Caracteritaci�� de models funcionals d'��mfores romanes mitjan��ant Finite Element Analysis

Projecte de recerca elaborat a partir d���una estada al Laboratory of Archaeometry del National Centre of Scientific Research ���Demokritos��� d���Atenes, Gr��cia, entre juny i setembre 2006. Aquest estudi s���emmarca dins d���un context m��s ampli d���estudi del canvi tecnol��gic que es documenta en la producci�� d�����mfores de tipologia romana durant els segles I aC i I dC en els territoris costaners de Catalunya. Una part d���aquest estudi contempla el c��lcul de les propietats mec��niques d���aquestes ��mfores i la seva avaluaci�� en funci�� de la tipologia amforal, a partir de l���An��lisi d���Elements Finits (AEF). L���AEF ��s una aproximaci�� num��rica que t�� el seu origen en les ci��ncies d���enginyeria i que ha estat emprada per estimar el comportament mec��nic d���un model en termes, per exemple, de deformaci�� i estr��s. Aix��, un objecte, o millor dit el seu model, es dividit en sub-dominis anomenats elements finits, als quals se���ls atribueixen les propietats mec��niques del material en estudi. Aquests elements finits estan connectats formant una xarxa amb constriccions que pot ser definida. En el cas d���aplicar una for��a determinada a un model, el comportament de l���objecte pot ser estimat mitjan��ant el conjunt d���equacions lineals que defineixen el rendiment dels elements finits, proporcionant una bona aproximaci�� per a la descripci�� de la deformaci�� estructural. Aix��, aquesta simulaci�� per ordinador suposa una important eina per entendre la funcionalitat de cer��miques arqueol��giques. Aquest procediment representa un model quantitatiu per predir el trencament de l���objecte cer��mic quan aquest ��s sotm��s a diferents condicions de pressi��. Aquest model ha estat aplicat a diferents tipologies amforals. Els resultats preliminars mostren difer��ncies significatives entre la tipologia pre-romana i les tipologies romanes, aix�� com entre els mateixos dissenys amforals romans, d���importants implicacions arqueol��giques.

A New Large-DNA-Fragment Delivery System Based on Integrase Activity from an Integrative and Conjugative Element.

During the past few decades, numerous plasmid vectors have been developed for cloning, gene expression analysis, and genetic engineering. Cloning procedures typically rely on PCR amplification, DNA fragment restriction digestion, recovery, and ligation, but increasingly, procedures are being developed to assemble large synthetic DNAs. In this study, we developed a new gene delivery system using the integrase activity of an integrative and conjugative element (ICE). The advantage of the integrase-based delivery is that it can stably introduce a large DNA fragment (at least 75 kb) into one or more specific sites (the gene for glycine-accepting tRNA) on a target chromosome. Integrase recombination activity in Escherichia coli is kept low by using a synthetic hybrid promoter, which, however, is unleashed in the final target host, forcing the integration of the construct. Upon integration, the system is again silenced. Two variants with different genetic features were produced, one in the form of a cloning vector in E. coli and the other as a mini-transposable element by which large DNA constructs assembled in E. coli can be tagged with the integrase gene. We confirmed that the system could successfully introduce cosmid and bacterial artificial chromosome (BAC) DNAs from E. coli into the chromosome of Pseudomonas putida in a site-specific manner. The integrase delivery system works in concert with existing vector systems and could thus be a powerful tool for synthetic constructions of new metabolic pathways in a variety of host bacteria.

Simulaci��n de fluidos inmiscibles con el Particle Finite Element Method (PFEM)

Proyecto de investigaci��n realizado a partir de una estancia en el Centro Internacional de M��todos Computacionales en Ingenier��a (CIMEC), Argentina, entre febrero y abril del 2007. La simulaci��n num��rica de problemas de mezclas mediante el Particle Finite Element Method (PFEM) es el marco de estudio de una futura tesis doctoral. ��ste es un m��todo desarrollado conjuntamente por el CIMEC y el Centre Internacional de M��todos Num��rics en l'Enginyeria (CIMNE-UPC), basado en la resoluci��n de las ecuaciones de Navier-Stokes en formulaci��n Lagrangiana. El mallador ha sido implementado y desarrollado por Dr. Nestor Calvo, investigador del CIMEC. El desarrollo del m��dulo de c��lculo corresponde al trabajo de tesis de la beneficiaria. La correcta interacci��n entre ambas partes es fundamental para obtener resultados v��lidos. En esta memoria se explican los principales aspectos del mallador que fueron modificados (criterios de refinamiento geom��trico) y los cambios introducidos en el m��dulo de c��lculo (librer��a PETSc, algoritmo predictor-corrector) durante la estancia en el CIMEC. Por ��ltimo, se muestran los resultados obtenidos en un problema de dos fluidos inmiscibles con transferencia de calor.

