Abstract multiple specialization and its application to program parallelization.

Program specialization optimizes programs for known valúes of the input. It is often the case that the set of possible input valúes is unknown, or this set is infinite. However, a form of specialization can still be performed in such cases by means of abstract interpretation, specialization then being with respect to abstract valúes (substitutions), rather than concrete ones. We study the múltiple specialization of logic programs based on abstract interpretation. This involves in principie, and based on information from global analysis, generating several versions of a program predicate for different uses of such predicate, optimizing these versions, and, finally, producing a new, "multiply specialized" program. While múltiple specialization has received theoretical attention, little previous evidence exists on its practicality. In this paper we report on the incorporation of múltiple specialization in a parallelizing compiler and quantify its effects. A novel approach to the design and implementation of the specialization system is proposed. The resulting implementation techniques result in identical specializations to those of the best previously proposed techniques but require little or no modification of some existing abstract interpreters. Our results show that, using the proposed techniques, the resulting "abstract múltiple specialization" is indeed a relevant technique in practice. In particular, in the parallelizing compiler application, a good number of run-time tests are eliminated and invariants extracted automatically from loops, resulting generally in lower overheads and in several cases in increased speedups.

Implementation of multiple specialization in logic programs

We study the múltiple specialization of logic programs based on abstract interpretation. This involves in general generating several versions of a program predícate for different uses of such predícate, making use of information obtained from global analysis performed by an abstract interpreter, and finally producing a new, "multiply specialized" program. While the topic of múltiple specialization of logic programs has received considerable theoretical attention, it has never been actually incorporated in a compiler and its effects quantified. We perform such a study in the context of a parallelizing compiler and show that it is indeed a relevant technique in practice. Also, we propose an implementation technique which has the same power as the strongest of the previously proposed techniques but requires little or no modification of an existing abstract interpreter.

Advances in the Simultaneous Multiple Surface optical design method for imaging and non-imaging applications

