Ensemble transcript interaction networks: A case study on Alzheimer's disease

Systems biology techniques are a topic of recent interest within the neurological field. Computational intelligence (CI) addresses this holistic perspective by means of consensus or ensemble techniques ultimately capable of uncovering new and relevant findings. In this paper, we propose the application of a CI approach based on ensemble Bayesian network classifiers and multivariate feature subset selection to induce probabilistic dependences that could match or unveil biological relationships. The research focuses on the analysis of high-throughput Alzheimer's disease (AD) transcript profiling. The analysis is conducted from two perspectives. First, we compare the expression profiles of hippocampus subregion entorhinal cortex (EC) samples of AD patients and controls. Second, we use the ensemble approach to study four types of samples: EC and dentate gyrus (DG) samples from both patients and controls. Results disclose transcript interaction networks with remarkable structures and genes not directly related to AD by previous studies. The ensemble is able to identify a variety of transcripts that play key roles in other neurological pathologies. Classical statistical assessment by means of non-parametric tests confirms the relevance of the majority of the transcripts. The ensemble approach pinpoints key metabolic mechanisms that could lead to new findings in the pathogenesis and development of AD

Anticorrelation between Ion Acceleration and Nonlinear Coherent Structures from Laser-Underdense Plasma Interaction

In laser-plasma experiments, we observed that ion acceleration from the Coulomb explosion of the plasma channel bored by the laser, is prevented when multiple plasma instabilities such as filamentation and hosing, and nonlinear coherent structures (vortices/post-solitons) appear in the wake of an ultrashort laser pulse. The tailoring of the longitudinal plasma density ramp allows us to control the onset of these insabilities. We deduced that the laser pulse is depleted into these structures in our conditions, when a plasma at about 10% of the critical density exhibits a gradient on the order of 250 {\mu}m (gaussian fit), thus hindering the acceleration. A promising experimental setup with a long pulse is demonstrated enabling the excitation of an isolated coherent structure for polarimetric measurements and, in further perspectives, parametric studies of ion plasma acceleration efficiency.

Transcriptional changes and oxidative stress associated with the synergistic interaction between potato virus X and potato virus Y and their relationship with symptom expression.

Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus---host interactions in mixed infections. Compared with single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves and death of the plant. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection and correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly infected leaves were compared with those from singly infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (downregulated), protein synthesis and degradation (upregulated), carbohydrate metabolism (upregulated), and response to biotic stimulus and stress (upregulated). The expressions of reactive oxygen species?generating enzymes as well as several mitogen-activated protein kinases were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely upregulated by the synergistic infection. Virus-induced gene silencing of ?-dioxygenase1 delayed cell death during PVX?PVY infection.

Integrated studies for the evaluation of conservation treatments on stone material from archaeological sites. Application to the case of Mérida (Spain)

In recent decades archaeological sites have been subject of many interventions. The application of conservation treatments, such us consolidation and protection ones by means of using, for instance, synthetic resins or organosilicic compounds, has been demonstrated inadequate in many cases, and even harmful for the heritage materials [1]. Evaluation studies should be a mandatory task, ideally before and after the intervention, but both tasks are complex and unusual in the case of archaeological heritage. Moreover, there is a general lack of knowledge in the mid and long term effects of these treatments, and how to act when these have resulted in deterioration of the original material. Remains of Roman Augusta Emerita, located in Merida (Spain), have gone through many interventions since the first archaeological campaign, in 1910. Some of them have demonstrated already to be harmful [2], others, more recent, must be evaluated in order to determine its effectiveness and durability, considering that many of these treatments are currently still applied. For this purpose a range of parameters has been measured such as color, surface hardness and roughness, mechanical or hydric properties, porosity, etc. on the original material (granite, marble and mortars mainly), and then the transformations of those same parameters analyzed after treatment, both in situ, in places where a intervention is documented, and in the laboratory, in samples. The study is being conducted both in the laboratory (Petrophysics Laboratory within IGEO) and in situ, on selected archaeological sites of Mérida (Theater and House of Mitreo). The comparison of results in untreated and treated areas of the site, and in treated-untreated samples, allows the distinction of variables that affect the interaction between products and stone material, issues such us effectiveness and durability of treatment and its validation or dismissal.

