HLA-A Typing in formalin-fixed paraffin embedded tissue samples : towards potential retrospective analysis

El Antígeno Leucocitario Humano (HLA en inglés) ha sido descrito en muchos casos como factor de pronóstico para cáncer. La característica principal de los genes de HLA, localizados en el cromosoma 6 (6p21.3), son sus numerosos polimorfismos. Los análisis de secuencia de nucleótidos muestran que la variación está restringida predominantemente a los exones que codifican los dominios de unión a péptidos de la proteína. Por lo tanto, el polimorfismo del HLA define el repertorio de péptidos que se unen a los alotipos de HLA y este hecho define la habilidad de un individuo para responder a la exposición a muchos agentes infecciosos durante su vida. La tipificación de HLA se ha convertido en un análisis importante en clínica. Muestras de tejido embebidas en parafina y fijadas con formalina (FFPE en inglés) son recolectadas rutinariamente en oncología. Este procedimiento podría ser utilizado como una buena fuente de ADN, dado que en estudios en el pasado los ensayos de recolección de ADN no eran normalmente llevados a cabo de casi ningún tejido o muestra en procedimientos clínicos regulares. Teniendo en cuenta que el problema más importante con el ADN de muestras FFPE es la fragmentación, nosotros propusimos un nuevo método para la tipificación del alelo HLA-A desde muestras FFPE basado en las secuencias del exón 2, 3 y 4. Nosotros diseñamos un juego de 12 cebadores: cuatro para el exón 2 de HLA-A, tres para el exón 3 de HLA-A y cinco para el exón 4 de HLA-A, cada uno de acuerdo las secuencias flanqueantes de su respectivo exón y la variación en la secuencia entre diferentes alelos. 17 muestran FFPE colectadas en el Hospital Universitario de Karolinska en Estocolmo Suecia fueron sometidas a PCR y los productos fueron secuenciados. Finalmente todas las secuencias obtenidas fueron analizadas y comparadas con la base de datos del IMGT-HLA. Las muestras FFPE habían sido previamente tipificadas para HLA y los resultados fueron comparados con los de este método. De acuerdo con nuestros resultados, las muestras pudieron ser correctamente secuenciadas. Con este procedimiento, podemos concluir que nuestro estudio es el primer método de tipificación basado en secuencia que permite analizar muestras viejas de ADN de las cuales no se tiene otra fuente. Este estudio abre la posibilidad de desarrollar análisis para establecer nuevas relaciones entre HLA y diferentes enfermedades como el cáncer también.

Synthesis of fused cyclic systems containing medium-sized rings through tandem ROM-RCM of norbornene derivatives embedded in a carbohydrate template

A general approach for the synthesis of fused cyclic systems containing medium-sized rings (7-9) has been developed. The key steps involve a diastereoface-selective Diels-Alder reaction of the dienophiles 4a-d attached to a furanosugar with cyclopentadiene and ring opening (ROM)-ring closing metathesis (RCM) of the resulting norbornene derivatives 10a-d and 11a-d. Diels-Alder reaction of the dienophiles 4a-d with cyclopentadiene in the absence of a catalyst produced 10a-d as the major product arising through addition of the diene to the unhindered Si-face. The most interesting and new aspect of the Diels-Alder reaction of these dienophiles is the accessibility of the Re-face that was blocked by the alkenyl chains under Lewis acid catalysis producing the diastereoisomers 11a-d exclusively. The reversal of facial selectivity from an uncatalyzed reaction to a catalyzed one is unprecedented. The observed stereochemical dichotomy is attributed to rotation of the enone moiety along the or bond linking the sugar moiety during formation of the chelate 13. This makes the Re-face of the enone moiety in 4a-d unhindered. Diels-Alder reaction of the carbocyclic analogue 15 under Lewis acid catalysis produced a 1: 1 mixture of the adducts 16 and 17 confirming the participation of sugar ring oxygen in chelate formation. Finally ROM-RCM of 10a-d and 11a-d with Grubbs' catalyst afforded the cis-syn-cis and cis-anti-cis bicyclo-annulated sugars 21a-d and 23a-d, respectively, containing 7-9 membered rings.

Integrative workflow-embedded support for process automation and management

This paper presents the on-going research performed in order to integrate process automation and process management support in the context of media production. This has been addressed on the basis of a holistic approach to software engineering applied to media production modelling to ensure design correctness, completeness and effectiveness. The focus of the research and development has been to enhance the metadata management throughout the process in a similar fashion to that achieved in Decision Support Systems (DSS) to facilitate well-grounded business decisions. The paper sets out the aims and objectives and the methodology deployed. The paper describes the solution in some detail and sets out some preliminary conclusions and the planned future work.

