Beauty and the beast: Aligning national curriculum standards with state (high school) graduation requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linder-Scholer, B.

1994-12-31

An overview of SCI/MATH/MN - Minnesota`s standards-based, systemic approach to the reform and improvement of the K-12 science and mathematics education delivery system - is offered as an illustration of the challenges of aligning state educational practices with the national curriculum standards, and as a model for business involvement in state educational policy issues that will enable fundamental, across-the-system reform. SCI/MATH/MN illustrates the major challenges involved in developing a statewide vision for math and science education reform, articulating frameworks aligned with the national standards, building capacity for system-oriented change at the local level, and involving business in systemic reform.

Toolkit for Evaluating Alignment of Instructional and Assessment Materials to the Common Core State Standards

ERIC Educational Resources Information Center

Achieve, Inc., 2014

2014-01-01

In joint partnership, Achieve, The Council of Chief State School Officers, and Student Achievement Partners have developed a Toolkit for Evaluating the Alignment of Instructional and Assessment Materials to the Common Core State Standards. The Toolkit is a set of interrelated, freely available instruments for evaluating alignment to the CCSS; each…

Methodological Choices in the Content Analysis of Textbooks for Measuring Alignment with Standards

ERIC Educational Resources Information Center

Polikoff, Morgan S.; Zhou, Nan; Campbell, Shauna E.

2015-01-01

With the recent adoption of the Common Core standards in many states, there is a need for quality information about textbook alignment to standards. While there are many existing content analysis procedures, these generally have little, if any, validity or reliability evidence. One exception is the Surveys of Enacted Curriculum (SEC), which has…

A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

NASA Astrophysics Data System (ADS)

Contino, Julie

2013-02-01

In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the standards. This study reports an analysis of the alignment between the National Science Education Standards (NSES), New York State Physical Setting/Earth Science Core Curriculum (Core Curriculum) and New York State Physical Setting/Earth Science Regents Examination (Regents Exam)—the sources teachers use for creating Earth Science curricula in New York State. The NSES were found to have a 49 % overlap with the Core Curriculum and a 27 % overlap with the Regents Exam. The Core Curriculum and Regents Exam, represented by matrices consisting of performance indicators and cognitive demands, were compared using the Porter Alignment Index. The alignment was 0.35, categorized as slightly aligned, due to the different emphases on cognitive levels. The Core focused on cognitive skills of Understand and Apply while the Regents concentrated more on Apply followed by Understand and Remember. It is suggested that the NSES be revised and the Core updated to include quantifiable emphasis on the major understandings such as percentage of time.

The Alignment of State Standards and Assessments in Elementary Reading. CIERA Report.

ERIC Educational Resources Information Center

Wixson, Karen K.; Fisk, Maria Chesley; Dutro, Elizabeth; McDaniel, Julie

A study examined the alignment between state standards and assessments in elementary reading. The impetus for the study was a request by the National Research Council's Committee on Title I Testing and Assessment for information on the extent to which students' performance on state assessments could be assumed to provide evidence of their level of…

A Seven-Step Process To Align Curriculum with Oregon State Content Standards.

ERIC Educational Resources Information Center

Golden, Nancy; Lane, Marilyn

1998-01-01

The University of Oregon (UO) and Captain Robert Gray Elementary School formed a partnership where UO students used the elementary school as a case study for curriculum research. This document gives an overview of the 7-step process the students used to align the school's curriculum with Oregon's content and performance standards. The text opens…

Alignment of Standards and Assessments as an Accountability Criterion.

ERIC Educational Resources Information Center

La Marca, Paul M.

2001-01-01

Provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. Discusses some methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment is not only a methodological requirement but also an ethical requirement.…

A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

ERIC Educational Resources Information Center

Contino, Julie

2013-01-01

In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the…

Effects of Enhanced Anchored Instruction on Skills Aligned to Common Core Math Standards

ERIC Educational Resources Information Center

Bottge, Brian A.; Cho, Sun-Joo

2013-01-01

This study compared how students with learning difficulties in math (MLD) who were randomly assigned to two instructional conditions answered items on problem solving tests aligned to the Common Core State Standards Initiative for Mathematics. Posttest scores showed improvement in the math performance of students receiving Enhanced Anchored…

Alignment as a Teacher Variable

ERIC Educational Resources Information Center

Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

2007-01-01

With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

2013-01-01

Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View.

PubMed

Zampogna, Biagio; Vasta, Sebastiano; Amendola, Annunziato; Uribe-Echevarria Marbach, Bastian; Gao, Yubo; Papalia, Rocco; Denaro, Vincenzo

2015-01-01

High tibial osteotomy (HTO) is a well-established and commonly utilized technique in medial knee osteoarthritis secondary to varus malalignment. Accurate measurement of the preoperative limb alignment, and the amount of correction required are essential when planning limb realignment surgery. The hip-knee-ankle angle (HKA) measured on a full length weightbearing (FLWB) X-ray in the standing position is considered the gold standard, since it allows for reliable and accurate measurement of the mechanical axis of the whole lower extremity. In general practice, alignment is often evaluated on standard anteroposterior weightbearing (APWB) X-rays, as the angle between the femur and tibial anatomic axis (TFa). It is, therefore, of value to establish if measuring the anatomical axis from limited APWB is an effective measure of knee alignment especially in patients undergoing osteotomy about the knee. Three independent observers measured preoperative and postoperative FTa with standard method (FTa1) and with circles method (FTa2) on APWB X-ray and the HKA on FLWB X-ray at three different time-points separated by a two-week period. Intra-observer and inter-observer reliabilities and the comparison and relationship between anatomical and mechanical alignment were calculated. Intra- and interclass coefficients for all the three methods indicated excellent reliability, having all the values above 0.80. Using the mean of paired t-student test, the comparison of HKA versus TFa1 and TFa2 showed a statistically significant difference (p<.0001) both for the pre-operative and post-operative sets of values. The correlation between the HKA and FTal was found poor for the preoperative set (R=0.26) and fair for the postoperative one (R=0.53), while the new circles method showed a higher correlation in both the preoperative (R=0.71) and postoperative sets (R=0.79). Intra-observer reliability was high for HKA, FTal and FTa2 on APWB x-rays in the pre- and post-operative setting. Inter

Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View

PubMed Central

Zampogna, Biagio; Vasta, Sebastiano; Amendola, Annunziato; Uribe-Echevarria Marbach, Bastian; Gao, Yubo; Papalia, Rocco; Denaro, Vincenzo

2015-01-01

Background High tibial osteotomy (HTO) is a well-established and commonly utilized technique in medial knee osteoarthritis secondary to varus malalignment. Accurate measurement of the preoperative limb alignment, and the amount of correction required are essential when planning limb realignment surgery. The hip-knee-ankle angle (HKA) measured on a full length weightbearing (FLWB) X-ray in the standing position is considered the gold standard, since it allows for reliable and accurate measurement of the mechanical axis of the whole lower extremity. In general practice, alignment is often evaluated on standard anteroposterior weightbearing (APWB) X-rays, as the angle between the femur and tibial anatomic axis (TFa). It is, therefore, of value to establish if measuring the anatomical axis from limited APWB is an effective measure of knee alignment especially in patients undergoing osteotomy about the knee. Methods Three independent observers measured preoperative and postoperative FTa with standard method (FTa1) and with circles method (FTa2) on APWB X-ray and the HKA on FLWB X-ray at three different time-points separated by a two-week period. Intra-observer and inter-observer reliabilities and the comparison and relationship between anatomical and mechanical alignment were calculated. Results Intra- and interclass coefficients for all the three methods indicated excellent reliability, having all the values above 0.80. Using the mean of paired t-student test, the comparison of HKA versus TFa1 and TFa2 showed a statistically significant difference (p<.0001) both for the pre-operative and post-operative sets of values. The correlation between the HKA and FTal was found poor for the preoperative set (R=0.26) and fair for the postoperative one (R=0.53), while the new circles method showed a higher correlation in both the preoperative (R=0.71) and postoperative sets (R=0.79). Conclusions Intra-observer reliability was high for HKA, FTal and FTa2 on APWB x-rays in the pre

Whole-genome alignment.

PubMed

Dewey, Colin N

2012-01-01

Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

Standards, Assessment, and Readiness: Addressing Postsecondary Transition Issues across State Lines

ERIC Educational Resources Information Center

Michelau, Demarée K.

2015-01-01

This brief describes major challenges ahead for states, institutions, and most importantly, students as the standards and assessments from the Common Core Standards (CCSS) are implemented. It also offers recommendations to create a network structure that would assist K-12 and higher education leaders in addressing those challenges. To begin the…

Early Learning Foundations. Indiana's Early Learning Development Framework Aligned to the Indiana Academic Standards, 2014

ERIC Educational Resources Information Center

Indiana Department of Education, 2015

2015-01-01

The "Foundations" (English/language arts, mathematics, social emotional skills, approaches to play and learning, science, social studies, creative arts, and physical health and growth) are Indiana's early learning development framework and are aligned to the 2014 Indiana Academic Standards. This framework provides core elements that…

Timeline and Approach to Standards and Assessments. State Implementation of College- and Career-Readiness Standards

ERIC Educational Resources Information Center

Anderson, Kimberly; Mira, Mary Elizabeth

2015-01-01

The following profiles address decisions and actions that state education policy-makers--in the state departments of education, unless otherwise noted--are taking to foster successful statewide implementation of their states' new college- and career-readiness standards and aligned assessments. These profiles provide a descriptive overview of each…

Professional Development. State Implementation of College- and Career-Readiness Standards

ERIC Educational Resources Information Center

Anderson, Kimberly; Mira, Mary Elizabeth

2015-01-01

The following profiles address how the state departments of education are helping educators prepare for and implement their states' new college- and career-readiness standards and aligned assessments, through professional learning. SREB researchers examined each state's major professional development efforts around its new standards in order to…

Supporting Science Teachers in Alignment with State Curriculum Standards through Professional Development: Teachers' Preparedness, Expectations and Their Fulfillment

NASA Astrophysics Data System (ADS)

Paik, Sunhee; Zhang, Meilan; Lundeberg, Mary A.; Eberhardt, Jan; Shin, Tae Seob; Zhang, Tianyi

2011-08-01

Since A Nation at Risk was released in the 1980s, standards-based reform has been the most dominant trend in American educational policy, and the No Child Left Behind Act pushed the trend further by requiring states to develop rigorous curriculum standards. Though much has been said about these new standards, less has been said about whether or how well professional development helps teachers link their instruction to these standards. This study examined the impact of a professional development program for K-12 science teachers in helping teachers meet state curriculum standards. Seventy-five science teachers in Michigan participated in a 2-week summer workshop that used Problem-Based Learning for improving teachers' content knowledge and pedagogical content knowledge. Researchers surveyed participating teachers about the change of teachers' preparedness for standards-based teaching, their expectations to meet state curriculum standards, and whether their expectations were met. In addition, the usefulness of workshop activities was examined. Data analysis showed that to align teaching with state curriculum standards, participating teachers expected to learn instructional strategies and enhance science content knowledge through professional development, and by and large their expectations were well met. Collaboration with colleagues and facilitators helped teachers achieve their goals in terms of teaching within state curriculum standards. These findings have important implications for designing professional development to help teachers align instruction with curriculum standards.

Standard Reference Material (SRM 1990) for Single Crystal Diffractometer Alignment

USGS Publications Warehouse

Wong-Ng, W.; Siegrist, T.; DeTitta, G.T.; Finger, L.W.; Evans, H.T.; Gabe, E.J.; Enright, G.D.; Armstrong, J.T.; Levenson, M.; Cook, L.P.; Hubbard, C.R.

2001-01-01

An international project was successfully completed which involved two major undertakings: (1) a round-robin to demonstrate the viability of the selected standard and (2) the certification of the lattice parameters of the SRM 1990, a Standard Reference Material?? for single crystal diffractometer alignment. This SRM is a set of ???3500 units of Cr-doped Al2O3, or ruby spheres [(0 420.011 mole fraction % Cr (expanded uncertainty)]. The round-robin consisted of determination of lattice parameters of a pair of crystals' the ruby sphere as a standard, and a zeolite reference to serve as an unknown. Fifty pairs of crystals were dispatched from Hauptman-Woodward Medical Research Institute to volunteers in x-ray laboratories world-wide. A total of 45 sets of data was received from 32 laboratories. The mean unit cell parameters of the ruby spheres was found to be a=4.7608 A?? ?? 0.0062 A??, and c=12.9979 A?? ?? 0.020 A?? (95 % intervals of the laboratory means). The source of errors of outlier data was identified. The SRM project involved the certification of lattice parameters using four well-aligned single crystal diffractometers at (Bell Laboratories) Lucent Technologies and at NRC of Canada (39 ruby spheres), the quantification of the Cr content using a combined microprobe and SEM/EDS technique, and the evaluation of the mosaicity of the ruby spheres using a double-crystal spectrometry method. A confirmation of the lattice parameters was also conducted using a Guinier-Ha??gg camera. Systematic corrections of thermal expansion and refraction corrections were applied. These rubies_ are rhombohedral, with space group R3c. The certified mean unit cell parameters are a=4.76080 ?? 0.00029 A??, and c=12 99568 A?? ?? 0.00087 A?? (expanded uncertainty). These certified lattice parameters fall well within the results of those obtained from the international round-robin study. The Guinier-Ha??gg transmission measurements on five samples of powdered rubies (a=4.7610 A?? ?? 0

Standard Reference Material (SRM 1990) For Single Crystal Diffractometer Alignment

PubMed Central

Wong-Ng, W.; Siegrist, T.; DeTitta, G. T.; Finger, L. W.; Evans, H. T.; Gabe, E. J.; Enright, G. D.; Armstrong, J. T.; Levenson, M.; Cook, L. P.; Hubbard, C. R.

2001-01-01

An international project was successfully completed which involved two major undertakings: (1) a round-robin to demonstrate the viability of the selected standard and (2) the certification of the lattice parameters of the SRM 1990, a Standard Reference Material® for single crystal diffractometer alignment. This SRM is a set of ≈3500 units of Cr-doped Al2O3, or ruby spheres [(0.420.011 mole fraction % Cr (expanded uncertainty)]. The round-robin consisted of determination of lattice parameters of a pair of crystals: the ruby sphere as a standard, and a zeolite reference to serve as an unknown. Fifty pairs of crystals were dispatched from Hauptman-Woodward Medical Research Institute to volunteers in x-ray laboratories world-wide. A total of 45 sets of data was received from 32 laboratories. The mean unit cell parameters of the ruby spheres was found to be a=4.7608 ű0.0062 Å, and c=12.9979 ű0.020 Å (95 % intervals of the laboratory means). The source of errors of outlier data was identified. The SRM project involved the certification of lattice parameters using four well-aligned single crystal diffractometers at (Bell Laboratories) Lucent Technologies and at NRC of Canada (39 ruby spheres), the quantification of the Cr content using a combined microprobe and SEM/EDS technique, and the evaluation of the mosaicity of the ruby spheres using a double-crystal spectrometry method. A confirmation of the lattice parameters was also conducted using a Guinier-Hägg camera. Systematic corrections of thermal expansion and refraction corrections were applied. These rubies– are rhombohedral, with space group R3¯c. The certified mean unit cell parameters are a=4.76080±0.00029 Å, and c=12.99568 ű0.00087 Å (expanded uncertainty). These certified lattice parameters fall well within the results of those obtained from the international round-robin study. The Guinier-Hägg transmission measurements on five samples of powdered rubies (a=4.7610 ű0.0013 Å, and c = 12

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

Alignment of Standards and Assessments as an Accountability Criterion. ERIC Digest.

ERIC Educational Resources Information Center

La Marca, Paul M.

This digest provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. It also discusses methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment refers to the degree of match between test content and subject…

How Rhetorical Theories of Genre Address Common Core Writing Standards

ERIC Educational Resources Information Center

Collin, Ross

2013-01-01

This article begins with a review of the forms of writing promoted in the Common Core State Standards. Across content areas, Common Core encourages teachers to attune students' writing to rhetorical concerns of audience, purpose, task, and disciplinary thinking. To address these concerns, teachers might take a rhetorical approach to the study…

Align-and-shine photolithography

NASA Astrophysics Data System (ADS)

Petrusis, Audrius; Rector, Jan H.; Smith, Kristen; de Man, Sven; Iannuzzi, Davide

2009-10-01

At the beginning of 2009, our group has introduced a new technique that allows fabrication of photolithographic patterns on the cleaved end of an optical fibre: the align-and-shine photolithography technique (see A. Petrušis et al., "The align-and-shine technique for series production of photolithography patterns on optical fibres", J. Micromech. Microeng. 19, 047001, 2009). Align-and-shine photolithography combines standard optical lithography with imagebased active fibre alignment processes. The technique adapts well to series production, opening the way to batch fabrication of fibre-top devices (D. Iannuzzi et al., "Monolithic fibre-top cantilever for critical environments and standard applications", Appl. Phys. Lett. 88, 053501, 2006) and all other devices that rely on suitable machining of engineered parts on the tip of a fibre. In this paper we review our results and briefly discuss its potential applications.

