A framework for mixed-criticality partitioned real-time embedded systems

Los sistemas empotrados son cada d��a m��s comunes y complejos, de modo que encontrar procesos seguros, eficaces y baratos de desarrollo software dirigidos espec��ficamente a esta clase de sistemas es m��s necesario que nunca. A diferencia de lo que ocurr��a hasta hace poco, en la actualidad los avances tecnol��gicos en el campo de los microprocesadores de los ��ltimos tiempos permiten el desarrollo de equipos con prestaciones m��s que suficientes para ejecutar varios sistemas software en una ��nica m��quina. Adem��s, hay sistemas empotrados con requisitos de seguridad (safety) de cuyo correcto funcionamiento depende la vida de muchas personas y/o grandes inversiones econ��micas. Estos sistemas software se dise��an e implementan de acuerdo con unos est��ndares de desarrollo software muy estrictos y exigentes. En algunos casos puede ser necesaria tambi��n la certificaci��n del software. Para estos casos, los sistemas con criticidades mixtas pueden ser una alternativa muy valiosa. En esta clase de sistemas, aplicaciones con diferentes niveles de criticidad se ejecutan en el mismo computador. Sin embargo, a menudo es necesario certificar el sistema entero con el nivel de criticidad de la aplicaci��n m��s cr��tica, lo que hace que los costes se disparen. La virtualizaci��n se ha postulado como una tecnolog��a muy interesante para contener esos costes. Esta tecnolog��a permite que un conjunto de m��quinas virtuales o particiones ejecuten las aplicaciones con unos niveles de aislamiento tanto temporal como espacial muy altos. Esto, a su vez, permite que cada partici��n pueda ser certificada independientemente. Para el desarrollo de sistemas particionados con criticidades mixtas se necesita actualizar los modelos de desarrollo software tradicionales, pues estos no cubren ni las nuevas actividades ni los nuevos roles que se requieren en el desarrollo de estos sistemas. Por ejemplo, el integrador del sistema debe definir las particiones o el desarrollador de aplicaciones debe tener en cuenta las caracter��sticas de la partici��n donde su aplicaci��n va a ejecutar. Tradicionalmente, en el desarrollo de sistemas empotrados, el modelo en V ha tenido una especial relevancia. Por ello, este modelo ha sido adaptado para tener en cuenta escenarios tales como el desarrollo en paralelo de aplicaciones o la incorporaci��n de una nueva partici��n a un sistema ya existente. El objetivo de esta tesis doctoral es mejorar la tecnolog��a actual de desarrollo de sistemas particionados con criticidades mixtas. Para ello, se ha dise��ado e implementado un entorno dirigido espec��ficamente a facilitar y mejorar los procesos de desarrollo de esta clase de sistemas. En concreto, se ha creado un algoritmo que genera el particionado del sistema autom��ticamente. En el entorno de desarrollo propuesto, se han integrado todas las actividades necesarias para desarrollo de un sistema particionado, incluidos los nuevos roles y actividades mencionados anteriormente. Adem��s, el dise��o del entorno de desarrollo se ha basado en la ingenier��a guiada por modelos (Model-Driven Engineering), la cual promueve el uso de los modelos como elementos fundamentales en el proceso de desarrollo. As�� pues, se proporcionan las herramientas necesarias para modelar y particionar el sistema, as�� como para validar los resultados y generar los artefactos necesarios para el compilado, construcci��n y despliegue del mismo. Adem��s, en el dise��o del entorno de desarrollo, la extensi��n e integraci��n del mismo con herramientas de validaci��n ha sido un factor clave. En concreto, se pueden incorporar al entorno de desarrollo nuevos requisitos no-funcionales, la generaci��n de nuevos artefactos tales como documentaci��n o diferentes lenguajes de programaci��n, etc. Una parte clave del entorno de desarrollo es el algoritmo de particionado. Este algoritmo se ha dise��ado para ser independiente de los requisitos de las aplicaciones as�� como para permitir al integrador del sistema implementar nuevos requisitos del sistema. Para lograr esta independencia, se han definido las restricciones al particionado. El algoritmo garantiza que dichas restricciones se cumplir��n en el sistema particionado que resulte de su ejecuci��n. Las restricciones al particionado se han dise��ado con una capacidad expresiva suficiente para que, con un peque��o grupo de ellas, se puedan expresar la mayor parte de los requisitos no-funcionales m��s comunes. Las restricciones pueden ser definidas manualmente por el integrador del sistema o bien pueden ser generadas autom��ticamente por una herramienta a partir de los requisitos funcionales y no-funcionales de una aplicaci��n. El algoritmo de particionado toma como entradas los modelos y las restricciones al particionado del sistema. Tras la ejecuci��n y como resultado, se genera un modelo de despliegue en el que se definen las particiones que son necesarias para el particionado del sistema. A su vez, cada partici��n define qu�� aplicaciones deben ejecutar en ella as�� como los recursos que