Temper and Temperature: The Missing Link of Climate on Armed Conflicts

We investigate the causes of a conflict by adding ambient climate factors to the existing bundle of most significant variables. It turns out that ��� controlling for possible associations ��� temperature could actually induce a conflict. We emphasise that temperature could not be a dominant reason in starting a conflict; however, it could escalate the chances when other factors are present. This paper references some of the related psychological studies to support this claim. We also show that grievance factors could actually be rightfully effective in starting an internal conflict alongside greed based reasons. In the end, we believe that it could be informative to study ambient factors more often in economics.

A mixed finite element method for nonlinear diffusion equations

We propose a mixed finite element method for a class of nonlinear diffusion equations, which is based on their interpretation as gradient flows in optimal transportation metrics. We introduce an appropriate linearization of the optimal transport problem, which leads to a mixed symmetric formulation. This formulation preserves the maximum principle in case of the semi-discrete scheme as well as the fully discrete scheme for a certain class of problems. In addition solutions of the mixed formulation maintain exponential convergence in the relative entropy towards the steady state in case of a nonlinear Fokker-Planck equation with uniformly convex potential. We demonstrate the behavior of the proposed scheme with 2D simulations of the porous medium equations and blow-up questions in the Patlak-Keller-Segel model.

Identification of two steroid-responsive promoters of different strength controlled by the same estrogen-responsive element in the 5'-end region of the Xenopus laevis vitellogenin gene A1.

A structural and functional analysis of the 5'-end region of the Xenopus laevis vitellogenin gene A1 revealed two transcription initiation sites located 1.8 kilobases apart. A RNA polymerase II binding assay indicates that both promoters form initiation complexes efficiently. In vitro, using a transcription assay derived from a HeLa whole-cell extract, the upstream promoter is more than 10-fold stronger than the downstream one. In contrast, both promoters have a similar strength in a HeLa nuclear extract. In vivo, that is in estrogen-stimulated hepatocytes, it is the downstream promoter homologous to the one used by the other members of the vitellogenin gene family, which is 50-fold stronger than the upstream promoter. Thus, if functional vitellogenin mRNA results from this latter activity, it would contribute less than 1% to the synthesis of vitellogenin by fully induced Xenopus hepatocytes expressing the four vitellogenin genes. In contrast, both gene A1 promoters are silent in uninduced hepatocytes. Transfection experiments using the Xenopus cell line B3.2 in which estrogen-responsiveness has been introduced reveal that the strong downstream promoter is controlled by an estrogen responsive element (ERE) located 330 bp upstream of it. The upstream promoter can also be controlled by the same ERE. Since the region comprising the upstream promoter is flanked by a 200 base pair long inverted repeat with stretches of homology to other regions of the X. laevis genome, we speculate that it might have been inserted upstream of the vitellogenin gene A1 by a recombination event and consequently brought under control of the ERE lying 1.5 kilobases downstream.

Natural killer cell mediated missing-self recognition can protect mice from primary chronic myeloid leukemia in vivo.

Background: Natural Killer (NK) cells are thought to protect from residual leukemic cells in patients receiving stem cell transplantation. However, multiple retrospective analyses of patient data have yielded conflicting conclusions regarding a putative role of NK cells and the essential NK cell recognition events mediating a protective effect against leukemia. Further, a NK cell mediated protective effect against primary leukemia in vivo has not been shown directly.Methodology/Principal Findings: Here we addressed whether NK cells have the potential to control chronic myeloid leukemia (CML) arising based on the transplantation of BCR-ABL1 oncogene expressing primary bone marrow precursor cells into lethally irradiated recipient mice. These analyses identified missing-self recognition as the only NK cell-mediated recognition strategy, which is able to significantly protect from the development of CML disease in vivo.Conclusion: Our data provide a proof of principle that NK cells can control primary leukemic cells in vivo. Since the presence of NK cells reduced the abundance of leukemia propagating cancer stem cells, the data raise the possibility that NK cell recognition has the potential to cure CML, which may be difficult using small molecule BCR-ABL1 inhibitors. Finally, our findings validate approaches to treat leukemia using antibody-based blockade of self-specific inhibitory MHC class I receptors.

Analysis of a finite volume element method for the Stokes problem

In this paper we propose a stabilized conforming finite volume element method for the Stokes equations. On stating the convergence of the method, optimal a priori error estimates in different norms are obtained by establishing the adequate connection between the finite volume and stabilized finite element formulations. A superconvergence result is also derived by using a postprocessing projection method. In particular, the stabilization of the continuous lowest equal order pair finite volume element discretization is achieved by enriching the velocity space with local functions that do not necessarily vanish on the element boundaries. Finally, some numerical experiments that confirm the predicted behavior of the method are provided.