Creating a Coherent System to Support Instruction Aligned with State Standards: Promising Practices of the Louisiana Department of Education

ERIC Educational Resources Information Center

Kaufman, Julia H.; Thompson, Lindsey E.; Opfer, V. Darleen

2016-01-01

The impetus for this report is new evidence that state department of education work to align instruction with standards may make a difference for teachers' practices and understanding about their state standards. Using data from the RAND American Teacher Panel, the authors found that Louisiana teachers were more likely than other teachers to…

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

Large format focal plane array integration with precision alignment, metrology and accuracy capabilities

NASA Astrophysics Data System (ADS)

Neumann, Jay; Parlato, Russell; Tracy, Gregory; Randolph, Max

2015-09-01

Focal plane alignment for large format arrays and faster optical systems require enhanced precision methodology and stability over temperature. The increase in focal plane array size continues to drive the alignment capability. Depending on the optical system, the focal plane flatness of less than 25μm (.001") is required over transition temperatures from ambient to cooled operating temperatures. The focal plane flatness requirement must also be maintained in airborne or launch vibration environments. This paper addresses the challenge of the detector integration into the focal plane module and housing assemblies, the methodology to reduce error terms during integration and the evaluation of thermal effects. The driving factors influencing the alignment accuracy include: datum transfers, material effects over temperature, alignment stability over test, adjustment precision and traceability to NIST standard. The FPA module design and alignment methodology reduces the error terms by minimizing the measurement transfers to the housing. In the design, the proper material selection requires matched coefficient of expansion materials minimizes both the physical shift over temperature as well as lowering the stress induced into the detector. When required, the co-registration of focal planes and filters can achieve submicron relative positioning by applying precision equipment, interferometry and piezoelectric positioning stages. All measurements and characterizations maintain traceability to NIST standards. The metrology characterizes the equipment's accuracy, repeatability and precision of the measurements.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

NASA Astrophysics Data System (ADS)

Lizotte, Todd E.

2011-10-01

Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

The South Carolina Amazing Coast Program: Using Ocean Sciences to Address Next Generation Science Standards in Grades 3-5

NASA Astrophysics Data System (ADS)

Bell, E. V.; Thomas, C.; Weiss, B.; Bliss, A.; Spence, L.

2013-12-01

The Next Generation Science Standards (NGSS) are more inclusive of ocean sciences than the National Science Standards and respective state science standards. In response, the Center for Ocean Sciences Education Excellence-SouthEast (COSEE SE) is piloting the South Carolina's Amazing Coast (SCAC) program: a three-year initiative that incorporates ocean science concepts in grades 3-5 with the goals of addressing NGSS, STEM (science-technology-engineering-math) disciplines, and inquiry skills. The SCAC program targeted two Charleston County, South Carolina elementary schools that were demographically similar: Title 1 status (75% free or reduced lunch), > 90% African American student population, grade level size <55, and proximity to tidal salt marsh or barrier islands (< 2 miles). Fourteen teachers and approximately 240 students participated in the SCAC program between 2010 and 2013. The SCAC framework uses a scaffolding and multi-pronged approach for teacher professional development and student engagement. The scaffolding approach to curriculum implementation focuses on one grade level per year (Year 1 = 3rd; Year 2 = 4th, and Year 3 = 5th), thus building student and teacher literacy in ocean sciences. The coach-mentor model of teacher professional development was also used for the implementation of the program which differs from the traditional 'train the trainer' method in allowing for more frequent and consistent interaction by COSEE SE staff with the students and teachers during the school year. The coach mentor model enabled the creation of a community of practice where teachers served as both learners and practitioners of student learning. Methods for student engagement aligned with the NGSS and included hands-on classroom activities, use of 'hook' species such as loggerhead sea turtles (Caretta caretta), diamondback terrapins (Malaclemys terrapin) and smooth cord grass (Spartina alterniflora), field experiences to explore local ecosystems, interactions with

Sub-cell turning to accomplish micron-level alignment of precision assemblies

NASA Astrophysics Data System (ADS)

Kumler, James J.; Buss, Christian

2017-08-01

Higher performance expectations for complex optical systems demand tighter alignment requirements for lens assembly alignment. In order to meet diffraction limited imaging performance over wide spectral bands across the UV and visible wavebands, new manufacturing approaches and tools must be developed if the optical systems will be produced consistently in volume production. This is especially applicable in the field of precision microscope objectives for life science, semiconductor inspection and laser material processing systems. We observe a rising need for the improvement in the optical imaging performance of objective lenses. The key challenge lies in the micron-level decentration and tilt of each lens element. One solution for the production of high quality lens systems is sub-cell assembly with alignment turning. This process relies on an automatic alignment chuck to align the optical axis of a mounted lens to the spindle axis of the machine. Subsequently, the mount is cut with diamond tools on a lathe with respect to the optical axis of the mount. Software controlled integrated measurement technology ensures highest precision. In addition to traditional production processes, further dimensions can be controlled in a very precise manner, e.g. the air gaps between the lenses. Using alignment turning simplifies further alignment steps and reduces the risk of errors. This paper describes new challenges in microscope objective design and manufacturing, and addresses difficulties with standard production processes. A new measurement and alignment technique is described, and strengths and limitations are outlined.

Onorbit IMU alignment error budget

NASA Technical Reports Server (NTRS)

Corson, R. W.

1980-01-01

The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

The effect of tibiotalar alignment on coronal plane mechanics following total ankle replacement.

PubMed

Grier, A Jordan; Schmitt, Abigail C; Adams, Samuel B; Queen, Robin M

2016-07-01

Gait mechanics following total ankle replacement (TAR) have reported improved ankle motion following surgery. However, no studies have addressed the impact of preoperative radiographic tibiotalar alignment on post-TAR gait mechanics. We therefore investigated whether preoperative tibiotalar alignment (varus, valgus, or neutral) resulted in significantly different coronal plane mechanics or ground reaction forces post-TAR. We conducted a non-randomized study of 93 consecutive end-stage ankle arthritis patients. Standard weight-bearing radiographs were obtained preoperatively to categorize patients as having neutral (±4°), varus (≥5° of varus), or valgus (≥5° of valgus) coronal plane tibiotalar alignment. All patients underwent a standard walking assessment including three-dimensional lower extremity kinetics and kinematics preoperatively, 12 and 24 months postoperatively. A significant group by time interaction was observed for the propulsive vertical ground reaction force (vGRF), coronal plane hip range of motion (ROM) and the peak hip abduction moment. The valgus group demonstrated an increase in the peak knee adduction angle and knee adduction angle at heel strike when compared to the other groups. Coronal plane ankle ROM, knee and hip angles at heel strike, and the peak hip angle exhibited significant increases across time. Peak ankle inversion moment, peak knee abduction moment and the weight acceptance vGRF also exhibited significant increases across time. Neutral ankle alignment was achieved for all patients by 2 years following TAR. Restoration of neutral ankle alignment at the time of TAR in patients with preoperative varus or valgus tibiotalar alignment resulted in biomechanics similar to those of patients with neutral preoperative tibiotalar alignment by 24-month follow-up. Copyright © 2016 Elsevier B.V. All rights reserved.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Instructional Alignment under No Child Left Behind

ERIC Educational Resources Information Center

Polikoff, Morgan S.

2012-01-01

The alignment of instruction with the content of standards and assessments is the key mediating variable separating the policy of standards-based reform (SBR) from the outcome of improved student achievement. Few studies have investigated SBR's effects on instructional alignment, and most have serious methodological limitations. This research uses…

Alignment and Brakes Mechanic. Apprenticeship Training Standards = Mecanicien regleur d'avant-train et reparateur de freins. Normes de formation en apprentissage.

ERIC Educational Resources Information Center

Ontario Ministry of Skills Development, Toronto.

These training standards for alignment and brakes mechanics are intended to be used by apprentice/trainees, instructors, and companies in Ontario, Canada, as a blueprint for training or as a prerequisite for accreditation/certification. The training standards identify skills required for this occupation and its related training program. They are…

75 FR 16837 - Public Review of Draft United States Thoroughfare, Landmark, and Postal Address Data Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-02

... the structure of their address information but have not defined the elements that constitute an address. Knowledge of structure, content, and quality is required to successfully share information in a... discrete elements of address information and provides standardized terminology and definitions to alleviate...

Energy level alignment at hybridized organic-metal interfaces from a GW projection approach

NASA Astrophysics Data System (ADS)

Chen, Yifeng; Tamblyn, Isaac; Quek, Su Ying

Energy level alignments at organic-metal interfaces are of profound importance in numerous (opto)electronic applications. Standard density functional theory (DFT) calculations generally give incorrect energy level alignments and missing long-range polarization effects. Previous efforts to address this problem using the many-electron GW method have focused on physisorbed systems where hybridization effects are insignificant. Here, we use state-of-the-art GW methods to predict the level alignment at the amine-Au interface, where molecular levels do hybridize with metallic states. This non-trivial hybridization implies that DFT result is a poor approximation to the quasiparticle states. However, we find that the self-energy operator is approximately diagonal in the molecular basis, allowing us to use a projection approach to predict the level alignments. Our results indicate that the metallic substrate reduces the HOMO-LUMO gap by 3.5 4.0 eV, depending on the molecular coverage/presence of Au adatoms. Our GW results are further compared with those of a simple image charge model that describes the level alignment in physisorbed systems. Syq and YC acknowledge Grant NRF-NRFF2013-07 and the medium-sized centre program from the National Research Foundation, Singapore.

Opportunities to Align California's PreK-3 Education System

ERIC Educational Resources Information Center

Policy Analysis for California Education, PACE, 2016

2016-01-01

"PreK-3 Alignment in California's Education System: Obstacles and Opportunities" by Rachel Valentino and Deborah J. Stipek reviews the opportunities and challenges that must be addressed to better align PreK-3 education in California. The report describes policies and practices that districts have implemented to strengthen alignment, and…

The Effects of Using Bloom's Taxonomy to Align Reading Instruction with the Virginia Standards of Learning Framework for English

ERIC Educational Resources Information Center

Crews, Charla Faulkner

2010-01-01

This study examined the effects of aligning the "Virginia Standards of Learning (SOL)" English Framework with Bloom's Taxonomy on student achievement. Changes prompted by "No Child Left Behind" legislation increased accountability for student success, as well as mandated testing to determine annual academic growth of all…

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2010-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with a state's standards. Yet no established criteria were available for judging strength of alignment. Previous studies of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to interpret…

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2011-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with the state's standards documents. Yet, there exist no established criteria for judging strength of alignment. Previous measures of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to…

Aligned-or Not?

ERIC Educational Resources Information Center

Roseman, Jo Ellen; Koppal, Mary

2015-01-01

When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

Functional Alignment of Metabolic Networks.

PubMed

Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

2016-05-01

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.

State Capacity for Leadership: Ensuring Meaningful Higher Education Involvement in State Implementation of New Assessments Aligned with the Common Core State Standards

ERIC Educational Resources Information Center

National Center for Higher Education Management Systems (NJ1), 2011

2011-01-01

The Common Core State Standards (CCSS) and assessments aligned to them represent a significant milestone in public education reform in the U.S. Developed with consultation from higher education, the rigorous new standards and the assessments now being drafted by two consortia promise to help students reach higher levels of academic achievement and…

New overlay measurement technique with an i-line stepper using embedded standard field image alignment marks for wafer bonding applications

NASA Astrophysics Data System (ADS)

Kulse, P.; Sasai, K.; Schulz, K.; Wietstruck, M.

2017-06-01

In the last decades the semiconductor technology has been driven by Moore's law leading to high performance CMOS technologies with feature sizes of less than 10 nm [1]. It has been pointed out that not only scaling but also the integration of novel components and technology modules into CMOS/BiCMOS technologies is becoming more attractive to realize smart and miniaturized systems [2]. Driven by new applications in the area of communication, health and automation, new components and technology modules such as BiCMOS embedded RF-MEMS, high-Q passives, Sibased microfluidics and InP-SiGe BiCMOS heterointegration have been demonstrated [3-6]. In contrast to standard VLSI processes fabricated on front side of the silicon wafer, these new technology modules require addition backside processing of the wafer; thus an accurate alignment between the front and backside of the wafer is mandatory. In previous work an advanced back to front side alignment technique and implementation into IHP's 0.25/0.13 μm high performance SiGe:C BiCMOS backside process module has been presented [7]. The developed technique enables a high resolution and accurate lithography on the backside of BiCMOS wafer for additional backside processing. In addition to the aforementioned back side process technologies, new applications like Through-Silicon Vias (TSV) for interposers and advanced substrate technologies for 3D heterogeneous integration demand not only single wafer fabrication but also processing of wafer stacks provided by temporary and permanent wafer bonding [8]. Therefore, the available overlay measurement techniques are not suitable if overlay and alignment marks are realized at the bonding interface of a wafer stack which consists of both a silicon device and a silicon carrier wafer. The former used EVG 40NT automated overlay measurement system, which use two opposite positioned microscopes inspecting simultaneous the wafer back and front side, is not capable measuring embedded overlay

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Alignment control study for the solar optical telescope

NASA Technical Reports Server (NTRS)

1976-01-01

Analysis of the alignment and focus errors than can be tolerated, methods of sensing such errors, and mechanisms to make the necessary corrections were addressed. Alternate approaches and their relative merits were considered. The results of this study indicate that adequate alignment control can be achieved.

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

Alignment verification procedures

NASA Technical Reports Server (NTRS)

Edwards, P. R.; Phillips, E. P.; Newman, J. C., Jr.

1988-01-01

In alignment verification procedures each laboratory is required to align its test machines and gripping fixtures to produce a nearly uniform tensile stress field on an un-notched sheet specimen. The blank specimens (50 mm w X 305 mm l X 2.3 mm th) supplied by the coordinators were strain gauged. Strain gauge readings were taken at all gauges (n = 1 through 10). The alignment verification procedures are as follows: (1) zero all strain gauges while specimen is in a free-supported condition; (2) put strain-gauged specimen in the test machine so that specimen front face (face 1) is in contact with reference jaw (standard position of specimen), tighten grips, and at zero load measure strains on all gauges. (epsilon sub nS0 is strain at gauge n, standard position, zero load); (3) with specimen in machine and at a tensile load of 10 kN measure strains (specimen in standard position). (Strain = epsilon sub nS10); (4) remove specimen from machine. Put specimen in machine so that specimen back face (face 2) is in contact with reference jaw (reverse position of specimen), tighten grips, and at zero load measure strains on all gauges. (Strain - epsilon sub nR0); and (5) with specimen in machine and at tensile load of 10 kN measure strains (specimen in reverse position). (epsilon sub nR10 is strain at gauge n, reverse position, 10 kN load).

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Kernel Manifold Alignment for Domain Adaptation.

PubMed

Tuia, Devis; Camps-Valls, Gustau

2016-01-01

The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

Surface tension-driven self-alignment.

PubMed

Mastrangeli, Massimo; Zhou, Quan; Sariola, Veikko; Lambert, Pierre

2017-01-04

Surface tension-driven self-alignment is a passive and highly-accurate positioning mechanism that can significantly simplify and enhance the construction of advanced microsystems. After years of research, demonstrations and developments, the surface engineering and manufacturing technology enabling capillary self-alignment has achieved a degree of maturity conducive to a successful transfer to industrial practice. In view of this transition, a broad and accessible review of the physics, material science and applications of capillary self-alignment is presented. Statics and dynamics of the self-aligning action of deformed liquid bridges are explained through simple models and experiments, and all fundamental aspects of surface patterning and conditioning, of choice, deposition and confinement of liquids, and of component feeding and interconnection to substrates are illustrated through relevant applications in micro- and nanotechnology. A final outline addresses remaining challenges and additional extensions envisioned to further spread the use and fully exploit the potential of the technique.

Aligning Assessment and Instruction with State Standards for Children with Significant Disabilities

ERIC Educational Resources Information Center

Parrish, Polly R.; Stodden, Robert A.

2009-01-01

This article presents a classroom teacher's perspective on one of the important requirements of the No Child Left Behind Act of 2001 (NCLB) legislation and aligned language found in the Individuals With Disabilities Education Improvement Act (IDEA 2004)--that of aligning assessment and instructional practices with state academic content standard…

Individually addressable vertically aligned carbon nanofiber-based electrochemical probes

NASA Astrophysics Data System (ADS)

Guillorn, M. A.; McKnight, T. E.; Melechko, A.; Merkulov, V. I.; Britt, P. F.; Austin, D. W.; Lowndes, D. H.; Simpson, M. L.

2002-03-01

In this paper we present the fabrication and initial testing results of high aspect ratio vertically aligned carbon nanofiber (VACNF)-based electrochemical probes. Electron beam lithography was used to define the catalytic growth sites of the VACNFs. Following catalyst deposition, VACNF were grown using a plasma enhanced chemical vapor deposition process. Photolithography was performed to realize interconnect structures. These probes were passivated with a thin layer of SiO2, which was then removed from the tips of the VACNF, rendering them electrochemically active. We have investigated the functionality of completed devices using cyclic voltammetry (CV) of ruthenium hexammine trichloride, a highly reversible, outer sphere redox system. The faradaic current obtained during CV potential sweeps shows clear oxidation and reduction peaks at magnitudes that correspond well with the geometry of these nanoscale electrochemical probes. Due to the size and the site-specific directed synthesis of the VACNFs, these probes are ideally suited for characterizing electrochemical phenomena with an unprecedented degree of spatial resolution.