necesita la partici��n para ejecutar correctamente. El problema del particionado y las restricciones al particionado se modelan matem��ticamente a trav��s de grafos coloreados. En dichos grafos, un coloreado propio de los v��rtices representa un particionado del sistema correcto. El algoritmo se ha dise��ado tambi��n para que, si es necesario, sea posible obtener particionados alternativos al inicialmente propuesto. El entorno de desarrollo, incluyendo el algoritmo de particionado, se ha probado con ��xito en dos casos de uso industriales: el sat��lite UPMSat-2 y un demostrador del sistema de control de una turbina e��lica. Adem��s, el algoritmo se ha validado mediante la ejecuci��n de numerosos escenarios sint��ticos, incluyendo algunos muy complejos, de m��s de 500 aplicaciones. ABSTRACT The importance of embedded software is growing as it is required for a large number of systems. Devising cheap, efficient and reliable development processes for embedded systems is thus a notable challenge nowadays. Computer processing power is continuously increasing, and as a result, it is currently possible to integrate complex systems in a single processor, which was not feasible a few years ago.Embedded systems may have safety critical requirements. Its failure may result in personal or substantial economical loss. The development of these systems requires stringent development processes that are usually defined by suitable standards. In some cases their certification is also necessary. This scenario fosters the use of mixed-criticality systems in which applications of different criticality levels must coexist in a single system. In these cases, it is usually necessary to certify the whole system, including non-critical applications, which is costly. Virtualization emerges as an enabling technology used for dealing with this problem. The system is structured as a set of partitions, or virtual machines, that can be executed with temporal and spatial isolation. In this way, applications can be developed and certified independently. The development of MCPS (Mixed-Criticality Partitioned Systems) requires additional roles and activities that traditional systems do not require. The system integrator has to define system partitions. Application development has to consider the characteristics of the partition to which it is allocated. In addition, traditional software process models have to be adapted to this scenario. The V-model is commonly used in embedded systems development. It can be adapted to the development of MCPS by enabling the parallel development of applications or adding an additional partition to an existing system. The objective of this PhD is to improve the available technology for MCPS development by providing a framework tailored to the development of this type of system and by defining a flexible and efficient algorithm for automatically generating system partitionings. The goal of the framework is to integrate all the activities required for developing MCPS and to support the different roles involved in this process. The framework is based on MDE (Model-Driven Engineering), which emphasizes the use of models in the development process. The framework provides basic means for modeling the system, generating system partitions, validating the system and generating final artifacts. The framework has been designed to facilitate its extension and the integration of external validation tools. In particular, it can be extended by adding support for additional non-functional requirements and support for final artifacts, such as new programming languages or additional documentation. The framework includes a novel partitioning algorithm. It has been designed to be independent of the types of applications requirements and also to enable the system integrator to tailor the partitioning to the specific requirements of a system. This independence is achieved by defining partitioning constraints that must be met by the resulting partitioning. They have sufficient expressive capacity to state the most common constraints and can be defined manually by the system integrator or generated automatically based on functional and non-functional requirements of the applications. The partitioning algorithm uses system models and partitioning constraints as its inputs. It generates a deployment model that is composed by a set of partitions. Each partition is in turn composed of a set of allocated applications and assigned resources. The partitioning problem, including applications and constraints, is modeled as a colored graph. A valid partitioning is a proper vertex coloring. A specially designed algorithm generates this coloring and is able to provide alternative partitions if required. The framework, including the partitioning algorithm, has been successfully used in the development of two industrial use cases: the UPMSat-2 satellite and the control system of a wind-power turbine. The partitioning algorithm has been successfully validated by using a large number of synthetic loads, including complex scenarios with more that 500 applications.