Trace-element and phosphorus contents in sediment associated with Cretaceous oceanic anoxic events

ABSTRACT : During my SNSF-funded Ph.D. thesis project, I studied the evolution of redox conditions and organic-carbon preservation in the western Tethyan realm during three major positive excursions in the Cretaceous δ13C record, corresponding to the Valanginian, Early Aptian and Late Cenomanian. These periods were characterized by important global environmental and climate change, which was associated with perturbations in the carbon cycle. For the period of the Valanginian δ13C excursion, total organic carbon (TOC) contents and the quality of preserved organic matter are typical of oxic pelagic settings in the western Tethys. This is confirmed by the absence of major excursions in the stratigraphic distribution of RSTE during the δ13C shift. Published TOC data from other parts of the Valanginian oceans indicate that dys- to anaerobic zones were restricted to marginal seas within the Atlantic and Southern Ocean, and to the Pacific. Phosphorus (P) and mineralogical contents suggest a stepwise climatic evolution during the Valanginian, with a humid and warm climate prior to the δ13C shift leading to an increase in continental runoff. During the δ13C shift, a decrease in detrital input and P contents suggests a change in the climate towards more and conditions. During the early Aptian oceanic anoxic event (OAE 1a), a general increase followed by a rapid decrease in P contents suggests enhanced nutrient input at the beginning of OAE 1a. The return to lower values during OAE 1 a, associated with an increase in RSTE contents, may have been related to the weakened capacity to retain P in the sedimentary reservoir due to bottom-water oxygen depletion. In basinal settings, the RSTE distribution indicates well-developed anoxic conditions during OAE la, whereas in the shallower-water environments, conditions were oxic to suboxic, rather than anoxic. Furthermore, in the deeper part of the Tethys, two distinct enrichments have been observed, indicating fluctuations in the intensity of water column anoxia during the δ73C excursion. We also studied the effect of the end-Cenomanian oceanic anoxic event (OAE 2) on an expanded section in the Chrummflueschlucht (E of Euthal, Ct Switzerland). The goal here was to identify paleoceanographic and paleoenvironmental conditions during OAE 2 in this part of the northern Tethyan margin. The results show that this section is one of the most complete sections for the Cenomanian-Turonian boundary interval known from the Helvetic realm, despite a small hiatus between sediments corresponding to peaks 1 and 2 in the δ13C record. The evolution of P contents points to an increase in the input of this nutrient at the onset of OAE 2. The trends in RSTE contents show, however, that this part of the Helvetic realm was not affected by a strong depletion in oxygen conditions during OAE 2, despite its hemipelagic position. A further goal of this project was to submit the samples to a total extraction method (a combined HF/HNO3/HCI acid digestion) and compare the results obtained by the partial HNO3 acid extraction in order to standardize the analytical pr��cedures in the extraction of RSTE. The obtained results for samples of OAE 1 a suggest that RSTE trends using the partial HNO3 digestion are very comparable to those obtained by the total digestion method and subsequently normalized with regards to AI contents. R��SUM�� : Durant ce projet de th��se, financ�� par le Swiss National Science Funding (SNSF), j'ai ��tudi�� l'��volution des conditions redox et de la pr��servation de carbone organique dans le domnaine ouestt��thysien pendant trois excursions majeures du δ13C au Cr��tac�� correspondant au Valanginien, �� l'Aptien inf��rieur et �� la limite C��nomanien-Turonien. Ces p��riodes sont caract��ris��es par des changements climatiques et environnementaux globaux associ��s �� des perturbations dans le cylce du carbone. Pour L'excursion positive en δ13C du Valanginien, les analyses du carbone organique total (COT) et les observations palynologiques du domaine t��thysien ont pr��sent�� des indications d'environnement p��lagique relativementbienoxyg��n��. L'absence d'enrichissements en ��l��ments traces sensibles aux conditions redox (TE) pendant l'excursion positive en δ13C confirme ces interpr��tations. Les donn��es publi��es de COT dans d'autres partie du globe indiquent cependant l'existence de conditions dys- �� ana��robiques dans certains bassins restreints de l'Atlantique, l'Oc��an Austral et du Pacifique. L'��volution du phosphore (P) et la composition min��ralogique des s��diments semblent indiquer un climat relativement chaud et humide avant l'excursion en δ13C entra��nant une augmentation de l'alt��ration continentale. Pendant le shift isotopique, une diminution des apports d��tritiques et du P sugg��rent une transition vers des conditions plus arides. �� l'Aptien Inf��rieur, le d��but de l'��v��nement anoxique (OAE 1a) est marqu�� par une augmentation g��n��rale du P dans les s��diments indiquant une augmentation du niveau trophique �� la base de l'excursion isotopique. Durant l'��v��nement anoxique, les s��diments sont relativement appauvris en P. Cette diminution rapide associ��e �� des enrichissements en TE est probablement li��e �� une remobilisation plus importante du P lors de la mise en place de conditions anoxiques dans les eaux de fond. Dans les environnements de bassin, le comportement des TE (enrichissements bien marqu��s) attestent de conditions r��ductrices bien marqu��es alors que dans les environnements moins profonds, les conditions semblent plut��t oxiques �� dysoxiques. De plus, deux niveaux d'enrichissement en TE ont ��t�� observ��s dans la partie plus profonde de la T��thys, indiquant des fluctuations assez rapides dans l'intensit�� de l'anoxie de la colonne d'eau. Nous avons ensuite ��tudi�� les effets de l'��v��nement anoxique de la fin du Cenomanien (OAE 2) dans un basin marginal de la marge nord de la T��thys avec la coupe de Chrummflueschlucht (�� l'est de Euthal, Ct Schwyz). Les r��sultats ont montr�� que cette coupe pr��sente un des enregistrements s��dimentaires des plus complets de l'OAE 2 dans le domaine helv��tique malgr�� un hiatus entre le pic 1 et 2 de l'excursion en δ13C. L'��volution du P montre une augmentation au d��but de l'OAE 2. Cependant, la distribution des TE indique que cette r��gion n'a pas ��t�� affect��e par des conditions r��ductrices trop importantes. Un second aspect de ce travail a ��t�� l'��tude des diff��rentes m��thodes sur l'analyse de la distribution des TE. Des ��chantillons de l'OAE 1a ont ��t�� soumis �� deux types d'extractions, l'une dite ��totale �� (attaque combin��e d'acides HF/HNO3/HCI) et l'autre dite partielle �� (HNO3). Les r��sultats obtenus sugg��rent que les courbes de tendances des TE acquises par extraction partielle sont semblables �� celle obtenues par extraction totale et normalis��es par l'AI.

