A statistical physics perspective on alignment-independent protein sequence comparison.

Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function, and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from “first passage probability distribution” to summarize statistics of ensemble averaged amino acid propensity values. In this paper, we introduce and elaborate this approach.

Weighted ICP Algorithm for Alignment of Stars from Scanned Astronomical Photographic Plates

ACM Computing Classification System (1998): I.2.8, I.2.10, I.5.1, J.2.

Transitive state alignment for the quantum jensen-shannon kernel

Kernel methods provide a convenient way to apply a wide range of learning techniques to complex and structured data by shifting the representational problem from one of finding an embedding of the data to that of defining a positive semidefinite kernel. One problem with the most widely used kernels is that they neglect the locational information within the structures, resulting in less discrimination. Correspondence-based kernels, on the other hand, are in general more discriminating, at the cost of sacrificing positive-definiteness due to their inability to guarantee transitivity of the correspondences between multiple graphs. In this paper we generalize a recent structural kernel based on the Jensen-Shannon divergence between quantum walks over the structures by introducing a novel alignment step which rather than permuting the nodes of the structures, aligns the quantum states of their walks. This results in a novel kernel that maintains localization within the structures, but still guarantees positive definiteness. Experimental evaluation validates the effectiveness of the kernel for several structural classification tasks. © 2014 Springer-Verlag Berlin Heidelberg.

Molecular alignment relaxation in polymer optical fibers for sensing applications

A systematic study of annealing behavior of drawn PMMA fibers was performed. Annealing dynamics were investigated under different environmental conditions by fiber longitudinal shrinkage monitoring. The shrinkage process was found to follow a stretched exponential decay function revealing the heterogeneous nature of the underlying molecular dynamics. The complex dependence of the fiber shrinkage on initial degree of molecular alignment in the fiber, annealing time and temperature was investigated and interpreted. Moreover, humidity was shown to have a profound effect on the annealing process, which was not recognized previously. Annealing was also shown to have considerable effect on the fiber mechanical properties associated with the relaxation of molecular alignment in the fiber. The consequences of fiber annealing for the climatic stability of certain polymer optical fiber-based sensors are discussed, emphasizing the importance of fiber controlled pre-annealing with respect to the foreseeable operating conditions.

Factors affecting the alignment of *grades and reading scores for third-grade students on the Florida Comprehensive Assessment Test

The purpose of this study was to aid in understanding the relationship between current Reading report card grading practices and standards-based state standardized testing results in Reading and factors associated with the alignment of this relationship. Report card and Florida Comprehensive Assessment Test (FLAT) data for 2004 were collected for 1064 third grade students in nine schools of one feeder pattern in Florida's Miami-Dade County Public Schools. A Third Grade Teacher Questionnaire was administered to 48 Reading teachers. The questionnaire contained items relating to teachers' education, teaching experience, grading practices, and beliefs about the FCAT, instructional Reading activities, methods, and materials. ^ Findings of this study support a strong relationship between report card grades and FCAT Reading achievement levels. However, individual school correlational analysis showed significant differences among schools' alignment measures. Higher teacher alignment between grades and FCAT levels was associated with teachers spending more time on individualized methods of Reading instruction and to teachers feeling there was not enough time to teach and help individual students. Lower teacher alignment of grades and achievement levels was associated with teachers taking homework into account in the final Reading grade. Teacher alignment of grades and achievement levels was not associated with teacher beliefs concerning the FCAT, instructional activities in Reading and Language Arts, the Reading program used, the model of delivery of the Reading program, instruction or type of instructional planning done by the teachers. ^ This study highlights the need for further investigations related to determining additional teacher factors that may affect the alignment relationship between report card grades and standards-based state standardized testing results. ^

Acoustic Manipulation and Alignment of Particles for Applications in Separation, Micro-Templating, and Device Fabrication