Classical imaging optics has been developed over centuries in many areas, such as its paraxial imaging theory and practical design methods like multi-parametric optimization techniques. Although these imaging optical design methods can provide elegant solutions to many traditional optical problems, there are more and more new design problems, like solar concentrator, illumination system, ultra-compact camera, etc., that require maximum energy transfer efficiency, or ultra-compact optical structure. These problems do not have simple solutions from classical imaging design methods, because not only paraxial rays, but also non-paraxial rays should be well considered in the design process. Non-imaging optics is a newly developed optical discipline, which does not aim to form images, but to maximize energy transfer efficiency. One important concept developed from non-imaging optics is the “edge-ray principle”, which states that the energy flow contained in a bundle of rays will be transferred to the target, if all its edge rays are transferred to the target. Based on that concept, many CPC solar concentrators have been developed with efficiency close to the thermodynamic limit. When more than one bundle of edge-rays needs to be considered in the design, one way to obtain solutions is to use SMS method. SMS stands for Simultaneous Multiple Surface, which means several optical surfaces are constructed simultaneously. The SMS method was developed as a design method in Non-imaging optics during the 90s. The method can be considered as an extension to the Cartesian Oval calculation. In the traditional Cartesian Oval calculation, one optical surface is built to transform an input wave-front to an out-put wave-front. The SMS method however, is dedicated to solve more than 1 wave-fronts transformation problem. In the beginning, only 2 input wave-fronts and 2 output wave-fronts transformation problem was considered in the SMS design process for rotational optical systems or free-form optical systems. Usually “SMS 2D” method stands for the SMS procedure developed for rotational optical system, and “SMS 3D” method for the procedure for free-form optical system. Although the SMS method was originally employed in non-imaging optical system designs, it has been found during this thesis that with the improved capability to design more surfaces and control more input and output wave-fronts, the SMS method can also be applied to imaging system designs and possesses great advantage over traditional design methods. In this thesis, one of the main goals to achieve is to further develop the existing SMS-2D method to design with more surfaces and improve the stability of the SMS-2D and SMS-3D algorithms, so that further optimization process can be combined with SMS algorithms. The benefits of SMS plus optimization strategy over traditional optimization strategy will be explained in details for both rotational and free-form imaging optical system designs. Another main goal is to develop novel design concepts and methods suitable for challenging non-imaging applications, e.g. solar concentrator and solar tracker. This thesis comprises 9 chapters and can be grouped into two parts: the first part (chapter 2-5) contains research works in the imaging field, and the second part (chapter 6-8) contains works in the non-imaging field. In the first chapter, an introduction to basic imaging and non-imaging design concepts and theories is given. Chapter 2 presents a basic SMS-2D imaging design procedure using meridian rays. In this chapter, we will set the imaging design problem from the SMS point of view, and try to solve the problem numerically. The stability of this SMS-2D design procedure will also be discussed. The design concepts and procedures developed in this chapter lay the path for further improvement. Chapter 3 presents two improved SMS 3 surfaces’ design procedures using meridian rays (SMS-3M) and skew rays (SMS-1M2S) respectively. The major improvement has been made to the central segments selections, so that the whole SMS procedures become more stable compared to procedures described in Chapter 2. Since these two algorithms represent two types of phase space sampling, their image forming capabilities are compared in a simple objective design. Chapter 4 deals with an ultra-compact SWIR camera design with the SMS-3M method. The difficulties in this wide band camera design is how to maintain high image quality meanwhile reduce the overall system length. This interesting camera design provides a playground for the classical design method and SMS design methods. We will show designs and optical performance from both classical design method and the SMS design method. Tolerance study is also given as the end of the chapter. Chapter 5 develops a two-stage SMS-3D based optimization strategy for a 2 freeform mirrors imaging system. In the first optimization phase, the SMS-3D method is integrated into the optimization process to construct the two mirrors in an accurate way, drastically reducing the unknown parameters to only few system configuration parameters. In the second optimization phase, previous optimized mirrors are parameterized into Qbfs type polynomials and set up in code V. Code V optimization results demonstrates the effectiveness of this design strategy in this 2-mirror system design. Chapter 6 shows an etendue-squeezing condenser optics, which were prepared for the 2010 IODC illumination contest. This interesting design employs many non-imaging techniques such as the SMS method, etendue-squeezing tessellation, and groove surface design. This device has theoretical efficiency limit as high as 91.9%. Chapter 7 presents a freeform mirror-type solar concentrator with uniform irradiance on the solar cell. Traditional parabolic mirror concentrator has many drawbacks like hot-pot irradiance on the center of the cell, insufficient use of active cell area due to its rotational irradiance pattern and small acceptance angle. In order to conquer these limitations, a novel irradiance homogenization concept is developed, which lead to a free-form mirror design. Simulation results show that the free-form mirror reflector has rectangular irradiance pattern, uniform irradiance distribution and large acceptance angle, which confirm the viability of the design concept. Chapter 8 presents a novel beam-steering array optics design strategy. The goal of the design is to track large angle parallel rays by only moving optical arrays laterally, and convert it to small angle parallel output rays. The design concept is developed as an extended SMS method. Potential applications of this beam-steering device are: skylights to provide steerable natural illumination, building integrated CPV systems, and steerable LED illumination. Conclusion and future lines of work are given in Chapter 9. Resumen La óptica de formación de imagen clásica se ha ido desarrollando durante siglos, dando lugar tanto a la teoría de óptica paraxial y los métodos de diseño prácticos como a técnicas de optimización multiparamétricas. Aunque estos métodos de diseño óptico para formación de imagen puede aportar