A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element.

The Bacillus subtilis strain 168 chromosomal region extending from 109 degrees to 112 degrees has been sequenced. Among the 35 ORFs identified, cotT and rapA were the only genes that had been previously mapped and sequenced. Out of ten ORFs belonging to a single putative transcription unit, seven are probably involved in hexuronate catabolism. Their sequences are homologous to Escherichia coli genes exuT, uidB, uxaA, uxaB, uxaC, uxuA and uxuB, which are all required for the uptake of free D-glucuronate, D-galacturonate and beta-glucuronide, and their transformation into glyceraldehyde 3-phosphate and pyruvate via 2-keto-3-deoxygluconate. The remaining three ORFs encode two dehydrogenases and a transcriptional regulator. The operon is preceded by a putative catabolite-responsive element (CRE), located between a hypothetical promoter and the RBS of the first gene. This element, the longest and the only so far described that is fully symmetrical, consists of a 26 bp palindrome matching the theoretical B. subtilis CRE sequence. The remaining predicted amino acid sequences that share homologies with other proteins comprise: a cytochrome P-450, a glycosyltransferase, an ATP-binding cassette transporter, a protein similar to the formate dehydrogenase alpha-subunit (FdhA), protein similar to NADH dehydrogenases, and three homologues of polypeptides that have undefined functions.

Atenci�� prim��ria: una aproximaci�� a l'experi��ncia vital de l'educand com a element educatiu

La recerca Atenci�� Prim��ria: una aproximaci�� a l'experi��ncia vital de l'educand com a element educatiu, posa de relleu la import��ncia de l'experi��ncia viscuda en un individu com a element motivador i capacitador de les pr��pies expectatives personals, de les ganes de superaci�� en el proc��s educatiu que s'est�� duent a terme entre l'educador o educadora i l'educand com a subjecte de l'experi��ncia. El treball que presento vol ser una primera aproximaci�� a un element tan important com ��s l'experi��ncia vital de l'educand. Preguntes com quin paper juga l'experi��ncia, el record, la posada en pr��ctica i la seva recuperaci��, sempre des d'un punt de vista educatiu i no terap��utic, s��n les que m'he plantejat en la recerca. Exploro com la recuperaci�� d���all�� que cadasc�� viu com a bon saber i posar-lo en pr��ctica de nou, pot ser un element facilitador en el proc��s educatiu. Reflexionar sobre unes accions ja realitzades ��s tornar-les a pensar des d'una mem��ria reflexiva, perqu�� no comencem de zero, sin�� que comencem des d'aquella acci�� que en el seu moment ja ens va dur a un resultat positiu. Suposa aprendre a pensar millor, a utilitzar el pensament com un processador de la experi��ncia i la informaci��. L���educador/a social, en aquesta relaci��, fa ���de mirall��� del propi educand, ajudant a sortir-se'n, acompanyant-lo en el recorregut de l'aprenentatge.