Mi-STAR: Designing Integrated Science Curriculum to Address the Next Generation Science Standards and Their Foundations

NASA Astrophysics Data System (ADS)

Gochis, E. E.; Huntoon, J. E.

2015-12-01

Mi-STAR (Michigan Science Teaching and Assessment Reform, http://mi-star.mtu.edu/) was funded by the Herbert H. and Grace A. Dow Foundation to reform K-12 science education to present science as an integrated body of knowledge that is applied to address societal issues. To achieve this goal, Mi-STAR is developing an integrated science curriculum for the middle grades that will be aligned with the Next Generation Science Standards (NGSS). Similar to the geosciences, the curriculum requires the integration of science, engineering and math content to explore 21st-century issues and demonstrates how these concepts can be used in service of society. The curriculum is based on the Mi-STAR Unit Specification Chart which pairs interdisciplinary themes with bundled NGSS Performance Expectations. Each unit is developed by a collaborative team of K-12 teachers, university STEM content experts and science education experts. Prior to developing a unit, each member on the team attends the on-line Mi-STAR Academy, completing 18+ hours of professional development (PD). This on-line PD program familiarizes teachers and experts with necessary pedagogical and content background knowledge, including NGSS and three-dimensional learning. With this background, teams use a staged, backwards design process to craft a multi-week unit based on a series of performance based tasks, or 'challenges' that engage students in actively doing science and engineering. Each unit includes Disciplinary Core Ideas from multiple disciplines, which focus on local and familiar examples that demonstrate the relevance of science in student's lives. Performance-based assessments are interwoven throughout the unit. Mi-STAR units will go through extensive pilot testing in several school districts across the state of Michigan. Additionally, the Mi-STAR program will develop teacher professional development programs to support implementation of the curriculum and design a pre-service teacher program in integrated

Local alignment of two-base encoded DNA sequence

PubMed Central

Homer, Nils; Merriman, Barry; Nelson, Stanley F

2009-01-01

Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Fourier transform power spectrum is a potential measure of tissue alignment in standard MRI: A multiple sclerosis study.

PubMed

Sharma, Shrushrita; Zhang, Yunyan

2017-01-01

Loss of tissue coherency in brain white matter is found in many neurological diseases such as multiple sclerosis (MS). While several approaches have been proposed to evaluate white matter coherency including fractional anisotropy and fiber tracking in diffusion-weighted imaging, few are available for standard magnetic resonance imaging (MRI). Here we present an image post-processing method for this purpose based on Fourier transform (FT) power spectrum. T2-weighted images were collected from 19 patients (10 relapsing-remitting and 9 secondary progressive MS) and 19 age- and gender-matched controls. Image processing steps included: computation, normalization, and thresholding of FT power spectrum; determination of tissue alignment profile and dominant alignment direction; and calculation of alignment complexity using a new measure named angular entropy. To test the validity of this method, we used a highly organized brain white matter structure, corpus callosum. Six regions of interest were examined from the left, central and right aspects of both genu and splenium. We found that the dominant orientation of each ROI derived from our method was significantly correlated with the predicted directions based on anatomy. There was greater angular entropy in patients than controls, and a trend to be greater in secondary progressive MS patients. These findings suggest that it is possible to detect tissue alignment and anisotropy using traditional MRI, which are routinely acquired in clinical practice. Analysis of FT power spectrum may become a new approach for advancing the evaluation and management of patients with MS and similar disorders. Further confirmation is warranted.

Interprofessional education workshops in the workplace for pre-registration learners: Aligning to National Standards.

PubMed

Kent, Fiona; Courtney, Jade; Thorpe, Jo

2018-03-01

The inclusion of formal interprofessional education activities within clinical placements aligns with the national agenda in Australia to increase the focus on collaborative practice. However, the challenge remains for health services to determine how to achieve this goal. The education team at one health service elected to align new interprofessional education initiatives to the National Standards for Quality in Healthcare, to increase student focus on the complex domains of practice that require collaborative practice. An interprofessional falls prevention workshop was created for students on clinical placement. In the pilot phase, the 2h workshops ran four times across three months. Simultaneously, a second group of students were invited to complete an online falls prevention module. Knowledge gains from the two interventions were compared using a Mann Whitney test and qualitative data was thematically coded. There was no significant difference in fall prevention knowledge between the two interventions. Thematic analysis illustrated workshops promoted an increased understanding of others roles, person-centred care, interprofessional communication and collaboration. This pilot study has demonstrated that 2h interprofessional educational workshops are a feasible, replicable and useful addition to profession-specific clinical placements. The interprofessional workshop offered the opportunity for students of different professions to come together, practice interprofessional communication, explore the roles and responsibilities of others and collaborate in the theoretical management of a clinical case. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Quality of National Standards for Preparing Teachers for Partnerships with Families? Briefing Paper.

ERIC Educational Resources Information Center

Kochhar-Bryant, Carol A.

Recent federal legislation has strengthened the role of parents in the education of their children, in school decision making, and in teacher preparation. The purpose of this study was to determine: (1) whether teacher preparation standards are aligned with current legislation related to parent partnerships; (2) if they address the direct…

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Design of practical alignment device in KSTAR Thomson diagnostic.

PubMed

Lee, J H; Lee, S H; Yamada, I

2016-11-01

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

The Optics and Alignment of the Divergent Beam Laboratory X-ray Powder Diffractometer and its Calibration Using NIST Standard Reference Materials.

PubMed

Cline, James P; Mendenhall, Marcus H; Black, David; Windover, Donald; Henins, Albert

2015-01-01

The laboratory X-ray powder diffractometer is one of the primary analytical tools in materials science. It is applicable to nearly any crystalline material, and with advanced data analysis methods, it can provide a wealth of information concerning sample character. Data from these machines, however, are beset by a complex aberration function that can be addressed through calibration with the use of NIST Standard Reference Materials (SRMs). Laboratory diffractometers can be set up in a range of optical geometries; considered herein are those of Bragg-Brentano divergent beam configuration using both incident and diffracted beam monochromators. We review the origin of the various aberrations affecting instruments of this geometry and the methods developed at NIST to align these machines in a first principles context. Data analysis methods are considered as being in two distinct categories: those that use empirical methods to parameterize the nature of the data for subsequent analysis, and those that use model functions to link the observation directly to a specific aspect of the experiment. We consider a multifaceted approach to instrument calibration using both the empirical and model based data analysis methods. The particular benefits of the fundamental parameters approach are reviewed.

Recommendations for Implementing the New Illinois Early Learning and Development Standards to Affect Classroom Practices for Social and Emotional Learning

ERIC Educational Resources Information Center

Zinsser, Katherine M.; Dusenbury, Linda

2015-01-01

The state of Illinois in the central United States has long been a trendsetter both in the development of learning standards and in addressing social and emotional learning in education settings. With a recent revision to the state's early learning standards, published in 2013, the Illinois State Board of Education (ISBE) fully aligned its…

Design of practical alignment device in KSTAR Thomson diagnostic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J. H., E-mail: jhlee@nfri.re.kr; University of Science and Technology; Lee, S. H.

2016-11-15

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broadmore » wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.« less

QUASAR--scoring and ranking of sequence-structure alignments.

PubMed

Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

2005-12-15

Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovacik, Meric A.; Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu; Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854

2013-09-15

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogeneticmore » relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.« less

Gauging Item Alignment through Online Systems While Controlling for Rater Effects

ERIC Educational Resources Information Center

Anderson, Daniel; Irvin, Shawn; Alonzo, Julie; Tindal, Gerald A.

2015-01-01

The alignment of test items to content standards is critical to the validity of decisions made from standards-based tests. Generally, alignment is determined based on judgments made by a panel of content experts with either ratings averaged or via a consensus reached through discussion. When the pool of items to be reviewed is large, or the…

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

Blanco, Enrique; Messeguer, Xavier; Smith, Temple F; Guigó, Roderic

2006-01-01

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments. PMID:16733547

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

Addressing refractive error visual impairment: volunteer organisations' alignment with Vision 2020 and public health principles.

PubMed

Pearce, Matthew G; Pearce, Nicole

2012-11-01

Eye care professionals have been making short visits to developing countries for decades in an effort to reduce visual impairment caused by refractive error. A 2006 survey revealed that volunteer organisations were not working within the Vision 2020 framework. Recommendations were made for volunteer organisations that would better align their work with accepted Vision 2020 and public health principles. This study re-evaluates the alignment of volunteer organisations with Vision 2020 and public health principles. To determine their philosophies and methods, a web-based survey was sent to 89 volunteer organisations identified from an internet search. The response rate was 48 per cent. Many (70.7 per cent) organisations exclusively mention direct service provision in their statement of purpose, often provided by student volunteers (75.6 per cent). A few (19.5 per cent) provide short training in refraction, not necessarily following best principles. The majority (82.1 per cent) dispenses recycled spectacles and many use medications not on national essential drug lists. Few attempt to follow aid effectiveness principles with only 26.8 per cent stating they follow Vision 2020 country plans. Overall, as in 2006, the work of these organisations is largely not in alignment with Vision 2020 and public health principles. Organisations interested in decreasing visual impairment due to refractive error in the developing world are encouraged to transition to organisations that not only recognise but also implement public health principles. This should include reprioritisation of their work to developing human resources and infrastructure, determining the burden and causes of disease, assisting in the training of mid-level personnel and providing professional and community education, collaborating via partnerships, discontinuing the use of recycled spectacles and inappropriate medications, and evaluating their outcomes. Following these recommendations as well as creating a better

Does Test Item Performance Increase with Test-to-Standards Alignment?

ERIC Educational Resources Information Center

Traynor, Anne

2017-01-01

Variation in test performance among examinees from different regions or national jurisdictions is often partially attributed to differences in the degree of content correspondence between local school or training program curricula, and the test of interest. This posited relationship between test-curriculum correspondence, or "alignment,"…

Towards the Development of a Model for Hardware Standards in Information Technology Procurement: Factors for Consideration

ERIC Educational Resources Information Center

Ryan, David L.

2010-01-01

While research in academic and professional information technology (IT) journals address the need for strategic alignment and defined IT processes, there is little research about what factors should be considered when implementing specific IT hardware standards in an organization. The purpose of this study was to develop a set of factors for…

Georgia science curriculum alignment and accountability: A blueprint for student success

NASA Astrophysics Data System (ADS)

Reining-Gray, Kimberly M.

Current trends and legislation in education indicate an increased dependency on standardized test results as a measure for learner success. This study analyzed test data in an effort to assess the impact of curriculum alignment on learner success as well as teacher perceptions of the changes in classroom instruction due to curriculum alignment. Qualitative and quantitative design methods were used to determine the impact of science curriculum alignment in grades 9-12. To determine the impact of science curriculum alignment from the Quality Core Curriculum (QCC) to the Georgia Performance Standards (GPS) test data and teacher opinion surveys from one Georgia School system were examined. Standardized test scores before and after curriculum alignment were analyzed as well as teacher perception survey data regarding the impact of curriculum change. A quantitative teacher perception survey was administered to science teachers in the school system to identify significant changes in teacher perceptions or teaching strategies following curriculum realignment. Responses to the survey were assigned Likert scale values for analysis purposes. Selected teachers were also interviewed using panel-approved questions to further determine teacher opinions of curriculum realignment and the impact on student success and teaching strategies. Results of this study indicate significant changes related to curriculum alignment. Teachers reported a positive change in teaching strategies and instructional delivery as a result of curriculum alignment and implementation. Student scores also showed improvement, but more research is recommended in this area.

Quasiparticle Level Alignment for Photocatalytic Interfaces.

PubMed

Migani, Annapaoala; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

2014-05-13

Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces.

Comparative Analysis of the Measurement of Total Instructional Alignment

ERIC Educational Resources Information Center

Kick, Laura C.

2013-01-01

In 2007, Lisa Carter created the Total Instructional Alignment system--a process that aligns standards, curriculum, assessment, and instruction. Employed in several hundred school systems, the TIA process is a successful professional development program. The researcher developed an instrument to measure the success of the TIA process with the…

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch

PubMed Central

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M. L.; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G.

2015-01-01

Introduction Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. Methods hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. Results SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Conclusions Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch.

PubMed

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M L; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G

2015-01-01

Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

An Analysis of Strategies for Teaching Standards-Based Lesson Plan Alignment to Preservice Teachers

ERIC Educational Resources Information Center

Drost, Bryan R.; Levine, Anita C.

2015-01-01

Research consistently shows that well-aligned lesson plans lead to better student learning outcomes. The development of these plans challenges both preservice teachers and the teacher educators who instruct them. This exploratory study examined strategies for teaching lesson plan alignment utilized by 87 teacher educators in the United States.…

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

PubMed

Oliver, Tim; Schmidt, Bertil; Nathan, Darran; Clemens, Ralf; Maskell, Douglas

2005-08-15

Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

Teacher Education, Experience, and the Practice of Aligned Instruction

ERIC Educational Resources Information Center

Polikoff, Morgan S.

2013-01-01

Research over the past two decades has shown the alignment of teachers’ instruction with state standards is generally weak. Proposing that alignment is a useful measure of teachers' curricular knowledge (Shulman, 1986), this study uses a large database of teacher reports of their content coverage to understand the relationship of teacher…

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

PubMed

Yu, Jia; Blom, Jochen; Sczyrba, Alexander; Goesmann, Alexander

2017-09-10

The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Identifying and Aligning Expectations in a Mentoring Relationship

PubMed Central

Huskins, W. Charles; Silet, Karin; Weber‐Main, Anne Marie; Begg, Melissa D.; Fowler, Jr, Vance G.; Hamilton, John; Fleming, Michael

2011-01-01

Abstract The mentoring relationship between a scholar and their primary mentor is a core feature of research training. Anecdotal evidence suggests this relationship is adversely affected when scholar and mentor expectations are not aligned. We examined three questions: (1) What is the value in assuring that the expectations of scholars and mentors are mutually identified and aligned? (2) What types of programmatic interventions facilitate this process? (3) What types of expectations are important to identify and align? We addressed these questions through a systematic literature review, focus group interviews of mentors and scholars, a survey of Clinical and Translational Science Award (CTSA) KL2 program directors, and review of formal programmatic mechanisms used by KL2 programs. We found broad support for the importance of identifying and aligning the expectations of scholars and mentors and evidence that mentoring contracts, agreements, and training programs facilitate this process. These tools focus on aligning expectations with respect to the scholar’s research, education, professional development and career advancement as well as support, communication, and personal conduct and interpersonal relations. Research is needed to assess test the efficacy of formal alignment activities. Clin Trans Sci 2011; Volume 4: 439–447 PMID:22212226

The Alignment of easyCBM[R] Math Measures to Curriculum Standards. Technical Report #1002

ERIC Educational Resources Information Center

Nese, Joseph F. T.; Lai, Cheng-Fei; Anderson, Daniel; Park, Bitnara Jasmine; Tindal, Gerald; Alonzo, Julie

2010-01-01

The purpose of this study was to examine the alignment of the easyCBM[R] mathematics benchmark and progress monitoring measures to the National Council of Teachers of Mathematics "Curriculum Focal Points" (NCTM, 2006). Based on Webb's alignment model (1997, 2002), we collected expert judgments on individual math items across a sampling of forms…

Common Core State Standards for Mathematics: How Well Do the Textbook and Instructional Methods Align?

ERIC Educational Resources Information Center

Rawding, Denise M.

2016-01-01

The Common Core Math Standards were written to address concerns that the math curriculum in the United States was not focused and coherent. Based on national and international assessments, the United States math scores have remained stagnant, while other countries have seen significant growth in their scores. This study, designed as an action…

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Using The GLOBE Program to address the Global Development Goals

NASA Astrophysics Data System (ADS)

Wegner, K.; Murphy, T.; Wigbels, L.; Mauriello, H.; Kucera, P. A.

2016-12-01

The GLOBE Program (globe.gov) is an international science and education program in more than 110 countries that provides students and the public worldwide the opportunity to participate in the scientific process through Earth observations and geospatial information. To address the Global Goals for Sustainable Development, The GLOBE Program has collaborated with with international organizations such as the UNEP, Peace Corps, USAID, UNESCO, Eco-Schools, and SciStarter to address the Goals for Sustainable Development. In this presentation, GLOBE will share the alignment materials that they have created to provide pathways to achieving the goals, as well as present case studies that demonstrate how the GLOBE community uses GLOBE protocols as Earth observations to monitor and communicate environmental indicators aligned to the Global Development Goals.

Leveraging FPGAs for Accelerating Short Read Alignment.

