Showing papers by "University of Turin published in 2007"

PLUTO: A Numerical Code for Computational Astrophysics

Abstract: We present a new numerical code, PLUTO, for the solution of hypersonic flows in 1, 2, and 3 spatial dimensions and different systems of coordinates. The code provides a multiphysics, multialgorithm modular environment particularly oriented toward the treatment of astrophysical flows in presence of discontinuities. Different hydrodynamic modules and algorithms may be independently selected to properly describe Newtonian, relativistic, MHD, or relativistic MHD fluids. The modular structure exploits a general framework for integrating a system of conservation laws, built on modern Godunov-type shock-capturing schemes. Although a plethora of numerical methods has been successfully developed over the past two decades, the vast majority shares a common discretization recipe, involving three general steps: a piecewise polynomial reconstruction followed by the solution of Riemann problems at zone interfaces and a final evolution stage. We have checked and validated the code against several benchmarks available in literature. Test problems in 1, 2, and 3 dimensions are discussed.

The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease

Abstract: The recycling of the amyloid precursor protein (APP) from the cell surface via the endocytic pathways plays a key role in the generation of amyloid beta peptide (Abeta) in Alzheimer disease. We report here that inherited variants in the SORL1 neuronal sorting receptor are associated with late-onset Alzheimer disease. These variants, which occur in at least two different clusters of intronic sequences within the SORL1 gene (also known as LR11 or SORLA) may regulate tissue-specific expression of SORL1. We also show that SORL1 directs trafficking of APP into recycling pathways and that when SORL1 is underexpressed, APP is sorted into Abeta-generating compartments. These data suggest that inherited or acquired changes in SORL1 expression or function are mechanistically involved in causing Alzheimer disease.

CMS physics technical design report, volume II: Physics performance

Abstract: CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider (LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking--through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start-up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb−1 or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, Bs production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb−1 to 30 fb−1. The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z0 boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing ET, B-mesons and τ's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model

N-doped TiO2: Theory and experiment

Abstract: Nitrogen doped titanium dioxide is attracting a continuously increasing attention because of its potential as material for environmental photocatalysis In this paper we review experimental and theoretical work done on this system in our groups in recent years The analysis is largely based on electron paramagnetic resonance (EPR) spectra and on their interpretation based on high-level ab initio calculations N-doped anatase TiO2 contains thermally stable single N-atom impurities either as charged diamagnetic Nb- centers or as neutral paramagnetic Nb centers (b stays for bulk) The N-atoms can occupy both interstitial or substitutional positions in the solid, with some evidence for a preference for interstitial sites All types of Nb centers give rise to localized states in the band-gap of the oxide, thus accounting for the related reduction of absorption band edge The relative abundance of these species depends on the oxidation state of the solid In fact, upon reduction, oxygen vacancies form and transfer electrons from Ti3+ ions to the Nb with formation of Ti4+ and Nb- EPR spectra measured under irradiation show that the Nb centers are responsible for visible light absorption with promotion of electrons from the localized N-impurity states to the conduction band or to electron scavengers like O2 adsorbed on the surface These results provide an unambiguous characterization of the electronic states associated with N-impurities in TiO2 and a realistic picture of the processes occurring in the solid under irradiation with visible light

Oncogenic Activation of the RAS/RAF Signaling Pathway Impairs the Response of Metastatic Colorectal Cancers to Anti–Epidermal Growth Factor Receptor Antibody Therapies

Abstract: Monoclonal antibodies (mAbs) against the extracellular domain of the epidermal growth factor receptor (EGFR) have been introduced for the treatment of metastatic colorectal cancer (mCRC). We have reported recently that increased copy number of the EGFR can predict response to anti-EGFR mAbs and that patients might be selected for treatment based on EGFR copy number. Here, we show that mutations activating the RAS/RAF signaling pathway are also predictive and prognostic indicators in mCRC patients, being inversely correlated with response to anti-EGFR mAbs. In cellular models of CRCs, activation of the RAS signaling pathway by introduction of an activated K-RAS allele (Gly12Val) impairs the therapeutic effect of anti-EGFR mAbs. In cancer cells carrying constitutively active RAS, the pharmacologic inhibition of the mitogen-activated protein kinase (MAPK) signaling cascade improves anti-EGFR treatment based on mAbs. These results have implications for the identification of patients who are likely to respond to anti-EGFR treatment. They also provide the rationale for combination therapies, targeted simultaneously to the EGFR and RAS/RAF/MAPK signaling pathways in CRC patients. [Cancer Res 2007;67(6):2643–8]

Correlation of the highest-energy cosmic rays with nearby extragalactic objects.