Los programas municipales de ocupaci��n guiada: instrumentos preferentes de habitabilidad b��sica versus la urbanizaci��n informal futura. El caso de Trujillo (Per��)

El crecimiento demogr��fico y el proceso de urbanizaci��n que ha experimentado el planeta en el ��ltimo siglo se ha traducido, en contextos de pobreza, en la generaci��n de tugurios y en el aumento de la poblaci��n viviendo en condiciones de habitabilidad precaria (HaP) fruto de la urbanizaci��n informal. Situaci��n que, seg��n las estimaciones de Naciones Unidas continuar�� teniendo lugar en las pr��ximas d��cadas, especialmente en las ciudades de las regiones menos desarrolladas. Este ha sido el problema espec��fico que se ha querido atender con el presente trabajo: la b��squeda de un instrumento urbano que incida en la reducci��n de las tasas de precariedad habitacional urbana futuras, la b��squeda de instrumentos que eviten que ese aumento de la urbanizaci��n se traduzca en aumento de poblaci��n condenada a vivir en tugurios durante d��cadas. Dicha b��squeda ha tenido lugar en el marco de la teor��a de la Habitabilidad B��sica (HaB) desarrollada por el ICHaBC��tedra UNESCO de Habitabilidad B��sica de la UPM. Una HaB que consiste en la satisfacci��n de las necesidades fundamentales de habitabilidad pero, a su vez, o m��s importante a��n, en una esperanza de mejora y progreso paulatino de esas condiciones elementales entendida como herramienta de desarrollo y lucha contra la pobreza. Como herramienta b��sica, no se trata de ofrecer las condiciones ideales, sino de brindar un camino razonable, que se considera posible, para que miles de millones de personas que viven en HaP o parecen condenadas a tener que hacerlo, puedan acceder a mejores condiciones de vida en tiempos m��s cortos. Entre las pol��ticas habitacionales no convencionales puestas en marcha desde H��bitat I en 1976, las de habilitaci��n urbana progresiva, y m��s en particular, la Ocupaci��n Guiada, resultan ser en contextos de escasez econ��mica, el mejor instrumento para hacer frente a la urbanizaci��n informal, un instrumento paradigm��tico m��nimo preferente de implantaci��n ex novo de HaB. Lo es, por la atenci��n prestada en la elecci��n del suelo y la parcelaci��n, las dos etapas cabecera del proceso, as�� como por los mecanismos implementados para atender la etapa de urbanizaci��n en su fase provisional, y por dejar la ��ltima etapa, la de la edificaci��n de las viviendas, en manos de la poblaci��n. El proceso de urbanizaci��n que se favorece es parecido al de los tugurios y ocupaciones ilegales en lo referente a las etapas y mecanismos de crecimiento. Sin embargo, la diferencia est�� en las condiciones en las que se produce, en los niveles de salubridad y de seguridad, y en la proyecci��n de futuro. El Programa de Ocupaci��n Guiada 'Alto Trujillo' (POG), puesto en marcha por la municipalidad de Trujillo (Per��) entre 1995 y 2006 fue concebido para hacer frente a los procesos de urbanizaci��n informal que estaban teniendo lugar en la ciudad y ha demostrado ser un mecanismo adecuado para garantizar el acceso regulado al suelo, las infraestructuras, los servicios b��sicos y la vivienda en condiciones de fuerte restricci��n econ��mica mediante un cogesti��n acertada entre municipalidad, poblaci��n y dem��s actores del proceso. El POG eligi�� un suelo no vulnerable y en continuidad con el tejido urbano, con la parcelaci��n estableci�� el orden geom��trico del asentamiento y reserv�� los espacios p��blicos destinados a equipamientos, zonas verdes y viario, y fij�� las dimensiones de las parcelas, acompa���� a la poblaci��n en el proceso de ocupaci��n guiada de las mismas, as�� como en el posterior desarrollo progresivo del asentamiento haciendo una fuerte apuesta por lo p��blico, relegando la construcci��n de las viviendas al esfuerzo de los pobladores. Los POG municipales resultan ser un instrumento replicable siempre que se den cinco condiciones: la existencia de un marco institucional adecuado que contemple la descentralizaci��n de competencias, que haya inter��s y continuidad pol��tica en el gobierno local, acceso a suelo urbano disponible y voluntad de co-gesti��n con la poblaci��n. El an��lisis del POG ha permitido elaborar una propuesta de replicabilidad del POG basada en la experiencia de soluciones ya implementadas, que han sido contrastadas emp��ricamente y analizadas para aprender de sus fortalezas, oportunidades, debilidades y amenazas, as�� como de sus aciertos y errores. La estrategia de replicabilidad del POG se plantea como alternativa a la urbanizaci��n informal con mecanismos mejorados para que las ciudades se desarrollen siguiendo unos par��metros m��nimos de HaB y no a trav��s de asentamientos informales que dificulten el progreso futuro de las familias que los habitan y de las mismas ciudades de las que forman parte. Esta propuesta de replicabilidad, que precisa ser adaptada a cada contexto, ten��a una clara vocaci��n: intentar ser instrumento en la regi��n del planeta donde, seg��n las estimaciones, en los pr��ximos treinta a��os el crecimiento demogr��fico y el proceso de urbanizaci��n ser��n m��s fuertes: ��frica Subsahariana. Por ello, con el apoyo de expertos mozambique��os en temas de habitabilidad, se estudi�� la replicabilidad en Mozambique incorporando las medidas necesarias que dar��an respuesta a los condicionantes particulares del pa��s. ABSTRACT The demographic growth and the urbanisation process that the planet has experienced in the last century has turned into the generation of slums and in the increase of population living in conditions of precarious habitability (HaP) result of the informal urbanisation, in contexts of poverty. According to the United Nations estimations, this situation will continue taking place in the next decades, especially in the cities of the least developed regions. The present work has wanted to attend this specific problem by the search of an urban instrument that has an impact on the reduction of the urban future precarious housing rates, a search of instruments that prevent that this urbanisation spread become an increase of population doomed to live in slums during decades. The above mentioned search has taken place in the frame of the Basic Habitability theory (HaB) developed by the ICHaB-C��tedra UNESCO of Basic Habitability of the UPM. HaB consists of the satisfaction of the fundamental habitability needs but, in turn, or still more important, it is the hope of improvement and gradual progress of these elementary conditions. The HaB is understood as a tool of development and fight against poverty. As a basic tool, it does not offer the ideal conditions, but it offers a reasonable way, which is considered to be possible, so that thousands of million persons who live in HaP or that seem to be doomed to have to do it, could gain access to better living conditions in shorter times. Between the non conventional housing policies started up from Habitat I in 1976, those of urban progressive fitting out, and more especially, the Guided Occupation, has turned out to be, in contexts of economic shortage, the best instrument to face the informal urbanisation, a preferential and minimum paradigmatic instrument of ex-novo HaB implementation. It is so due to the attention given to the appropriate site selection and the land allotment, both headboard stages of the process, as well as to the mechanisms implemented to attend the urbanisation stage in its provisional phase, and to leave the last stage, the building process, in population hands. The urbanisation process that is favored is similar to that of the slums and squatting in what concerns the stages and mechanisms of growth. Nevertheless, the difference is in the conditions in which it takes place, in the levels of health and safety, and in the future projection. The Program of Guided Occupation 'Alto Trujillo' (PGO), turned on by the Provincial City Hall of Trujillo (Peru) between 1995 and 2006, was conceived to face the processes of informal urbanisation that took place in the city and it has demonstrated to be a mechanism adapted to guarantee the regulated access to soil, infrastructures, basic services and housing in conditions of strong economic restriction by means of a succeeded co-management between municipality, population and other process actors. The PGO chose a non vulnerable soil in continuity with the urban fabric, with the land allotment established the settlement geometric order, reserved the public spaces allocated for urban facilities, green spaces and streets, and fixed the plot dimensions, accompanied the population in the plot guided occupation process, as well as in the later progressive settlement development betting strongly for the public components, relegating the housing construction to the settlers effort. The municipal PGO turn out to be a replicable instrument under five conditions: the existence of an institutional suitable frame that contemplates the decentralization competitions, interest and political continuity in the local government, access to urban available soil and will of co-management with the population. The PGO analysis has allowed to elaborate a replicability proposal of the PGO based on the experience of the already implemented solutions, which have been empirically confirmed and analyzed to learn of its strengths, opportunities, weaknesses and threats, as well as of its successes and mistakes. The replicability strategy of the PGO is considered an alternative to the informal urbanisation with improved mechanisms in order that the cities can develop following a few HaB's minimal parameters, but not through informal settlements that would make difficult the families future progress and that of the cities where they live. This replicability proposal, that needs to be adapted to every context, had a clear vocation: try to be an instrument in the region of the planet where, according to the estimations, in the next thirty years the demographic growth and the urbanisation process will be stronger: Sub-Saharan Africa. Therefore, with the support of Mozambican experts in habitability topics, the replicability was studied in Mozambique incorporating the necessary measures that would give response to the country's determinants.

