Cromosomal location of four genes encoding Class III peroxidases in wheat

In a previous work, deduced amino acid sequences from twenty wheat peroxidase genes were assigned to seven groups designated as TaPrx108 to TaPrx114. Some of these apoplastic peroxidases have previously shown to play different roles in the plant defense responses to infection by the cereal cyst nematode Heterodera avenae. In the present study, PCR marker analysis using Sears’s aneuploid wheat lines cv. ‘Chinese Spring’ was used to locate four genes encoding peroxidase isozymes. The TaPrx111-A, TaPrx112-D and TaPrx113-F genes were located on the short arm of chromosome 2B and the TaPrx109-C on the long arm of chromosome 1B. These results would agree with the synteny between wheat and rice chromosomes previously established in other studies.

Fault isolation schemes for a class of continuous-time stochastic dynamical systems

In this paper a new method for fault isolation in a class of continuous-time stochastic dynamical systems is proposed. The method is framed in the context of model-based analytical redundancy, consisting in the generation of a residual signal by means of a diagnostic observer, for its posterior analysis. Once a fault has been detected, and assuming some basic a priori knowledge about the set of possible failures in the plant, the isolation task is then formulated as a type of on-line statistical classification problem. The proposed isolation scheme employs in parallel different hypotheses tests on a statistic of the residual signal, one test for each possible fault. This isolation method is characterized by deriving for the unidimensional case, a sufficient isolability condition as well as an upperbound of the probability of missed isolation. Simulation examples illustrate the applicability of the proposed scheme.

MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Steady state analysis of a storage integrated solar thermophotovoltaic (SISTPV) system

This paper presents the theoretical analysis of a storage integrated solar thermophotovoltaic (SISTPV) system operating in steady state. These systems combine thermophotovoltaic (TPV) technology and high temperature thermal storage phase-change materials (PCM) in the same unit, providing a great potential in terms of efficiency, cost reduction and storage energy density. The main attraction in the proposed system is its simplicity and modularity compared to conventional Concentrated Solar Power (CSP) technologies. This is mainly due to the absence of moving parts. In this paper we analyze the use of Silicon as the phase change material (PCM). Silicon is an excellent candidate because of its high melting point (1680 K) and its very high latent heat of fusion of 1800 kJ/kg, which is about ten times greater than the conventional PCMs like molten salts. For a simple system configuration, we have demonstrated that overall conversion efficiencies up to ?35% are approachable. Although higher efficiencies are expected by incorporating more advanced devices like multijunction TPV cells, narrow band selective emitters or adopting near-field TPV configurations as well as by enhancing the convective/conductive heat transfer within the PCM. In this paper, we also discuss about the optimum system configurations and provide the general guidelines for designing these systems. Preliminary estimates of night time operations indicate it is possible to achieve over 10 h of operation with a relatively small quantity of Silicon.

Linear latent force models using Gaussian Processes

Purely data-driven approaches for machine learning present difficulties when data are scarce relative to the complexity of the model or when the model is forced to extrapolate. On the other hand, purely mechanistic approaches need to identify and specify all the interactions in the problem at hand (which may not be feasible) and still leave the issue of how to parameterize the system. In this paper, we present a hybrid approach using Gaussian processes and differential equations to combine data-driven modeling with a physical model of the system. We show how different, physically inspired, kernel functions can be developed through sensible, simple, mechanistic assumptions about the underlying system. The versatility of our approach is illustrated with three case studies from motion capture, computational biology, and geostatistics.

Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis

The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm3 and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers.

Numerical analysis of shell and spatial structures

Since the advent of the computer into the engineering field, the application of the numerical methods to the solution of engineering problems has grown very rapidly. Among the different computer methods of structural analysis the Finite Element (FEM) has been predominantly used. Shells and space structures are very attractive and have been constructed to solve a large variety of functional problems (roofs, industrial building, aqueducts, reservoirs, footings etc). In this type of structures aesthetics, structural efficiency and concept play a very important role. This class of structures can be divided into three main groups, namely continuous (concrete) shells, space frames and tension (fabric, pneumatic, cable etc )structures. In the following only the current applications of the FEM to the analysis of continuous shell structures will be discussed. However, some of the comments on this class of shells can be also applied to some extend to the others, but obviously specific computational problems will be restricted to the continuous shells. Different aspects, such as, the type of elements,input-output computational techniques etc, of the analysis of shells by the FEM will be described below. Clearly, the improvements and developments occurring in general for the FEM since its first appearance in the fifties have had a significative impact on the particular class of structures under discussion.

