Grammar-based distance in progressive multiple sequence alignment

Background: We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algorithm uses a grammar-based distance metric to determine the order in which biological sequences are to be pairwise aligned. The progressive alignment occurs via pairwise aligning new sequences with an ensemble of the sequences previously aligned. Results: The performance of the proposed algorithm is validated via comparison to popular progressive multiple alignment approaches, ClustalW and T-Coffee, and to the more recently developed algorithms MAFFT, MUSCLE, Kalign, and PSAlign using the BAliBASE 3.0 database of amino acid alignment files and a set of longer sequences generated by Rose software. The proposed algorithm has successfully built multiple alignments comparable to other programs with significant improvements in running time. The results are especially striking for large datasets. Conclusion: We introduce a computationally efficient progressive alignment algorithm using a grammar based sequence distance particularly useful in aligning large datasets

A Multi-agent Controller to enable Cognition in Software Defined Networks

© 2018 IEEE. Current SDN controllers are not cognitive. We propose a new architecture for an SDN controller to enable intelligence. The proposed new architecture is based on Multi-agent systems. As a prototype, we have built a MAS-SDN controller using the GOAL agent programming language. We highlight the motivation behind the new architecture, describe the architecture and provide some initial results

‘Measure to yourself a prophet’s place’: Biblical Heroines, Jewish Difference, and Victorian Women’s Poetry

In Book II of Aurora Leigh, Elizabeth Barrett Browning has her male protagonist, Romney Leigh, voice a number of Victorian stereotypes about women poets. Because it was assumed that women could not ‘understand’ philosophical, theoretical or abstract ideas, and because women were seen as creatures of their own emotional responses, women were rarely granted the cultural authority to speak prophetically, to voice their own experience as an authoritative mode ‘to teach the living’. Defined as essentially non-prophetic in their very existence, women were thus excluded from being the dominant figure for the poet in the period. For in order to be a poet/prophet, a speaker must be understood as moving between two realms, the earthly, individual realm and the universal, divine realm; likewise, he must be able to move between two rhetorical realms, private devotional utterance and public persuasive utterance. In Victorian England, those realms tended to be gender specific, coded female and male respectively. And while many male poets constructed their lyric identities by balancing those two rhetorical modes, Romney’s speech in Book II of Aurora Leigh re-creates the scorn and censure women poets faced when they dared to ‘measure [themselves] to a prophet’s place’ in Victorian England

Kristallnacht in Context: Jewish War Veterans in America And Britain and the Crisis of German Jewry

Based on work conducted by scholars as part of a Summer Research Workshop organized bythe Center for Advanced Holocaust Studies/United States Holocaust ..

Jewishness and Judaism

Jewish and Christian women writers expressed a dazzling variety of approaches to issues of Judaism, Jewishness, and Jewish identity in nineteenth-century England. Their work demonstrates the complexity of the issue itself, highlighting how Jewishness is always an intersectional identity in its religious, ethnic, and cultural manifestations

The origin of coarse garnet peridotites in cratonic lithosphere: New data on xenoliths from the Udachnaya kimberlite, central Siberia

We report new textural and chemical data for 10 garnet peridotite xenoliths from the Udachnaya kimberlite and examine them together with recent data on another 21 xenoliths from the 80-220 km depth range. The samples are very fresh (LOI near zero), modally homogeneous and large ( > 100 g). Some coarse-grained peridotites show incipient stages of deformation with < 10 % neoblasts at grain boundaries of coarse olivine. Such microstructures can only be recognized in very fresh rocks, because fine-grained interstitial olivine is strongly affected by alteration, and may have been overlooked in previous studies of altered peridotite xenoliths in the Siberian and other cratons. Some of the garnet peridotites are similar in composition to low-opx Udachnaya spinel harzburgites (previously interpreted as pristine melt extraction residues), but the majority show post-melting enrichments in Fe and Ti. The least metasomatized coarse peridotites were formed by 30-38 % of polybaric fractional melting between 7 and 4 GPa and =1-3 GPa. Our data together with experimental results suggest that garnet in these rocks, as well as in some other cratonic peridotites elsewhere, may be a residual mineral, which has survived partial melting together with olivine and opx. Many coarse and all deformed garnet peridotites from Udachnaya underwent modal metasomatism through interaction of the melting residues with Fe-, Al-, Si-, Ti-, REE-rich melts, which precipitated cpx, less commonly additional garnet. The xenoliths define a complex geotherm probably affected by thermal perturbations shortly before the intrusion of the host kimberlite magmas. The deformation in the lower lithosphere may be linked to metasomatism. © 2013 Springer-Verlag Berlin Heidelberg