Abstract: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrate that there is a correlation between the arrival directions of cosmic rays with energy above {approx} 6 x 10{sup 19} eV and the positions of active galactic nuclei (AGN) lying within {approx} 75 Mpc. We reject the hypothesis of an isotropic distribution of these cosmic rays at over 99% confidence level from a prescribed a priori test. The correlation we observe is compatible with the hypothesis that the highest energy particles originate from nearby extragalactic sources whose flux has not been significantly reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.

Tidal hyperinflation during low tidal volume ventilation in acute respiratory distress syndrome.

Abstract: Rationale: Tidal volume and plateau pressure limitation decreases mortality in acute respiratory distress syndrome. Computed tomography demonstrated a small, normally aerated compartment on the top of poorly aerated and nonaerated compartments that may be hyperinflated by tidal inflation.Objectives: We hypothesized that despite tidal volume and plateau pressure limitation, patients with a larger nonaerated compartment are exposed to tidal hyperinflation of the normally aerated compartment.Measurements and Main Results: Pulmonary computed tomography at end-expiration and end-inspiration was obtained in 30 patients ventilated with a low tidal volume (6 ml/kg predicted body weight). Cluster analysis identified 20 patients in whom tidal inflation occurred largely in the normally aerated compartment (69.9 ± 6.9%; “more protected”), and 10 patients in whom tidal inflation occurred largely within the hyperinflated compartments (63.0 ± 12.7%; “less protected”). The nonaerated compartment was smaller and the norma...

Adjuvant mitotane treatment for adrenocortical carcinoma.

Abstract: Background Adrenocortical carcinoma is a rare neoplasm characterized by a high risk of recurrence after radical resection. Whether the use of mitotane is beneficial as an adjuvant treatment has been controversial. Our aim was to evaluate the efficacy of adjuvant mitotane in prolonging recurrence-free survival. Methods We performed a retrospective analysis involving 177 patients with adrenocortical cancer who had undergone radical surgery at 8 centers in Italy and 47 centers in Germany between 1985 and 2005. Adjuvant mitotane was administered to 47 Italian patients after radical surgery (mitotane group), whereas 55 Italian patients and 75 German patients (control groups 1 and 2, respectively) did not receive adjuvant treatment after surgery. Results Baseline features in the mitotane group and the control group from Italy were similar; the German patients were significantly older (P=0.03) and had more stage I or II adrenocortical carcinomas (P=0.02) than did patients in the mitotane group. Recurrence-free s...

Myeloid sarcoma: clinico-pathologic, phenotypic and cytogenetic analysis of 92 adult patients.

Abstract: Myeloid sarcoma (MS) is a rare neoplasm whose knowledge is largely based on case reports and/or technically dated contributions. Ninety-two MSs in adulthood with clinical data available were evaluated both morphologically and immunohistochemically. Seventy-four cases were also studied by fluorescent in situ hybridization on tissue sections and/or conventional karyotyping on bone marrow or peripheral blood. Histologically, 50% of the tumors were of the blastic type, 43.5% either monoblastic or myelomonocytic and 6.5% corresponded to different histotypes. CD68/KP1 was the most commonly expressed marker (100%), followed by myeloperoxidase (83.6%), CD117 (80.4%), CD99 (54.3%), CD68/PG-M1 (51%), CD34 (43.4%), terminal-deoxy-nucleotidyl-transferase (31.5%), CD56 (13%), CD61/linker for activation of T cells (2.2%), CD30 (2.2%) and CD4 (1.1%). Foci of plasmacytoid monocyte differentiation were observed in intestinal cases carrying inv16. Chromosomal aberrations were detected in about 54% of cases: monosomy 7(10.8%), trisomy 8(10.4%) and mixed lineage leukemia-splitting (8.5%) were the commonest abnormalities, whereas t(8;21) was rare (2.2%). The behavior was dramatic irrespective of presentation, age, sex, phenotype and cytogenetics. Most if not all, long survivors received bone-marrow transplantation. The present report expands the spectrum of our knowledge showing that MS has frequent monoblastic/myelomonocytic differentiation, displays distinctive phenotypic profile, carries chromosomal aberrations other than t(8;21), and requires supra-maximal therapy.

Estimate of B(B̄→X s γ) at O(α s 2 )

Abstract: Combining our results for various $O({\ensuremath{\alpha}}_{s}^{2})$ corrections to the weak radiative $B$-meson decay, we are able to present the first estimate of the branching ratio at the next-to-next-to-leading order in QCD. We find $\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{X}_{s}\ensuremath{\gamma})=(3.15\ifmmode\pm\else\textpm\fi{}0.23)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$ for ${E}_{\ensuremath{\gamma}}g1.6\text{ }\text{ }\mathrm{GeV}$ in the $\overline{B}$-meson rest frame. The four types of uncertainties: nonperturbative (5%), parametric (3%), higher-order (3%), and ${m}_{c}$-interpolation ambiguity (3%) have been added in quadrature to obtain the total error.