Polymer interaction with macroscopic carbon nanotube fibres and fabrication of nanostructured composites

El ensamblado de nanotubos de carbono (CNT) como una fibra macroscópica en la cual están orientados preferentemente paralelos entre sí y al eje de la fibra, ha dado como resultado un nuevo tipo de fibra de altas prestaciones derivadas de la explotación eficiente de las propiedades axiales de los CNTs, y que tiene un gran número de aplicaciones potenciales. Fibras continuas de CNTs se produjeron en el Instituto IMDEA Materiales mediante el proceso de hilado directo durante la reacción de síntesis por deposición química de vapores. Uno de los objetivos de esta tesis es el estudio de la estructura de estas fibras mediante técnicas del estado del arte de difracción de rayos X de sincrotrón y la elaboración de un modelo estructural de dicho material. Mediciones texturales de adsorción de gases, análisis de micrografías de electrones y dispersión de rayos X de ángulo alto y bajo (WAXS/SAXS) indican que el material tiene una estructura mesoporosa con una distribución de tamaño de poros ancha derivada del amplio rango de separaciones entre manojos de CNTs, así como una superficie específica de 170m2/g. Los valores de dimensión fractal obtenidos mediante SAXS y análisis Barrett-Joyner-Halenda (BJH) de mediciones texturales coinciden en 2.4 y 2.5, respectivamente, resaltando el carácter de red de la estructura de dichas fibras. La estructura mesoporosa y tipo hilo de las fibra de CNT es accesible a la infiltración de moléculas externas (líquidos o polímeros). En este trabajo se estudian los cambios en la estructura multiescala de las fibras de CNTs al interactuar con líquidos y polímeros. Los efectos de la densificación en la estructura de fibras secas de CNT son estudiados mediante WAXS/SAXS. El tratamiento de densificación junta los manojos de la fibra (los poros disminuyen de tamaño), resultando en un incremento de la densidad de la fibra. Sin embargo, los dominios estructurales correspondientes a la transferencia de esfuerzo mecánica y carga eléctrica en los nanotubos no son afectados durante este proceso de densificación; como consecuencia no se produce un efecto sustancial en las propiedades mecánicas y eléctricas. Mediciones de SAXS and fibra de CNT antes y después de infiltración de líquidos confirman la penetración de una gran cantidad de líquidos que llena los poros internos de la fibra pero no se intercalan entre capas de nanotubos adyacentes. La infiltración de cadenas poliméricas de bajo peso molecular tiende a expandir los manojos en la fibra e incrementar el ángulo de apertura de los poros. Los resultados de SAXS indican que la estructura interna de la fibra en términos de la organización de las capas de tubos y su orientación no es afectada cuando las muestras consisten en fibras infiltradas con polímeros de alto peso molecular. La cristalización de varios polímeros semicristalinos es acelerada por la presencia de fibras de CNTs alineados y produce el crecimiento de una capa transcristalina normal a la superficie de la fibra. Esto es observado directamente mediante microscopía óptica polarizada, y detectado mediante calorimetría DSC. Las lamelas en la capa transcristalina tienen orientación de la cadena polimérica paralela a la fibra y por lo tanto a los nanotubos, de acuerdo con los patrones de WAXS. Esta orientación preferencial se sugiere como parte de la fuerza impulsora en la nucleación. La nucleación del dominio cristalino polimérico en la superficie de los CNT no es epitaxial. Ocurre sin haber correspondencia entre las estructuras cristalinas del polímero y los nanotubos. Estas observaciones contribuyen a la compresión del fenómeno de nucleación en CNTs y otros nanocarbonos, y sientan las bases para el desarrollo de composites poliméricos de gran escala basados en fibra larga de CNTs alineados. ABSTRACT The assembly of carbon nanotubes into a macroscopic fibre material where they are preferentially aligned parallel to each other and to the fibre axis has resulted in a new class of high-performance fibres, which efficiently exploits the axial properties of the building blocks and has numerous applications. Long, continuous CNT fibres were produced in IMDEA Materials Institute by direct fibre spinning from a chemical vapour deposition reaction. These fibres have a complex hierarchical structure covering multiple length scales. One objective of this thesis is to reveal this structure by means of state-of-the-art techniques such as synchrotron X-ray diffraction, and to build a model to link the fibre structural elements. Texture and gas absorption measurements, using electron microscopy, wide angle and small angle X-ray scattering (WAXS/SAXS), and pore size distribution analysis by Barrett-Joyner-Halenda (BJH), indicate that the material has a mesoporous structure with a wide pore size distribution arising from the range of fibre bundle separation, and a high surface area _170m2/g. Fractal dimension values of 2.4_2.5 obtained from the SAXS and BJH measurements highlight the network structure of the fibre. Mesoporous and yarn-like structure of CNT fibres make them accessible to the infiltration of foreign molecules (liquid or polymer). This work studies multiscale structural changes when CNT fibres interact with liquids and polymers. The effects of densification on the structure of dry CNT fibres were measured by WAXS/SAXS. The densification treatment brings the fibre bundles closer (pores become smaller), leading to an increase in fibre density. However, structural domains made of the load and charge carrying nanotubes are not affected; consequently, it has no substantial effect on mechanical and electrical properties. SAXS measurements on the CNT fibres before and after liquid infiltration imply that most liquids are able to fill the internal pores but not to intercalate between nanotubes. Successful infiltration of low molecular weight polymer chains tends to expand the fibre bundles and increases the pore-opening angle. SAXS results indicate that the inner structure of the fibre, in terms of the nanotube layer arrangement and the fibre alignment, are not largely affected when infiltrated with polymers of relatively high molecular weight. The crystallisation of a variety of semicrystalline polymers is accelerated by the presence of aligned fibres of CNTs and results in the growth of a transcrystalline layer perpendicular to the fibre surface. This can be observed directly under polarised optical microscope, and detected by the exothermic peaks during differential scanning calorimetry. The discussion on the driving forces for the enhanced nucleation points out the preferential chain orientation of polymer lamella with the chain axis parallel to the fibre and thus to the nanotubes, which is confirmed by two-dimensional WAXS patterns. A non-epitaxial polymer crystal growth habit at the CNT-polymer interface is proposed, which is independent of lattice matching between the polymer and nanotubes. These findings contribute to the discussion on polymer nucleation on CNTs and other nanocarbons, and their implication for the development of large polymer composites based on long and aligned fibres of CNTs.