Improved static analysis and verification of energy consumption and other resources via abstract interpretation

Resource analysis aims at inferring the cost of executing programs for any possible input, in terms of a given resource, such as the traditional execution steps, time ormemory, and, more recently energy consumption or user defined resources (e.g., number of bits sent over a socket, number of database accesses, number of calls to particular procedures, etc.). This is performed statically, i.e., without actually running the programs. Resource usage information is useful for a variety of optimization and verification applications, as well as for guiding software design. For example, programmers can use such information to choose different algorithmic solutions to a problem; program transformation systems can use cost information to choose between alternative transformations; parallelizing compilers can use cost estimates for granularity control, which tries to balance the overheads of task creation and manipulation against the benefits of parallelization. In this thesis we have significatively improved an existing prototype implementation for resource usage analysis based on abstract interpretation, addressing a number of relevant challenges and overcoming many limitations it presented. The goal of that prototype was to show the viability of casting the resource analysis as an abstract domain, and howit could overcome important limitations of the state-of-the-art resource usage analysis tools. For this purpose, it was implemented as an abstract domain in the abstract interpretation framework of the CiaoPP system, PLAI.We have improved both the design and implementation of the prototype, for eventually allowing an evolution of the tool to the industrial application level. The abstract operations of such tool heavily depend on the setting up and finding closed-form solutions of recurrence relations representing the resource usage behavior of program components and the whole program as well. While there exist many tools, such as Computer Algebra Systems (CAS) and libraries able to find closed-form solutions for some types of recurrences, none of them alone is able to handle all the types of recurrences arising during program analysis. In addition, there are some types of recurrences that cannot be solved by any existing tool. This clearly constitutes a bottleneck for this kind of resource usage analysis. Thus, one of the major challenges we have addressed in this thesis is the design and development of a novel modular framework for solving recurrence relations, able to combine and take advantage of the results of existing solvers. Additionally, we have developed and integrated into our novel solver a technique for finding upper-bound closed-form solutions of a special class of recurrence relations that arise during the analysis of programs with accumulating parameters. Finally, we have integrated the improved resource analysis into the CiaoPP general framework for resource usage verification, and specialized the framework for verifying energy consumption specifications of embedded imperative programs in a real application, showing the usefulness and practicality of the resulting tool.---ABSTRACT---El Análisis de recursos tiene como objetivo inferir el coste de la ejecución de programas para cualquier entrada posible, en términos de algún recurso determinado, como pasos de ejecución, tiempo o memoria, y, más recientemente, el consumo de energía o recursos definidos por el usuario (por ejemplo, número de bits enviados a través de un socket, el número de accesos a una base de datos, cantidad de llamadas a determinados procedimientos, etc.). Ello se realiza estáticamente, es decir, sin necesidad de ejecutar los programas. La información sobre el uso de recursos resulta muy útil para una gran variedad de aplicaciones de optimización y verificación de programas, así como para asistir en el diseño de los mismos. Por ejemplo, los programadores pueden utilizar dicha información para elegir diferentes soluciones algorítmicas a un problema; los sistemas de transformación de programas pueden utilizar la información de coste para elegir entre transformaciones alternativas; los compiladores paralelizantes pueden utilizar las estimaciones de coste para realizar control de granularidad, el cual trata de equilibrar el coste debido a la creación y gestión de tareas, con los beneficios de la paralelización. En esta tesis hemos mejorado de manera significativa la implementación de un prototipo existente para el análisis del uso de recursos basado en interpretación abstracta, abordando diversos desafíos relevantes y superando numerosas limitaciones que éste presentaba. El objetivo de dicho prototipo era mostrar la viabilidad de definir el análisis de recursos como un dominio abstracto, y cómo se podían superar las limitaciones de otras herramientas similares que constituyen el estado del arte. Para ello, se implementó como un dominio abstracto en el marco de interpretación abstracta presente en el sistema CiaoPP, PLAI. Hemos mejorado tanto el diseño como la implementación del mencionado prototipo para posibilitar su evolución hacia una herramienta utilizable en el ámbito industrial. Las operaciones abstractas de dicha herramienta dependen en gran medida de la generación, y posterior búsqueda de soluciones en forma cerrada, de relaciones recurrentes, las cuales modelizan el comportamiento, respecto al consumo de recursos, de los componentes del programa y del programa completo. Si bien existen actualmente muchas herramientas capaces de encontrar soluciones en forma cerrada para ciertos tipos de recurrencias, tales como Sistemas de Computación Algebraicos (CAS) y librerías de programación, ninguna de dichas herramientas es capaz de tratar, por sí sola, todos los tipos de recurrencias que surgen durante el análisis de recursos. Existen incluso recurrencias que no las puede resolver ninguna herramienta actual. Esto constituye claramente un cuello de botella para este tipo de análisis del uso de recursos. Por lo tanto, uno de los principales desafíos que hemos abordado en esta tesis es el diseño y desarrollo de un novedoso marco modular para la resolución de relaciones recurrentes, combinando y aprovechando los resultados de resolutores existentes. Además de ello, hemos desarrollado e integrado en nuestro nuevo resolutor una técnica para la obtención de cotas superiores en forma cerrada de una clase característica de relaciones recurrentes que surgen durante el análisis de programas lógicos con parámetros de acumulación. Finalmente, hemos integrado el nuevo análisis de recursos con el marco general para verificación de recursos de CiaoPP, y hemos instanciado dicho marco para la verificación de especificaciones sobre el consumo de energía de programas imperativas embarcados, mostrando la viabilidad y utilidad de la herramienta resultante en una aplicación real.