PubMed

Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

2017-01-01

One of the key challenges facing genomics today is how to efficiently analyze the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialized processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper, we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to two mismatches. Our design is based on the FM-index, with optimizations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seed-and-compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with eight Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and nine times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

Content and Alignment of State Writing Standards and Assessments as Predictors of Student Writing Achievement: An Analysis of 2007 National Assessment of Educational Progress Data

ERIC Educational Resources Information Center

Troia, Gary A.; Olinghouse, Natalie G.; Zhang, Mingcai; Wilson, Joshua; Stewart, Kelly A.; Mo, Ya; Hawkins, Lisa

2018-01-01

We examined the degree to which content of states' writing standards and assessments (using measures of content range, frequency, balance, and cognitive complexity) and their alignment were related to student writing achievement on the 2007 National Assessment of Educational Progress (NAEP), while controlling for student, school, and state…

Aligning IT and Business Strategy: An Australian University Case Study

ERIC Educational Resources Information Center

Dent, Alan

2015-01-01

Alignment with business objectives is considered to be an essential outcome of information technology (IT) strategic planning. This case study examines the process of creating an IT strategy for an Australian university using an industry standard methodology. The degree of alignment is determined by comparing the strategic priorities supported by…

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multiple nodes transfer alignment for airborne missiles based on inertial sensor network

NASA Astrophysics Data System (ADS)

Si, Fan; Zhao, Yan

2017-09-01

Transfer alignment is an important initialization method for airborne missiles because the alignment accuracy largely determines the performance of the missile. However, traditional alignment methods are limited by complicated and unknown flexure angle, and cannot meet the actual requirement when wing flexure deformation occurs. To address this problem, we propose a new method that uses the relative navigation parameters between the weapons and fighter to achieve transfer alignment. First, in the relative inertial navigation algorithm, the relative attitudes and positions are constantly computed in wing flexure deformation situations. Secondly, the alignment results of each weapon are processed using a data fusion algorithm to improve the overall performance. Finally, the feasibility and performance of the proposed method were evaluated under two typical types of deformation, and the simulation results demonstrated that the new transfer alignment method is practical and has high-precision.

Customer-Provider Strategic Alignment: A Maturity Model

NASA Astrophysics Data System (ADS)

Luftman, Jerry; Brown, Carol V.; Balaji, S.

This chapter presents a new model for assessing the maturity of a ­customer-provider relationship from a collaborative service delivery perspective: the Customer-Provider Strategic Alignment Maturity (CPSAM) Model. This model builds on recent research for effectively managing the customer-provider relationship in IT service outsourcing contexts and a validated model for assessing alignment across internal IT service units and their business customers within the same organization. After reviewing relevant literature by service science and information systems researchers, the six overarching components of the maturity model are presented: value measurements, governance, partnership, communications, human resources and skills, and scope and architecture. A key assumption of the model is that all of the components need be addressed to assess and improve customer-provider alignment. Examples of specific metrics for measuring the maturity level of each component over the five levels of maturity are also presented.

libgapmis: extending short-read alignments

PubMed Central

2013-01-01

Background A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. Results In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. Conclusions We present libgapmis, a library for extending

Use artificial neural network to align biological ontologies.

PubMed

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

How does a Next Generation Science Standard Aligned, Inquiry Based, Science Unit Impact Student Achievement of Science Practices and Student Science Efficacy in an Elementary Classroom?

NASA Astrophysics Data System (ADS)

Whittington, Kayla Lee

This study examined the impact of an inquiry based Next Generation Science Standard aligned science unit on elementary students' understanding and application of the eight Science and Engineering Practices and their relation in building student problem solving skills. The study involved 44 second grade students and three participating classroom teachers. The treatment consisted of a school district developed Second Grade Earth Science unit: What is happening to our playground? that was taught at the beginning of the school year. Quantitative results from a Likert type scale pre and post survey and from student content knowledge assessments showed growth in student belief of their own abilities in the science classroom. Qualitative data gathered from student observations and interviews performed at the conclusion of the Earth Science unit further show gains in student understanding and attitudes. This study adds to the existing literature on the importance of standard aligned, inquiry based science curriculum that provides time for students to engage in science practices.

Alignment limit of the NMSSM Higgs sector

DOE PAGES

Carena, Marcela; Haber, Howard E.; Low, Ian; ...

2016-02-17

The Next-to-Minimal Supersymmetric extension of the Standard Model (NMSSM) with a Higgs boson of mass 125 GeV can be compatible with stop masses of order of the electroweak scale, thereby reducing the degree of fine-tuning necessary to achieve electroweak symmetry breaking. Moreover, in an attractive region of the NMSSM parameter space, corresponding to the \\alignment limit" in which one of the neutral Higgs fields lies approximately in the same direction in field space as the doublet Higgs vacuum expectation value, the observed Higgs boson is predicted to have Standard- Model-like properties. We derive analytical expressions for the alignment conditions andmore » show that they point toward a more natural region of parameter space for electroweak symmetry breaking, while allowing for perturbativity of the theory up to the Planck scale. Additionally, the alignment limit in the NMSSM leads to a well defined spectrum in the Higgs and Higgsino sectors, and yields a rich and interesting Higgs boson phenomenology that can be tested at the LHC. Here, we discuss the most promising channels for discovery and present several benchmark points for further study.« less

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

Instructional Alignment as a Measure of Teaching Quality

ERIC Educational Resources Information Center

Polikoff, Morgan S.; Porter, Andrew C.

2014-01-01

Recent years have seen the convergence of two major policy streams in U.S. K-12 education: standards/accountability and teacher quality reforms. Work in these areas has led to the creation of multiple measures of teacher quality, including measures of their instructional alignment to standards/assessments, observational and student survey measures…

New FASB standard addresses revenue recognition considerations.

PubMed

McKee, Thomas E

2015-12-01

Healthcare organizations are expected to apply the following steps in revenue recognition under the new standard issued in May 2014 by the Financial Accounting Standards Board: Identify the customer contract. Identify the performance obligations in the contract. Determine the transaction price. Allocate the transaction price to the performance obligations in the contract. Recognize revenue when--or in some circumstances, as--the entity satisfies the performance obligation.

The Effect of Professional Learning Activities on Implementation of California's Quality Professional Learning Standards in Alignment with the Local Control Funding Formula Priority 2

ERIC Educational Resources Information Center

Pinotti, Sadie

2017-01-01

The purpose of this Delphi study was to identify the professional learning activities that experts perceive are necessary for local education agencies (LEAs) to effectively implement California's Quality Professional Learning Standards (QPLS) in alignment with the Local Control Funding Formula (LCFF) Priority 2. The study also examined the degree…

Choosing iPad Apps with a Purpose: Aligning Skills and Standards

ERIC Educational Resources Information Center

Powell, Selma

2014-01-01

With the number of apps available today, browsing the iTunes store can become overwhelming for any teacher. A teacher can quickly try free apps, but to have full access, cost is often involved. Purchasing numerous apps can be expensive and time consuming and, most important, may not produce an outcome of acquiring tools that are well aligned with…

Bypass, Augment, or Integrate: How Secondary Mathematics Teachers Address the Literacy Demands of Standards-Based Curriculum Materials

ERIC Educational Resources Information Center

Chandler-Olcott, Kelly; Doerr, Helen M.; Hinchman, Kathleen A.; Masingila, Joanna O.

2015-01-01

This 3-year qualitative study examined how 26 teachers in four U.S. secondary schools addressed the literacy demands of curriculum materials based on standards from the National Council of Teachers of Mathematics. It was grounded in sociocultural perspectives that encourage study of language in local contexts, including classrooms, communities,…

Null test fourier domain alignment technique for phase-shifting point diffraction interferometer

DOEpatents

Naulleau, Patrick; Goldberg, Kenneth Alan

2000-01-01

Alignment technique for calibrating a phase-shifting point diffraction interferometer involves three independent steps where the first two steps independently align the image points and pinholes in rotation and separation to a fixed reference coordinate system, e.g, CCD. Once the two sub-elements have been properly aligned to the reference in two parameters (separation and orientation), the third step is to align the two sub-element coordinate systems to each other in the two remaining parameters (x,y) using standard methods of locating the pinholes relative to some easy to find reference point.

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

PubMed Central

DeBlasio, Dan

2013-01-01

Abstract We develop a novel and general approach to estimating the accuracy of multiple sequence alignments without knowledge of a reference alignment, and use our approach to address a new task that we call parameter advising: the problem of choosing values for alignment scoring function parameters from a given set of choices to maximize the accuracy of a computed alignment. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its error with respect to true accuracy using mathematical optimization. Compared to prior approaches for estimating accuracy, our new approach (a) introduces novel feature functions that measure nonlocal properties of an alignment yet are fast to evaluate, (b) considers more general classes of estimators beyond linear combinations of features, and (c) develops new regression formulations for learning an estimator from examples; in addition, for parameter advising, we (d) determine the optimal parameter set of a given cardinality, which specifies the best parameter values from which to choose. Our estimator, which we call Facet (for “feature-based accuracy estimator”), yields a parameter advisor that on the hardest benchmarks provides more than a 27% improvement in accuracy over the best default parameter choice, and for parameter advising significantly outperforms the best prior approaches to assessing alignment quality. PMID:23489379

Smart and precise alignment of optical systems

NASA Astrophysics Data System (ADS)

Langehanenberg, Patrik; Heinisch, Josef; Stickler, Daniel

2013-09-01

For the assembly of any kind of optical systems the precise centration of every single element is of particular importance. Classically the precise alignment of optical components is based on the precise centering of all components to an external axis (usually a high-precision rotary spindle axis). Main drawback of this timeconsuming process is that it is significantly sensitive to misalignments of the reference (e.g. the housing) axis. In order to facilitate process in this contribution we present a novel alignment strategy for the TRIOPTICS OptiCentric® instrument family that directly aligns two elements with respect to each other by measuring the first element's axis and using this axis as alignment reference without the detour of considering an external reference. According to the optical design any axis in the system can be chosen as target axis. In case of the alignment to a barrel this axis is measured by using a distance sensor (e.g., the classically used dial indicator). Instead of fine alignment the obtained data is used for the calculation of its orientation within the setup. Alternatively, the axis of an optical element (single lens or group of lenses) whose orientation is measured with the standard OptiCentric MultiLens concept can be used as a reference. In the instrument's software the decentering of the adjusting element to the calculated axis is displayed in realtime and indicated by a target mark that can be used for the manual alignment. In addition, the obtained information can also be applied for active and fully automated alignment of lens assemblies with the help of motorized actuators.

"Authentic Alignment"--A New Framework of Entrepreneurship Education

ERIC Educational Resources Information Center

Macht, Stephanie Alexandra; Ball, Steve

2016-01-01

Purpose: This paper seeks to address an underdeveloped aspect of entrepreneurship education (EE), which is still criticised for not explicitly linking educational practice with established educational theory. As such, the purpose of this paper is to propose a novel educational framework--Authentic Alignment--that the authors evolved based on their…

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

PubMed

Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

2016-03-01

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Electromagnetic versus Lense-Thirring alignment of black hole accretion discs

NASA Astrophysics Data System (ADS)

Polko, Peter; McKinney, Jonathan C.

2017-01-01

Accretion discs and black holes (BHs) have angular momenta that are generally misaligned, which can lead to warped discs and bends in any jets produced. We examine whether a disc that is misaligned at large radii can be aligned more efficiently by the torque of a Blandford-Znajek (BZ) jet than by Lense-Thirring (LT) precession. To obtain a strong result, we will assume that these torques maximally align the disc, rather than cause precession, or disc tearing. We consider several disc states that include radiatively inefficient thick discs, radiatively efficient thin discs, and super-Eddington accretion discs. The magnetic field strength of the BZ jet is chosen as either from standard equipartition arguments or from magnetically arrested disc (MAD) simulations. We show that standard thin accretion discs can reach spin-disc alignment out to large radii long before LT would play a role, due to the slow infall time that gives even a weak BZ jet time to align the disc. We show that geometrically thick radiatively inefficient discs and super-Eddington discs in the MAD state reach spin-disc alignment near the BH when density profiles are shallow as in magnetohydrodynamical simulations, while the BZ jet aligns discs with steep density profiles (as in advection-dominated accretion flows) out to larger radii. Our results imply that the BZ jet torque should affect the cosmological evolution of BH spin magnitude and direction, spin measurements in active galactic nuclei and X-ray binaries, and the interpretations for Event Horizon Telescope observations of discs or jets in strong-field gravity regimes.

Pairwise alignment of chromatograms using an extended Fisher-Rao metric.

PubMed

Wallace, W E; Srivastava, A; Telu, K H; Simón-Manso, Y

2014-09-02

A conceptually new approach for aligning chromatograms is introduced and applied to examples of metabolite identification in human blood plasma by liquid chromatography-mass spectrometry (LC-MS). A square-root representation of the chromatogram's derivative coupled with an extended Fisher-Rao metric enables the computation of relative differences between chromatograms. Minimization of these differences using a common dynamic programming algorithm brings the chromatograms into alignment. Application to a complex sample, National Institute of Standards and Technology (NIST) Standard Reference Material 1950, Metabolites in Human Plasma, analyzed by two different LC-MS methods having significantly different ranges of elution time is described. Published by Elsevier B.V.

Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecework alignment algorithm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

2007-02-02

First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to

Long Read Alignment with Parallel MapReduce Cloud Platform

PubMed Central

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

Long Read Alignment with Parallel MapReduce Cloud Platform.

PubMed

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

PubMed

Hoffmann, Nils; Stoye, Jens

2009-08-15

We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

Kinematically aligned TKA can align knee joint line to horizontal.

PubMed

Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

2016-08-01

The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically

Robustly Aligning a Shape Model and Its Application to Car Alignment of Unknown Pose.

PubMed

Li, Yan; Gu, Leon; Kanade, Takeo

2011-09-01

Precisely localizing in an image a set of feature points that form a shape of an object, such as car or face, is called alignment. Previous shape alignment methods attempted to fit a whole shape model to the observed data, based on the assumption of Gaussian observation noise and the associated regularization process. However, such an approach, though able to deal with Gaussian noise in feature detection, turns out not to be robust or precise because it is vulnerable to gross feature detection errors or outliers resulting from partial occlusions or spurious features from the background or neighboring objects. We address this problem by adopting a randomized hypothesis-and-test approach. First, a Bayesian inference algorithm is developed to generate a shape-and-pose hypothesis of the object from a partial shape or a subset of feature points. For alignment, a large number of hypotheses are generated by randomly sampling subsets of feature points, and then evaluated to find the one that minimizes the shape prediction error. This method of randomized subset-based matching can effectively handle outliers and recover the correct object shape. We apply this approach on a challenging data set of over 5,000 different-posed car images, spanning a wide variety of car types, lighting, background scenes, and partial occlusions. Experimental results demonstrate favorable improvements over previous methods on both accuracy and robustness.

Medical and Transmission Vector Vocabulary Alignment with Schema.org

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, William P.; Chappell, Alan R.; Corley, Courtney D.

Available biomedical ontologies and knowledge bases currently lack formal and standards-based interconnections between disease, disease vector, and drug treatment vocabularies. The PNNL Medical Linked Dataset (PNNL-MLD) addresses this gap. This paper describes the PNNL-MLD, which provides a unified vocabulary and dataset of drug, disease, side effect, and vector transmission background information. Currently, the PNNL-MLD combines and curates data from the following research projects: DrugBank, DailyMed, Diseasome, DisGeNet, Wikipedia Infobox, Sider, and PharmGKB. The main outcomes of this effort are a dataset aligned to Schema.org, including a parsing framework, and extensible hooks ready for integration with selected medical ontologies. The PNNL-MLDmore » enables researchers more quickly and easily to query distinct datasets. Future extensions to the PNNL-MLD will include Traditional Chinese Medicine, broader interlinks across genetic structures, a larger thesaurus of synonyms and hypernyms, explicit coding of diseases and drugs across research systems, and incorporating vector-borne transmission vocabularies.« less

Building Strategically Aligned Individualized Education Programs for Transition

ERIC Educational Resources Information Center

Flannery, K. Brigid; Hellemn, Lisa A.

2015-01-01

The Individualized Education Programs (IEPs) for students 16 years of age or above must address specific transition components. Studies to date have focused on the presence and quality of these transition components, yet the alignment of these components and their role in leading the development of the IEP is just as critical. This qualitative…

Efficient alignment-free DNA barcode analytics.

PubMed

Kuksa, Pavel; Pavlovic, Vladimir

2009-11-10

In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

Efficient alignment-free DNA barcode analytics

PubMed Central

Kuksa, Pavel; Pavlovic, Vladimir

2009-01-01

Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

78 FR 987 - Hazardous Materials: Harmonization with International Standards (RRR)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-07

...PHMSA is amending the Hazardous Materials Regulations to maintain alignment with international standards by incorporating various amendments, including changes to proper shipping names, hazard classes, packing groups, special provisions, packaging authorizations, air transport quantity limitations, and vessel stowage requirements. These revisions are necessary to harmonize the Hazardous Materials Regulations (HMR) with recent changes made to the International Maritime Dangerous Goods (IMDG) Code, the International Civil Aviation Organization's Technical Instructions for the Safe Transport of Dangerous Goods by Air (ICAO Technical Instructions), and the United Nations Recommendations on the Transport of Dangerous Goods--Model Regulations (UN Model Regulations) and address a petition for rulemaking.

