Comparison between off-resonance and electron Bernstein waves heating regime in a microwave discharge ion sourcea)

A microwave discharge ion source (MDIS) operating at the Laboratori Nazionali del Sud of INFN, Catania has been used to compare the traditional electron cyclotron resonance (ECR) heating with an innovative mechanisms of plasma ignition based on the electrostatic Bernstein waves (EBW). EBW are obtained via the inner plasma electromagnetic-to-electrostatic wave conversion and they are absorbed by the plasma at cyclotron resonance harmonics. The heating of plasma by means of EBW at particular frequencies enabled us to reach densities much larger than the cutoff ones. Evidences of EBW generation and absorption together with X-ray emissions due to high energy electrons will be shown. A characterization of the discharge heating process in MDISs as a generalization of the ECR heating mechanism by means of ray tracing will be shown in order to highlight the fundamental physical differences between ECR and EBW heating

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

Involvement of GTA protein NC2β in Neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation

<p>Abstract</p> <p>Background</p> <p>The General Transcription Apparatus (GTA) comprises more than one hundred proteins, including RNA Polymerases, GTFs, TAFs, Mediator, and cofactors such as heterodimeric NC2. This complexity contrasts with the simple mechanical role that these proteins are believed to perform and suggests a still uncharacterized participation to important biological functions, such as the control of cell proliferation.</p> <p>Results</p> <p>To verify our hypothesis, we analyzed the involvement in Neuroblastoma (NB) pathogenesis of GTA genes localized at 1p, one of NB critical regions: through RT-PCR of fifty eight NB biopsies, we demonstrated the statistically significant reduction of the mRNA for NC2β (localized at 1p22.1) in 74% of samples (p = 0.0039). Transcripts from TAF13 and TAF12 (mapping at 1p13.3 and 1p35.3, respectively) were also reduced, whereas we didn't detect any quantitative alteration of the mRNAs from GTF2B and NC2α (localized at 1p22-p21 and 11q13.3, respectively). We confirmed these data by comparing tumour and constitutional DNA: most NB samples with diminished levels of NC2β mRNA had also genomic deletions at the corresponding locus.</p> <p>Conclusion</p> <p>Our data show that NC2β is specifically involved in NB pathogenesis and may be considered a new NB biomarker: accordingly, we suggest that NC2β, and possibly other GTA members, are physiologically involved in the control of cell proliferation. Finally, our studies unearth complex selective mechanisms within NB cells.</p

SIGMA: A SET-COVER-BASED INEXACT GRAPH MATCHING ALGORITHM

Network querying is a growing domain with vast applications ranging from screening compounds against a database of known molecules to matching sub-networks across species. Graph indexing is a powerful method for searching a large database of graphs. Most graph indexing methods to date tackle the exact matching (isomorphism) problem, limiting their applicability to specific instances in which such matches exist. Here we provide a novel graph indexing method to cope with the more general, inexact matching problem. Our method, SIGMA, builds on approximating a variant of the set-cover problem that concerns overlapping multi-sets. We extensively test our method and compare it to a baseline method and to the state-of-the-art Grafil. We show that SIGMA outperforms both, providing higher pruning power in all the tested scenario

A set-cover-based approach for inexact graph matching

Network querying is a growing domain with vast applications ranging from screening compounds against a database of known molecules to matching subnetworks across species. Graph indexing is a powerful method for searching for queries in a large database of graphs. Most graph indexing methods to date tackle the exact matching (isomorphism) problem, limiting their applicability to speci\uafc instances in which such matches exist. Here we provide a novel graph indexing method to cope with the more general, inexact matching problem. Our method, SIGMA, builds on approximating a new variant of the set-cover problem that concerns overlapping multi-sets. We extensively test our method and compare it to a layman approach and to the state-of-the-art Grafil. We show that SIGMA outperforms both, providing higher pruning power in all the tested scenarios