soluciones elegantes a muchos problemas convencionales, siguen apareciendo nuevos problemas de diseño óptico, concentradores solares, sistemas de iluminación, cámaras ultracompactas, etc. que requieren máxima transferencia de energía o dimensiones ultracompactas. Este tipo de problemas no se pueden resolver fácilmente con métodos clásicos de diseño porque durante el proceso de diseño no solamente se deben considerar los rayos paraxiales sino también los rayos no paraxiales. La óptica anidólica o no formadora de imagen es una disciplina que ha evolucionado en gran medida recientemente. Su objetivo no es formar imagen, es maximazar la eficiencia de transferencia de energía. Un concepto importante de la óptica anidólica son los “rayos marginales”, que se pueden utilizar para el diseño de sistemas ya que si todos los rayos marginales llegan a nuestra área del receptor, todos los rayos interiores también llegarán al receptor. Haciendo uso de este principio, se han diseñado muchos concentradores solares que funcionan cerca del límite teórico que marca la termodinámica. Cuando consideramos más de un haz de rayos marginales en nuestro diseño, una posible solución es usar el método SMS (Simultaneous Multiple Surface), el cuál diseña simultáneamente varias superficies ópticas. El SMS nació como un método de diseño para óptica anidólica durante los años 90. El método puede ser considerado como una extensión del cálculo del óvalo cartesiano. En el método del óvalo cartesiano convencional, se calcula una superficie para transformar un frente de onda entrante a otro frente de onda saliente. El método SMS permite transformar varios frentes de onda de entrada en frentes de onda de salida. Inicialmente, sólo era posible transformar dos frentes de onda con dos superficies con simetría de rotación y sin simetría de rotación, pero esta limitación ha sido superada recientemente. Nos referimos a “SMS 2D” como el método orientado a construir superficies con simetría de rotación y llamamos “SMS 3D” al método para construir superficies sin simetría de rotación o free-form. Aunque el método originalmente fue aplicado en el diseño de sistemas anidólicos, se ha observado que gracias a su capacidad para diseñar más superficies y controlar más frentes de onda de entrada y de salida, el SMS también es posible aplicarlo a sistemas de formación de imagen proporcionando una gran ventaja sobre los métodos de diseño tradicionales. Uno de los principales objetivos de la presente tesis es extender el método SMS-2D para permitir el diseño de sistemas con mayor número de superficies y mejorar la estabilidad de los algoritmos del SMS-2D y SMS-3D, haciendo posible combinar la optimización con los algoritmos. Los beneficios de combinar SMS y optimización comparado con el proceso de optimización tradicional se explican en detalle para sistemas con simetría de rotación y sin simetría de rotación. Otro objetivo importante de la tesis es el desarrollo de nuevos conceptos de diseño y nuevos métodos en el área de la concentración solar fotovoltaica. La tesis está estructurada en 9 capítulos que están agrupados en dos partes: la primera de ellas (capítulos 2-5) se centra en la óptica formadora de imagen mientras que en la segunda parte (capítulos 6-8) se presenta el trabajo del área de la óptica anidólica. El primer capítulo consta de una breve introducción de los conceptos básicos de la óptica anidólica y la óptica en formación de imagen. El capítulo 2 describe un proceso de diseño SMS-2D sencillo basado en los rayos meridianos. En este capítulo se presenta el problema de diseñar un sistema formador de imagen desde el punto de vista del SMS y se intenta obtener una solución de manera numérica. La estabilidad de este proceso se analiza con detalle. Los conceptos de diseño y los algoritmos desarrollados en este capítulo sientan la base sobre la cual se realizarán mejoras. El capítulo 3 presenta dos procedimientos para el diseño de un sistema con 3 superficies SMS, el primero basado en rayos meridianos (SMS-3M) y el segundo basado en rayos oblicuos (SMS-1M2S). La mejora más destacable recae en la selección de los segmentos centrales, que hacen más estable todo el proceso de diseño comparado con el presentado en el capítulo 2. Estos dos algoritmos representan dos tipos de muestreo del espacio de fases, su capacidad para formar imagen se compara diseñando un objetivo simple con cada uno de ellos. En el capítulo 4 se presenta un diseño ultra-compacto de una cámara SWIR diseñada usando el método SMS-3M. La dificultad del diseño de esta cámara de espectro ancho radica en mantener una alta calidad de imagen y al mismo tiempo reducir drásticamente sus dimensiones. Esta cámara es muy interesante para comparar el método de diseño clásico y el método de SMS. En este capítulo se presentan ambos diseños y se analizan sus características ópticas. En el capítulo 5 se describe la estrategia de optimización basada en el método SMS-3D. El método SMS-3D calcula las superficies ópticas de manera precisa, dejando sólo unos pocos parámetros libres para decidir la configuración del sistema. Modificando el valor de estos parámetros se genera cada vez mediante SMS-3D un sistema completo diferente. La optimización se lleva a cabo variando los mencionados parámetros y analizando el sistema generado. Los resultados muestran que esta estrategia de diseño es muy eficaz y eficiente para un sistema formado por dos espejos. En el capítulo 6 se describe un sistema de compresión de la Etendue, que fue presentado en el concurso de iluminación del IODC en 2010. Este interesante diseño hace uso de técnicas propias de la óptica anidólica, como el método SMS, el teselado de las lentes y el diseño mediante grooves. Este dispositivo tiene un límite teórica en la eficiencia del 91.9%. El capítulo 7 presenta un concentrador solar basado en un espejo free-form con irradiancia uniforme sobre la célula. Los concentradores parabólicos tienen numerosas desventajas como los puntos calientes en la zona central de la célula, uso no eficiente del área de la célula al ser ésta cuadrada y además tienen ángulos de aceptancia de reducido. Para poder superar estas limitaciones se propone un novedoso concepto de homogeneización de la irrandancia que se materializa en un diseño con espejo free-form. El análisis mediante simulación demuestra que la irradiancia es homogénea en una región rectangular y con mayor ángulo de aceptancia, lo que confirma la viabilidad del concepto de diseño. En el capítulo 8 se presenta un novedoso concepto para el diseño de sistemas afocales dinámicos. El objetivo del diseño es realizar un sistema cuyo haz de rayos de entrada pueda llegar con ángulos entre ±45º mientras que el haz de rayos a la salida sea siempre perpendicular al sistema, variando únicamente la posición de los elementos ópticos lateralmente. Las aplicaciones potenciales de este dispositivo son varias: tragaluces que proporcionan iluminación natural, sistemas de concentración fotovoltaica integrados en los edificios o iluminación direccionable con LEDs. Finalmente, el último capítulo contiene las conclusiones y las líneas de investigación futura.

