Exploring the Oxygen Order in Hg-1223 and Hg-1201 by 199Hg MAS NMR

We demonstrate the use of a high-resolution solid-state fast (45 kHz) magic angle spinning (MAS) NMR for mapping the oxygen distribution in Hg-based cuprate superconductors. We identify observed three peaks in 199Hg spectrum as belonging to the different chemical environments in the HgO? layer with no oxygen neighbors, single oxygen neighbor, and two oxygen neighbors. We discuss observed differences between Hg-1201 and Hg-1223 materials.Comment: 4 pages, 2 figures included. Submitted to NATO Advanced Research Workshop Proceedings (Miami January 2004

Genonets server-a web server for the construction, analysis and visualization of genotype networks.

A genotype network is a graph in which vertices represent genotypes that have the same phenotype. Edges connect vertices if their corresponding genotypes differ in a single small mutation. Genotype networks are used to study the organization of genotype spaces. They have shed light on the relationship between robustness and evolvability in biological systems as different as RNA macromolecules and transcriptional regulatory circuits. Despite the importance of genotype networks, no tool exists for their automatic construction, analysis and visualization. Here we fill this gap by presenting the Genonets Server, a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education. The Genonets Server is freely available at http://ieu-genonets.uzh.ch

The anatomy of the tendon of the Infundibulum revisited

The heart is a muscular organ supported by collagenous tissue. The collagenous tissue is condensed in certain areas to form a supporting framework, often called the fibrous skeleton. The so-called tendon of the infundibulum has previously been described as part of this skeleton, but its structure and incidence remain ill defined. The tendon was initially described as a strip of fibrous tissue running between the aortic root and the pulmonary trunk. Since information on its structure is vague, we sought to evaluate its existence in 100 formalin-fixed adult human hearts obtained from subjects ranging in age from 22 to 86 years, in 20 hearts from infants and children aged from 2 months to 6 years at the time of their death and in 10 cattle hearts. We used classical macroscopic anatomical techniques to demonstrate all the possible connections between the sinuses of the aorta and the pulmonary trunk. We then supplemented the macroscopic techniques with serial transverse histological sections taken through the vascular roots, staining the sections with the haematoxylin-eosin, van Gieson, Masson trichrome and orcein staining methods. Fascial bands surrounded by connective tissue were observed in all hearts. In 80 adult hearts and in 16 neonatal hearts we found fascial bands or strips, which connected the aortic and pulmonary roots. Only in two hearts, however, were we able to identify tendon-like structures, and histology revealed that these were formed by tightly packed collagen fibres intermingled with fat, most likely due to advanced age. Thus in those cases where a "tendon" was present it was no more than condensed fascial bands joining together the apposing sinuses of the arterial trunks. In our opinion, therefore, accounts in the literature describing the "tendon of the infundibulum" as a tendinous structure connecting the aortic and pulmonary roots do not accurately represent this anatomical structure

RNA-mediated gene regulation is less evolvable than transcriptional regulation.

Much of gene regulation is carried out by proteins that bind DNA or RNA molecules at specific sequences. One class of such proteins is transcription factors, which bind short DNA sequences to regulate transcription. Another class is RNA binding proteins, which bind short RNA sequences to regulate RNA maturation, transport, and stability. Here, we study the robustness and evolvability of these regulatory mechanisms. To this end, we use experimental binding data from 172 human and fruit fly transcription factors and RNA binding proteins as well as human polymorphism data to study the evolution of binding sites in vivo. We find little difference between the robustness of regulatory protein-RNA interactions and transcription factor-DNA interactions to DNA mutations. In contrast, we find that RNA-mediated regulation is less evolvable than transcriptional regulation, because mutations are less likely to create interactions of an RNA molecule with a new RNA binding protein than they are to create interactions of a gene regulatory region with a new transcription factor. Our observations are consistent with the high level of conservation observed for interactions between RNA binding proteins and their target molecules as well as the evolutionary plasticity of regulatory regions bound by transcription factors. They may help explain why transcriptional regulation is implicated in many more evolutionary adaptations and innovations than RNA-mediated gene regulation

