NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae

BACKGROUND: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications: a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. RESULTS: Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons. DISCUSSION: This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol. Availability: the program is freely available a

Topological Protection and Quantum Noiseless Subsystems

Encoding and manipulation of quantum information by means of topological degrees of freedom provides a promising way to achieve natural fault-tolerance that is built-in at the physical level. We show that this topological approach to quantum information processing is a particular instance of the notion of computation in a noiseless quantum subsystem. The latter then provide the most general conceptual framework for stabilizing quantum information and for preserving quantum coherence in topological and geometric systems.Comment: 4 Pages LaTeX. Published versio

On the transition from complex to real scalar fields in modern cosmology

We study some problems arising from the introduction of a complex scalar field in cosmology, modelling its possible behaviors in both the inflationary and dark energy stages of the universe. Such examples contribute to show that, while the complex nature of the scalar field can be indeed important during inflation, it loses its meaning in the later dark-energy dominated era of cosmology, when the phase of the complex field is practically constant, and there is indeed a transition from complex to real scalar field. In our considerations, the Noether symmetry approach turns out to be a useful tool once again. We arrive eventually at a potential containing the sixth and fourth powers of the scalar field, and the resulting semiclassical quantum cosmology is studied to gain a better understanding of the inflationary stage.Comment: 21 pages, 6 figures. In the new version, sections I, IV and VI have been improved, and two words have been added at the beginning of the titl

Response to Letter by Gupta

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Acoustic Measurements on a Sonic Crystals Barrier

Abstract This paper describes the measurements carried out over a sonic crystal at normal incidence according to EN 1793-6, which allows to cancel ground reflection and edge diffraction by applying suitable windowing techniques. The sample was made of hollow PVC pipes with an outer diameter of 160 mm arranged in a square lattice with lattice constant 0.2 m. FE predictions were computed in order to verify the experimental campaign. A good match between simulations and measurements was found in the first sonic Bragg band gap. As expected, increasing the number of rows does not translate into a shift of the Bragg band gap but into an increase of the insulation properties

Advent of a Link between Ayurveda and Modern Health Science: The Proceedings of the First International Congress on Ayurveda, “Ayurveda: The Meaning of Life—Awareness, Environment, and Health” March 21-22, 2009, Milan, Italy

The First International Congress on Ayurveda was held in Milan, Italy in March 2009 and it has been the first scientific event of this kind in western world. This groundbreaking international congress was devoted to human being as the product of interactions between Awareness, Environment and Health, subjects that the West tends to consider separate and independent, but that are believed deeply connected in Ayurveda, whose interdependence defines “The Meaning of Life”. The Congress established a bridge between indian and western philosophy, scientific and biomedical thinking in order to expand knowledge and healthcare. Main attention and address of the invited speakers was on the concept of “relationships” that, connecting living beings with environment, shape Nature itself. This concept is central in Ayurveda but is also common to other western scientific disciplines such as quantum physics and epigenetics that, in the four Sessions of the Congress, were represented by eminent experts. The importance of this event was underlined by the attendance of more than 400 participants and by noteworthy institutional endorsements, that added a significative political dimension of high social impact due to the topical period for CAM acceptance and integration in Europe

The role of insulin-like growth factor-I receptor in the development of Herceptin resistance

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Morphological and Immunohistochemical Description of a Splenic Haemangioma in a Captive European Wolf (<i>Canis lupus lupus</i>) and a Review of the Current Literature

Neoplastic diseases are rarely described in wild carnivores; only a few reports have been published on this topic. Here, we describe the histological and immunohistochemical features of a haemangioma in the spleen of a grey wolf (Canis lupus lupus) and we compare the results with the dog (Canis lupus familiaris). Additionally, we list the different publications found in the literature with neoplastic lesions in wolves. Our results show similar immunohistochemical features to dogs, in which neoplastic cells express Vimentin, von Willebrand factor, alpha smooth muscle actin antibody, vascular endothelial growth factor C and low vascular endothelial growth factor receptor 3. Toluidine blue special stain shows moderated increased numbers of mast cells infiltrating the tumor, a feature observed in benign vascular tumors in domestic dogs, but not in the malignant counterparts. To our knowledge, this is the first article describing the gross, histological and immunohistochemical features of a splenic haemangioma in a wolf

Evaluation of infill strut properties based on in-plane cyclic tests

U nelinearnoj analizi AB okvira sa zidanom ispunom jednostavni se zamjenjujući tlačni štap često primjenjuje za modeliranje ispune, posebice u slučaju opsežnih numeričkih proračuna. Stoga je pažljiv odabir odgovarajućih svojstava tlačnog štapa od iznimne važnosti za vjerodostojni prikaz odziva zgrade. U ovom je radu predložen i primijenjen postupak određivanja svojstava tlačnog štapa za prikaz zidane ispune temeljem interpretacije rezultata cikličkih, statičkih ispitivanja u ravnini na uzorcima jednoetažnih, jednorasponskih armiranobetonskih okvira s ispunom i bez nje.In the nonlinear analysis of masonry infilled RC frame structures, simple strut models are often adopted to represent the masonry infill, particularly in the case of extensive parametric numerical studies. Therefore, a careful definition of the corresponding strut properties is of exceptional significance for achieving a realistic building response. A method for evaluation of masonry infill strut properties is proposed and applied in this paper, based on the interpretation of results obtained by cyclic in-plane testing of single-storey, single-bay bare and infilled RC frame specimens