An automatic translation scheme from prolog to the andorra kernel language

The Andorra family of languages (which includes the Andorra Kernel Language -AKL) is aimed, in principie, at simultaneously supporting the programming styles of Prolog and committed choice languages. On the other hand, AKL requires a somewhat detailed specification of control by the user. This could be avoided by programming in Prolog to run on AKL. However, Prolog programs cannot be executed directly on AKL. This is due to a number of factors, from more or less trivial syntactic differences to more involved issues such as the treatment of cut and making the exploitation of certain types of parallelism possible. This paper provides basic guidelines for constructing an automatic compiler of Prolog programs into AKL, which can bridge those differences. In addition to supporting Prolog, our style of translation achieves independent and-parallel execution where possible, which is relevant since this type of parallel execution preserves, through the translation, the user-perceived "complexity" of the original Prolog program.

Contribution to the design of waveguide-fed compound-slot arrays by means of equivalent circuit modelling

Los arrays de ranuras son sistemas de antennas conocidos desde los años 40, principalmente destinados a formar parte de sistemas rádar de navíos de combate y grandes estaciones terrenas donde el tamaño y el peso no eran altamente restrictivos. Con el paso de los años y debido sobre todo a importantes avances en materiales y métodos de fabricación, el rango de aplicaciones de este tipo de sistemas radiantes creció en gran medida. Desde nuevas tecnologías biomédicas, sistemas anticolisión en automóviles y navegación en aviones, enlaces de comunicaciones de alta tasa binaria y corta distancia e incluso sistemas embarcados en satélites para la transmisión de señal de televisión. Dentro de esta familia de antennas, existen dos grupos que destacan por ser los más utilizados: las antennas de placas paralelas con las ranuras distribuidas de forma circular o espiral y las agrupaciones de arrays lineales construidos sobre guia de onda. Continuando con las tareas de investigación desarrolladas durante los últimos años en el Instituto de Tecnología de Tokyo y en el Grupo de Radiación de la Universidad Politécnica de Madrid, la totalidad de esta tesis se centra en este último grupo, aunque como se verá se separa en gran medida de las técnicas de diseño y metodologías convencionales. Los arrays de ranuras rectas y paralelas al eje de la guía rectangular que las alimenta son, sin ninguna duda, los modelos más empleados debido a la fiabilidad que presentan a altas frecuencias, su capacidad para gestionar grandes cantidades de potencia y la sencillez de su diseño y fabricación. Sin embargo, también presentan desventajas como estrecho ancho de banda en pérdidas de retorno y rápida degradación del diagrama de radiación con la frecuencia. Éstas son debidas a la naturaleza resonante de sus elementos radiantes: al perder la resonancia, el sistema global se desajusta y sus prestaciones degeneran. En arrays bidimensionales de slots rectos, el campo eléctrico queda polarizado sobre el plano transversal a las ranuras, correspondiéndose con el plano de altos lóbulos secundarios. Esta tesis tiene como objetivo el desarrollo de un método sistemático de diseño de arrays de ranuras inclinadas y desplazadas del centro (en lo sucesivo “ranuras compuestas”), definido en 1971 como uno de los desafíos a superar dentro del mundo del diseño de antennas. La técnica empleada se basa en el Método de los Momentos, la Teoría de Circuitos y la Teoría de Conexión Aleatoria de Matrices de Dispersión. Al tratarse de un método circuital, la primera parte de la tesis se corresponde con el estudio de la aplicabilidad de las redes equivalentes fundamentales, su capacidad para recrear fenómenos físicos de la ranura, las limitaciones y ventajas que presentan para caracterizar las diferentes configuraciones de slot compuesto. Se profundiza en las diferencias entre las redes en T y en ! y se condiciona la selección de una u otra dependiendo del tipo de elemento radiante. Una vez seleccionado el tipo de red a emplear en el diseño del sistema, se ha desarrollado un algoritmo de cascadeo progresivo desde el puerto alimentador hacia el cortocircuito que termina el modelo. Este algoritmo es independiente del número de elementos, la frecuencia central de funcionamiento, del ángulo de inclinación de las ranuras y de la red equivalente seleccionada (en T o en !). Se basa en definir el diseño del array como un Problema de Satisfacción de Condiciones (en inglés, Constraint Satisfaction Problem) que se resuelve por un método de Búsqueda en Retroceso (Backtracking algorithm). Como resultado devuelve un circuito equivalente del array completo adaptado a su entrada y cuyos elementos consumen una potencia acorde a una distribución de amplitud dada para el array. En toda agrupación de antennas, el acoplo mutuo entre elementos a través del campo radiado representa uno de los principales problemas para el ingeniero y sus efectos perjudican a las prestaciones globales del sistema, tanto en adaptación como en capacidad de radiación. El empleo de circuito equivalente se descartó por la dificultad que suponía la caracterización de estos efectos y su inclusión en la etapa de diseño. En esta tesis doctoral el acoplo también se ha modelado como una red equivalente cuyos elementos son transformadores ideales y admitancias, conectada al conjunto de redes equivalentes que representa el array. Al comparar los resultados estimados en términos de pérdidas de retorno y radiación con aquellos obtenidos a partir de programas comerciales populares como CST Microwave Studio se confirma la validez del método aquí