A comparison of allografting with autografting for newly diagnosed myeloma.

Abstract: Background In this trial of the treatment of newly diagnosed multiple myeloma, we compared a protocol that entailed a hematopoietic stem-cell autograft followed by an allograft from an HLA-identical sibling with a protocol of tandem autografts. Methods We enrolled 162 consecutive patients with newly diagnosed myeloma who were 65 years of age or younger and who had at least one sibling. All patients were initially treated with vincristine, doxorubicin, and dexamethasone, followed by melphalan and autologous stem-cell rescue. Patients with an HLA-identical sibling then received nonmyeloablative total-body irradiation and stem cells from the sibling. Patients without an HLA-identical sibling received two consecutive myeloablative doses of melphalan, each of which was followed by autologous stem-cell rescue. The primary end points were overall survival and event-free survival. Results After a median follow-up of 45 months (range, 21 to 90), the median overall survival and event-free survival were longer in th...

FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data

Abstract: Data clustering analysis has been extensively applied to extract information from gene expression profiles obtained with DNA microarrays. To this aim, existing clustering approaches, mainly developed in computer science, have been adapted to microarray data analysis. However, previous studies revealed that microarray datasets have very diverse structures, some of which may not be correctly captured by current clustering methods. We therefore approached the problem from a new starting point, and developed a clustering algorithm designed to capture dataset-specific structures at the beginning of the process. The clustering algorithm is named Fuzzy clustering by Local Approximation of MEmbership (FLAME). Distinctive elements of FLAME are: (i) definition of the neighborhood of each object (gene or sample) and identification of objects with "archetypal" features named Cluster Supporting Objects, around which to construct the clusters; (ii) assignment to each object of a fuzzy membership vector approximated from the memberships of its neighboring objects, by an iterative converging process in which membership spreads from the Cluster Supporting Objects through their neighbors. Comparative analysis with K-means, hierarchical, fuzzy C-means and fuzzy self-organizing maps (SOM) showed that data partitions generated by FLAME are not superimposable to those of other methods and, although different types of datasets are better partitioned by different algorithms, FLAME displays the best overall performance. FLAME is implemented, together with all the above-mentioned algorithms, in a C++ software with graphical interface for Linux and Windows, capable of handling very large datasets, named Gene Expression Data Analysis Studio (GEDAS), freely available under GNU General Public License. The FLAME algorithm has intrinsic advantages, such as the ability to capture non-linear relationships and non-globular clusters, the automated definition of the number of clusters, and the identification of cluster outliers, i.e. genes that are not assigned to any cluster. As a result, clusters are more internally homogeneous and more diverse from each other, and provide better partitioning of biological functions. The clustering algorithm can be easily extended to applications different from gene expression analysis.

Poorly differentiated thyroid carcinoma: the Turin proposal for the use of uniform diagnostic criteria and an algorithmic diagnostic approach.

Abstract: Poorly differentiated (PD) thyroid carcinomas lie both morphologically and behaviorally between well-differentiated and undifferentiated (anaplastic) carcinomas. Following the original description of this entity, different diagnostic criteria have been employed, resulting in wide discrepancies and c

Long-Term Follow-Up and Outcome of a Large Cohort of Patients with Common Variable Immunodeficiency

Abstract: Common Variable Immunodeficiency belongs to the group of rare diseases encompassing antibody deficiency syndromes of highly variable clinical presentation and outcome. The multicenter prospective study on a cohort of 224 patients with Common Variable Immunodeficiency provides an updated view of the spectrum of illnesses which occurred at the clinical onset and over a long period of follow-up (mean time: 11 years) and information on the effects of long-term immunoglobulin treatment. The mean age at the time of diagnosis was 26.6 years. Seventy-five patients were younger than 14 years of age. The mean age at the onset of symptoms was 16.9 years. This implicates with a mean diagnostic delay of 8.9 years. Respiratory tract infections were the most prominent clinical problem observed at diagnosis and during the follow-up. Intravenous immunoglobulin administration induced a significant reduction in the incidence of acute infections, mainly acute pneumonia and acute otitis. However, a progressive increase in the prevalence of patients with chronic diseases, mainly sinusitis and lung disease, was observed in all age groups, including the pediatric population. The morbidity of Common Variable Immunodeficiency due to all associated clinical conditions increased over time despite an adequate replacement with intravenous immunoglobulins. Our data stressed the need to develop international guidelines for the prevention and therapy of chronic lung disease, chronic sinusitis, chronic diarrhoea, and chronic granulomatosis in patients with humoral immunodeficiencies.