Quasi-aplanatic free-form V-groove collimators for LED colour mixing

Two quasi-aplanatic free-form solid V-groove collimators are presented in this work. Both optical designs are originally designed using the Simultaneous Multiple Surface method in three dimensions (SMS 3D). The second optically active surface in both free-form V-groove devices is designed a posteriori as a grooved surface. First two mirror (XX) design is designed in order to clearly show the design procedure and working principle of these devices. Second, RXI free-form design is comparable with existing RXI collimators; it is a compact and highly efficient design made of polycarbonate (PC) performing very good colour mixing of the RGGB LED sources placed off-axis. There have been presented rotationally symmetric non-aplanatic high efficiency collimators with colour mixing property to be improved and rotationally symmetric aplanatic devices with good colour mixing property and efficiency to be improved. The aim of this work was to design a free-form device in order to improve colour mixing property of the rotationally symmetric nonaplanatic RXI devices and the efficiency of the aplanatic ones.

Effects of internal luminescence and internal optics on V-oc and J(sc) of III-V solar cells

For solar cells dominated by radiative recombination, the performance can be significantly enhanced by improving the internal optics. Internally radiated photons can be directly emitted from the cell, but if confined by good internal reflectors at the front and back of the cell they can also be re-absorbed with a significant probability. This so-called photon recycling leads to an increase in the equilibrium minority carrier concentration and therefore the open-circuit voltage, Voc. In multijunction cells, the internal luminescence from a particular junction can also be coupled into a lower bandgap junction where it generates photocurrent in addition to the externally generated photocurrent, and affects the overall performance of the tandem. We demonstrate and discuss the implications of a detailed model that we have developed for real, non-idealized solar cells that calculates the external luminescent efficiency, accounting for wavelength-dependent optical properties in each layer, parasitic optical and electrical losses, multiple reflections within the cell and isotropic internal emission. The calculation leads to Voc, and we show data on high quality GaAs cells that agree with the trends in the model as the optics are systematically varied. For multijunction cells the calculation also leads to the luminescent coupling efficiency, and we show data on GaInP/GaAs tandems where the trends also agree as the coupling is systematically varied. In both cases, the effects of the optics are most prominent in cells with good material quality. The model is applicable to any solar cell for which the optical properties of each layer are well-characterized, and can be used to explore a wide phase space of design for single junction and multijunction solar cells.

