent, with lineages from these genera consistently found in individuals across years and with no differences in individual parasitaemia being recorded at subsequent captures. Conversely, Leucocytozoon parasites showed higher turnover with regard to lineage changes or transitions in infection status (infected vs non-infected) across years. Parasitaemia was found to be lineage specific and there was no relationship between Plasmodium parasitaemia or host body condition and the presence of Leucocytozoon parasites. CONCLUSIONS: The findings of this study suggest that different genera of haemosporidian parasites interact differently with their host and other co-infecting parasites, influencing parasite persistence most likely through inter-parasite competition or host-parasite immune interactions. Even-though co-infections do not seem to result in increased virulence (higher parasitaemia or poorer host body condition), further investigation into infection potential of these parasites, both individually and as co-infections, is necessary.