The Interstellar Neutral He haze in the heliosphere: what can we learn?

Neutral interstellar helium has been observed by the Interstellar Boundary Explorer (IBEX) since 2009, with a signal-to-noise ratio well above 1000. Because of the geometry of the observations, the signal observed from January to March each year is the easiest to identify. However, as we show via simulations, the portion of the signal in the range of intensities from 10(-3) to 10(-2) of the peak value, previously mostly left out from the analysis, may provide important information about the details of the distribution function of interstellar He gas in front of the heliosphere. In particular, these observations may inform us about possible departures of the parent interstellar He population from equilibrium. We compare the expected distribution of the signal for the canonical assumption of a single Maxwell-Boltzmann population with the distributions for a superposition of the Maxwell-Boltzmann primary population and the recently discovered Warm Breeze, and for a single primary population given by a kappa function. We identify the regions on the sky where the differences between those cases are expected to be the most visible against the background. We discuss the diagnostic potential of the fall peak of the interstellar signal, reduced by a factor of 50 due to the Compton-Getting effect but still above the detection limit of IBEX. We point out the strong energy dependence of the fall signal and suggest that searching for this signal in the data could bring an independent assessment of the low-energy measurement threshold of the IBEX-Lo sensor.

The transcriptional repressor Delta EF1 controls resistance to the EGFR inhibitor erlotinib in human HNSCC lines

Epidermal Growth Factor Receptor (EGFR) overexpression occurs in about 90% of Head and Neck Squamous Cell Carcinoma (HNSCC) cases. Aberrant EGFR signaling has been implicated in the malignant features of HNSCC. Thus, EGFR appears to be a logical therapeutic target with increased tumor specificity for the treatment of HNSCC. Erlotinib, a small molecule tyrosine kinase inhibitor, specifically inhibits aberrant EGFR signaling in HNSCC. Only a minority of HNSCC patients were able to derive a substantial clinical benefit from erlotinib. ^ This dissertation identifies Epithelial to Mesenchymal Transition (EMT) as the biological marker that distinguishes EGFR-dependent (erlotinib-sensitive) tumors from the EGFR-independent (erlotinib-resistant) tumors. This will allow us to prospectively identify the patients who are most likely to benefit from EGFR-directed therapy. More importantly, our data identifies the transcriptional repressor DeltaEF1 as the mesenchymal marker that controls EMT phenotype and resistance to erlotinib in human HNSCC lines. si-RNA mediated knockdown of DeltaEF1 in the erlotinib-resistant lines resulted in reversal of the mesenchymal phenotype to an epithelial phenotype and significant increase in sensitivity to erlotinib. ^ DeltaEF1 represses the expression of the epithelial markers by recruiting HDACs to chromatin. This observation allows us to translate our findings into clinical application. To test whether the transcriptional repression by DeltaEF1 underlines the mechanism responsible for erlotinib resistance, erlotinib-resistant lines were treated with an HDAC inhibitor (SAHA) followed by erlotinib. This resulted in a synergistic effect and substantial increase in sensitivity to erlotinib in the resistant cell lines. Thus, combining an HDAC inhibitor with erlotinib represents a novel promising pharmacologic strategy for reversing resistance to erlotinib in HNSCC patients. ^