Luz industrial e imagen tecnificada: de Moholy Nagy al C.A.V.S. (Center for Advanced Visual Studies)

El desarrollo de la tecnología de la luz implicará la transformación de la vida social, cultural y económica. Tanto las consideraciones espaciales del Movimiento Moderno, como los efectos producidos por la segunda Guerra Mundial, tendrán efectos visibles en las nuevas configuraciones espaciales y en la relación simbiótica y recíproca que se dará entre ideología y tecnología. La transformación en la comprensión de la articulación espacial, asociada al desarrollo tecnológico, afectará al modo en que este espacio es experimentado y percibido. El espacio expositivo y el espacio escénico se convertirán en laboratorio práctico donde desarrollar y hacer comprensible todo el potencial ilusorio de la luz, la proyección y la imagen, como parámetros modificadores y dinamizadores del espacio arquitectónico. Esta experimentación espacial estará precedida por la investigación y creación conceptual en el mundo plástico, donde los nuevos medios mecánicos serán responsables de la construcción de una nueva mirada moderna mediatizada por los elementos técnicos. La experimentación óptica, a través de la fotografía, el cine, o el movimiento de la luz y su percepción, vinculada a nuevos modos de representación y comunicación, se convertirá en elemento fundamental en la configuración espacial. Este ámbito de experimentación se hará patente en la Escuela de la Bauhaus, de la mano de Gropius, Schlemmer o Moholy Nagy entre otros; tanto en reflexiones teóricas como en el desarrollo de proyectos expositivos, arquitectónicos o teatrales, que evolucionarán en base a la tecnología y la modificación de la relación con el espectador. El espacio expositivo y el espacio escénico se tomarán como oportunidad de investigación espacial y de análisis de los modos de percepción, convirtiéndose en lugares de experimentación básicos para el aprendizaje. El teatro se postula como punto de encuentro entre el arte y la técnica, cobrando especial importancia la intersección con otras disciplinas en la definición espacial. Las múltiples innovaciones técnicas ligadas a los nuevos fundamentos teatrales en la modificación de la relación con la escena, que se producen a principios del siglo XX, tendrán como consecuencia la transformación del espacio en un espacio dinámico, tanto física como perceptivamente, que dará lugar a nuevas concepciones espaciales, muchas de ellas utópicas. La luz, la proyección y la creación de ilusión en base a estímulos visuales y sonoros, aparecen como elementos proyectuales efímeros e inmateriales, que tendrán una gran incidencia en el espacio y su modo de ser experimentado. La implicación de la tecnología en el arte conllevará modificaciones en la visualización, así como en la configuración espacial de los espacios destinados a esta. Destacaremos como propuesta el Teatro Total de Walter Gropius, en cuyo desarrollo se recogen de algún modo las experiencias espaciales y las investigaciones desarrolladas sobre la estructura formal de la percepción realizadas por Moholy Nagy, además de los conceptos acerca del espacio escénico desarrollados en el taller de Teatro de la Bauhaus por Oskar Schlemmer. En el Teatro Total, Gropius incorporará su propia visión de cuestiones que pertenecen a la tradición de la arquitectura teatral y las innovaciones conceptuales que estaban teniendo lugar desde finales del s.XIX, tales como la participación activa del público o la superación entre escena y auditorio, estableciendo en el proyecto una nueva relación perceptual entre sala, espectáculo y espectador; aumentando la sensación de inmersión, a través del uso de la física, la óptica, y la acústica, creando una energía concéntrica capaz de extenderse en todas direcciones. El Teatro Total será uno de los primeros ejemplos en los que desde el punto de partida del proyecto, se conjuga la imagen como elemento comunicativo con la configuración espacial. Las nuevas configuraciones escénicas tendrán como premisa de desarrollo la capacidad de transformación tanto perceptiva, como física. En la segunda mitad del s.XX, la creación de centros de investigación como el CAVS (The Center for Advanced Visual Studies,1967), o el EAT (Experiments in Art and Technology, 1966), favorecerán la colaboración interdisciplinar entre arte y ciencia, implicando a empresas de carácter tecnológico, como Siemens, HP, IBM o Philips, facilitando soporte técnico y económico para el desarrollo de nuevos sistemas. Esta colaboración interdisciplinar dará lugar a una serie de intervenciones espaciales que tendrán su mayor visibilidad en algunas Exposiciones Universales. El resultado será, en la mayoría de los casos, la creación de espacios de carácter inmersivo, donde se establecerá una relación simbiótica entre espacio, imagen, sonido, y espectador. La colocación del espectador en el centro de la escena y la disposición dinámica de imagen y sonido, crearán una particular narrativa espacial no lineal, concebida para la experiencia. Desde las primeras proyecciones de