Multiscale analysis of the mechanical behavior of needle-punched nonwoven fabrics

Los fieltros son una familia de materiales textiles constituidos por una red desordenada de fibras conectadas por medio de enlaces térmicos, químicos o mecánicos. Presentan menor rigidez y resistencia (al igual que un menor coste de procesado) que sus homólogos tejidos, pero mayor deformabilidad y capacidad de absorción de energía. Los fieltros se emplean en diversas aplicaciones en ingeniería tales como aislamiento térmico, geotextiles, láminas ignífugas, filtración y absorción de agua, impacto balístico, etc. En particular, los fieltros punzonados fabricados con fibras de alta resistencia presentan una excelente resistencia frente a impacto balístico, ofreciendo las mismas prestaciones que los materiales tejidos con un tercio de la densidad areal. Sin embargo, se sabe muy poco acerca de los mecanismos de deformación y fallo a nivel microscópico, ni sobre como influyen en las propiedades mecánicas del material. Esta carencia de conocimiento dificulta la optimización del comportamiento mecánico de estos materiales y también limita el desarrollo de modelos constitutivos basados en mecanismos físicos, que puedan ser útiles en el diseño de componentes estructurales. En esta tesis doctoral se ha llevado a cabo un estudio minucioso con el fin de determinar los mecanismos de deformación y las propiedades mecánicas de fieltros punzonados fabricados con fibras de polietileno de ultra alto peso molecular. Los procesos de deformación y disipación de energía se han caracterizado en detalle por medio de una combinación de técnicas experimentales (ensayos mecánicos macroscópicos a velocidades de deformación cuasi-estáticas y dinámicas, impacto balístico, ensayos de extracción de una o múltiples fibras, microscopía óptica, tomografía computarizada de rayos X y difracción de rayos X de gran ángulo) que proporcionan información de los mecanismos dominantes a distintas escalas. Los ensayos mecánicos macroscópicos muestran que el fieltro presenta una resistencia y ductilidad excepcionales. El estado inicial de las fibras es curvado, y la carga se transmite por el fieltro a través de una red aleatoria e isótropa de nudos creada por el proceso de punzonamiento, resultando en la formación de una red activa de fibra. La rotación y el estirado de las fibras activas es seguido por el deslizamiento y extracción de la fibra de los puntos de anclaje mecánico. La mayor parte de la resistencia y la energía disipada es proporcionada por la extracción de las fibras activas de los nudos, y la fractura final tiene lugar como consecuencia del desenredo total de la red en una sección dada donde la deformación macroscópica se localiza. No obstante, aunque la distribución inicial de la orientación de las fibras es isótropa, las propiedades mecánicas resultantes (en términos de rigidez, resistencia y energía absorbida) son muy anisótropas. Los ensayos de extracción de múltiples fibras en diferentes orientaciones muestran que la estructura de los nudos conecta más fibras en la dirección transversal en comparación con la dirección de la máquina. La mejor interconectividad de las fibras a lo largo de la dirección transversal da lugar a una esqueleto activo de fibras más denso, mejorando las propiedades mecánicas. En términos de afinidad, los fieltros deformados a lo largo de la dirección transversal exhiben deformación afín (la deformación macroscópica transfiere directamente a las fibras por el material circundante), mientras que el fieltro deformado a lo largo de la dirección de la máquina presenta deformación no afín, y la mayor parte de la deformación macroscópica no es transmitida a las fibras. A partir de estas observaciones experimentales, se ha desarrollado un modelo constitutivo para fieltros punzonados confinados por enlaces mecánicos. El modelo considera los efectos de la deformación no afín, la conectividad anisótropa inducida durante el punzonamiento, la curvatura y re-orientación de la fibra, así como el desenredo y extracción de la fibra de los nudos. El modelo proporciona la respuesta de un mesodominio del material correspondiente al volumen asociado a un elemento finito, y se divide en dos bloques. El primer bloque representa el comportamiento de la red y establece la relación entre el gradiente de deformación macroscópico y la respuesta microscópica, obtenido a partir de la integración de la respuesta de las fibras en el mesodominio. El segundo bloque describe el comportamiento de la fibra, teniendo en cuenta las características de la deformación de cada familia de fibras en el mesodominio, incluyendo deformación no afín, estiramiento, deslizamiento y extracción. En la medida de lo posible, se ha asignado un significado físico claro a los parámetros del modelo, por lo que se pueden identificar por medio de ensayos independientes. Las simulaciones numéricas basadas en el modelo se adecúan a los resultados experimentales de ensayos cuasi-estáticos y balísticos desde el punto de vista de la respuesta mecánica macroscópica y de los micromecanismos de deformación. Además, suministran información adicional sobre la