Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm

Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known individual bioinformatics tools. This PASA is statistically the most accurate protein alignment method today. It can have potential applications in drug discovery processes in the biotechnology industry

Oscillatory Shear Flow-Induced Alignment of Lamellar Melts of Hydrogen-Bonded Comb Copolymer Supramolecules

In this work we present the orientational behavior of comb copolymer-like supramolecules P4VP(PDP)1.0, obtained by hydrogen bonding between poly(4-vinylpyridine) and pentadecylphenol, during large-amplitude oscillatory shear flow experiments over a broad range of frequencies (0.001-10 Hz). The alignment diagram, presenting the macroscopic alignment in T/TODT vs ω/ωc, contains three regions of parallel alignment separated by a region of perpendicular alignment. For our material, the order-disorder temperature TODT = 67 °C and ωc, the frequency above which the distortion of the chain conformation dominates the materials’ viscoelasticity, is around 0.1 Hz at 61 °C. For the first time flipping from a pure transverse alignment via biaxial transverse/perpendicular alignment to a perpendicular alignment as a function of the strain amplitude was found.

Education alignment

This essay reviews recent developments in embedding data management and curation skills into information technology, library and information science, and research-based postgraduate courses in various national contexts. The essay also investigates means of joining up formal education with professional development training opportunities more coherently. The potential for using professional internships as a means of improving communication and understanding between disciplines is also explored. A key aim of this essay is to identify what level of complementarity is needed across various disciplines to most effectively and efficiently support the entire data curation lifecycle

Hinode Calibration for Precise Image Co-alignment between SOT and XRT (November 2006 -- April 2007)

To understand the physical mechanisms for activity and heating in the solar atmosphere, the magnetic coupling from the photosphere to the corona is an important piece of information from the Hinode observations, and therefore precise positional alignment is required among the data acquired by different telescopes. The Hinode spacecraft and its onboard telescopes were developed to allow us to investigate magnetic coupling with co-alignment accuracy better than 1 arcsec. Using the Mercury transit observed on 8 November 2006 and co-alignment measurements regularly performed on a weekly basis, we have determined the information necessary for precise image co-alignment and have confirmed that co-alignment better than 1 arcsec can be realized between Solar Optical Telescope (SOT) and X-Ray Telescope (XRT) with our baseline co-alignment method. This paper presents results from the calibration for precise co-alignment of CCD images from SOT and XRT.Comment: 8 pages, 9 figures, accepted for publication in PASJ (Hinode Special issue

Source-side context-informed hypothesis alignment for combining outputs from machine translation systems

This paper presents a new hypothesis alignment method for combining outputs of multiple machine translation (MT) systems. Traditional hypothesis alignment algorithms such as TER, HMM and IHMM do not directly utilise the context information of the source side but rather address the alignment issues via the output data itself. In this paper, a source-side context-informed (SSCI) hypothesis alignment method is proposed to carry out the word alignment and word reordering issues. First of all, the source–target word alignment links are produced as the hidden variables by exporting source phrase spans during the translation decoding process. Secondly, a mapping strategy and normalisation model are employed to acquire the 1- to-1 alignment links and build the confusion network (CN). The source-side context-based method outperforms the state-of-the-art TERbased alignment model in our experiments on the WMT09 English-to-French and NIST Chinese-to-English data sets respectively. Experimental results demonstrate that our proposed approach scores consistently among the best results across different data and language pair conditions

Primordial alignment of elliptical galaxies in intermediate redshift clusters

We measure primordial alignments for the red galaxies in the sample of eight massive galaxy clusters in the southern sky from the CLASH-VLT Large Programme, at a median redshift of 0.375. We find primordial alignment with about $3\sigma$ significance in the four dynamically young clusters, but null detection of primordial alignment in the four highly relaxed clusters. The observed primordial alignment is not dominated by any single one of the four dynamically young clusters, and is primarily due to a population of bright galaxies ($M_r<-20.5\ \rm{m}$) residing in the region 300 to 810 kpc from the cluster centers. For the first time, we point out that the combination of radial alignment and halo alignment can cause fake primordial alignment. Finally, we find that the detected alignment for the dynamically young clusters is real rather than fake primordial alignment.Comment: 10 pages, 8 figures, 1 table. Accepted for publication in MNRA