Vortex-induced vibrations on bridges : the interaction mechanism in complex sections and a new proposed semi-empirical model

El presente trabajo de investigación se ocupa del estudio de las vibraciones verticales inducidas por vórtices (VIV) en aquellos puentes que, por sus características geométricas y propiedades dinámicas, muestran cierta sensibilidad este tipo de fenómeno aeroelástico. El objeto principal es el análisis del mecanismo de interacción viento-estructura sobre secciones no fuseladas de geometría simple, con objeto de realizar una adecuada caracterización del problema y poder abordar posteriormente el análisis de otras secciones de geometría más compleja, representativas de los principales elementos estructurales de los puentes, como arcos, tableros, torres y pilas. Este aspecto es fundamental durante la fase de diseño del puente, donde deberán tenerse en cuenta también una serie de detalles que pueden influir significativamente su sensibilidad ante problemas aerodinámicos, como la morfología y dimensiones principales de la sección transversal del tablero, la disposición de barreras de seguridad y barreras cortaviento, o las riostras que unen diferentes elementos estructurales. La configuración de dos elementos en tándem o la construcción de un puente en las inmediaciones de otro existente son otros aspectos a considerar respecto a la sensibilidad frente a efectos aeroelásticos. El estudio se ha llevado a cabo principalmente mediante la implementación de simulaciones numéricas que reproducen la interacción entre la corriente de aire y secciones representativas de modelos estructurales, a partir de un código CFD basado en el método de las partículas de vórtices (VPM), siguiendo por tanto un esquema Lagrangiano. Los resultados han sido validados con datos experimentales existentes, valores procedentes de ensayos en túnel de viento y registros reales a partir de diferentes casos de estudio: Alconétar (2006), Niterói (1980), Trans- Tokyo Bay (1995) y Volgogrado (2010). Finalmente, se propone un modelo semi-empírico para la estimación del rango de velocidades críticas y amplitudes de oscilación basado en la utilización de las derivadas de flameo de Scanlan, y la densidad espectral de las fuerzas aerodinámicas en el dominio de la frecuencia. The present research work concerns the study of vertical vortex-induced vibrations (VIV) in bridges which show certain sensitivity to this type of aeroelastic phenomenon. It focuses on the analysis of the wind-structure interaction mechanism on bluff sections, with the objective of making a good characterisation of the problem and subsequently addressing the analysis of sections with a complex geometry, which are representative of the bridge structural elements, such as arches, decks, towers and piers. This issue is of relative importance during the bridge design phase, since minor details of the aforementioned elements can significantly influence its sensitivity to aerodynamic problems. The shape and main dimensions of the deck cross section, the addition of safety barriers and windshields, the presence of braces to enhance the structure mechanical properties, the utilisation of cross sections in tandem arrangement, or the erection of a new bridge in the vicinity of another existing one are some of the aspects to be considered regarding the sensitivity to the aeroelastic effects. The study has been carried out mainly through the implementation of numerical simulations that reproduces the interaction between the airflow and the representative cross section of a structural bridge model, by the use of a CFD code based on the vortex particle method (VPM), thus following a Lagrangian scheme. The results have been validated with existing experimental data, values from wind tunnel tests and full scale observations from the different case studies: Alconétar (2006), Niterói (1980), Trans-Tokyo Bay (1995) and Volgograd (2010). Finally, a new semi-empirical model is proposed for the estimation of the critical wind velocity ranges and oscillation amplitudes based on the use of the Scanlan’s flutter derivatives and the power spectral density of aerodynamic force time history in the frequency domain.