influencia de las características microstructurales (orientación de la fibra, conectividad de la fibra anisótropa, afinidad, etc) en el comportamiento mecánico de los fieltros punzonados. Nonwoven fabrics are a class of textile material made up of a disordered fiber network linked by either thermal, chemical or mechanical bonds. They present lower stiffness and strength (as well as processing cost) than the woven counterparts but much higher deformability and energy absorption capability and are used in many different engineering applications (including thermal insulation, geotextiles, fireproof layers, filtration and water absorption, ballistic impact, etc). In particular, needle-punched nonwoven fabrics manufactured with high strength fibers present an excellent performance for ballistic protection, providing the same ballistic protection with one third of the areal weight as compared to dry woven fabrics. Nevertheless, very little is known about their deformation and fracture micromechanisms at the microscopic level and how they contribute to the macroscopic mechanical properties. This lack of knowledge hinders the optimization of their mechanical performance and also limits the development of physically-based models of the mechanical behavior that can be used in the design of structural components with these materials. In this thesis, a thorough study was carried out to ascertain the micromechanisms of deformation and the mechanical properties of a needle-punched nonwoven fabric made up by ultra high molecular weight polyethylene fibers. The deformation and energy dissipation processes were characterized in detail by a combination of experimental techniques (macroscopic mechanical tests at quasi-static and high strain rates, ballistic impact, single fiber and multi fiber pull-out tests, optical microscopy, X-ray computed tomography and wide angle X-ray diffraction) that provided information of the dominant mechanisms at different length scales. The macroscopic mechanical tests showed that the nonwoven fabric presented an outstanding strength and energy absorption capacity. It was found that fibers were initially curved and the load was transferred within the fabric through the random and isotropic network of knots created by needlepunching, leading to the formation of an active fiber network. Uncurling and stretching of the active fibers was followed by fiber sliding and pull-out from the entanglement points. Most of the strength and energy dissipation was provided by the extraction of the active fibers from the knots and final fracture occurred by the total disentanglement of the fiber network in a given section at which the macroscopic deformation was localized. However, although the initial fiber orientation distribution was isotropic, the mechanical properties (in terms of stiffness, strength and energy absorption) were highly anisotropic. Pull-out tests of multiple fibers at different orientations showed that structure of the knots connected more fibers in the transverse direction as compared with the machine direction. The better fiber interconnection along the transverse direction led to a denser active fiber skeleton, enhancing the mechanical response. In terms of affinity, fabrics deformed along the transverse direction essentially displayed affine deformation {i.e. the macroscopic strain was directly transferred to the fibers by the surrounding fabric, while fabrics deformed along the machine direction underwent non-affine deformation, and most of the macroscopic strain was not transferred to the fibers. Based on these experimental observations, a constitutive model for the mechanical behavior of the mechanically-entangled nonwoven fiber network was developed. The model accounted for the effects of non-affine deformation, anisotropic connectivity induced by the entanglement points, fiber uncurling and re-orientation as well as fiber disentanglement and pull-out from the knots. The model provided the constitutive response for a mesodomain of the fabric corresponding to the volume associated to a finite element and is divided in two blocks. The first one was the network model which established the relationship between the macroscopic deformation gradient and the microscopic response obtained by integrating the response of the fibers in the mesodomain. The second one was the fiber model, which took into account the deformation features of each set of fibers in the mesodomain, including non-affinity, uncurling, pull-out and disentanglement. As far as possible, a clear physical meaning is given to the model parameters, so they can be identified by means of independent tests. The numerical simulations based on the model were in very good agreement with the experimental results of in-plane and ballistic mechanical response of the fabrics in terms of the macroscopic mechanical response and of the micromechanisms of deformation. In addition, it provided additional information about the influence of the microstructural features (fiber orientation, anisotropic fiber connectivity, affinity) on the mechanical performance of mechanically-entangled nonwoven fabrics.