A parallel convolutional coder including embedded puncturing with application to consumer devices

As consumers demand more functionality) from their electronic devices and manufacturers supply the demand then electrical power and clock requirements tend to increase, however reassessing system architecture can fortunately lead to suitable counter reductions. To maintain low clock rates and therefore reduce electrical power, this paper presents a parallel convolutional coder for the transmit side in many wireless consumer devices. The coder accepts a parallel data input and directly computes punctured convolutional codes without the need for a separate puncturing operation while the coded bits are available at the output of the coder in a parallel fashion. Also as the computation is in parallel then the coder can be clocked at 7 times slower than the conventional shift-register based convolutional coder (using DVB 7/8 rate). The presented coder is directly relevant to the design of modern low-power consumer devices

Uniformization of affine dependence programs for parallel embedded system design

This paper is concerned with the uniformization of a system of afine recurrence equations. This transformation is used in the design (or compilation) of highly parallel embedded systems (VLSI systolic arrays, signal processing filters, etc.). In this paper, we present and implement an automatic system to achieve uniformization of systems of afine recurrence equations. We unify the results from many earlier papers, develop some theoretical extensions, and then propose effective uniformization algorithms. Our results can be used in any high level synthesis tool based on polyhedral representation of nested loop computations.

Determiner spreading as DP-predication

Determiner Spreading (DS) occurs in adjectivally modified nominal phrases comprising more than one definite article, a phenomenon that has received considerable attention and has been extensively described in Greek. This paper discusses the syntactic properties of DS in detail and argues that DS structures are both arguments and predication configurations involving two DPs. This account successfully captures the word-order facts and the distinctive interpretation of DS, while also laying the groundwork towards unifying it with other structures linking two DPs in a predicative relation.

Observations of ice multiplication in a weakly convective cell embedded in supercooled mid-level stratus

Simultaneous observations of cloud microphysical properties were obtained by in-situ aircraft measurements and ground based Radar/Lidar. Widespread mid-level stratus cloud was present below a temperature inversion (~5 °C magnitude) at 3.6 km altitude. Localised convection (peak updraft 1.5 m s−1) was observed 20 km west of the Radar station. This was associated with convergence at 2.5 km altitude. The convection was unable to penetrate the inversion capping the mid-level stratus. The mid-level stratus cloud was vertically thin (~400 m), horizontally extensive (covering 100 s of km) and persisted for more than 24 h. The cloud consisted of supercooled water droplets and small concentrations of large (~1 mm) stellar/plate like ice which slowly precipitated out. This ice was nucleated at temperatures greater than −12.2 °C and less than −10.0 °C, (cloud top and cloud base temperatures, respectively). No ice seeding from above the cloud layer was observed. This ice was formed by primary nucleation, either through the entrainment of efficient ice nuclei from above/below cloud, or by the slow stochastic activation of immersion freezing ice nuclei contained within the supercooled drops. Above cloud top significant concentrations of sub-micron aerosol were observed and consisted of a mixture of sulphate and carbonaceous material, a potential source of ice nuclei. Particle number concentrations (in the size range 0.1

Under what conditions does embedded convection enhance orographic precipitation?

Idealised convection-permitting simulations are used to quantify the impact of embedded convection on the precipitation generated by moist flow over midlatitude mountain ridges. A broad range of mountain dimensions and moist stabilities are considered to encompass a spectrum of physically plausible flows. The simulations reveal that convection only enhances orographic precipitation in cap clouds that are otherwise unable to efficiently convert cloud condensate into precipitate. For tall and wide mountains (e.g. the Washington Cascades or the southern Andes), precipitate forms efficiently through vapour deposition and collection, even in the absence of embedded convection. When embedded convection develops in such clouds, it produces competing effects (enhanced condensation in updraughts and enhanced evaporation through turbulent mixing and compensating subsidence) that cancel to yield little net change in precipitation. By contrast, convection strongly enhances precipitation over short and narrow mountains (e.g. the UK Pennines or the Oregon Coastal Range) where precipitation formation is otherwise highly inefficient. Although cancellation between increased condensation and evaporation still occurs, the enhanced precipitation formation within the convective updraughts leads to a net increase in precipitation efficiency. The simulations are physically interpreted through non-dimensional diagnostics and relevant time-scales that govern advective, microphysical, and convective processes.