cine a la pantalla múltiple de los Eames, las técnicas espaciales de difusión del sonido en Stockhausen, o los experimentos con el movimiento físico interactivo, la imagen, la luz en movimiento y el sonido, quedan inevitablemente convertidos en material arquitectónico. ABSTRACT. Light technology development would lead to a social, cultural and economic transformation. Both spatial consideration of “Modern Movement” and Second World War effects on technology, would have a visible aftereffect on spatial configuration and on the symbiotic and mutual relationship between ideology & technology. Comprehension adjustment on the articulation of space together with technology development, would impact on how space is perceived and felt. Exhibition space and scenic space would turn into a laboratory where developing and making comprehensive all illusory potential of light, projection and image. These new parameters would modify and revitalize the architectonic space. as modifying and revitalizing parameters of architectonic space. Spatial experimentation would be preceded by conceptual creation and investigation on the sculptural field, where new mechanic media would be responsible for a fresh and modern look influenced by technical elements. Optical experimentation, through photography, cinema or light movement and its perception, would turn into essential components for spatial arrangement linked to new ways of performance and communication. This experimentation sphere would be clear at The Bauhaus School, by the hand of Gropius, Schlemmer or Moholy Nag among others; in theoretical, theatrical or architectural performance’s projects, that would evolve based on technology and also based on the transformation of the relationship with the observer. Exhibition and perfor-mance areas would be taken as opportunities of spatial investigation and for the analysis of the different ways of perception, thus becoming key places for learning. Theater is postulated as a meeting point between art and technique, taking on a new significance at its intersection with other disciplines working with spatial definition too. The multiple innovation techniques linked to the new foundations for the theater regarding stage relation, would have as a consequence the regeneration of the space. Space would turn dynamic, both physically and perceptibly, bringing innovative spatial conceptions, many of them unrealistic. Light, projection and illusory creation based on sound and visual stimulus would appear as intangible and momentary design components, which would have a great impact on the space and on the way it is experienced. Implication of technology in art would bring changes on the observer as well as on the spatial configuration of the art spaces2. It would stand out as a proposal Walter Groupis Total Theater, whose development would include somehow the spatial experiments and studies about formal structure of perception accomplished by Moholy Nagy besides the concepts regarding stage space enhanced at the Bauhaus Theater Studio by Oskar Schlemmer. Within Total Theater, Groupis would incorporate his own view about traditional theatric architecture and conceptual innovations that were taking place since the end of the nineteenth century, such as active audience participation or the diffusing limits between scene and audience, establishing a new perception relationship between auditorium, performance and audience, improving the feeling of immersion through the use of physics, optics and acoustics, creating a concentric energy capable of spreading in all directions. Total Theater would be one of the first example in which, from the beginning of the Project, image is combined as a communicating element with the spatial configuration. As a premise of development, new stage arrangement would have the capacity of transformation, both perceptive and physically. During the second half or the twentieth century, the creation of investigation centers such as CAVS (Center for Advanced Visual Studies, 1967) or EAT (Experiments in Art and Technology, 1966), would help to the interdisciplinary collaboration between art and science, involving technology companies like Siemens, HP, IBM or Philips, providing technical and economic support to the development of new systems. This interdisciplinary collaboration would give room to a series of spatial interventions which would have visibility in some Universal Exhibitions. The result would be, in most cases, the creation of immersive character spaces, where a symbiotic relationship would be stablished between space, image, sound and audience. The new location of the audience in the middle of the display, together with the dynamic arrangement of sound and image would create a particular, no lineal narrative conceived to be experienced. Since the first cinema projections, the multiple screen of Eames, the spatial techniques for sound dissemination at Stockhausen or the interactive physical movement experimentation, image, motion light and sound would turn inevitably into architectural material.

