Improved genetic algorithm for multiple sequence alignment using segment profiles (GASP)

This paper presents a novel genetic algorithm (GA) for multiple sequence alignment in protein analysis. The most significant improvement afforded by this algorithm results from its use of segment profiles to generate the diversified initial population and prevent the destruction of conserved regions by crossover and mutation operations. Segment profiles contain rich local information, thereby speeding up convergence. Secondly, it introduces the use of the norMD function in a genetic algorithm to measure multiple alignment Finally, as an approach to the premature problem, an improved progressive method is used to optimize the highest-scoring individual of each new generation. The new algorithm is compared with the ClustalX and T-Coffee programs on several data cases from the BAliBASE benchmark alignment database. The experimental results show that it can yield better performance on data sets with long sequences, regardless of similarity

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Solving Large Sparse Lyapunov Equations on Parallel Computers

Abstract. This paper describes the parallelization of the low-rank ADI iteration for the solution of large-scale, sparse Lyapunov equations. The only relevant operations involved in the method are matrix-vector prod-ucts and the solution of linear systems. Experimental results on a cluster, using the SuperLU library, show the performance of this approach

Learning to look : evaluating the student experience of an interactive image appraisal activity

Introduction: Student radiographers have expressed difficulty in performing image appraisal tasks. The purpose of this study was to investigate the value of a workshop delivered to level 4 undergraduate students. All students completed an image appraisal activity, inputting their appraisal into software that displayed their response alongside an expert opinion. They were asked to identify and discuss any discrepancy. Methods: All Level 4 students participated in an image appraisal workshop and were subsequently invited to take part in a focus group immediately after the activity. Twenty-three students took part in three focus groups (n = 7; n = 8; n = 8). A thematic analysis of transcripts was performed alongside validation from observations during the image appraisal activity. Results: Findings demonstrate that despite teaching and resources being available, students had focused on learning a generic checklist for image appraisal, had not appreciated the application of projection specific criteria and felt underprepared. The use of specific criteria and repetition within the task was considered useful. They identified learning needs and misconceptions through peer discussion and via the expert opinion, highlighting the value of feedback. Students enjoyed the workshop and made suggestions for implementation into the curriculum. Conclusion: Educators must not assume that the provision of resources will result in students developing deep knowledge. Teaching and learning strategies that are task specific are recommended to avoid a surface approach to learning. Time, repetition and appropriate feedback are essential to enable learners to develop competence and confidence for complex visual tasks, such as image appraisal

Two-sided Grassmann-Rayleigh quotient iteration

The two-sided Rayleigh quotient iteration proposed by Ostrowski computes a pair of corresponding left-right eigenvectors of a matrix $C$. We propose a Grassmannian version of this iteration, i.e., its iterates are pairs of $p$-dimensional subspaces instead of one-dimensional subspaces in the classical case. The new iteration generically converges locally cubically to the pairs of left-right $p$-dimensional invariant subspaces of $C$. Moreover, Grassmannian versions of the Rayleigh quotient iteration are given for the generalized Hermitian eigenproblem, the Hamiltonian eigenproblem and the skew-Hamiltonian eigenproblem.Comment: The text is identical to a manuscript that was submitted for publication on 19 April 200

2018 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1005/thumbnail.jp

Producing the magnum opus: a metaphor for nephrology nursing expertise acquisition

Aim. This paper elucidates the nature of metaphor and the conditions necessary to its use as an analytic device in qualitative research, and describes how the use of metaphor assisted in the analytic processes of a grounded theory study of nephrology nursing expertise. Background. The use of metaphor is pervasive in everyday thought, language and action. It is an important means for the comprehension and management of everyday life, and makes challenging or problematic concepts easier to explain. Metaphors are also pervasive in quantitative and qualitative research for the same reason. In both everyday life and in research, their use may be implicit or explicit. Methods. The study using grounded theory methodology took place in one renal unit in New South Wales, Australia between 1999 and 2000 and included six non-expert and 11 expert nurses. It involved simultaneous data collection and analysis using participant observation, semi-structured interviews and review of nursing documentation. Findings. A three stage skills-acquisitive process was identified in which an orchestral metaphor was used to explain the relationships between stages and to satisfactorily capture the data coded within each stage. Conclusion. Metaphors create images, clarify and add depth to meanings and, if used appropriately and explicitly in qualitative research, can capture data at highly conceptual levels. Metaphors also assist in explaining the relationship between findings in a clear and coherent manner. © 2005 Blackwell Publishing Ltd

Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers.

MRI tractography is the mapping of neural fiber pathways based on diffusion MRI of tissue diffusion anisotropy. Tractography based on diffusion tensor imaging (DTI) cannot directly image multiple fiber orientations within a single voxel. To address this limitation, diffusion spectrum MRI (DSI) and related methods were developed to image complex distributions of intravoxel fiber orientation. Here we demonstrate that tractography based on DSI has the capacity to image crossing fibers in neural tissue. DSI was performed in formalin-fixed brains of adult macaque and in the brains of healthy human subjects. Fiber tract solutions were constructed by a streamline procedure, following directions of maximum diffusion at every point, and analyzed in an interactive visualization environment (TrackVis). We report that DSI tractography accurately shows the known anatomic fiber crossings in optic chiasm, centrum semiovale, and brainstem; fiber intersections in gray matter, including cerebellar folia and the caudate nucleus; and radial fiber architecture in cerebral cortex. In contrast, none of these examples of fiber crossing and complex structure was identified by DTI analysis of the same data sets. These findings indicate that DSI tractography is able to image crossing fibers in neural tissue, an essential step toward non-invasive imaging of connectional neuroanatomy

Eating During Hemodialysis Treatment: A Consensus Statement From the International Society of Renal Nutrition and Metabolism.

Poor nutritional status and protein-energy wasting are common among maintenance dialysis patients and associated with unfavorable outcomes. Providing foods, meal trays, snack boxes, and/or oral nutritional supplements during hemodialysis can improve nutritional status and might also reduce inflammation, enhance health-related quality of life, boost patient satisfaction, and improve survival. Potential challenges include postprandial hypotension and other hemodynamic instabilities, aspiration risk, gastrointestinal symptoms, hygiene issues, staff burden, reduced solute removal, and increased costs. Differing in-center nutrition policies exist within organizations and countries around the world. Recent studies have demonstrated clinical benefits and highlight the need to work toward clear guidelines. Meals or supplements during hemodialysis may be an effective strategy to improve nutritional status with limited reports of complications in real-world scenarios. Whereas larger multicenter randomized trials are needed, meals and supplements during hemodialysis should be considered as a part of the standard-of-care practice for patients without contraindications