Comparison between the numerical solutions and the Thomas-Fermi approximation for atomic-molecular Bose-Einstein condensates

We study the stationary solution of an atomic Bose-Einstein condensate coupled coherently to a molecular condensate with both repulsive and attractive interspecies interactions confined in an isotropic harmonic trap. We use the Thomas-Fermi approximation and find four kinds of analytical solution for the cases. These analytical solutions are adopted as trial function for the diffusive numerical solution of the Gross-Pitaevskii equations. For the repulsive interspecies interaction, the case in which the atomic and molecular wavefunctions are out-phase, the densities have similar profiles for both methods, however, the case where the wavefunctions are in-phase, there are considerable difference between the density profiles. For the attractive interspecies interaction, there are two cases in the Thomas Fermi approximation where the wavefunctions are in-phase. One of them has numerical solution that agree with the approximation and the other does not have corresponding numerical solution.Comment: 15 pages, 6 figure

How to tell a gravastar from a black hole

Gravastars have been recently proposed as potential alternatives to explain the astrophysical phenomenology traditionally associated to black holes, raising the question of whether the two objects can be distinguished at all. Leaving aside the debate about the processes that would lead to the formation of a gravastar and the astronomical evidence in their support, we here address two basic questions: Is a gravastar stable against generic perturbations? If stable, can an observer distinguish it from a black hole of the same mass? To answer these questions we construct a general class of gravastars and determine the conditions they must satisfy in order to exist as equilibrium solutions of the Einstein equations. For such models we perform a systematic stability analysis against axial-perturbations, computing the real and imaginary parts of the eigenfrequencies. Overall, we find that gravastars are stable to axial perturbations, but also that their quasi-normal modes differ from those of a black hole of the same mass and thus can be used to discern, beyond dispute, a gravastar from a black hole.Comment: 16 pages, 13 figures, minor improvemen

A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs

Background: MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been found in extracellular human body fluids (e.g. plasma and serum) and some circulating miRNAs in the blood have been successfully revealed as biomarkers for diseases including cardiovascular diseases and cancer. Released miRNAs do not necessarily reflect the abundance of miRNAs in the cell of origin. It is claimed that release of miRNAs from cells into blood and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. Moreover, miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. In particular, the use of drugs should be taken into consideration while analyzing plasma miRNA levels as drug treatment. This may impair their employment as biomarkers. Description: We enriched our manually curated extracellular/circulating microRNAs database, miRandola, by providing (i) a systematic comparison of expression profiles of cellular and extracellular miRNAs, (ii) a miRNA targets enrichment analysis procedure, (iii) information on drugs and their effect on miRNA expression, obtained by applying a natural language processing algorithm to abstracts obtained from PubMed. Conclusions: This allows users to improve the knowledge about the function, diagnostic potential, and the drug effects on cellular and circulating miRNAs

GraphFind: enhancing graph searching by low support data mining techniques

<p>Abstract</p> <p>Background</p> <p>Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by systems that search for all exact or approximate occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed.</p> <p>Results</p> <p>This paper presents GraphFind. The system implements efficient graph searching algorithms together with advanced filtering techniques that allow approximate search. It allows users to select candidate subgraphs rather than entire graphs. It implements an effective data storage based also on low-support data mining.</p> <p>Conclusions</p> <p>GraphFind is compared with Frowns, GraphGrep and gIndex. Experiments show that GraphFind outperforms the compared systems on a very large collection of small graphs. The proposed low-support mining technique which applies to any searching system also allows a significant index space reduction.</p

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

BACKGROUND: Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species. RESULTS: This paper describes EasyBack, a new parameter-free, fully-automated software for backtranslation using Hidden Markov Models. EasyBack is not based on imitation of codon usage within the target species, but instead uses a sequence-similarity criterion. The model is trained with a set of proteins with known cDNA coding sequences, constructed from the input protein by querying the NCBI databases with BLAST. Unlike existing software, the proposed method allows the quality of prediction to be estimated. When tested on a group of proteins that show different degrees of sequence conservation, EasyBack outperforms other published methods in terms of precision. CONCLUSION: The prediction quality of a protein backtranslation methis markedly increased by replacing the criterion of most used codon in the same species with a Hidden Markov Model trained with a set of most similar sequences from all species. Moreover, the proposed method allows the quality of prediction to be estimated probabilistically

Field propagation in de Sitter black holes

We present an exhaustive analysis of scalar, electromagnetic and gravitational perturbations in the background of Schwarzchild-de Sitter and Reissner-Nordstrom-de Sitter spacetimes. The field propagation is considered by means of a semi-analytical (WKB) approach and two numerical schemes: the characteristic and general initial value integrations. The results are compared near the extreme cosmological constant regime, where analytical results are presented. A unifying picture is established for the dynamics of different spin fields.Comment: 15 pages, 16 figures, published versio

GSK-3\u3b2-induced Tau pathology drives hippocampal neuronal cell death in Huntington's disease: involvement of astrocyte-neuron interactions

Glycogen synthase kinase-3\u3b2 (GSK-3\u3b2) has emerged as a critical factor in several pathways involved in hippocampal neuronal maintenance and function. In Huntington's disease (HD), there are early hippocampal deficits both in patients and transgenic mouse models, which prompted us to investigate whether disease-specific changes in GSK-3\u3b2 expression may underlie these abnormalities. Thirty-three postmortem hippocampal samples from HD patients (neuropathological grades 2-4) and age- and sex-matched normal control cases were analyzed using real-time quantitative reverse transcription PCRs (qPCRs) and immunohistochemistry. In vitro and in vivo studies looking at hippocampal pathology and GSK-3\u3b2 were also undertaken in transgenic R6/2 and wild-type mice. We identified a disease and stage-dependent upregulation of GSK-3\u3b2 mRNA and protein levels in the HD hippocampus, with the active isoform pGSK-3\u3b2-Tyr(216) being strongly expressed in dentate gyrus (DG) neurons and astrocytes at a time when phosphorylation of Tau at the AT8 epitope was also present in these same neurons. This upregulation of pGSK-3\u3b2-Tyr(216) was also found in the R6/2 hippocampus in vivo and linked to the increased vulnerability of primary hippocampal neurons in vitro. In addition, the increased expression of GSK-3\u3b2 in the astrocytes of R6/2 mice appeared to be the main driver of Tau phosphorylation and caspase3 activation-induced neuronal death, at least in part via an exacerbated production of major proinflammatory mediators. This stage-dependent overactivation of GSK-3\u3b2 in HD-affected hippocampal neurons and astrocytes therefore points to GSK-3\u3b2 as being a critical factor in the pathological development of this condition. As such, therapeutic targeting of this pathway may help ameliorate neuronal dysfunction in HD