propuesto, el primer método de diseño sistemático de arrays de ranuras compuestos alimentados por guía de onda rectangular. Al tratarse de ranuras no resonantes, el ancho de banda en pérdidas de retorno es mucho mas amplio que el que presentan arrays de slots rectos. Para arrays bidimensionales, el ángulo de inclinación puede ajustarse de manera que el campo quede polarizado en los planos de bajos lóbulos secundarios. Además de simulaciones se han diseñado, construido y medido dos prototipos centrados en la frecuencia de 12GHz, de seis y diez elementos. Las medidas de pérdidas de retorno y diagrama de radiación revelan excelentes resultados, certificando la bondad del método genuino Method of Moments - Forward Matching Procedure desarrollado a lo largo de esta tésis. Abstract The slot antenna arrays are well known systems from the decade of 40s, mainly intended to be part of radar systems of large warships and terrestrial stations where size and weight were not highly restrictive. Over the years, mainly due to significant advances in materials and manufacturing methods, the range of applications of this type of radiating systems grew significantly. From new biomedical technologies, collision avoidance systems in cars and aircraft navigation, short communication links with high bit transfer rate and even embedded systems in satellites for television broadcast. Within this family of antennas, two groups stand out as being the most frequent in the literature: parallel plate antennas with slots placed in a circular or spiral distribution and clusters of waveguide linear arrays. To continue the vast research work carried out during the last decades in the Tokyo Institute of Technology and in the Radiation Group at the Universidad Politécnica de Madrid, this thesis focuses on the latter group, although it represents a technique that drastically breaks with traditional design methodologies. The arrays of slots straight and parallel to the axis of the feeding rectangular waveguide are without a doubt the most used models because of the reliability that they present at high frequencies, its ability to handle large amounts of power and their simplicity of design and manufacturing. However, there also exist disadvantages as narrow bandwidth in return loss and rapid degradation of the radiation pattern with frequency. These are due to the resonant nature of radiating elements: away from the resonance status, the overall system performance and radiation pattern diminish. For two-dimensional arrays of straight slots, the electric field is polarized transverse to the radiators, corresponding to the plane of high side-lobe level. This thesis aims to develop a systematic method of designing arrays of angled and displaced slots (hereinafter "compound slots"), defined in 1971 as one of the challenges to overcome in the world of antenna design. The used technique is based on the Method of Moments, Circuit Theory and the Theory of Scattering Matrices Connection. Being a circuitry-based method, the first part of this dissertation corresponds to the study of the applicability of the basic equivalent networks, their ability to recreate the slot physical phenomena, their limitations and advantages presented to characterize different compound slot configurations. It delves into the differences of T and ! and determines the selection of the most suitable one depending on the type of radiating element. Once the type of network to be used in the system design is selected, a progressive algorithm called Forward Matching Procedure has been developed to connect the proper equivalent networks from the feeder port to shorted ending. This algorithm is independent of the number of elements, the central operating frequency, the angle of inclination of the slots and selected equivalent network (T or ! networks). It is based on the definition of the array design as a Constraint Satisfaction Problem, solved by means of a Backtracking Algorithm. As a result, the method returns an equivalent circuit of the whole array which is matched at its input port and whose elements consume a power according to a given amplitude distribution for the array. In any group of antennas, the mutual coupling between elements through the radiated field represents one of the biggest problems that the engineer faces and its effects are detrimental to the overall performance of the system, both in radiation capabilities and return loss. The employment of an equivalent circuit for the array design was discarded by some authors because of the difficulty involved in the characterization of the coupling effects and their inclusion in the design stage. In this thesis the coupling has also been modeled as an equivalent network whose elements are ideal transformers and admittances connected to the set of equivalent networks that represent the antennas of the array. By comparing the estimated results in terms of return loss and radiation with those obtained from popular commercial software as CST Microwave Studio, the validity of the proposed method is fully confirmed, representing the first method of systematic design of compound-slot arrays fed by rectangular waveguide. Since these slots do not work under the resonant status, the bandwidth in return loss is much wider than the longitudinal-slot arrays. For the case of two-dimensional arrays, the angle of inclination can be adjusted so that the field is polarized at the low side-lobe level plane. Besides the performed full-wave simulations two prototypes of six and ten elements for the X-band have been designed, built and measured, revealing excellent results and agreement with the expected results. These facts certify that the genuine technique Method of Moments - Matching Forward Procedure developed along this thesis is valid and trustable.