A mixed-phase bulk orographic precipitation model with embedded convection

A novel analytical model for mixed-phase, unblocked and unseeded orographic precipitation with embedded convection is developed and evaluated. The model takes an idealised background flow and terrain geometry, and calculates the area-averaged precipitation rate and other microphysical quantities. The results provide insight into key physical processes, including cloud condensation, vapour deposition, evaporation, sublimation, as well as precipitation formation and sedimentation (fallout). To account for embedded convection in nominally stratiform clouds, diagnostics for purely convective and purely stratiform clouds are calculated independently and combined using weighting functions based on relevant dynamical and microphysical time scales. An in-depth description of the model is presented, as well as a quantitative assessment of its performance against idealised, convection-permitting numerical simulations with a sophisticated microphysics parameterisation. The model is found to accurately reproduce the simulation diagnostics over most of the parameter space considered.

Determination of the embedded thermo-optical expansion coefficients of PbTe and ZnSe thin film infrared multilayers

This paper reports the first derived thermo-optical properties for vacuum deposited infrared thin films embedded in multilayers. These properties were extracted from the temperature-dependence of manufactured narrow bandpass filters across the 4-17 µm mid-infrared wavelength region. Using a repository of spaceflight multi-cavity bandpass filters, the thermo-optical expansion coefficients of PbTe and ZnSe were determined across an elevated temperature range 20-160 ºC. Embedded ZnSe films showed thermo-optical properties similar to reported bulk values, whilst the embedded PbTe films of lower optical density, deviate from reference literature sources. Detailed knowledge of derived coefficients is essential to the multilayer design of temperature-invariant narrow bandpass filters for use in non-cooled infrared detection systems. We further present manufacture of the first reported temperature-invariant multi-cavity narrow bandpass filter utilizing PbS chalcogenide layer material.

The embedded cluster DBSB 48 in the nebula Hoffleit 18: Comparison with Trumpler 14

We derive fundamental parameters of the embedded cluster DBSB 48 in the southern nebula Hoffleit 18 and the very young open cluster Trumpler 14, by means of deep JHK(s) infrared photometry. We build colour-magnitude and colour-colour diagrams to derive reddening and age, based on main sequence and pre-main sequence distributions. Radial stellar density profiles are used to study cluster structure and guide photometric diagram extractions. Field-star decontamination is applied to uncover the intrinsic cluster sequences in the diagrams. Ages are inferred from K-excess fractions. A prominent pre-main sequence population is present in DBSB 48, and the K-excess fraction f(K) = 55 +/- 6% gives an age of 1.1 +/- 0.5 Myr. A mean reddening of A(Ks) = 0.9 +/- 0.03 was found, corresponding to A(v) = 8.2 +/- 0.3. The cluster CMD is consistent with the far kinematic distance of 5 kpc for Hoffleit 18. For Trumpler 14 we derived similar parameters as in previous studies in the optical, in particular an age of 1.7 +/- 0.7 Myr. The fraction of stars with infrared excess in Trumpler 14 is f(K) = 28 +/- 4%. Despite the young ages, both clusters are described by a King profile with core radii R-core = 0.46 +/- 0.05 pc and R-core = 0.35 +/- 0.04 pc, respectively, for DBSB 48 and Trumpler 14. Such cores are smaller than those of typical open clusters. Small cores are probably related to the cluster formation and/or parent molecular cloud fragmentation. In DBSB 48, the magnitude extent of the upper main sequence is Delta K-s approximate to 2 mag, while in Trumpler 14 it is Delta K-s approximate to 5 mag, consistent with the estimated ages. (c) 2008 Elsevier B.V. All rights reserved.

GEMINI near-infrared spectroscopic observations of young massive stars embedded in molecular clouds

K-band spectra of young stellar candidates in four Southern hemisphere clusters have been obtained with the Gemini Near-Infrared Spectrograph in Gemini South. The clusters are associated with IRAS sources that have colours characteristic of ultracompact H II regions. Spectral types were obtained by comparison of the observed spectra with those of a near-infrared (NIR) library; the results include the spectral classification of nine massive stars and seven objects confirmed as background late-type stars. Two of the studied sources have K-band spectra compatible with those characteristic of very hot stars, as inferred from the presence of C IV, N III and N V emission lines at 2.078, 2.116 and 2.100 mu m, respectively. One of them, I16177_IRS1, has a K-band spectrum similar to that of Cyg OB2 7, an O3If* supergiant star. The nebular K-band spectrum of the associated Ultra-Compact (UC) H II region shows the s-process [Kr III] and [Se IV] high excitation emission lines, previously identified only in planetary nebula. One young stellar object was found in each cluster, associated with either the main IRAS source or a nearby resolved Midecourse Space eXperiment (MSX) component, confirming the results obtained from previous NIR photometric surveys. The distances to the stars were derived from their spectral types and previously determined JHK magnitudes; they agree well with the values obtained from the kinematic method, except in the case of IRAS 15408-5356, for which the spectroscopic distance is about a factor of 2 smaller than the kinematic value.