Opening of a monomer-monomer interface of the trimeric bacteriophage T4-coded GP45 sliding clamp is required for clamp loading onto DNA

The replication system of bacteriophage T4 uses a trimeric ring-shaped processivity clamp (gp45) to tether the replication polymerase (gp43) to the template-primer DNA. This ring is placed onto the DNA by an ATPase-driven clamp-loading complex (gp44/62) where it then transfers, in closed form, to the polymerase. It generally has been assumed that one of the functions of the loading machinery is to open the clamp to place it around the DNA. However, the mechanism by which this occurs has not been fully defined. In this study we design and characterize a double-mutant gp45 protein that contains pairs of cysteine residues located at each monomer-monomer interface of the trimeric clamp. This mutant protein is functionally equivalent to wild-type gp45. However, when all three monomer-monomer interfaces are tethered by covalent crosslinks formed (reversibly or irreversibly) between the cysteine pairs these closed clamps can no longer be loaded onto the DNA nor onto the polymerase, effectively eliminating processive strand-displacement DNA synthesis. Analysis of the individual steps of the clamp-loading process shows that the ATPase-dependent interactions between the clamp and the clamp loader that precede DNA binding are hyperstimulated by the covalently crosslinked ring, suggesting that binding of the closed ring induces a futile, ATP-driven, ring-opening cycle. These findings and others permit further characterization and ordering of the steps involved in the T4 clamp-loading process.

Proton transfer from the bulk to the bound ubiquinone QB of the reaction center in chromatophores of Rhodobacter sphaeroides: Retarded conveyance by neutral water

The mechanism of proton transfer from the bulk into the membrane protein interior was studied. The light-induced reduction of a bound ubiquinone molecule QB by the photosynthetic reaction center is accompanied by proton trapping. We used kinetic spectroscopy to measure (i) the electron transfer to QB (at 450 nm), (ii) the electrogenic proton delivery from the surface to the QB site (by electrochromic carotenoid response at 524 nm), and (iii) the disappearance of protons from the bulk solution (by pH indicators). The electron transfer to QB��� and the proton-related electrogenesis proceeded with the same time constant of ���100 ��s (at pH 6.2), whereas the alkalinization in the bulk was distinctly delayed (�� ��� 400 ��s). We investigated the latter reaction as a function of the pH indicator concentration, the added pH buffers, and the temperature. The results led us to the following conclusions: (i) proton transfer from the surface-located acidic groups into the QB site followed the reduction of QB without measurable delay; (ii) the reprotonation of these surface groups by pH indicators and hydronium ions was impeded, supposedly, because of their slow diffusion in the surface water layer; and (iii) as a result, the protons were slowly donated by neutral water to refill the proton vacancies at the surface. It is conceivable that the same mechanism accounts for the delayed relaxation of the surface pH changes into the bulk observed previously with bacteriorhodopsin membranes and thylakoids. Concerning the coupling between proton pumps in bioenergetic membranes, our results imply a tendency for the transient confinement of protons at the membrane surface.

Ascorbate recycling in human neutrophils: Induction by���bacteria

Ascorbate (vitamin C) recycling occurs when extracellular ascorbate is oxidized, transported as dehydroascorbic acid, and reduced intracellularly to ascorbate. We investigated microorganism induction of ascorbate recycling in human neutrophils and in microorganisms themselves. Ascorbate recycling was determined by measuring intracellular ascorbate accumulation. Ascorbate recycling in neutrophils was induced by both Gram-positive and Gram-negative pathogenic bacteria, and the fungal pathogen Candida albicans. Induction of recycling resulted in as high as a 30-fold increase in intracellular ascorbate compared with neutrophils not exposed to microorganisms. Recycling occurred at physiologic concentrations of extracellular ascorbate within 20 min, occurred over a 100-fold range of effector/target ratios, and depended on oxidation of extracellular ascorbate to dehydroascorbic acid. Ascorbate recycling did not occur in bacteria nor in C. albicans. Ascorbate did not enter microorganisms, and dehydroascorbic acid entry was less than could be accounted for by diffusion. Because microorganism lysates reduced dehydroascorbic acid to ascorbate, ascorbate recycling was absent because of negligible entry of the substrate dehydroascorbic acid. Because ascorbate recycling occurs in human neutrophils but not in microorganisms, it may represent a eukaryotic defense mechanism against oxidants with possible clinical implications.

Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence

Several microbial systems have been shown to yield advantageous mutations in slowly growing or nongrowing cultures. In one assay system, the stationary-phase mutation mechanism differs from growth-dependent mutation, demonstrating that the two are different processes. This system assays reversion of a lac frameshift allele on an F��� plasmid in Escherichia coli. The stationary-phase mutation mechanism at lac requires recombination proteins of the RecBCD double-strand-break repair system and the inducible error-prone DNA polymerase IV, and the mutations are mostly ���1 deletions in small mononucleotide repeats. This mutation mechanism is proposed to occur by DNA polymerase errors made during replication primed by recombinational double-strand-break repair. It has been suggested that this mechanism is confined to the F plasmid. However, the cells that acquire the adaptive mutations show hypermutation of unrelated chromosomal genes, suggesting that chromosomal sites also might experience recombination protein-dependent stationary-phase mutation. Here we test directly whether the stationary-phase mutations in the bacterial chromosome also occur via a recombination protein- and pol IV-dependent mechanism. We describe an assay for chromosomal mutation in cells carrying the F��� lac. We show that the chromosomal mutation is recombination protein- and pol IV-dependent and also is associated with general hypermutation. The data indicate that, at least in these male cells, recombination protein-dependent stationary-phase mutation is a mechanism of general inducible genetic change capable of affecting genes in the bacterial chromosome.

Complex dynamics of multilocus systems subjected to cyclical selection.

Earlier we have shown that oscillations with a long period ("supercycles") may arise in two-locus systems experiencing cyclical selection with a short period. However, this mode of complex limiting behavior appeared to be possible for narrow ranges of parameters. Here we demonstrate that a multilocus system subjected to stabilizing selection with cyclically moving optimum can generate ubiquitous complex limiting behavior including supercycles, T-cycles, and chaotic-like phenomena. This mode of multilocus dynamics far exceeds the potential attainable under ordinary selection models resulting in simple behavior. It may represent a novel evolutionary mechanism increasing genetic diversity over long-term time periods.

A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA.

RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.

A general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions.

When NMR hydrogen exchange was used previously to monitor the kinetics of RNase A unfolding, some peptide NH protons were found to show EX2 exchange (detected by base catalysis) in addition to the expected EX1 exchange, whose rate is limited by the kinetic unfolding process. In earlier work, two groups showed independently that a restricted two-process model successfully fits published hydrogen exchange rates of native RNase A in the range 0-0.7 M guanidinium chloride. We find that this model predicts properties that are very different from the observed properties of the EX2 exchange reactions of RNase A in conditions where guanidine-induced unfolding takes place. The model predicts that EX2 exchange should be too fast to measure by the technique used, whereas it is readily measurable. Possible explanations for the contradiction are considered here, and we show that removing the restriction from the earlier two-process model is sufficient to resolve the contradiction; instead of specifying that exchange caused by global unfolding occurs by the EX2 mechanism, we allow it to occur by the general mechanism, which includes both the EX1 and EX2 cases. It is logical to remove this restriction because global unfolding of RNase A is known to give rise to EX1 exchange in these unfolding conditions. Resolving the contradiction makes it possible to determine whether populated unfolding intermediates contribute to the EX2 exchange, and this question is considered elsewhere. The results and simulations indicate that moderate or high denaturant concentrations readily give rise to EX1 exchange in native proteins. Earlier studies showed that hydrogen exchange in native proteins typically occurs by the EX2 mechanism but that high temperatures or pH values above 7 may give rise to EX1 exchange. High denaturant concentrations should be added to the list of variables likely to cause EX1 exchange.

Control of cell division in Escherichia coli: regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction.