ANTI-TUMOR EFFECTS OF THE NOTCH PATHWAY IN GASTROINTESTINAL STROMAL TUMORS

Gastrointestinal Stromal Tumors (GIST) are sarcomas driven by gain-of-function mutations of KIT or PDGFRA. Although, the introduction of tyrosine kinase inhibitors has dramatically changed the history of this disease, evidences emerge that inhibition of KIT or PDGFRA are not sufficient to cure patients. The developmental pathway Notch has a critical role in the cell fate, regulating cell proliferation and differentiation. Dysregulation of Notch pathway has been implicated in a wide variety of cancers functioning as a tumor promoter or a tumor suppressor in a cell context dependent manner. Given that Notch activation deregulates the morphogenesis of mesenchymal cells in the GI track, that Notch acts as a tumor suppressor in neuroendocrine tumors, and finally that the cell of origin of GIST are the Interstitial Cell of Cajal that arise from a mesenchymal origin with some neuroendocrine features, we hypothesized that Notch pathway signaling may play a role in growth, survival and differentiation of GIST cells. To test this hypothesis, we genetically and pharmacologically manipulated the Notch pathway in human GIST cells. In this study, we demonstrated that constitutively active intracellular domain of Notch1 (ICN-1) expression potently induced growth arrest and downregulated KIT expression. We have performed a retrospective analysis of 15 primary GIST patients and found that high mRNA level of Hes1, a major target gene of Notch pathway, correlated with a significantly longer relapse-free survival. Therefore, we have established that treatment with the FDA approved histone deacetylase inhibitor SAHA (Vorinostat) caused dose-dependent upregulation of Notch1 expression and a parallel decrease in viability in these cells. Retroviral silencing of downstream targets of Notch with dominant negative Hes-1 as well as pharmacological inhibition of Notch pathway with a γ-secretase inhibitor partially rescued GIST cells from SAHA treatment. Taken together these results identify anti-tumor effect of Notch1 and a negative cross-talk between Notch1 and KIT pathways in GIST. Consequently, we propose that activation of this pathway with HDAC inhibitors may be a potential therapeutic strategy for GIST patients.

Performance data of the coral Pocillopora verrucosa and environmental conditions along the Saudi Arabian Red Sea coast as assessed during 3 expeditions in the years 2011 and 2012

Large scale patterns of ecologically relevant traits may help identify drivers of their variability and conditions beneficial or adverse to the expression of these traits. Antimicrofouling defenses in scleractinian corals regulate the establishment of the associated biofilm as well as the risks of infection. The Saudi Arabian Red Sea coast features a pronounced thermal and nutritional gradient including regions and seasons with potentially stressful conditions to corals. Assessing the patterns of antimicrofouling defenses across the Red Sea may hint at the susceptibility of corals to global change. We investigated microfouling pressure as well as the relative strength of 2 alternative antimicrofouling defenses (chemical antisettlement activity, mucus release) along the pronounced environmental gradient along the Saudi Arabian Red Sea coast in 2 successive years. Microfouling pressure was exceptionally low along most of the coast but sharply increased at the southernmost sites. Mucus release correlated with temperature. Chemical defense tended to anti-correlate with mucus release. As a result, the combined action of mucus release and chemical antimicrofouling defense seemed to warrant sufficient defense against microbes along the entire coast. In the future, however, we expect enhanced energetic strain on corals when warming and/or eutrophication lead to higher bacterial fouling pressure and a shift towards putatively more costly defense by mucus release.

Defence chemistry modulation by light and temperature (results in 4 excel files, zipped)

The goals of this study were (1) to investigate whether Fucus vesiculosus regulates the production of its antifouling defence chemicals against microfoulers in response to light limitation and temperature shifts and (2) to investigate if different surface concentrations of defence compounds shape epibacterial communities. F. vesiculosus was incubated in indoor mesocosms at five different temperature conditions (5 to 25°C) and in outdoor mesocosms under six differently reduced sunlight conditions (0 to 100%), respectively. Algal surface concentrations of previously identified antifouling compounds - dimethylsulphopropionate (DMSP), fucoxanthin and proline - were determined and the bacterial community composition was characterized by in-depth sequencing of the 16S-rRNA gene. Altogether, the effect of different treatment levels upon defence compound concentrations was limited. Under all conditions DMSP alone appeared to be sufficiently concentrated to warrant for at least a partial inhibitory action against epibiotic bacteria of F. vesiculosus. In contrast, proline and fucoxanthin rarely reached the necessary concentration ranges for self-contained inhibition. Nonetheless, in both experiments along with the direct influence of temperature and light, all three compounds apparently affected (and thereby shaped) the overall bacterial community composition associated with F. vesiculosus since tendencies for insensitivity towards all three compounds were observed among bacterial taxa that typically dominate those communities. Given that the concentrations of at least one of the compounds (in most cases DMSP) were always high enough to inhibit bacterial settlement, we conclude that the capacity of F. vesiculosus for such defence will hardly be compromised by shading or warming to temperatures up to 25°C.