77 FR 49167 - Hazardous Materials: Harmonization with International Standards (RRR)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-15

...PHMSA proposes to amend the Hazardous Materials Regulations to maintain alignment with international standards by incorporating various amendments, including changes to proper shipping names, hazard classes, packing groups, special provisions, packaging authorizations, air transport quantity limitations, and vessel stowage requirements. These revisions are necessary to harmonize the Hazardous Materials Regulations with recent changes made to the International Maritime Dangerous Goods Code, the International Civil Aviation Organization's Technical Instructions for the Safe Transport of Dangerous Goods by Air, and the United Nations Recommendations on the Transport of Dangerous Goods--Model Regulations and subsequently address a petition for rulemaking.

American Indian Standards for History.

ERIC Educational Resources Information Center

Bureau of Indian Affairs (Dept. of Interior), Washington, DC. Office of Indian Education Programs.

This document presents American Indian history standards that are closely aligned with the 1996 expanded edition of the U.S. national standards for history. The American Indian standards should be used in conjunction with the national standards document itself and therefore, follow the same format, organization, and language. The Indian-specific…

Math: Basic Skills Content Standards

ERIC Educational Resources Information Center

CASAS - Comprehensive Adult Student Assessment Systems (NJ1), 2008

2008-01-01

This document presents content standards tables for math. [CASAS content standards tables are designed for educators at national, state and local levels to inform the alignment of content standards, instruction and assessment. The Content Standards along with the CASAS Competencies form the basis of the CASAS integrated assessment and curriculum…

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

Comparison of custom to standard TKA instrumentation with computed tomography.

PubMed

Ng, Vincent Y; Arnott, Lindsay; Li, Jia; Hopkins, Ronald; Lewis, Jamie; Sutphen, Sean; Nicholson, Lisa; Reader, Douglas; McShane, Michael A

2014-08-01

There is conflicting evidence whether custom instrumentation for total knee arthroplasty (TKA) improves component position compared to standard instrumentation. Studies have relied on long-limb radiographs limited to two-dimensional (2D) analysis and subjected to rotational inaccuracy. We used postoperative computed tomography (CT) to evaluate preoperative three-dimensional templating and CI to facilitate accurate and efficient implantation of TKA femoral and tibial components. We prospectively evaluated a single-surgeon cohort of 78 TKA patients (51 custom, 27 standard) with postoperative CT scans using 3D reconstruction and contour-matching technology to preoperative imaging. Component alignment was measured in coronal, sagittal and axial planes. Preoperative templating for custom instrumentation was 87 and 79 % accurate for femoral and tibial component size. All custom components were within 1 size except for the tibial component in one patient (2 sizes). Tourniquet time was 5 min longer for custom (30 min) than standard (25 min). In no case was custom instrumentation aborted in favour of standard instrumentation nor was original alignment of custom instrumentation required to be adjusted intraoperatively. There were more outliers greater than 2° from intended alignment with standard instrumentation than custom for both components in all three planes. Custom instrumentation was more accurate in component position for tibial coronal alignment (custom: 1.5° ± 1.2°; standard: 3° ± 1.9°; p = 0.0001) and both tibial (custom: 1.4° ± 1.1°; standard: 16.9° ± 6.8°; p < 0.0001) and femoral (custom: 1.2° ± 0.9°; standard: 3.1° ± 2.1°; p < 0.0001) rotational alignment, and was similar to standard instrumentation in other measurements. When evaluated with CT, custom instrumentation performs similar or better to standard instrumentation in component alignment and accurately templates component size. Tourniquet time was mildly increased for custom compared

Aligning ERP systems with companies' real needs: an `Operational Model Based' method

NASA Astrophysics Data System (ADS)

Mamoghli, Sarra; Goepp, Virginie; Botta-Genoulaz, Valérie

2017-02-01

Enterprise Resource Planning (ERP) systems offer standard functionalities that have to be configured and customised by a specific company depending on its own requirements. A consistent alignment is therefore an essential success factor of ERP projects. To manage this alignment, an 'Operational Model Based' method is proposed. It is based on the design and the matching of models, and conforms to the modelling views and constructs of the ISO 19439 and 19440 enterprise-modelling standards. It is characterised by: (1) a predefined design and matching order of the models; (2) the formalisation, in terms of modelling constructs, of alignment and misalignment situations; and (3) their association with a set of decisions in order to mitigate the misalignment risk. Thus, a comprehensive understanding of the alignment management during ERP projects is given. Unlike existing methods, this one includes decisions related to the organisational changes an ERP system can induce, as well as criteria on which the best decision can be based. In this way, it provides effective support and guidance to companies implementing ERP systems, as the alignment process is detailed and structured. The method is applied on the ERP project of a Small and Medium Enterprise, showing that it can be used even in contexts where the ERP project expertise level is low.

78 FR 43145 - Announcing Approval of Federal Information Processing Standard 186-4, Digital Signature Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-19

... correction of wording and typographical errors, and further aligns the FIPS with Key Cryptography Standard... Cryptography Standard (PKCS) 1. NIST published a Federal Register Notice (77 FR 21538) on April 10, 2012 to...

The dynamic nature of alignment and variations in normal knees.

PubMed

Deep, K; Eachempati, K K; Apsingi, S

2015-04-01

The restoration of knee alignment is an important goal during total knee arthroplasty (TKA). In the past surgeons aimed to restore neutral limb alignment during surgery. However, previous studies have demonstrated alignment to be dynamic, varying depending on the position of the limb and the degree of weight-bearing, and between patients. We used a validated computer navigation system to measure the femorotibial mechanical angle (FTMA) in 264 knees in 77 male and 55 female healthy volunteers aged 18 to 35 years (mean 26.2). We found the mean supine alignment to be a varus angle of 1.2° (standard deviation (sd) 4), with few patients having neutral alignment. FTMA differs significantly between males and females (with a mean varus of 1.7° (sd 4) and 0.4° (sd 3.9), respectively; p = 0.008). It changes significantly with posture, the knee hyperextending by a mean of 5.6°, and coronal plane alignment becoming more varus by 2.2° (sd 3.6) on standing compared with supine. Knee alignment is different in different individuals and is dynamic in nature, changing with different postures. This may have implications for the assessment of alignment in TKA, which is achieved in non-weight-bearing conditions and which may not represent the situation observed during weight-bearing. ©2015 The British Editorial Society of Bone & Joint Surgery.

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

PubMed Central

2010-01-01

Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

CAFE: aCcelerated Alignment-FrEe sequence analysis

PubMed Central

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.

2017-01-01

Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388

Comparison of single-incision mini-slings (Ajust) and standard transobturator midurethral slings (Align) in the management of female stress urinary incontinence: A 1-year follow-up.

PubMed

Chang, Chia-Pei; Chang, Wen-Hsun; Hsu, Yen-Mei; Chen, Yi-Jen; Wen, Kuo-Chang; Chao, Kuan-Chong; Yen, Ming-Shyen; Horng, Huann-Cheng; Wang, Peng-Hui

2015-12-01

To investigate the effectiveness and safety of a new single-incision mini-sling (SIMS)-Ajust-compared with the standard transobturator midurethral sling (SMUS)-Align-for the treatment of female stress urinary incontinence (SUI). A retrospective cohort study was conducted between January 1, 2010 and August 31, 2012. Women with SUI who underwent either SMUS-Align or SIMS-Ajust were recruited. The primary outcomes included operation time, estimated operative blood loss, postoperative pain, and complications. The secondary outcomes included subjective and objective success, defined as an International Consultation on Incontinence Questionnaire (ICIQ) score of 0 or improvement as felt by the patient and a long-term complication, such as dyspareunia and mesh erosion after 6 months and 12 months of follow-up. A total of 136 patients were enrolled, including 76 receiving SMUS-Align and 60 receiving SIMS-Ajust. Baseline characteristics of the patients in both groups were similar, without a statistically significant difference. Primary outcomes between both groups were similar, except that women treated with SIMS-Ajust had statistically significantly shorter operation time (p = 0.003), less intent to treat (p < 0.05), and earlier postoperative discharge (p = 0.001) than women treated with SMUS-Align. Secondary outcomes were similar without a significant difference between the two groups (93% vs. 88% success rate in each group). Our results showed that SIMS-Ajust was not inferior to SMUS-Align with respect to success rate, and might have a slight advantage in early discharge. A long-term follow-up or prospective study is needed to confirm the above findings. Copyright © 2015. Published by Elsevier B.V.

Addressing Theory and Performance Enhancements for the Independent Sustain and Address AC Plasma Display

NASA Astrophysics Data System (ADS)

Warren, Kevin Wilson

The Independent Sustain and Address (ISA) AC plasma panel is a flat, flicker-free, gas discharge type of display device. This display technology promises to reduce both the cost of manufacturing and operation of AC plasma displays. The ISA technology uses a vastly different mechanism to change the state of the display pixels than the standard AC plasma technology. This addressing mechanism is an exploitation of some of the natural characteristics associated with the plasma that can form during strong gas discharges. This thesis presents detailed data from experiments that were designed to evaluate and test the effectiveness of this mechanism. Through these experiments, the theory that the addressing methodology is based upon is developed and evaluated. These experiments show that the address margin windows for this technology are very large, minimally two to three times larger than the address margins for the standard XY AC plasma addressing techniques. New capabilities are also described, such as global brightness control for the ISA technology and a technique for increasing the addressing rate. These advances were designed into working prototypes and transferred to industry where there are currently commercial products available based upon these advances. A technique for implementing gray scale using some of these advances is also proposed.

Addressing standards of care in resource-limited settings.

PubMed

Dawson, Liza; Klingman, Karin L; Marrazzo, Jeanne

2014-01-01

: The choice between "best-known" standards of care (SOC) or "best available" standards as the control arm in a clinical trial is a fundamental dilemma in clinical research in resource-limited settings (RLS). When the health system is delivering less than an optimal level of care, using highest standard of care in a clinical trial may produce results that cannot be implemented or sustained locally. On the other hand, using interventions that are more feasible in the local setting may involve suboptimal care, and clinical outcomes may be affected. The need for improved standards in health systems in RLS, and the difficulty in securing them, has led many researchers advocate for policy changes at the national or international level to improve clinical care more systemically. SOC decisions in a clinical trial affect the level of benefit provided to study participants and the policy implications of the trial findings. SOC choices should provide high-quality care to help advance the health care system in host countries participating in the trial, but balancing the scientific and ethical objectives of SOC choices is difficult, and there is no single formula for selecting the appropriate SOC. Despite the challenges, well-designed and conducted clinical trials can and should make significant contributions to health systems in RLS.

Biclustering as a method for RNA local multiple sequence alignment.

PubMed

Wang, Shu; Gutell, Robin R; Miranker, Daniel P

2007-12-15

Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/

Electronic laboratory quality assurance program: A method of enhancing the prosthodontic curriculum and addressing accreditation standards.

PubMed

Moghadam, Marjan; Jahangiri, Leila

2015-08-01

An electronic quality assurance (eQA) program was developed to replace a paper-based system and to address standards introduced by the Commission on Dental Accreditation (CODA) and to improve educational outcomes. This eQA program provides feedback to predoctoral dental students on prosthodontic laboratory steps at New York University College of Dentistry. The purpose of this study was to compare the eQA program of performing laboratory quality assurance with the former paper-based format. Fourth-year predoctoral dental students (n=334) who experienced both the paper-based and the electronic version of the quality assurance program were surveyed about their experiences. Additionally, data extracted from the eQA program were analyzed to identify areas of weakness in the curriculum. The study findings revealed that 73.8% of the students preferred the eQA program to the paper-based version. The average number of treatments that did not pass quality assurance standards was 119.5 per month. This indicated a 6.34% laboratory failure rate. Further analysis of these data revealed that 62.1% of the errors were related to fixed prosthodontic treatment, 27.9% to partial removable dental prostheses, and 10% to complete removable dental prostheses in the first 18 months of program implementation. The eQA program was favored by dental students who have experienced both electronic and paper-based versions of the system. Error type analysis can yield the ability to create customized faculty standardization sessions and refine the didactic and clinical teaching of the predoctoral students. This program was also able to link patient care activity with the student's laboratory activities, thus addressing the latest requirements of the CODA regarding the competence of graduates in evaluating laboratory work related to their patient care. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

Investigating How to Align Schools' Marketing Environments with Federal Standards for Competitive Foods

ERIC Educational Resources Information Center

Polacsek, Michele; O'Brien, Liam M.; Pratt, Elizabeth; Whatley-Blum, Janet; Adler, Sabrina

2017-01-01

Background: Limiting food and beverage marketing to children is a promising approach to influence children's nutrition behavior. School-based marketing influences nutrition behavior and studies have consistently found marketing for nonnutritious foods and beverages in schools. No studies have examined the resources necessary to align school…

Transition of vertically aligned liquid crystal driven by fan-shaped electric field

NASA Astrophysics Data System (ADS)

Tsung, J. W.; Ting, T. L.; Chen, C. Y.; Liang, W. L.; Lai, C. W.; Lin, T. H.; Hsu, W. H.

2017-09-01

Interdigital electrodes are implemented in many commercial and novel liquid crystal devices to align molecules. Although many empirical principles and patents apply to electrode design, only a few numerical simulations of alignment have been conducted. Why and how the molecules align in an ordered manner has never been adequately explained. Hence, this investigation addresses the Fréedericksz transition of vertically aligned liquid crystal that is driven by fishbone electrodes, and thereafter identifies the mechanism of liquid crystal alignment. Theoretical calculations suggest that the periodic deformation that is caused by the fan-shaped fringe field minimizes the free energy in the liquid crystal cell, and the optimal alignment can be obtained when the cell parameters satisfy the relation p /2 d =√{k11/k33 } , where p is the spatial period of the strips of the electrode; d denotes the cell gap; and k11 and k33 are the splay and bend elastic constants of the liquid crystal, respectively. Polymer-stabilized vertical alignment test cells with various p values and spacings between the electrodes were fabricated, and the process of liquid crystal alignment was observed under an optical microscope. The degree of alignment was evaluated by measuring the transmittance of the test cell. The experimental results were consistent with the theoretical predictions. The principle of design, p /2 d =√{k11/k33 } , greatly improves the uniformity and stability of the aligned liquid crystal. The methods that are presented here can be further applied to cholesteric liquid crystal and other self-assembled soft materials.

Structural re-alignment in an immunologic surface region of ricin A chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Melody Alignment and Similarity Metric for Content-Based Music Retrieval

NASA Astrophysics Data System (ADS)

Zhu, Yongwei; Kankanhalli, Mohan S.

2003-01-01

Music query-by-humming has attracted much research interest recently. It is a challenging problem since the hummed query inevitably contains much variation and inaccuracy. Furthermore, the similarity computation between the query tune and the reference melody is not easy due to the difficulty in ensuring proper alignment. This is because the query tune can be rendered at an unknown speed and it is usually an arbitrary subsequence of the target reference melody. Many of the previous methods, which adopt note segmentation and string matching, suffer drastically from the errors in the note segmentation, which affects retrieval accuracy and efficiency. Some methods solve the alignment issue by controlling the speed of the articulation of queries, which is inconvenient because it forces users to hum along a metronome. Some other techniques introduce arbitrary rescaling in time but this is computationally very inefficient. In this paper, we introduce a melody alignment technique, which addresses the robustness and efficiency issues. We also present a new melody similarity metric, which is performed directly on melody contours of the query data. This approach cleanly separates the alignment and similarity measurement in the search process. We show how to robustly and efficiently align the query melody with the reference melodies and how to measure the similarity subsequently. We have carried out extensive experiments. Our melody alignment method can reduce the matching candidate to 1.7% with 95% correct alignment rate. The overall retrieval system achieved 80% recall in the top 10 rank list. The results demonstrate the robustness and effectiveness the proposed methods.

Global Alignment and Proportion (GAP) Score: Development and Validation of a New Method of Analyzing Spinopelvic Alignment to Predict Mechanical Complications After Adult Spinal Deformity Surgery.

PubMed

Yilgor, Caglar; Sogunmez, Nuray; Boissiere, Louis; Yavuz, Yasemin; Obeid, Ibrahim; Kleinstück, Frank; Pérez-Grueso, Francisco Javier Sánchez; Acaroglu, Emre; Haddad, Sleiman; Mannion, Anne F; Pellise, Ferran; Alanay, Ahmet

2017-10-04

The restoration of normal sagittal alignment is a critical goal in adult spinal deformity surgery to achieve favorable outcomes and prevent mechanical complications. Schwab sagittal modifiers have been accepted as targets for appropriate alignment, but addressing these targets does not always prevent high mechanical complication or revision rates. This may be because the linear absolute numerical parameters do not cover the whole pelvic incidence spectrum and the distribution of lordosis, pelvic anteversion, and negative malalignment are not considered as potential causes of failure. The aim of the present study was to develop and validate a score based on pelvic-incidence-based proportional parameters to better predict mechanical complications. Two hundred and twenty-two patients (168 women and 54 men) followed for ≥2 years after posterior fusion at ≥4 levels were included in the study. The mean age (and standard deviation) was 52.2 ± 19.3 years (range, 18 to 84 years), and the mean duration of follow-up was 28.8 ± 8.2 months (range, 24 to 62 months). The global alignment and proportion (GAP) score was developed and validated in groups of patients randomly assigned to derivation (n = 148, 66.7%) and validation (n = 74, 33.3%) cohorts. GAP score parameters were relative pelvic version (the measured minus the ideal sacral slope), relative lumbar lordosis (the measured minus the ideal lumbar lordosis), lordosis distribution index (the L4-S1 lordosis divided by the L1-S1 lordosis multiplied by 100), relative spinopelvic alignment (the measured minus the ideal global tilt), and an age factor. Proximal and distal junctional kyphosis and/or failure, rod breakage, and other implant-related complications were considered mechanical complications. The predictive accuracy of the GAP score was analyzed using receiver operating characteristic (ROC) analyses. Associations between GAP categories and mechanical complications and revisions were analyzed using Cochran

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Keynote Address: ACR-NEMA standards and their implications for teleradiology

NASA Astrophysics Data System (ADS)

Horii, Steven C.