Diseases shared between wildlife and livestock: a European perspective

Abstract: Wildlife diseases are in fashion. This is creating an explosion of related knowledge. Despite this, the dynamics of both wildlife and diseases and the changes in livestock and wildlife management make it increasingly difficult to overview the current situation of wildlife diseases in Europe. This paper aims to discuss the available management possibilities and to highlight current research priorities. One area that causes severe concern to authorities is diseases largely under control in domestic populations but still existing as a reservoir in wildlife. Multihost situations are also of concern for wildlife management and conservation, as diseases can affect the productivity and density of wildlife populations with an economic or recreational value. Concern about emerging diseases is rising in recent years, and these may well occur at the fertile livestock-wildlife interface. Wildlife-related zoonoses are a diverse and complex issue that requires a close collabora- tion between wildlife ecologists, veterinarians and public health professionals. A few risk factors can be identified in most of the relevant wildlife diseases. Among them are (1) the introduction of diseases through movements or trans- locations of wild or domestic animals, (2) the consequences of wildlife overabundance, (3) the risks of open air livestock breeding, (4) vector expansion and (5) the expansion or introduction of hosts. Wildlife disease control requires the integration of veterinary, ecology and wildlife management expertise. In addition to surveillance, attempts to control wildlife diseases or to avoid disease transmission between wildlife and livestock have been based on setting up barriers, culling, hygienic measures, habitat manage- ment, vector control, treatments and vaccination. Surveil- lance and descriptive studies are still valuable in regions, species or diseases that have received less attention or are (at least apparently) emerging. Nonetheless, limiting the research effort to the mere reporting of wildlife disease outbreaks is of limited value if management recommenda- tions are not given at the same time. Thus, more experimental approaches are needed to produce substantial knowledge that enables authorities to make targeted management recommendations. This requires policy mak- ers to be more aware of the value of science and to provide extra-funding for the establishment of multidisciplinary scientific teams.

Bacteria of the genus Asaia stably associate with Anopheles stephensi, an Asian malarial mosquito vector

Abstract: Here, we show that an α-proteobacterium of the genus Asaia is stably associated with larvae and adults of Anopheles stephensi, an important mosquito vector of Plasmodium vivax, a main malaria agent in Asia. Asaia bacteria dominate mosquito-associated microbiota, as shown by 16S rRNA gene abundance, quantitative PCR, transmission electron microscopy and in situ-hybridization of 16S rRNA genes. In adult mosquitoes, Asaia sp. is present in high population density in the female gut and in the male reproductive tract. Asaia sp. from An. stephensi has been cultured in cell-free media and then transformed with foreign DNA. A green fluorescent protein-tagged Asaia sp. strain effectively lodged in the female gut and salivary glands, sites that are crucial for Plasmodium sp. development and transmission. The larval gut and the male reproductive system were also colonized by the transformed Asaia sp. strain. As an efficient inducible colonizer of mosquitoes that transmit Plasmodium sp., Asaia sp. may be a candidate for malaria control.

CMS physics technical design report: Addendum on high density QCD with heavy ions

Abstract: This report presents the capabilities of the CMS experiment to explore the rich heavy-ion physics programme offered by the CERN Large Hadron Collider (LHC). The collisions of lead nuclei at energies , will probe quark and gluon matter at unprecedented values of energy density. The prime goal of this research is to study the fundamental theory of the strong interaction ? Quantum Chromodynamics (QCD) ? in extreme conditions of temperature, density and parton momentum fraction (low-x).This report covers in detail the potential of CMS to carry out a series of representative Pb-Pb measurements. These include bulk observables, (charged hadron multiplicity, low pT inclusive hadron identified spectra and elliptic flow) which provide information on the collective properties of the system, as well as perturbative probes such as quarkonia, heavy-quarks, jets and high pT hadrons which yield tomographic information of the hottest and densest phases of the reaction.

Adsorption properties of HKUST-1 toward hydrogen and other small molecules monitored by IR

Abstract: Among microporous systems metal organic frameworks are considered promising materials for molecular adsorption. In this contribution infrared spectroscopy is successfully applied to highlight the positive role played by coordinatively unsaturated Cu2+ ions in HKUST-1, acting as specific interaction sites. A properly activated material, obtained after solvent removal, is characterized by a high fraction of coordinatively unsaturated Cu2+ ions acting as preferential adsorption sites that show specific activities towards some of the most common gaseous species (NO, CO2, CO, N2 and H2). From a temperature dependent IR study, it has been estimated that the H2 adsorption energy is as high as 10 kJ mol−1. A very complex spectral evolution has been observed upon lowering the temperature. A further peculiarity of this material is the fact that it promotes ortho–para conversion of the adsorbed H2 species.

The ODE/IM correspondence

Abstract: This paper reviews a recently discovered link between integrable quantum field theories and certain ordinary differential equations in the complex domain. Along the way, aspects of PT-symmetric quantum mechanics are discussed, and some elementary features of the six-vertex model and the Bethe ansatz are explained.