3D Soil Images Structure Quantification using Relative Entropy

Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice?Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.

Self-similar motion of laser half-space plasmas. I. Deflagration regime

The one-dimensional self-similar motion of an initially cold, half-space plasma of electron density 0,produced by the (anomalous) absorption of a laser pulse of irradiation = (j>0f/T(0< (< T) at the critical density nc(«c/«0=eoKe)213, where k, m, are Boltzmann's constant and the ion mass, and Ke X (electron temperature)5'2 = heat conductivity. If a >e- 4 ' 3 , a deflagration wave separates an isentropic compression with a shock bounding the undisturbed plasma, and an isentropic expansion flow to the vacuum. The structures of these three regions are completely determined; in particular, the Chapman-Jouguet condition is proved and the density behind the deflagration is found. The deflagration-compression thickness ratio is large (small) for a^e- 5 ' 3(a>e- 5 ' 3 ) . The compression to expansion ratio for both energy and thickness is 0(e"2). For Z,- large, a deflagration exists even if a~e~413. Condition a>e~4'3 may be applied to pulses that are not linear.

Ion charge number and flux saturation effects in the corona of a laser-irradiated pellet

The quasisteady structure of the corona of a laser-irradiated pellet is completely determined for arbitrary Z, (ion charge number} and re/ra (ratio of critical and ablation radii), and for heat-flux saturation factor/above approximately 0.04. The ion-to-electron temperature ratio at rc grows sensibly with Z,; all other quantities depend weakly and nonmonotonically on Z,. For rc /ra close to unity, and all Z, of interest (Z, < 47}, the flow is subsonic at rc. For a given laser power W, flux saturation may decrease (low/) or increase (high/) the ablation pressure Pa relative to the value obtained when saturation is not considered; in some cases a decrease in/with W fixed increases Pa. For intermediate^ ~0.1), Pa cc (W/r* )2/3 p\n\pc = critical density), independently of rc/ra; for/~0.6, Pa «s larger by a factor of about [rc/raf13. For rjra > 1.2 roughly, the mass ablation rate is C{Z,) [{m/kZ.f^Kr^Pl) l,\ independent of pc and/, and barely dependent on Z,(m, is ion mass; k, Boltzmann's constant; K, conductivity coefficient; and C, a tabulated function).