This dissertation studies the manipulation of particles using acoustic stimulation for applications in microfluidics and templating of devices. The term particle is used here to denote any solid, liquid or gaseous material that has properties, which are distinct from the fluid in which it is suspended. Manipulation means to take over the movements of the particles and to position them in specified locations. Using devices, microfabricated out of silicon, the behavior of particles under the acoustic stimulation was studied with the main purpose of aligning the particles at either low-pressure zones, known as the nodes or high-pressure zones, known as anti-nodes. By aligning particles at the nodes in a flow system, these particles can be focused at the center or walls of a microchannel in order to ultimately separate them. These separations are of high scientific importance, especially in the biomedical domain, since acoustopheresis provides a unique approach to separate based on density and compressibility, unparalleled by other techniques. The study of controlling and aligning the particles in various geometries and configurations was successfully achieved by controlling the acoustic waves. Apart from their use in flow systems, a stationary suspended-particle device was developed to provide controllable light transmittance based on acoustic stimuli. Using a glass compartment and a carbon-particle suspension in an organic solvent, the device responded to acoustic stimulation by aligning the particles. The alignment of light-absorbing carbon particles afforded an increase in visible light transmittance as high as 84.5%, and it was controlled by adjusting the frequency and amplitude of the acoustic wave. The device also demonstrated alignment memory rendering it energy-efficient. A similar device for suspended-particles in a monomer enabled the development of electrically conductive films. These films were based on networks of conductive particles. Elastomers doped with conductive metal particles were rendered surface conductive at particle loadings as low as 1% by weight using acoustic focusing. The resulting films were flexible and had transparencies exceeding 80% in the visible spectrum (400-800 nm) These films had electrical bulk conductivities exceeding 50 S/cm.

Aspects of postural alignment and postural control relevant for the evaluation and the treatment of idiopathic scoliosis patients

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Aspects of postural alignment and postural control relevant for the evaluation and the treatment of idiopathic scoliosis patients

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Item and task difficulty in a B2 reading examination: perceptions of test-takers and CEFR alignment experts compared with psychometric measurements

The article presents a study of a CEFR B2-level reading subtest that is part of the Slovenian national secondary school leaving examination in English as a foreign language, and compares the test-taker actual performance (objective difficulty) with the test-taker and expert perceptions of item difficulty (subjective difficulty). The study also analyses the test-takers’ comments on item difficulty obtained from a while-reading questionnaire. The results are discussed in the framework of the existing research in the fields of (the assessment of) reading comprehension, and are addressed with regard to their implications for item-writing, FL teaching and curriculum development.

Towards a Contingency Theory perspective of Quality Management in Enabling Strategic Alignment

The aim of this paper is to explore the role of Quality Management (QM) theory and practice using a contingency theory perspective. The study is grounded in the role of QM in improving strategic alignment within Small and Medium Sized Enterprises (SMEs) using Contingency Theory rather than adopting best practice approaches. An inductive theory building research methodology was used involving multiple case analyses of five SMEs, involving repeat interviews (n=45), focus groups (n=5) and document analysis. From the findings, it was found that Contingency Variables (strategy, culture, lifecycle and customer focus) and their respective typologies were found to interact with QM practices in helping to shape strategic alignment between the SMEs and their environments. This shaping process based on contingency approaches occurred in a manner unique to each SME and their respective environments rather than in an overarching best practice manner.

Partition alignment in three dimensional unstructured mesh multi-physics modelling

Unstructured mesh codes for modelling continuum physics phenomena have evolved to provide the facility to model complex interacting systems. Parallelisation of such codes using single Program Multi Data (SPMD) domain decomposition techniques implemented with message passing has been demonstrated to provide high parallel efficiency, scalability to large numbers of processors P and portability across a wide range of parallel platforms. High efficiency, especially for large P requires that load balance is achieved in each parallel loop. For a code in which loops span a variety of mesh entity types, for example, elements, faces and vertices, some compromise is required between load balance for each entity type and the quantity of inter-processor communication required to satisfy data dependence between processors.

From policy development to effectiveness and alignment: An analysis of the UK’s Higher Education Open Access policy landscape

The number of Open Access (OA) policies that have been adopted by universities, research institutes and research funders has been increasing at a fast pace. The Registry of Open Access Repository Mandates and Policies (ROARMAP) records the existence of 724 OA policies across the world, of which 512 have been adopted by universities and research institutions. The UK is one of the leading countries in terms of OA policy development and implementation with a total of 85 institutional1 and an estimated 35 funder2 OA policies. In order to understand and contextualise how OA policies are developed and how they can be effectively implemented and aligned, this brief looks at two areas. The first section provides an overview on the processes evolving around policy making, policy effectiveness and policy alignment. In particular, it summarises the criteria and elements generally specified in OA policies, it points out some of the relevant steps informing the development, monitoring and revision of OA policies, it outlines what OA policy elements contribute to policy effectiveness, and highlights the benefits in aligning OA policies. The second section revisits the issues previously discussed within the context of the UK institutional (universities) OA policy landscape.