Molecular analysis of CaMnt1p, a mannosyl transferase important for adhesion and virulence of Candida albicans

There is an immediate need for identification of new antifungal targets in opportunistic pathogenic fungi like Candida albicans. In the past, efforts have focused on synthesis of chitin and glucan, which confer mechanical strength and rigidity upon the cell wall. This paper describes the molecular analysis of CaMNT1, a gene involved in synthesis of mannoproteins, the third major class of macromolecule found in the cell wall. CaMNT1 encodes an α-1,2-mannosyl transferase, which adds the second mannose residue in a tri-mannose oligosaccharide structure which represents O-linked mannan in C. albicans. The deduced amino acid sequence suggests that CaMnt1p is a type II membrane protein residing in a medial Golgi compartment. The absence of CaMnt1p reduced the ability of C. albicans cells to adhere to each other, to human buccal epithelial cells, and to rat vaginal epithelial cells. Both heterozygous and homozygous Camnt1 null mutants of C. albicans showed strong attenuation of virulence in guinea pig and mouse models of systemic candidosis, which, in guinea pigs, could be attributed to a decreased ability to reach and/or adhere internal organs. Therefore, correct CaMnt1p-mediated O-linked mannosylation of proteins is critical for adhesion and virulence of C. albicans.

Diversification, expression, and γδ T cell recognition of evolutionarily distant members of the MIC family of major histocompatibility complex class I-related molecules

Distant relatives of major histocompatibility complex (MHC) class I molecules, human MICA and MICB, function as stress-induced antigens that are broadly recognized by intestinal epithelial γδ T cells. They may thus play a central role in the immune surveillance of damaged, infected, or otherwise stressed intestinal epithelial cells. However, the generality of this system in evolution and the mode of recognition of MICA and MICB are undefined. Analysis of cDNA sequences from various primate species defined translation products that are homologous to MICA and MICB. All of the MIC polypeptides have common characteristics, although they are extraordinarily diverse. The most notable alterations are several deletions and frequent amino acid substitutions in the putative α-helical regions of the α1α2 domains. However, the primate MIC molecules were expressed on the surfaces of normal and transfected cells. Moreover, despite their sharing of relatively few identical amino acids in potentially accessible regions of their α1α2 domains, they were recognized by diverse human intestinal epithelial γδ T cells that are restricted by MICA and MICB. Thus, MIC molecules represent a family of MHC proteins that are structurally diverse yet appear to be functionally conserved. The promiscuous mode of γδ T cell recognition of these antigens may be explained by their sharing of a single conserved interaction site.

Expression of HLA class I-specific inhibitory natural killer cell receptors in HIV-specific cytolytic T lymphocytes: Impairment of specific cytolytic functions

Human T lymphocytes have been shown to express inhibitory natural killer cell receptors (NKR), which can down-regulate T cell antigen receptor-mediated T cell function, including cytolytic activity. In the present study, we demonstrate that CD3+NKR+ cells can be identified in HIV-infected patients. HIV-specific cytolytic activity was analyzed in five patients in whom autologous lymphoblastoid B cell lines could be derived as a source of autologous target cells. Phytohemagglutinin-activated T cell populations that had been cultured in interleukin 2 displayed HIV-specific cytotoxic T lymphocyte (CTL) activity against HIV env, gag, pol, and nef in 3 of 5 patients. Addition of anti-NKR mAb of IgM isotype could increase the specific CTL activity. Moreover, in one additional patient, HIV-specific CTL activity was undetectable; however, after addition of anti-NKR mAb such CTL activity appeared de novo. Similar results were obtained by analysis of CD3+NKR+ clones derived from two patients. These data provide direct evidence that CD3+NKR+ cells may include antigen (HIV)-specific CTLs and that mAb-mediated masking of inhibitory NKR may revert the down-regulation of CTL function.