The conditioning of culture medium by the production of growth-regulatory substances is a well-established phenomenon with eukaryotic cells. It has recently been shown that many prokaryotes are also capable of modulating growth, and in some cases sensing cell density, by production of extracellular signaling molecules, thereby allowing single celled prokaryotes to function in some respects as multicellular organisms. As Escherichia coli shifts from exponential growth to stationary growth, many changes occur, including cell division leading to formation of short minicells and expression of numerous genes not expressed in exponential phase. An understanding of the coordination between the morphological changes associated with cell division and the physiological and metabolic changes is of fundamental importance to understanding regulation of the prokaryotic cell cycle. The ftsQA genes, which encode functions required for cell division in E. coli, are regulated by promoters P1 and P2, located upstream of the ftsQ gene. The P1 promoter is rpoS-stimulated and the second, P2, is regulated by a member of the LuxR subfamily of transcriptional activators, SdiA, exhibiting features characteristic of an autoinduction (quorum sensing) mechanism. The activity of SdiA is potentiated by N-acyl-homoserine lactones, which are the autoinducers of luciferase synthesis in luminous marine bacteria as well as of pathogenesis functions in several pathogenic bacteria. A compound(s) produced by E. coli itself during growth in Luria Broth stimulates transcription from P2 in an SdiA-dependent process. Another substance(s) enhances transcription of rpoS and (perhaps indirectly) of ftsQA via promoter P1. It appears that this bimodal control mechanism may comprise a fail-safe system, such that transcription of the ftsQA genes may be properly regulated under a variety of different environmental and physiological conditions.

Commonplace book, October 29, 1728-January 15, 1735

The small hardcover volume contains excerpts copied by John Winthrop beginning at the age of thirteen as a freshman at Harvard College. Winthrop���s own description of this book as ���a book of Extracts from many Authors��� is accurate, as it includes neither personal information about Winthrop nor reflections on what he read. With the exception of occasional notations indicating the date he finished reading particular books, the volume consists of passages he copied from a wide range of sources. It begins with an index of the various sections of the book (History, Poetry, Miscellanies, Geography, Divinity, History, Philosophy, Philosophy, Miscellanies, Poetry, Divinity, Philosophy) and ends with an index of the extracts' authors.

Turkey after the start of negotiations with the European Union - foreign relations and the domestic situation, Part I. OSW Report, June 2007

The start of accession negotiations between Ankara and the EU is vital for the future of both Turkey and the Union, including Poland as its member state, as well as for the geopolitical situation in Eurasia (the Black Sea region, Caucasus, Central Asia and the Middle East). Appreciating the significance of these issues, the Centre for Eastern Studies in early 2005 decided to launch a project entitled "Turkey after the start of negotiations with the European Union - foreign relations and the domestic situation". The goal of this project is to present, within the context of accession negotiations, Turkey's greatest internal challenges as well as Ankara's relations with its neighbour regions, the EU and the USA. This Report is the first of three which will be published as part of the project. The Report includes texts on Turkish-US relations since 2003, major political and social challenges on Turkey's path towards the EU and the current condition of the Turkish economy. The Report was developed between July 2005 and November 2006, over which time CES workers and associates searched for publicly available materials in Poland, Turkey and EU countries, and went on three research trips to Turkey, where they met local researchers, analysts, politicians and officials. The authors of the Report would like to express their gratitude to everyone who have shared their opinions with them, and to the Polish Embassy in Ankara, especially to Ambassador Grzegorz Michalski and Minister Andrzej Ananicz for their expert support and assistance in the authors' work on this Report. This Report does not present the official stance of the Polish government on the issues discussed therein; instead it reflects the personal views of its authors, who have made their best efforts to ensure that their work is reliable.

The WTO and Female Labor Rights in Developing Countries. IES WORKING PAPER 3/2008

The impacts of WTO on women���s labour rights in the developing countries have been raised to the international agenda by various nongovernmental organizations. On the one hand it is assumed that international trade policies are gender neutral. On the other hand a number of authors hold the view that the negative impacts of WTO policies are more pronounced on female than male workers. This paper takes a critical look at these claims. It argues that the impact of the WTO system, the driving force of trade liberalization, on women���s labour rights in the developing countries is a complicated issue, because the effects have been both negative and positive. In support of this claim, this paper first briefly reviews the international framework for the protection of women���s labour rights. Next, the WTO agreements and policies are analysed insofar as they are relevant for the protection of women���s labour rights. The analysis covers, for example, the use of the trade policy review mechanism and restrictions of trade on grounds of violation of public morals.. Finally, a case study is conducted on the situation of female workers in Bangladesh and Pakistan, countries that have recently undergone a liberalization of trade in the textiles and clothing sectors. It is concluded that the increase of international trade in the developing countries has created many work opportunities for women, helped them to become more independent and allowed them to participate in the society more actively. However, it is at the same time posited that in order to comply with its own objectives of raising standards of living and full employment, the WTO should engage itself in active policies to overcome the negative aspects of trade on female workers in the developing countries.