The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling

ABSTRACT: Transcription factors (TFs) are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger) TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns). These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley. RESULTS: Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs). Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds) has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination). CONCLUSIONS: Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal species considered here, deduced from the phylogenetic analysis, indicates that although the expression profile has been conserved in many of the putative orthologs, in some cases duplication followed by subsequent divergence may have occurred (neo-functionalization).

The family of DOF transcription factors in Brachypodium distachyon: BdDof24 in germinating seeds

The DOF (DNA binding with One Finger) transcription factor (TF) family is characterized by a binding domain of 52 amino acid residues that is structured as a Cys2/Cys2 Zn2+ finger that recognizes the common core 5?-T/AAAAG-3? in the promoter regions of their target genes. DOF TFs have been associated with biological processes exclusive to higher plants and their close ancestors (algae, mosses and ferns).

When defense backfires: Detrimental effect of a plant’s protective trichomes on an insect beneficial to the plant

The plant Mentzelia pumila (family Loasaceae) has leaves and stems densely covered with tiny hooked trichomes. The structures entrap and kill insects and therefore are most probably protective. But they are also maladaptive in that they incapacitate a coccinellid beetle (Hippodamia convergens) that preys upon an aphid enemy (Macrosiphum mentzeliae) of the plant. The adaptive benefit provided by the trichomes is evidently offset by a cost.

The small GTP-binding protein Rho links G protein-coupled receptors and Gα12 to the serum response element and to cellular transformation

Receptors coupled to heterotrimeric G proteins can effectively stimulate growth promoting pathways in a large variety of cell types, and if persistently activated, these receptors can also behave as dominant-acting oncoproteins. Consistently, activating mutations for G proteins of the Gαs and Gαi2 families were found in human tumors; and members of the Gαq and Gα12 families are fully transforming when expressed in murine fibroblasts. In an effort aimed to elucidate the molecular events involved in proliferative signaling through heterotrimeric G proteins we have focused recently on gene expression regulation. Using NIH 3T3 fibroblasts expressing m1 muscarinic acetylcholine receptors as a model system, we have observed that activation of this transforming G protein-coupled receptors induces the rapid expression of a variety of early responsive genes, including the c-fos protooncogene. One of the c-fos promoter elements, the serum response element (SRE), plays a central regulatory role, and activation of SRE-dependent transcription has been found to be regulated by several proteins, including the serum response factor and the ternary complex factor. With the aid of reporter plasmids for gene expression, we observed here that stimulation of m1 muscarinic acetylcholine receptors potently induced SRE-driven reporter gene activity in NIH 3T3 cells. In these cells, only the Gα12 family of heterotrimeric G protein α subunits strongly induced the SRE, while Gβ1γ2 dimers activated SRE to a more limited extent. Furthermore, our study provides strong evidence that m1, Gα12 and the small GTP-binding protein RhoA are components of a novel signal transduction pathway that leads to the ternary complex factor-independent transcriptional activation of the SRE and to cellular transformation.