Constraints on the pMSSM from LAT Observations of Dwarf Spheroidal Galaxies

We examine the ability for the Large Area Telescope (LAT) to constrain Minimal Supersymmetric Standard Model (MSSM) dark matter through a combined analysis of Milky Way dwarf spheroidal galaxies. We examine the Lightest Supersymmetric Particles (LSPs) for a set of ~71k experimentally valid supersymmetric models derived from the phenomenological-MSSM (pMSSM). We find that none of these models can be excluded at 95% confidence by the current analysis; nevertheless, many lie within the predicted reach of future LAT analyses. With two years of data, we find that the LAT is currently most sensitive to light LSPs (m_LSP < 50 GeV) annihilating into tau-pairs and heavier LSPs annihilating into b-bbar. Additionally, we find that future LAT analyses will be able to probe some LSPs that form a sub-dominant component of dark matter. We directly compare the LAT results to direct detection experiments and show the complementarity of these search methods.Comment: 24 pages, 9 figures, submitted to JCA

An Immunocompetent Mouse Model of HPV16(+) Head and Neck Squamous Cell Carcinoma

The incidence of human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) is increasing and implicated in more than 60% of all oropharyngeal carcinomas (OPSCCs). Although whole-genome, transcriptome, and proteome analyses have identified altered signaling pathways in HPV-induced HNSCCs, additional tools are needed to investigate the unique pathobiology of OPSCC. Herein, bioinformatics analyses of human HPV(+) HNSCCs revealed that all tumors express full-length E6 and identified molecular subtypes based on relative E6 and E7 expression levels. To recapitulate the levels, stoichiometric ratios, and anatomic location of E6/E7 expression, we generated a genetically engineered mouse model whereby balanced expression of E6/E7 is directed to the oropharyngeal epithelium. The addition of a mutant PIK3CAE545K allele leads to the rapid development of pre-malignant lesions marked by immune cell accumulation, and a subset of these lesions progress to OPSCC. This mouse provides a faithful immunocompetent model for testing treatments and investigating mechanisms of immunosuppression

N-body simulations with generic non-Gaussian initial conditions I: Power Spectrum and halo mass function

We address the issue of setting up generic non-Gaussian initial conditions for N-body simulations. We consider inflationary-motivated primordial non-Gaussianity where the perturbations in the Bardeen potential are given by a dominant Gaussian part plus a non-Gaussian part specified by its bispectrum. The approach we explore here is suitable for any bispectrum, i.e. it does not have to be of the so-called separable or factorizable form. The procedure of generating a non-Gaussian field with a given bispectrum (and a given power spectrum for the Gaussian component) is not univocal, and care must be taken so that higher-order corrections do not leave a too large signature on the power spectrum. This is so far a limiting factor of our approach. We then run N-body simulations for the most popular inflationary-motivated non-Gaussian shapes. The halo mass function and the non-linear power spectrum agree with theoretical analytical approximations proposed in the literature, even if they were so far developed and tested only for a particular shape (the local one). We plan to make the simulations outputs available to the community via the non-Gaussian simulations comparison project web site http://icc.ub.edu/~liciaverde/NGSCP.html.Comment: 23 pages, 10 figure

Properties of projectile-fragments in the 40^{40}Ar + 27^{27}Al reaction at 44 A MeV. Comparison with a multisequential decay model

GANIL-EXPResults on projectile fragment–fragment coincidences in the forward direction and for the reaction 40Ar + 27Al at 44 A MeV are presented and compared with the predictions of two different entrance channel models, a two-body and a three-body mechanism both followed by a binary multisequential decay including fission. This analysis shows that many features of the projectile decay products are well accounted for by the binary multisequential decay model. However the results depend critically upon the initial masses and excitation energies of the primary projectile fragments. In this respect, the three-body approach underestimates the excitation energy imparted to the primary fragments whereas the two-body scenario overestimates it. The present data put strong constraints on the initial excitation energy imparted to the primary fragments which appears to be intermediate between the predictions of the two models