Post-war economic policy and planning. Preliminary report of the Special committee on post-war economic policy and planning, pursuant to S.Res.102, a resolution creating a Special committee on post-war economic policy and planning ... [and Report[s]].

Submitted by Mr. George.

O PAPEL DA C��MARA T��CNICA DE PESCA DO COMIT�� DE BACIA HIDROGR��FICA LAGOS S��O JO��O NA GEST��O DA PESCA ARTESANAL NA LAGOA DE ARARUAMA

Este trabalho apresenta um estudo de caso sobre o papel da C��mara T��cnica de Pesca (CTP) do Cons��rcio Intermunicipal Lagos S��o Jo��o (CILSJ) na media����o de conflitos de gest��o da pesca artesanal na regi��o da Lagoa de Araruama (LA). A CTP �� gerida pelas prioridades da Pol��tica Nacional de Recursos H��dricos (PNRH), preservacionista, em oposi����o a Pol��tica Nacional de Desenvolvimento Sustent��vel da Atividade Pesqueira (PNDSAP), com fins de explora����o econ��mica. Na Bacia Hidrogr��fica Lagos S��o Jo��o, o CILSJ, prioriza as a����es de conserva����o e manuten����o dos corpos de ��gua para o abastecimento, deixando em segundo plano a recupera����o dos estu��rios em que lan��a o esgoto tratado e o n��o tratado, justamente os locais onde ocorre a pesca. O sujeito da pesquisa foi a representa����o dos pescadores, que s��o os presidentes das col��nias. O levantamento de dados ocorreu por meio de entrevistas, observa����o direta, observa����o participante, documentos, filmes, fotografias, depoimentos, considerando tamb��m os atores da gest��o p��blica da pesca local, estadual e federal. As entrevistas foram examinadas com base em an��lise textual. A abordagem da pesquisa �� qualitativa. A pesca artesanal praticada na localidade �� de pequena escala, se utiliza de embarca����es mi��das, o trabalho ocorre em regime de companha e/ou familiar. O co-manejo �� a metodologia de gest��o dos recursos comuns mais utilizadas na atualidade na pesca artesanal. Os dados revelaram que o modelo de co-manejo da CTP n��o �� o mais adequado para mediar os conflitos da pesca na localidade. Este estudo constatou que existe a uni��o das col��nias por meio da CTP, mas mesmo assim, o mecanismo CTP, n��o permite que maiores conquistas sejam alcan��adas pelos pescadores, tendo em vista que o modelo de co-manejo �� apenas consultivo, em que o poder p��blico consulta, mas toma a decis��o de forma aut��noma sem compartilhar o poder de gest��o, desse modo n��o h�� o empoderamento por parte dos pescadores. Assim, se faz urgente a substitui����o do sistema de co-manejo exercido pela CTP, por outro que possibilite maior participa����o dos pescadores e n��o s�� das suas representa����es; autonomia de gest��o dos pescadores; possibilidade de financiamento al��m das atividades de preserva����o, mas tamb��m de desenvolvimento econ��mico da pesca. Outros modelos de co-gest��o pass��veis de substituir a CTP s��o a Reserva Extrativista (RESEX), a Reserva de Desenvolvimento Sustent��vel ou F��rum de Pesca tendo em vista serem esses os modelos de co-manejo mais bem sucedidos no pa��s e inclusive em parte da regi��o, a RESEX de Arraial do Cabo. A constata����o desta pesquisa do papel exercido pela CTP no que tange o co-manejo na LA �� compat��vel com as defici��ncias dos modelos de co-manejo da pesca no Brasil, com menor empoderamento dos pescadores diante do poder p��blico e da pr��pria submiss��o da gest��o p��blica da pesca diante da gest��o p��blica do ambiente. Apesar de haver certa produ����o acad��mica sobre a pesca, a literatura sobre a gest��o da pesca na localidade da LA �� escassa, o que dificulta o desenvolvimento da sustentabilidade pesqueira e da aplica����o de qualquer plano de manejo e indica a urg��ncia do desenvolvimento de maiores investiga����es, no que este trabalho procura oferecer alguma contribui����o.