1990-06-01

The ACR-NEMA Standard was developed initially as an interface standard for the interconnection of two pieces of imaging equipment Essentially the Standard defmes a point-to-point hardware connection with the necessary protocol and data structure so that two differing devices which meet the specification will be able to communicate with each other. The Standard does not defme a particular PACS architecture nor does it specify a database structure. In part these are the reasons why implementers have had difficulty in using the Standard in a full PACS. Recent activity of the Working Groups formed by the Committee overseeing work on the ACR-NEMA Standard has changed some of the " flavor" of the Standard. It was realized that connection of PACS with hospital and radiology information systems (HIS and RIS) is necessary if a PACS is ever to be succesful. The idea of interconnecting heterogeneous computer systems has pushed Standards development beyond the scope of the original work. Teleradiology which inherenfly involves wide-area networking may be a direct beneficiary of the new directions taken by the Standards Working Groups. This paper will give a brief history of the ACR-NEMA effort describe the " parent" Standard and its " offspring" and describe the activity of the current Working Groups with particular emphasis on the potential impacts on teleradiology.

A comparison of short term radiological alignment outcomes of the patient specific and standard instrumentation for primary total knee arthroplasty: A systematic review and meta-analysis.

PubMed

Alcelik, Ilhan; Blomfield, Mark; Öztürk, Cenk; Soni, Ashish; Charity, Richard; Acornley, Alex

2017-05-01

The aim of this study was to review the radiological alignment outcomes of patient Specific (PS) cutting blocks and Standard Instrumentation in Primary Total Knee Arthroplasty. We hypothesized that the use of PS techniques would significantly improve sagittal, coronal and rotational alignment of the prosthesis on short term. We performed a systematic review and a meta-analysis including all the randomised controlled trials (RCT) using PS and standard (ST) total knee arthroplasty to date. A total of 538 PS TKA and 549 ST TKA were included in the study. Statistical analysis of the outliers for femoral component sagittal, coronal and rotational positioning, tibial component sagittal and coronal positioning and the overall mechanical axis were assessed. We found that there was no significant benefit from using PS instrumentation in primary knee arthroplasty to aid in the positioning of either the tibial or femoral components. Furthermore sagittal plane tibial component positioning was worse in the PS than the traditional ST group. Our results suggest that at present PS instrumentation is not superior to ST instrumentation in primary total knee arthroplasty. Level 1, Systematic review of therapeutic studies. Copyright © 2017 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Precise Synaptic Efficacy Alignment Suggests Potentiation Dominated Learning.

PubMed

Hartmann, Christoph; Miner, Daniel C; Triesch, Jochen

2015-01-01

Recent evidence suggests that parallel synapses from the same axonal branch onto the same dendritic branch have almost identical strength. It has been proposed that this alignment is only possible through learning rules that integrate activity over long time spans. However, learning mechanisms such as spike-timing-dependent plasticity (STDP) are commonly assumed to be temporally local. Here, we propose that the combination of temporally local STDP and a multiplicative synaptic normalization mechanism is sufficient to explain the alignment of parallel synapses. To address this issue, we introduce three increasingly complex models: First, we model the idealized interaction of STDP and synaptic normalization in a single neuron as a simple stochastic process and derive analytically that the alignment effect can be described by a so-called Kesten process. From this we can derive that synaptic efficacy alignment requires potentiation-dominated learning regimes. We verify these conditions in a single-neuron model with independent spiking activities but more realistic synapses. As expected, we only observe synaptic efficacy alignment for long-term potentiation-biased STDP. Finally, we explore how well the findings transfer to recurrent neural networks where the learning mechanisms interact with the correlated activity of the network. We find that due to the self-reinforcing correlations in recurrent circuits under STDP, alignment occurs for both long-term potentiation- and depression-biased STDP, because the learning will be potentiation dominated in both cases due to the potentiating events induced by correlated activity. This is in line with recent results demonstrating a dominance of potentiation over depression during waking and normalization during sleep. This leads us to predict that individual spine pairs will be more similar after sleep compared to after sleep deprivation. In conclusion, we show that synaptic normalization in conjunction with coordinated

Kinematic Alignment and Bonding of Silicon Mirrors for High-Resolution Astronomical X-Ray Optics

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Mazzarella, James R.; Saha, Timo T.; Zhang, William W.; Mcclelland, Ryan S.; Biskack, Michael P.; Riveros, Raul E.; Allgood, Kim D.; Kearney, John D.; Sharpe, Marton V.;

Increasing ocean sciences in K and 1st grade classrooms through ocean sciences curriculum aligned to A Framework for K-12 Science Education, and implementation support.

NASA Astrophysics Data System (ADS)

Pedemonte, S.; Weiss, E. L.

2016-02-01

Ocean and climate sciences are rarely introduced at the early elementary levels. Reasons for this vary, but include little direct attention at the national and state levels; lack of quality instructional materials; and, lack of teacher content knowledge. Recent recommendations by the National Research Council, "revise the Earth and Space sciences core ideas and grade band endpoints to include more attention to the ocean whenever possible" (NRC, 2012, p. 336) adopted in the Next Generation Science Standards (NGSS), may increase the call for ocean and climate sciences to be addressed. In response to these recommendations' and the recognition that an understanding of some of the Disciplinary Core Ideas (DCIs) would be incomplete without an understanding of processes or phenomena unique to the ocean and ocean organisms; the ocean Literacy community have created documents that show the alignment of NGSS with the Ocean Literacy Principles and Fundamental Concepts (Ocean Literacy, 2013) as well as the Ocean Literacy Scope and Sequence for Grades K-12 (Ocean Literacy, 2010), providing a solid argument for how and to what degree ocean sciences should be part of the curriculum. However, the percentage of science education curricula focused on the ocean remains very low. This session will describe a new project, that draws on the expertise of curriculum developers, ocean literacy advocates, and researchers to meet the challenges of aligning ocean sciences curriculum to NGSS, and supporting its implementation. The desired outcomes of the proposed project are to provide a rigorous standards aligned curricula that addresses all of the Life Sciences, and some Earth and Space Sciences and Engineering Design Core Ideas for Grades K and 1; and provides teachers with the support they need to understand the content and begin implementation. The process and lessons learned will be shared.

Two Influential Primate Classifications Logically Aligned

PubMed Central

Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-01-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across

Using Quasi-Horizontal Alignment in the absence of the actual alignment.

PubMed

Banihashemi, Mohamadreza

2016-10-01

Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of Virginia's 2009 Mathematics Standards of Learning with the Common Core State Standards for Mathematics

ERIC Educational Resources Information Center

Virginia Department of Education, 2011

2011-01-01

This first draft of the "Comparison of Virginia's 2009 Mathematics Standards of Learning (SOL) with the Common Core State Standards (CCSS) for Mathematics" provides a side-by-side overview demonstrating how the 2009 Mathematics SOL are aligned to the CCSS. The comparison was made using Virginia's complete standards program for supporting…

A Kalman Filter for SINS Self-Alignment Based on Vector Observation.

PubMed

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-29

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.

A Kalman Filter for SINS Self-Alignment Based on Vector Observation

PubMed Central

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-01

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q-method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate. PMID:28146059

The impact of training under different visual-spatial conditions on reverse-alignment laparoscopic skills development.

PubMed

Holznecht, Catherine; Schmidt, Travis; Gould, Jon

2012-01-01

Circumstances may arise during laparoscopic procedures in which alignment of the laparoscope and the instruments is off by 180°, creating a mirror image of the operative field. It has been shown that task performance is degraded under these reverse-alignment conditions, and that the magnitude of performance impairment is directly related to laparoscopic experience and skill. The aim of this study was to determine if reverse-alignment surgical skills could be developed through training. Twenty-two medical students were randomized to train in either reverse- or forward-alignment conditions on a standardized laparoscopic task in a video trainer (peg transfer). Baseline scores were attained for each group under both orientations. Subjects participated in three 1-h training sessions during an 8-week period. Post-training scores were then obtained under both alignment conditions. Pre and post-training scores were compared for users in each study group under both conditions. Post-training assessments in the forward orientation demonstrated that subjects in the forward-training group improved significantly compared to pre-testing, while the performance of subjects in the reverse-training group did not improve. Under reverse-alignment conditions, both groups improved on post-test assessment, with dramatic improvements observed for those in the reverse-training group. Laparoscopic novices can learn to adapt to a sensorimotor discordance in a simulated training environment. While it is possible that skills developed by training under standard forward-alignment conditions can be utilized in situations of extreme visual-spatial discordance, the intentional development of reverse-alignment skills by training under these conditions may prove beneficial to novice surgeons.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

A strategic approach for managing conflict in hospitals: responding to the Joint Commission leadership standard, Part 1.

PubMed

Scott, Charity; Gerardi, Debra

2011-02-01

The Joint Commission's leadership standard for conflict management in hospitals, LD.02.04.01, states, "The hospital manages conflict between leadership groups to protect the quality and safety of care." This standard is one of numerous standards and alerts issued by The Joint Commission that address conflict and communication. They underscore the significant impact of relational dynamics on patient safety and quality of care and the critical need for a strategic approach to conflict in health care organizations. Whether leadership conflicts openly threaten a major disruption of hospital operations or whether unresolved conflicts lurk beneath the surface of daily interactions, unaddressed conflict can undermine a hospital's efforts to ensure safe, high-quality patient care. How leaders manage organizational conflict has a significant impact on achieving strategic objectives. Aligning conflict management approaches with quality and safety goals is the first step in adopting a strategic approach to conflict management. A strategic approach goes beyond reducing costs of litigation or improving grievance processes--it integrates a collaborative mind-set and individual conflict competency with nonadversarial processes. Conflict assessment should determine how conflicts are handled among the leaders at the hospital, the degree of conflict competence already present among the leaders, where the most significant conflicts occur, and how leaders think a conflict management system might work for them. Strategically aligning a conflict management approach that addresses conflict among leadership groups as a means of protecting the quality and safety of patient care is at the heart of LD.02.04.01.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Self-aligned quadruple patterning-compliant placement

NASA Astrophysics Data System (ADS)

Nakajima, Fumiharu; Kodama, Chikaaki; Nakayama, Koichi; Nojima, Shigeki; Kotani, Toshiya

2015-03-01

Self-Aligned Quadruple Patterning (SAQP) will be one of the leading candidates for sub-14nm node and beyond. However, compared with triple patterning, making a feasible standard cell placement has following problems. (1) When coloring conflicts occur between two adjoining cells, they may not be solved easily since SAQP layout has stronger coloring constraints. (2) SAQP layout cannot use stitch to solve coloring conflict. In this paper, we present a framework of SAQP-aware standard cell placement considering the above problems. When standard cell is placed, the proposed method tries to solve coloring conflicts between two cells by exchanging two of three colors. If some conflicts remain between adjoining cells, dummy space will be inserted to keep coloring constraints of SAQP. We show some examples to confirm effectiveness of the proposed framework. To our best knowledge, this is the first framework of SAQP-aware standard cell placement.

Novel Models of Visual Topographic Map Alignment in the Superior Colliculus

PubMed Central

El-Ghazawi, Tarek A.; Triplett, Jason W.

2016-01-01

The establishment of precise neuronal connectivity during development is critical for sensing the external environment and informing appropriate behavioral responses. In the visual system, many connections are organized topographically, which preserves the spatial order of the visual scene. The superior colliculus (SC) is a midbrain nucleus that integrates visual inputs from the retina and primary visual cortex (V1) to regulate goal-directed eye movements. In the SC, topographically organized inputs from the retina and V1 must be aligned to facilitate integration. Previously, we showed that retinal input instructs the alignment of V1 inputs in the SC in a manner dependent on spontaneous neuronal activity; however, the mechanism of activity-dependent instruction remains unclear. To begin to address this gap, we developed two novel computational models of visual map alignment in the SC that incorporate distinct activity-dependent components. First, a Correlational Model assumes that V1 inputs achieve alignment with established retinal inputs through simple correlative firing mechanisms. A second Integrational Model assumes that V1 inputs contribute to the firing of SC neurons during alignment. Both models accurately replicate in vivo findings in wild type, transgenic and combination mutant mouse models, suggesting either activity-dependent mechanism is plausible. In silico experiments reveal distinct behaviors in response to weakening retinal drive, providing insight into the nature of the system governing map alignment depending on the activity-dependent strategy utilized. Overall, we describe novel computational frameworks of visual map alignment that accurately model many aspects of the in vivo process and propose experiments to test them. PMID:28027309

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

2016-01-01

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

Real-time high-resolution measurement of collagen alignment in dynamically loaded soft tissue.

PubMed

York, Timothy; Kahan, Lindsey; Lake, Spencer P; Gruev, Viktor

2014-06-01

A technique for creating maps of the direction and strength of fiber alignment in collagenous soft tissues is presented. The method uses a division of focal plane polarimeter to measure circularly polarized light transmitted through the tissue. The architecture of the sensor allows measurement of the retardance and fiber alignment at the full frame rate of the sensor without any moving optics. The technique compares favorably to the standard method of using a rotating polarizer. How the new technique enables real-time capture of the full angular spread of fiber alignment and retardance under various cyclic loading conditions is illustrated.

The Battle for Higher Standards

ERIC Educational Resources Information Center

Luna, Tom; Rush, Mike; Gramer, Rod; Stewart, Roger

2014-01-01

To remain internationally competitive, states needed clearer, higher, and comparable K-12 learning standards aligned with college and career expectations, and as ambitious as those of the countries that lead the world in education. Idaho's old academic standards were not preparing students for postsecondary education, which contributed to the…

Alignment of sensor arrays in optical instruments using a geometric approach.

PubMed

Sawyer, Travis W

2018-02-01

Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87  deg in rotation and ±0.86  μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.

Aligning for Innovation - Alignment Strategy to Drive Innovation

NASA Technical Reports Server (NTRS)

Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

2010-01-01

With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

PubMed Central

Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

2015-01-01

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

PubMed Central

Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

2011-01-01

Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.

PubMed

Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André

2016-08-01

The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment.

Individual responses to alignment perturbations in socket reaction moments while walking in transtibial prostheses.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Zhang, Ming; Boone, David A

2014-05-01

The alignment of transtibial prostheses has a systematic effect on the mean socket reaction moments in amputees. However, understanding their individual differences in response to alignment perturbations is also important for prosthetists to fully utilize the socket reaction moments for dynamic alignment in each unique patient. The aim of this study was to investigate individual responses to alignment perturbations in transtibial prostheses with solid-ankle-cushion-heel feet. A custom instrumented prosthesis alignment component was used to measure the socket reaction moments while walking in 11 amputees with transtibial prostheses under 17 alignment conditions, including 3° and 6° of flexion, extension, abduction, and adduction of the socket, 5mm and 10mm of anterior, posterior, lateral, and medial translation of the socket, and an initial baseline alignment. Coronal moments at 30% of stance and maximum sagittal moments were extracted for comparisons from each amputee. In the coronal plane, varus moment at 30% of stance was generally reduced by adduction or medial translation of the socket in all the amputees. In the sagittal plane, extension moment was generally increased by posterior translation or flexion of the socket; however, this was not necessarily the case for all the amputees. Individual responses to alignment perturbations are not always consistent, and prosthetists would need to be aware of this variance when addressing individual socket reaction moments during dynamic alignment in clinical setting. Copyright © 2014 Elsevier Ltd. All rights reserved.

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

State Testing Standards versus Creativity.

ERIC Educational Resources Information Center

Ediger, Marlow

The balance between conformity to state standards and creativity in providing for individual differences in the classroom is discussed. With the current emphases on accountability and standards, learning opportunities for students are supposed to be aligned with state-mandated objectives. This may lead to a situation in which rote learning,…

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.

Passively aligned multichannel fiber-pigtailing of planar integrated optical waveguides

NASA Astrophysics Data System (ADS)

Kremmel, Johannes; Lamprecht, Tobias; Crameri, Nino; Michler, Markus

2017-02-01

A silicon device to simplify the coupling of multiple single-mode fibers to embedded single-mode waveguides has been developed. The silicon device features alignment structures that enable a passive alignment of fibers to integrated waveguides. For passive alignment, precisely machined V-grooves on a silicon device are used and the planar lightwave circuit board features high-precision structures acting as a mechanical stop. The approach has been tested for up to eight fiber-to-waveguide connections. The alignment approach, the design, and the fabrication of the silicon device as well as the assembly process are presented. The characterization of the fiber-to-waveguide link reveals total coupling losses of (0.45±0.20 dB) per coupling interface, which is significantly lower than the values reported in earlier works. Subsequent climate tests reveal that the coupling losses remain stable during thermal cycling but increases significantly during an 85°C/85 Rh-test. All applied fabrication and bonding steps have been performed using standard MOEMS fabrication and packaging processes.