RB-mediated suppression of spontaneous multiple neuroendocrine neoplasia and lung metastases in Rb+/− mice

Alterations in pathways mediated by retinoblastoma susceptibility gene (RB) product are among the most common in human cancer. Mice with a single copy of the Rb gene are shown to develop a syndrome of multiple neuroendocrine neoplasia. The earliest Rb-deficient atypical cells were identified in the intermediate and anterior lobes of the pituitary, the thyroid and parathyroid glands, and the adrenal medulla within the first 3 months of postnatal development. These cells form gross tumors with various degrees of malignancy by postnatal day 350. By age of 380 days, 84% of Rb+/− mice exhibited lung metastases from C-cell thyroid carcinomas. Expression of a human RB transgene in the Rb+/− mice suppressed carcinogenesis in all tissues studied. Of particular clinical relevance, the frequency of lung metastases also was reduced to 12% in Rb+/− mice by repeated i.v. administration of lipid-entrapped, polycation-condensed RB complementary DNA. Thus, in spite of long latency periods during which secondary alterations can accumulate, the initial loss of Rb function remains essential for tumor progression in multiple types of neuroendocrine cells. Restoration of RB function in humans may prove an effective general approach to the treatment of RB-deficient disseminated tumors.

“You Can't Always Get What You Want” : A Novel Research Paradigm to Explore the Relationship between Multiple Intentions and Behaviours

Funded by •Centre for Translational Research in Public Health •United Kingdom Clinical Research Collaboration Public Health Research Centre •British Heart Foundation •Cancer Research United Kingdom •Economic and Social Research Council •Medical Research Council •National Institute for Health

Multiple domains of repressor activator protein 1 contribute to facilitated binding of glycolysis regulatory protein 1

The function of repressor activator protein 1 (Rap1p) at glycolytic enzyme gene upstream activating sequence (UAS) elements in Saccharomyces cerevisiae is to facilitate binding of glycolysis regulatory protein 1 (Gcr1p) at adjacent sites. Rap1p has a modular domain structure. In its amino terminus there is an asymmetric DNA-bending domain, which is distinct from its DNA-binding domain, which resides in the middle of the protein. In the carboxyl terminus of Rap1p lie its silencing and putative activation domains. We carried out a molecular dissection of Rap1p to identify domains contributing to its ability to facilitate binding of Gcr1p. We prepared full-length and three truncated versions of Rap1p and tested their ability to facilitate binding of Gcr1p by gel shift assay. The ability to detect ternary complexes containing Rap1p⋅DNA⋅Gcr1p depended on the presence of binding sites for both proteins in the probe DNA. The DNA-binding domain of Rap1p, although competent to bind DNA, was unable to facilitate binding of Gcr1p. Full-length Rap1p and the amino- and carboxyl-truncated versions of Rap1p were each able to facilitate binding of Gcr1p at an appropriately spaced binding site. Under these conditions, Gcr1p displayed an approximately 4-fold greater affinity for Rap1p-bound DNA than for otherwise identical free DNA. When spacing between Rap1p- and Gcr1p-binding sites was altered by insertion of five nucleotides, the ability to form ternary Rap1p⋅DNA⋅Gcr1p complexes was inhibited by all but the DNA-binding domain of Rap1p itself; however, the ability of each individual protein to bind the DNA probe was unaffected.

Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing

Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The maps assembled from these fingerprints order both the clones and the restriction fragments. Maps are coordinated across three enzymes in the examples presented. Starting with yeast artificial chromosome contigs from the 7q31.3 and 7p14 regions of the human genome, we have produced cosmid-based maps spanning more than one million base pairs. Each yeast artificial chromosome is first subcloned into cosmids at a redundancy of ×15–30. Complete-digest fragments are electrophoresed on agarose gels, poststained, and imaged on a fluorescent scanner. Aberrant clones that are not representative of the underlying genome are rejected in the map construction process. Almost every restriction fragment is ordered, allowing selection of minimal tiling paths with clone-to-clone overlaps of only a few thousand base pairs. These maps demonstrate the practicality of applying the experimental and software-based steps in multiple-complete-digest mapping to a target of significant size and complexity. We present evidence that the maps are sufficiently accurate to validate both the clones selected for sequencing and the sequence assemblies obtained once these clones have been sequenced by a “shotgun” method.