Aplicación de la física estadística a los medios granulares

Esta tesis se centra en el estudio de medios granulares blandos y atascados mediante la aplicación de la física estadística. Esta aproximación se sitúa entre los tradicionales enfoques macro y micromecánicos: trata de establecer cuáles son las propiedades macroscópicas esperables de un sistema granular en base a un análisis de las propiedades de las partículas y las interacciones que se producen entre ellas y a una consideración de las restricciones macroscópicas del sistema. Para ello se utiliza la teoría estadística junto con algunos principios, conceptos y definiciones de la teoría de los medios continuos (campo de tensiones y deformaciones, energía potencial elástica, etc) y algunas técnicas de homogeneización. La interacción entre las partículas es analizada mediante las aportaciones de la teoría del contacto y de las fuerzas capilares (producidas por eventuales meniscos de líquido cuando el medio está húmedo). La idea básica de la mecánica estadística es que entre todas soluciones de un problema físico (como puede ser el ensamblaje en equilibrio estático de partículas de un medio granular) existe un conjunto que es compatible con el conocimiento macroscópico que tenemos del sistema (por ejemplo, su volumen, la tensión a la que está sometido, la energía potencial elástica que almacena, etc.). Este conjunto todavía contiene un número enorme de soluciones. Pues bien, si no hay ninguna información adicional es razonable pensar que no existe ningún motivo para que alguna de estas soluciones sea más probable que las demás. Entonces parece natural asignarles a todas ellas el mismo peso estadístico y construir una función matemática compatible. Actuando de este modo se obtiene cuál es la función de distribución más probable de algunas cantidades asociadas a las soluciones, para lo cual es muy importante asegurarse de que todas ellas son igualmente accesibles por el procedimiento de ensamblaje o protocolo. Este enfoque se desarrolló en sus orígenes para el estudio de los gases ideales pero se puede extender para sistemas no térmicos como los analizados en esta tesis. En este sentido el primer intento se produjo hace poco más de veinte años y es la colectividad de volumen. Desde entonces esta ha sido empleada y mejorada por muchos investigadores en todo el mundo, mientras que han surgido otras, como la de la energía o la del fuerza-momento (tensión multiplicada por volumen). Cada colectividad describe, en definitiva, conjuntos de soluciones caracterizados por diferentes restricciones macroscópicas, pero de todos ellos resultan distribuciones estadísticas de tipo Maxwell-Boltzmann y controladas por dichas restricciones. En base a estos trabajos previos, en esta tesis se ha adaptado el enfoque clásico de la física estadística para el caso de medios granulares blandos. Se ha propuesto un marco general para estudiar estas colectividades que se basa en la comparación de todas las posibles soluciones en un espacio matemático definido por las componentes del fuerza-momento y en unas funciones de densidad de estados. Este desarrollo teórico se complementa con resultados obtenidos mediante simulación de la compresión cíclica de sistemas granulares bidimensionales. Se utilizó para ello un método de dinámica molecular, MD (o DEM). Las simulaciones consideran una interacción mecánica elástica, lineal y amortiguada a la que se ha añadido, en algunos casos, la fuerza cohesiva producida por meniscos de agua. Se realizaron cálculos en serie y en paralelo. Los resultados no solo prueban que las funciones de distribución de las componentes de fuerza-momento del sistema sometido a un protocolo específico parecen ser universales, sino que también revelan que existen muchos aspectos computacionales que pueden determinar cuáles son las soluciones accesibles. This thesis focuses on the application of statistical mechanics for the study of static and jammed packings of soft granular media. Such approach lies between micro and macromechanics: it tries to establish what the expected macroscopic properties of a granular system are, by starting from a micromechanical analysis of the features of the particles, and the interactions between them, and by considering the macroscopic constraints of the system. To do that, statistics together with some principles, concepts and definitions of continuum mechanics (e.g. stress and strain fields, elastic potential energy, etc.) as well as some homogenization techniques are used. The interaction between the particles of a granular system is examined too and theories on contact and capillary forces (when the media are wet) are revisited. The basic idea of statistical mechanics is that among the solutions of a physical problem (e.g. the static arrangement of particles in mechanical equilibrium) there is a class that is compatible with our macroscopic knowledge of the system (volume, stress, elastic potential energy,...). This class still contains an enormous number of solutions. In the absence of further information there is not any a priori reason for favoring one of these more than any other. Hence we shall naturally construct the equilibrium function by assigning equal statistical weights to all the functions compatible with our requirements. This procedure leads to the most probable statistical distribution of some quantities, but it is necessary to guarantee that all the solutions are likely accessed. This approach was originally set up for the study of ideal gases, but it can be extended to non-thermal systems too. In this connection, the first attempt for granular systems was the volume ensemble, developed about 20 years ago. Since then, this model has been followed and improved upon by many researchers around the world, while other two approaches have also been set up: energy and force-moment (i.e. stress multiplied by volume) ensembles. Each ensemble is described by different macroscopic constraints but all of them result on a Maxwell-Boltzmann statistical distribution, which is precisely controlled by the respective constraints. According to this previous work, in this thesis the classical statistical mechanics approach is introduced and adapted to the case of soft granular media. A general framework, which includes these three ensembles and uses a force-moment phase space and a density of states function, is proposed. This theoretical development is complemented by molecular dynamics (or DEM) simulations of the cyclic compression of 2D granular systems. Simulations were carried out by considering spring-dashpot mechanical interactions and attractive capillary forces in some cases. They were run on single and parallel processors. Results not only prove that the statistical distributions of the force-moment components obtained with a specific protocol seem to be universal, but also that there are many computational issues that can determine what the attained packings or solutions are.