Quantitative high performance liquid chromatography/tandem mass spectrometric analysis of the four classes of F2-isoprostanes in human urine

Isoprostanes (iPs) are free radical catalyzed prostaglandin isomers. Analysis of individual isomers of PGF2α—F2-iPs—in urine has reflected lipid peroxidation in humans. However, up to 64 F2-iPs may be formed, and it is unknown whether coordinate generation, disposition, and excretion of F2-iPs occurs in humans. To address this issue, we developed methods to measure individual members of the four structural classes of F2-iPs, using liquid chromatography/tandem mass spectrometry (LC/MS/MS), in which sample preparation is minimized. Authentic standards of F2-iPs of classes III, IV, V, and VI were used to identify class-specific ions for multiple reaction monitoring. Using iPF2α-VI as a model compound, we demonstrated the reproducibility of the assay in human urine. Urinary levels of all F2-iPs measured were elevated in patients with familial hypercholesterolemia. However, only three of eight F2-iPs were elevated in patients with congestive heart failure, compared with controls. Paired analyses by GC/MS and LC/MS/MS of iPF2α-VI in hypercholesterolemia and of 8,12-iso-iPF2α-VI in congestive heart failure were highly correlated. This approach will permit high throughput analysis of multiple iPs in human disease.

Ol-Prx 3, a member of an additional class of homeobox genes, is unimodally expressed in several domains of the developing and adult central nervous system of the medaka (Oryzias latipes)

Large-scale genetic screens for mutations affecting early neurogenesis of vertebrates have recently been performed with an aquarium fish, the zebrafish. Later stages of neural morphogenesis have attracted less attention in small fish species, partly because of the lack of molecular markers of developing structures that may facilitate the detection of discrete structural alterations. In this context, we report the characterization of Ol-Prx 3 (Oryzias latipes-Prx 3). This gene was isolated in the course of a large-scale screen for brain cDNAs containing a highly conserved DNA binding region, the homeobox helix-three. Sequence analysis revealed that this gene belongs to another class of homeobox genes, together with a previously isolated mouse ortholog, called OG-12 [Rovescalli, A. C., Asoh, S. & Nirenberg, M. (1996) Proc. Natl. Acad. Sci. USA 93, 10691–10696] and with the human SHOX gene [Rao, E., Weiss, B., Fukami, M., Rump, A., Niesler, B., et al. (1997) Nat. Genet. 16, 54–62], thought to be involved in the short-stature phenotype of Turner syndrome patients. These three genes exhibit a moderate level of identity in the homeobox with the other genes of the paired-related (PRX) gene family. Ol-Prx 3, as well as the PRX genes, are expressed in various cartilaginous structures of head and limbs. These genes might thus be involved in common regulatory pathways during the morphogenesis of these structures. Moreover, this paper reports a complex and monophasic pattern of Ol-Prx 3 expression in the central nervous system, which differs markedly from the patterns reported for the PRX genes, Prx 3 excluded: this gene begins to be expressed in a variety of central nervous system territories at late neurula stage. Strikingly, it remains turned on in some of the derivatives of each territory during the entire life of the fish. We hope this work will thus help identify common features for the PRX 3 family of homeobox genes.

Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy

Although highly active antiretroviral therapy (HAART) in the form of triple combinations of drugs including protease inhibitors can reduce the plasma viral load of some HIV-1-infected individuals to undetectable levels, it is unclear what the effects of these regimens are on latently infected CD4+ T cells and what role these cells play in the persistence of HIV-1 infection in individuals receiving such treatment. The present study demonstrates that highly purified CD4+ T cells from 13 of 13 patients receiving HAART with an average treatment time of 10 months and with undetectable (<500 copies HIV RNA/ml) plasma viremia by a commonly used bDNA assay carried integrated proviral DNA and were capable of producing infectious virus upon cellular activation in vitro. Phenotypic analysis of HIV-1 produced by activation of latently infected CD4+ T cells revealed the presence in some patients of syncytium-inducing virus. In addition, the presence of unintegrated HIV-1 DNA in infected resting CD4+ T cells from patients receiving HAART, even those with undetectable plasma viremia, suggests persistent active virus replication in vivo.