A new method and device of aligning patient setup lasers in radiation therapy.

PubMed

Hwang, Ui-Jung; Jo, Kwanghyun; Lim, Young Kyung; Kwak, Jung Won; Choi, Sang Hyuon; Jeong, Chiyoung; Kim, Mi Young; Jeong, Jong Hwi; Shin, Dongho; Lee, Se Byeong; Park, Jeong-Hoon; Park, Sung Yong; Kim, Siyong

2016-01-08

The aim of this study is to develop a new method to align the patient setup lasers in a radiation therapy treatment room and examine its validity and efficiency. The new laser alignment method is realized by a device composed of both a metallic base plate and a few acrylic transparent plates. Except one, every plate has either a crosshair line (CHL) or a single vertical line that is used for alignment. Two holders for radiochromic film insertion are prepared in the device to find a radiation isocenter. The right laser positions can be found optically by matching the shadows of all the CHLs in the gantry head and the device. The reproducibility, accuracy, and efficiency of laser alignment and the dependency on the position error of the light source were evaluated by comparing the means and the standard deviations of the measured laser positions. After the optical alignment of the lasers, the radiation isocenter was found by the gantry and collimator star shots, and then the lasers were translated parallel to the isocenter. In the laser position reproducibility test, the mean and standard deviation on the wall of treatment room were 32.3 ± 0.93 mm for the new method whereas they were 33.4 ± 1.49 mm for the conventional method. The mean alignment accuracy was 1.4 mm for the new method, and 2.1 mm for the conventional method on the walls. In the test of the dependency on the light source position error, the mean laser position was shifted just by a similar amount of the shift of the light source in the new method, but it was greatly magnified in the conventional method. In this study, a new laser alignment method was devised and evaluated successfully. The new method provided more accurate, more reproducible, and faster alignment of the lasers than the conventional method.

A new method and device of aligning patient setup lasers in radiation therapy

PubMed Central

Hwang, Ui‐Jung; Jo, Kwanghyun; Kwak, Jung Won; Choi, Sang Hyoun; Jeong, Chiyoung; Kim, Mi Young; Jeong, Jong Hwi; Shin, Dongho; Lee, Se Byeong; Park, Jeong‐Hoon; Park, Sung Yong; Kim, Siyong

2016-01-01

The aim of this study is to develop a new method to align the patient setup lasers in a radiation therapy treatment room and examine its validity and efficiency. The new laser alignment method is realized by a device composed of both a metallic base plate and a few acrylic transparent plates. Except one, every plate has either a crosshair line (CHL) or a single vertical line that is used for alignment. Two holders for radiochromic film insertion are prepared in the device to find a radiation isocenter. The right laser positions can be found optically by matching the shadows of all the CHLs in the gantry head and the device. The reproducibility, accuracy, and efficiency of laser alignment and the dependency on the position error of the light source were evaluated by comparing the means and the standard deviations of the measured laser positions. After the optical alignment of the lasers, the radiation isocenter was found by the gantry and collimator star shots, and then the lasers were translated parallel to the isocenter. In the laser position reproducibility test, the mean and standard deviation on the wall of treatment room were 32.3±0.93 mm for the new method whereas they were 33.4±1.49 mm for the conventional method. The mean alignment accuracy was 1.4 mm for the new method, and 2.1 mm for the conventional method on the walls. In the test of the dependency on the light source position error, the mean laser position was shifted just by a similar amount of the shift of the light source in the new method, but it was greatly magnified in the conventional method. In this study, a new laser alignment method was devised and evaluated successfully. The new method provided more accurate, more reproducible, and faster alignment of the lasers than the conventional method. PACS numbers: 87.56.Fc, 87.53.Bn, 87.53.Kn, 87.53.Ly, 87.55.Gh PMID:26894331

Do small changes in rotation affect measurements of lower extremity limb alignment?

PubMed

Jamali, Amir A; Meehan, John P; Moroski, Nathan M; Anderson, Matthew J; Lamba, Ramit; Parise, Carol

2017-05-22

The alignment of the lower extremity has important implications in the development of knee arthritis. The effect of incremental rotations of the limb on common parameters of alignment has not been studied. The purpose of the study was to (1) determine the standardized neutral position measurements of alignment and (2) determine the effect of rotation on commonly used measurements of alignment. Eighty-seven full length CT angiography studies (49 males and 38 females, average age 66 years old) were included. Three-dimensional models were created using a rendering software program and placed on a virtual plane. An image of the extremity was obtained. Thirty scans were randomly selected, and those models were rotated in 3° intervals around the longitudinal axis and additional images were obtained. In the neutral position, the mechanical lateral distal femoral articular angle (mLDFA) was 85.6 ± 2.3°, medial proximal tibial angle (MPTA) was 86.1 ± 2.8°, and mechanical tibiofemoral angle (mTFA) was -0.7 ± 3.1°. Females had a more valgus alignment with a mTFA of 0.5 ± 2.9° while males had a more varus alignment with a mTFA of -1.7 ± 2.9°. The anatomic tibiofemoral angle (aTFA) was 4.8 ± 2.6°, the anatomic lateral distal femoral angle (aLDFA) measured 80.2 ± 2.2°, and the anatomical-mechanical angle (AMA) was 5.4 ± 0.7°. The prevalence of constitutional varus was 18%. The effect of rotation on the rotated scans led to statistically significant differences relative to the 0° measurement for all measurements. These effects may be small, and their clinical importance is unknown. This study provides new information on standardized measures of lower extremity alignment and the relationship between discreet axial rotations of the entire lower extremity and these parameters.

Experimental findings on the underwater measurements uncertainty of speed of sound and the alignment system

NASA Astrophysics Data System (ADS)

Santos, T. Q.; Alvarenga, A. V.; Oliveira, D. P.; Mayworm, R. C.; Souza, R. M.; Costa-Félix, R. P. B.

2016-07-01

Speed of sound is an important quantity to characterize reference materials for ultrasonic applications, for instance. The alignment between the transducer and the test body is an key activity in order to perform reliable and consistent measurement. The aim of this work is to evaluate the influence of the alignment system to the expanded uncertainty of such measurement. A stainless steel cylinder was previously calibrated on an out of water system typically used for calibration of non-destructive blocks. Afterwards, the cylinder was calibrated underwater with two distinct alignment system: fixed and mobile. The values were statistically compared to the out-of-water measurement, considered the golden standard for such application. For both alignment systems, the normalized error was less than 0.8, leading to conclude that the both measurement system (under and out-of-water) do not diverge significantly. The gold standard uncertainty was 2.7 m-s-1, whilst the fixed underwater system resulted in 13 m-s-1, and the mobile alignment system achieved 6.6 m-s-1. After the validation of the underwater system for speed of sound measurement, it will be applied to certify Encapsulated Tissue Mimicking Material as a reference material for biotechnology application.

Two Influential Primate Classifications Logically Aligned.

PubMed

Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-07-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents

PubMed Central

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-01-01

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties. PMID:27660048

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.

PubMed

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-12-16

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

Superposition and alignment of labeled point clouds.

PubMed

Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

2011-01-01

Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

Year 3 of Implementing the Common Core State Standards: Transitioning to CCSS-Aligned Curriculum and Assessments for Students with Disabilities

ERIC Educational Resources Information Center

Frizzell, Matthew

2013-01-01

This report, based on a spring 2013 survey of state education agency officials in Common Core-adopting states, focuses on state efforts to prepare students with disabilities for the Common Core State Standards. The report also addresses the challenges states face with supporting teachers of students with disabilities and state plans for assessing…

Aligning, Bonding, and Testing Mirrors for Lightweight X-ray Telescopes

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Zhang, William W.; Saha, Timo T.; McClelland, Ryan S.; Biskach, Michael P.; Niemeyer, Jason; Schofield, Mark J.; Mazzarella, James R.; Kolos, Linette D.; Hong, Melinda M.;

Comparison of Virginia's 2010 English Standards of Learning with the Common Core State Standards for English and Literacy

ERIC Educational Resources Information Center

Virginia Department of Education, 2010

2010-01-01

The "Comparison of Virginia's 2010 English Standards of Learning (SOL) with the Common Core State Standards (CCSS) for English Language Arts and Literacy (ELAL)" provides a side-by-side overview demonstrating how the 2010 English SOL are aligned to the CCSS for ELAL. The comparison was made using Virginia's complete standards program for…

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

PubMed Central

2007-01-01

Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction

Standards Draw Heat in States

ERIC Educational Resources Information Center

Ujifusa, Andrew

2013-01-01

Opponents of the Common Core State Standards are ramping up legislative pressure and public relations efforts aimed at getting states to scale back--or even abandon--the high-profile initiative, even as implementation proceeds and tests aligned with the standards loom. Critics of the common core have focused recent lobbying and media efforts on…

An efficient multi-resolution GA approach to dental image alignment

NASA Astrophysics Data System (ADS)

Nassar, Diaa Eldin; Ogirala, Mythili; Adjeroh, Donald; Ammar, Hany

2006-02-01

Automating the process of postmortem identification of individuals using dental records is receiving an increased attention in forensic science, especially with the large volume of victims encountered in mass disasters. Dental radiograph alignment is a key step required for automating the dental identification process. In this paper, we address the problem of dental radiograph alignment using a Multi-Resolution Genetic Algorithm (MR-GA) approach. We use location and orientation information of edge points as features; we assume that affine transformations suffice to restore geometric discrepancies between two images of a tooth, we efficiently search the 6D space of affine parameters using GA progressively across multi-resolution image versions, and we use a Hausdorff distance measure to compute the similarity between a reference tooth and a query tooth subject to a possible alignment transform. Testing results based on 52 teeth-pair images suggest that our algorithm converges to reasonable solutions in more than 85% of the test cases, with most of the error in the remaining cases due to excessive misalignments.

Theory of electrical conductivity and dielectric permittivity of highly aligned graphene-based nanocomposites.

PubMed

Xia, Xiaodong; Hao, Jia; Wang, Yang; Zhong, Zheng; Weng, George J

2017-05-24

Highly aligned graphene-based nanocomposites are of great interest due to their excellent electrical properties along the aligned direction. Graphene fillers in these composites are not necessarily perfectly aligned, but their orientations are highly confined to a certain angle, [Formula: see text] with 90° giving rise to the randomly oriented state and 0° to the perfectly aligned one. Recent experiments have shown that electrical conductivity and dielectric permittivity of highly aligned graphene-polymer nanocomposites are strongly dependent on this distribution angle, but at present no theory seems to exist to address this issue. In this work we present a new effective-medium theory that is derived from the underlying physical process including the effects of graphene orientation, filler loading, aspect ratio, percolation threshold, interfacial tunneling, and Maxwell-Wagner-Sillars polarization, to determine these two properties. The theory is formulated in the context of preferred orientational average. We highlight this new theory with an application to rGO/epoxy nanocomposites, and demonstrate that the calculated in-plane and out-of-plane conductivity and permittivity are in agreement with the experimental data as the range of graphene orientations changes from the randomly oriented to the highly aligned state. We also show that the percolation thresholds of highly aligned graphene nanocomposites are in general different along the planar and the normal directions, but they converge into a single one when the statistical distribution of graphene fillers is spherically symmetric.

Self-Alignment MEMS IMU Method Based on the Rotation Modulation Technique on a Swing Base

PubMed Central

Chen, Zhiyong; Yang, Haotian; Wang, Chengbin; Lin, Zhihui; Guo, Meifeng

2018-01-01

The micro-electro-mechanical-system (MEMS) inertial measurement unit (IMU) has been widely used in the field of inertial navigation due to its small size, low cost, and light weight, but aligning MEMS IMUs remains a challenge for researchers. MEMS IMUs have been conventionally aligned on a static base, requiring other sensors, such as magnetometers or satellites, to provide auxiliary information, which limits its application range to some extent. Therefore, improving the alignment accuracy of MEMS IMU as much as possible under swing conditions is of considerable value. This paper proposes an alignment method based on the rotation modulation technique (RMT), which is completely self-aligned, unlike the existing alignment techniques. The effect of the inertial sensor errors is mitigated by rotating the IMU. Then, inertial frame-based alignment using the rotation modulation technique (RMT-IFBA) achieved coarse alignment on the swing base. The strong tracking filter (STF) further improved the alignment accuracy. The performance of the proposed method was validated with a physical experiment, and the results of the alignment showed that the standard deviations of pitch, roll, and heading angle were 0.0140°, 0.0097°, and 0.91°, respectively, which verified the practicality and efficacy of the proposed method for the self-alignment of the MEMS IMU on a swing base. PMID:29649150

Evaluation of mathematical algorithms for automatic patient alignment in radiosurgery.

PubMed

Williams, Kenneth M; Schulte, Reinhard W; Schubert, Keith E; Wroe, Andrew J

2015-06-01

Image registration techniques based on anatomical features can serve to automate patient alignment for intracranial radiosurgery procedures in an effort to improve the accuracy and efficiency of the alignment process as well as potentially eliminate the need for implanted fiducial markers. To explore this option, four two-dimensional (2D) image registration algorithms were analyzed: the phase correlation technique, mutual information (MI) maximization, enhanced correlation coefficient (ECC) maximization, and the iterative closest point (ICP) algorithm. Digitally reconstructed radiographs from the treatment planning computed tomography scan of a human skull were used as the reference images, while orthogonal digital x-ray images taken in the treatment room were used as the captured images to be aligned. The accuracy of aligning the skull with each algorithm was compared to the alignment of the currently practiced procedure, which is based on a manual process of selecting common landmarks, including implanted fiducials and anatomical skull features. Of the four algorithms, three (phase correlation, MI maximization, and ECC maximization) demonstrated clinically adequate (ie, comparable to the standard alignment technique) translational accuracy and improvements in speed compared to the interactive, user-guided technique; however, the ICP algorithm failed to give clinically acceptable results. The results of this work suggest that a combination of different algorithms may provide the best registration results. This research serves as the initial groundwork for the translation of automated, anatomy-based 2D algorithms into a real-world system for 2D-to-2D image registration and alignment for intracranial radiosurgery. This may obviate the need for invasive implantation of fiducial markers into the skull and may improve treatment room efficiency and accuracy. © The Author(s) 2014.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Associations of Varus Thrust and Alignment with Pain in Knee Osteoarthritis

PubMed Central

Lo, Grace H.; Harvey, William F.; McAlindon, Timothy E.

2012-01-01

Objective To compare associations of varus thrust and varus static alignment with pain in those with knee osteoarthritis (OA). Method This was a cross-sectional study of participants from a randomized controlled trial of vitamin D for knee OA. Participants were video recorded walking and scored for presence of varus thrust. Standard PA knee X-rays were measured for static alignment. Pain questions from the Western Ontario McMasters Osteoarthritis (WOMAC) questionnaire assessed symptoms. We calculated means for total WOMAC pain by varus thrust and varus alignment (i.e. corrected anatomic alignment < 178°). We performed ordinal logistic regressions; outcomes: individual WOMAC pain questions; predictors: varus thrust and varus alignment. Results There were 82 participants, mean age 65.1 (±8.5), mean body mass index 30.2 (±5.4), and 60% female. Total WOMAC pain was 6.3 versus 3.9, p = 0.007 in those with versus without definite varus thrust. For varus alignment, total WOMAC pain was 5.2 versus 4.2, p = 0.30. Odds ratios for pain with walking and standing were 5.5 (95%CI 2.0 – 15.1) and 6.0 (95%CI 2.2 – 16.2) in those with versus without definite varus thrust. There were no significant associations between varus alignment and individual WOMAC pain questions. Sensitivity analyses suggested a more stringent definition of varus might have been associated with walking and standing pain. Conclusion In those with knee OA, varus thrust and possibly varus static alignment, were associated with pain, specifically during weight-bearing activities. Treatment of varus thrust (e.g. via bracing or gait modification) may lead to improvement of symptoms. PMID:22307813

Reference News Release: U.S. Files Complaint, Announces Settlement to Address Alleged Renewable Fuel Standard Violations by NGL Crude Logistics and Western Dubuque Biodiesel

EPA Pesticide Factsheets

Reference news release on the complaint against NGL Crude Logistics, LLC and Western Dubuque Biodiesel, LLC and a settlement with Western Dubuque to address alleged violations of the Renewable Fuel Standard.