A cytochrome P450 terpenoid hydroxylase linked to the suppression of insect juvenile hormone synthesis

A cDNA encoding a cytochrome P450 enzyme was isolated from a cDNA library of the corpora allata (CA) from reproductively active Diploptera punctata cockroaches. This P450 from the endocrine glands that produce the insect juvenile hormone (JH) is most closely related to P450 proteins of family 4 and was named CYP4C7. The CYP4C7 gene is expressed selectively in the CA; its message could not be detected in the fat body, corpora cardiaca, or brain, but trace levels of expression were found in the midgut and caeca. The levels of CYP4C7 mRNA in the CA, measured by ribonuclease protection assays, were linked to the activity cycle of the glands. In adult females, CYP4C7 expression increased immediately after the peak of JH synthesis, reaching a maximum on day 7, just before oviposition. mRNA levels then declined after oviposition and during pregnancy. The CYP4C7 protein was produced in Escherichia coli as a C-terminal His-tagged recombinant protein. In a reconstituted system with insect NADPH cytochrome P450 reductase, cytochrome b5, and NADPH, the purified CYP4C7 metabolized (2E,6E)-farnesol to a more polar product that was identified by GC-MS and by NMR as (10E)-12-hydroxyfarnesol. CYP4C7 converted JH III to 12-trans-hydroxy JH III and metabolized other JH-like sesquiterpenoids as well. This ω-hydroxylation of sesquiterpenoids appears to be a metabolic pathway in the corpora allata that may play a role in the suppression of JH biosynthesis at the end of the gonotrophic cycle.

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established.

Pontin52, an interaction partner of β-catenin, binds to the TATA box binding protein

β-catenin, the vertebrate homolog of the Drosophila Armadillo protein, has been shown to have dual cellular functions, as a component of both the cadherin-catenin cell adhesion complex and the Wnt signaling pathway. At Wnt signaling, β-catenin becomes stabilized in the cytoplasm and subsequently available for interaction with transcription factors of the lymphocyte enhancer factor-1/T-cell factor family, resulting in a nuclear localization of β-catenin. Although β-catenin does not bind DNA directly, its carboxyl- and amino-terminal regions exhibit a transactivating activity still not well understood molecularly. Here we report the identification of an interaction partner of β-catenin, a nuclear protein designated Pontin52. Pontin52 binds β-catenin in the region of Armadillo repeats 2–5 and, more importantly, also binds the TATA box binding protein. We provide evidence for an in vivo multiprotein complex composed of Pontin52, β-catenin, and lymphocyte enhancer factor-1/T-cell factor. Our results suggest involvement of Pontin52 in the nuclear function of β-catenin.

GERp95, a Membrane-associated Protein that Belongs to a Family of Proteins Involved in Stem Cell Differentiation

A panel of mAbs was elicited against intracellular membrane fractions from rat pancreas. One of the antibodies reacted with a 95-kDa protein that localizes primarily to the Golgi complex or the endoplasmic reticulum (ER), depending on cell type. The corresponding cDNA was cloned and sequenced and found to encode a protein of 97.6 kDa that we call GERp95 (Golgi ER protein 95 kDa). The protein copurifies with intracellular membranes but does not contain hydrophobic regions that could function as signal peptides or transmembrane domains. Biochemical analysis suggests that GERp95 is a cytoplasmically exposed peripheral membrane protein that exists in a protease-resistant complex. GERp95 belongs to a family of highly conserved proteins in metazoans and Schizosaccharomyces pombe. It has recently been determined that plant and Drosophila homologues of GERp95 are important for controlling the differentiation of stem cells (Bohmert et al., 1998; Cox et al., 1998; Moussian et al., 1998). In Caenorhabditis elegans, there are at least 20 members of this protein family. To this end, we have used RNA interference to show that the GERp95 orthologue in C. elegans is important for maturation of germ-line stem cells in the gonad. GERp95 and related proteins are an emerging new family of proteins that have important roles in metazoan development. The present study suggests that these proteins may exert their effects on cell differentiation from the level of intracellular membranes.

The conserved SOCS box motif in suppressors of cytokine signaling binds to elongins B and C and may couple bound proteins to proteasomal degradation

The suppressors of cytokine signaling (SOCS) family of proteins act as intracellular inhibitors of several cytokine signal transduction pathways. Their expression is induced by cytokine activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway and they act as a negative feedback loop by subsequently inhibiting the JAK/STAT pathway either by direct interaction with activated JAKs or with the receptors. These interactions are mediated at least in part by the SH2 domain of SOCS proteins but these proteins also contain a highly conserved C-terminal homology domain termed the SOCS box. Here we show that the SOCS box mediates interactions with elongins B and C, which in turn may couple SOCS proteins and their substrates to the proteasomal protein degradation pathway. Analogous to the family of F-box-containing proteins, it appears that the SOCS proteins may act as adaptor molecules that target activated cell signaling proteins to the protein degradation pathway.

Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix–loop–helix factor PIF3 in a reaction requiring the PAS domain of PIF3

The signaling pathways by which the phytochrome (phy) family of photoreceptors transmits sensory information to light-regulated genes remain to be fully defined. Evidence for a relatively direct pathway has been provided by the binding of one member of the family, phyB, to a promoter-element-bound, basic helix–loop–helix protein, PIF3, specifically upon light-induced conversion of the photoreceptor molecule to its biologically active conformer (Pfr). Here, we show that phyA also binds selectively and reversibly to PIF3 upon photoconversion to Pfr, but that the apparent affinity of PIF3 for phyA is 10-fold lower than for phyB. This result is consistent with previous in vivo data from PIF3-deficient Arabidopsis, indicating that PIF3 has a major role in phyB signaling, but a more minor role in phyA signaling. We also show that phyB binds stoichiometrically to PIF3 at an equimolar ratio, suggesting that the resultant complex is the unit active in transcriptional regulation at target promoters. Deletion mapping suggests that a 37-aa segment present at the N terminus of phyB, but absent from phyA, contributes strongly to the high binding affinity of phyB for PIF3. Conversely, deletion mapping and point mutation analysis of PIF3 for determinants involved in recognition of phyB indicates that the PAS domain of PIF3 is a major contributor to this interaction, but that a second determinant in the C-terminal domain is also necessary.

Murine Nkg2d and Cd94 are clustered within the natural killer complex and are expressed independently in natural killer cells

Natural killer (NK) cells express C-type lectin-like receptors, encoded in the NK gene complex, that interact with major histocompatibility complex class I and either inhibit or activate functional activity. Human NK cells express heterodimers consisting of CD94 and NKG2 family molecules, whereas murine NK cells express homodimers belonging to the Ly-49 family. The corresponding orthologues for other species, however, have not been described. In this report, we used probes derived from the expressed sequence tag database to clone C57BL/6-derived cDNAs homologous to human NKG2-D and CD94. Among normal tissues, murine NKG2-D and CD94 transcripts are highly expressed only in activated NK cells, including both Ly-49A+ and Ly-49A− subpopulations. Additionally, mNKG2-D is expressed in murine NK cell clones KY-1 and KY-2, whereas mCD94 expression is observed only in KY-1 cells but not KY-2. Last, we have finely mapped the physical location of the Cd94 (centromeric) and Nkg2d (telomeric) genes between Cd69 and the Ly49 cluster in the NK complex. Thus, these data indicate the expanding complexity of the NK complex and the corresponding repertoire of C-type lectin-like receptors on murine NK cells.

Analysis of the Xenopus laevis CCAAT-enhancer binding protein α gene promoter demonstrates species-specific differences in the mechanisms for both auto-activation and regulation by Sp1

Transcription factors belonging to the CCAAT-enhancer binding protein (C/EBP) family have been implicated in the regulation of gene expression during differentiation, development and disease. Autoregulation is relatively common in the modulation of C/EBP gene expression and the murine and human C/EBPα genes have been shown to be auto-activated by different mechanisms. In the light of this finding, it is essential that autoregulation of C/EBPα genes from a wider range of different species be investigated in order to gauge the degree of commonality, or otherwise, that may exist. We report here studies that investigate the regulation of the Xenopus laevis C/EBPα gene (xC/EBPα). The –1131/+41 promoter region was capable of directing high levels of expression in both the human hepatoma Hep3B and the Xenopus kidney epithelial A6 cell lines, and was auto-activated by expression vectors specifying for xC/EBPα or xC/EBPβ. Deletion analysis showed that the –321/+41 sequence was sufficient for both the constitutive promoter activity and auto-activation and electrophoretic mobility shift assays identified the interaction of C/EBPs and Sp1 to this region. Although deletion of either the C/EBP or the Sp1 site drastically reduced the xC/EBPα promoter activity, multimers of only the C/EBP site could confer autoregulation to a heterologous SV40 promoter. These results indicate that, in contrast to the human promoter and in common with the murine gene, the xC/EBPα promoter was subject to direct autoregulation. In addition, we demonstrate a novel species-specific action of Sp1 in the regulation of C/EBPα expression, with the factor able to repress the murine promoter but activate the Xenopus gene.