Development of Extended Content Standards for Biodiversity Data

NASA Astrophysics Data System (ADS)

Hugo, Wim; Schmidt, Jochen; Saarenmaa, Hannu

2013-04-01

Interoperability in the field of Biodiversity observation has been strongly driven by the development of a number of global initiatives (GEO, GBIF, OGC, TDWG, GenBank, …) and its supporting standards (OGC-WxS, OGC-SOS, Darwin Core (DwC), NetCDF, …). To a large extent, these initiatives have focused on discoverability and standardization of syntactic and schematic interoperability. Semantic interoperability is more complex, requiring development of domain-dependent conceptual data models, and extension of these models with appropriate ontologies (typically manifested as controlled vocabularies). Biodiversity content has been standardized partly, for example through Darwin Core for occurrence data and associated taxonomy, and through Genbank for genetic data, but other contexts of biodiversity observation have lagged behind - making it difficult to achieve semantic interoperability between distributed data sources. With this in mind, WG8 of GEO BON (charged with data and systems interoperability) has started a work programme to address a number of concerns, one of which is the gap in content standards required to make Biodiversity data truly interoperable. The paper reports on the framework developed by WG8 for the classification of Biodiversity observation data into 'families' of use cases and its supporting data schema, where gaps, if any, in the availability if content standards have been identified, and how these are to be addressed by way of an abstract data model and the development of associated content standards. It is proposed that a minimum set of standards (1) will be required to address the scope of Biodiversity content, aligned with levels and dimensions of observation, and based on the 'Essential Biodiversity Variables' (2) being developed by GEO BON . The content standards are envisaged as loosely separated from the syntactic and schematic standards used for the base data exchange: typically, services would offer an existing data standard (DwC, WFS

Tidal alignment of galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Tidal alignment of galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš, E-mail: blazek@berkeley.edu, E-mail: zvlah@stanford.edu, E-mail: useljak@berkeley.edu

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Homeotropic alignment of multiple bent-core liquid crystal phases using a polydimethylsiloxane alignment layer

NASA Astrophysics Data System (ADS)

Carlson, Eric D.; Foley, Lee M.; Guzman, Edward; Korblova, Eva D.; Visvanathan, Rayshan; Ryu, SeongHo; Gim, Min-Jun; Tuchband, Michael R.; Yoon, Dong Ki; Clark, Noel A.; Walba, David M.

2017-08-01

The control of the molecular orientation of liquid crystals (LCs) is important in both understanding phase properties and the continuing development of new LC technologies including displays, organic transistors, and electro-optic devices. Many techniques have been developed for successfully inducing alignment of calamitic LCs, though these techniques typically do not translate to the alignment of bent-core liquid crystals (BCLCs). Some techniques have been utilized to align various phases of BCLCs, but these techniques are often unsuccessful for general alignment of multiple materials and/or multiple phases. Here, we demonstrate that glass cells treated with polydimethylsiloxane (PDMS) thin films induce high quality homeotropic alignment of multiple mesophases of four BCLCs. On cooling to the lowest temperature phase the homeotropic alignment is lost, and spherulitic growth is seen in crystal and crystal-like phases including the dark conglomerate (DC) and helical nanofilament (HNF) phases. Evidence of homeotropic alignment is observed using polarized optical microscopy. We speculate that the methyl groups on the surface of the PDMS films strongly interact with the aliphatic tails of each mesogens, resulting in homeotropic alignment.

From Standards to Frameworks for IL: How the ACRL Framework Addresses Critiques of the Standards

ERIC Educational Resources Information Center

Foasberg, Nancy M.

2015-01-01

The Association of College and Research Libraries (ACRL) Information Literacy Competency Standards for Higher Education, since their publication in 2000, have drawn criticism for ignoring the social and political aspects of information literacy. The ACRL Information Literacy Competency Standards Task Force responded with the Framework for…

High-power modular LED-based illumination systems for mask-aligner lithography.

PubMed

Bernasconi, Johana; Scharf, Toralf; Vogler, Uwe; Herzig, Hans Peter

2018-04-30

Mask-aligner lithography is traditionally performed using mercury arc lamps with wavelengths ranging from 250 nm to 600 nm with intensity peaks at the i, g and h lines. Since mercury arc lamps present several disadvantages, it is of interest to replace them with high power light emitting diodes (LEDs), which recently appeared on the market at those wavelengths. In this contribution, we present a prototype of an LED-based mask-aligner illumination. An optical characterization is made and the prototype is tested in a mask-aligner. Very good performances are demonstrated. The measured uniformity in the mask plane is 2.59 ± 0.24 % which is within the uniformity of the standard lamp. Print tests show resolution of 1 micron in contact printing and of 3 microns in proximity printing with a proximity gap of 30 microns.

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

PubMed

Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

2011-01-01

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Nuclear reactor alignment plate configuration

DOEpatents

Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

2014-01-28

An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

High School Science Teachers' Receptivity to the Next Generation Science Standards: An Examination of Discipline Specific Factors

NASA Astrophysics Data System (ADS)

Shapiro, Lesley Jacqueline

The Next Generation Science Standards (NGSS), are the biggest change to American science education since the National Science Education Standards (NSES) were published. While inquiry was central to the NSES, science assessment largely addressed factual knowledge acquisition. The NGSS represent a significant practical change for teachers as they mark a return to the ideals specified in the National Science Education Standards (NSES) and Benchmarks for Science Literacy. The purpose of this explanatory sequential, mixed-methods study was to identify and compare the factors that influenced high school science teachers' receptivity to the curricular shifts necessitated by the adoption of the NGSS. The survey data identified three factors as significant predictors of teacher receptivity: teachers' non-monetary cost-benefit analysis, alignment between the NGSS and their current teaching style, and concerns about student readiness. To understand how these factors operate in the classroom, both receptive and non-receptive teachers were interviewed. In terms of cost-benefit analysis, all teachers agree that time is a significant cost. This includes the time it takes to adapt lessons to the NGSS, and the time it takes to teach in a way that integrates the three parts of the NGSS which are the practices of science and engineering, the crosscutting concepts, and the disciplinary core ideas. In terms of alignment between their teaching style and the NGSS, teachers talked about the lack of examples of what NGSS-aligned instruction looks like and the dearth of accessible high quality professional development. Finally, concerns about students' readiness focused on both inadequate preparation for college-level science coursework and deficits in science instruction in the lower grades.

Implementing the Next Generation Science Standards: How Instructional Coaches Mediate Standards-Based Educational Reform to Teacher Practice

NASA Astrophysics Data System (ADS)

Laxton, Katherine E.

This dissertation takes a close look at how district-level instructional coaches support teachers in learning to shifting their instructional practice, related to the Next Generation Science Standards. This dissertation aims to address how re-structuring professional development to a job-embedded coaching model supports individual teacher learning of new reform-related instructional practice. Implementing the NGSS is a problem of supporting professional learning in a way that will enable educators to make fundamental changes to their teaching practice. However, there are few examples in the literature that explain how coaches interact with teachers to improve teacher learning of reform-related instructional practice. There are also few examples in the literature that specifically address how supporting teachers with extended professional learning opportunities, aligned with high-leverage practices, tools and curriculum, impacts how teachers make sense of new standards-based educational reforms and what manifests in classroom instruction. This dissertation proposes four conceptual categories of sense-making that influence how instructional coaches interpret the nature of reform, their roles and in instructional improvement and how to work with teachers. It is important to understand how coaches interpret reform because their interpretations may have unintended consequences related to privileging certain views about instruction, or establishing priorities for how to work with teachers. In this dissertation, we found that re-structuring professional development to a job-embedded coaching model supported teachers in learning new reform-related instructional practice. However, individual teacher interpretations of reform emerged and seemed to be linked to how instructional coaches supported teacher learning.

Addressing Standardized Testing through a Novel Assesment Model

ERIC Educational Resources Information Center

Schifter, Catherine C.; Carey, Martha

2014-01-01

The No Child Left Behind (NCLB) legislation spawned a plethora of standardized testing services for all the high stakes testing required by the law. We argue that one-size-fits all assessments disadvantage students who are English Language Learners, in the USA, as well as students with limited economic resources, special needs, and not reading on…

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align

Addressing the Standards for Mathematical Practice in a Calculus Class

ERIC Educational Resources Information Center

Pilgrim, Mary E.

2014-01-01

The Common Core State Standards (CCSS) provide teachers with the expectations and requirements that are meant to prepare K-12 students for college and the workforce (CCSSI 2010b). The Common Core State Standards for Mathematical Practice (SMPs) emphasize the development of skills and conceptual understanding for students to become proficient in…

Does Tibial Slope Affect Perception of Coronal Alignment on a Standing Anteroposterior Radiograph?

PubMed

Schwartz, Adam J; Ravi, Bheeshma; Kransdorf, Mark J; Clarke, Henry D

2017-07-01

A standing anteroposterior (AP) radiograph is commonly used to evaluate coronal alignment following total knee arthroplasty (TKA). The impact of coronal alignment on TKA outcomes is controversial, perhaps due to variability in imaging and/or measurement technique. We sought to quantify the effect of image rotation and tibial slope on coronal alignment. Using a standard extramedullary tibial alignment guide, 3 cadaver legs were cut to accept a tibial tray at 0°, 3°, and 7° of slope. A computed tomography scan of the entire tibia was obtained for each specimen to confirm neutral coronal alignment. Images were then obtained at progressive 10° intervals of internal and external rotation up to 40° maximum in each direction. Images were then randomized and 5 blinded TKA surgeons were asked to determine coronal alignment. Continuous data values were transformed to categorical data (neutral [0], valgus [L], and varus [R]). Each 10° interval of external rotation of a 7° sloped tibial cut (or relative internal rotation of a tibial component viewed in the AP plane) resulted in perception of an additional 0.75° of varus. The slope of the proximal tibia bone cut should be taken into account when measuring coronal alignment on a standing AP radiograph. Copyright © 2017 Elsevier Inc. All rights reserved.

Zipping, entanglement, and the elastic modulus of aligned single-walled carbon nanotube films

PubMed Central

Won, Yoonjin; Gao, Yuan; Panzer, Matthew A.; Xiang, Rong; Maruyama, Shigeo; Kenny, Thomas W.; Cai, Wei; Goodson, Kenneth E.

2013-01-01

Reliably routing heat to and from conversion materials is a daunting challenge for a variety of innovative energy technologies––from thermal solar to automotive waste heat recovery systems––whose efficiencies degrade due to massive thermomechanical stresses at interfaces. This problem may soon be addressed by adhesives based on vertically aligned carbon nanotubes, which promise the revolutionary combination of high through-plane thermal conductivity and vanishing in-plane mechanical stiffness. Here, we report the data for the in-plane modulus of aligned single-walled carbon nanotube films using a microfabricated resonator method. Molecular simulations and electron microscopy identify the nanoscale mechanisms responsible for this property. The zipping and unzipping of adjacent nanotubes and the degree of alignment and entanglement are shown to govern the spatially varying local modulus, thereby providing the route to engineered materials with outstanding combinations of mechanical and thermal properties. PMID:24309375

Fluorescein thiocarbamyl amino acids as internal standards for migration time correction in capillary sieving electrophoresis

PubMed Central

Pugsley, Haley R.; Swearingen, Kristian E.; Dovichi, Norman J.

2009-01-01

A number of algorithms have been developed to correct for migration time drift in capillary electrophoresis. Those algorithms require identification of common components in each run. However, not all components may be present or resolved in separations of complex samples, which can confound attempts for alignment. This paper reports the use of fluorescein thiocarbamyl derivatives of amino acids as internal standards for alignment of 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ)-labeled proteins in capillary sieving electrophoresis. The fluorescein thiocarbamyl derivative of aspartic acid migrates before FQ-labeled proteins and the fluorescein thiocarbamyl derivative of arginine migrates after the FQ-labeled proteins. These compounds were used as internal standards to correct for variations in migration time over a two-week period in the separation of a cellular homogenate. The experimental conditions were deliberately manipulated by varying electric field and sample preparation conditions. Three components of the homogenate were used to evaluate the alignment efficiency. Before alignment, the average relative standard deviation in migration time for these components was 13.3%. After alignment, the average relative standard deviation in migration time for these components was reduced to 0.5%. PMID:19249052

An Investigation of the Engagement of Elementary Students in the NCTM Process Standards after One Year of Standards-Based Instruction

ERIC Educational Resources Information Center

Fillingim, Jennifer Gale

2010-01-01

Contemporary mathematics education reform has placed increased emphasis on K-12 mathematics curriculum. Reform-based curricula, often referred to as "Standards-based" due to philosophical alignment with the NCTM Process Standards, have generated controversy among families, educators, and researchers. The mathematics education research…

The Caterpillar Game: A SW-PBIS Aligned Classroom Management System

ERIC Educational Resources Information Center

Floress, Margaret T.; Jacoby, Amber L.

2017-01-01

The Caterpillar Game is a classroom management system that is aligned with School-wide Positive Behavioral Interventions and Supports standards. A single-case, multiple-baseline design was used to evaluate the effects of the Caterpillar Game on disruptive student behavior and teacher praise. Three classrooms were included in the study (preschool,…

The Association of State Policy Attributes with Teachers' Instructional Alignment

ERIC Educational Resources Information Center

Polikoff, Morgan S.

2012-01-01

States vary greatly in their implementation of standards-based accountability under No Child Left Behind, yet little evidence is available to guide policymakers on what attributes of state policy advance more tightly aligned instruction. This study uses survey data and content analyses from the Surveys of Enacted Curriculum to describe elements of…

Modeling Phase-Aligned Gamma-Ray And Radio Millisecond Pulsar Light Curves

DOE PAGES

Venter, C.; Johnson, T. J.; Harding, A. K.

2011-12-12

The gamma-ray population of millisecond pulsars (MSPs) detected by the Fermi Large Area Telescope (LAT) has been steadily increasing. A number of the more recent detections, including PSR J0034-0534, PSR J1939+2134 (B1937+21; the first MSP ever discovered), PSR J1959+2048 (B1957+20; the first black widow system), and PSR J2214+3000, exhibit an unusual phenomenon: nearly phase-aligned radio and gamma- ray light curves (LCs). To account for the phase alignment, we explore geometric models where both the radio and gamma-ray emission originate either in the outer magnetosphere near the light cylinder (R LC) or near the polar caps (PCs). We obtain reasonable fitsmore » for the first three of these MSPs in the context of “altitude- limited” outer gap (alOG) and two-pole caustic (alTPC) geometries. The outer magnetosphere phase-aligned models differ from the standard outer gap (OG) / two-pole caustic (TPC) models in two respects: first, the radio emission originates in caustics at relatively high altitudes compared to the usual low-altitude conal radio beams; second, we allow the maximum altitude of the gamma-ray emission region as well as both the minimum and maximum altitudes of the radio emission region to vary within a limited range. Alternatively, there also exist phase-aligned LC solutions for emission originating near the stellar surface in a slot gap (SG) scenario (“low-altitude slot gap” (laSG) models). We find best-fit LCs using a Markov chain Monte Carlo (MCMC) max- imum likelihood approach [30]. Our fits imply that the phase-aligned LCs are likely of caustic origin, produced in the outer magnetosphere, and that the radio emission may come from close to R LC. We lastly constrain the emission altitudes with typical uncertainties of ~ 0.3RLC. Our results describe a third gamma-ray MSP subclass, in addition to the two (with non-aligned LCs) previously found [50]: those with LCs fit by standard OG / TPC models, and those with LCs fit by pair-starved polar

Vertically aligned carbon nanotubes for microelectrode arrays applications.

PubMed

Castro Smirnov, J R; Jover, Eric; Amade, Roger; Gabriel, Gemma; Villa, Rosa; Bertran, Enric

2012-09-01

In this work a methodology to fabricate carbon nanotube based electrodes using plasma enhanced chemical vapour deposition has been explored and defined. The final integrated microelectrode based devices should present specific properties that make them suitable for microelectrode arrays applications. The methodology studied has been focused on the preparation of highly regular and dense vertically aligned carbon nanotube (VACNT) mat compatible with the standard lithography used for microelectrode arrays technology.

Precision alignment and mounting apparatus

NASA Technical Reports Server (NTRS)

Preston, Dennis R. (Inventor)

1993-01-01

An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

KISS for STRAP: user extensions for a protein alignment editor.

PubMed

Gille, Christoph; Lorenzen, Stephan; Michalsky, Elke; Frömmel, Cornelius

2003-12-12

The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. JAVA-1.4 or higher. http://www.charite.de/bioinf/strap/

Robust face alignment under occlusion via regional predictive power estimation.

PubMed

Heng Yang; Xuming He; Xuhui Jia; Patras, Ioannis

2015-08-01

Face alignment has been well studied in recent years, however, when a face alignment model is applied on facial images with heavy partial occlusion, the performance deteriorates significantly. In this paper, instead of training an occlusion-aware model with visibility annotation, we address this issue via a model adaptation scheme that uses the result of a local regression forest (RF) voting method. In the proposed scheme, the consistency of the votes of the local RF in each of several oversegmented regions is used to determine the reliability of predicting the location of the facial landmarks. The latter is what we call regional predictive power (RPP). Subsequently, we adapt a holistic voting method (cascaded pose regression based on random ferns) by putting weights on the votes of each fern according to the RPP of the regions used in the fern tests. The proposed method shows superior performance over existing face alignment models in the most challenging data sets (COFW and 300-W). Moreover, it can also estimate with high accuracy (72.4% overlap ratio) which image areas belong to the face or nonface objects, on the heavily occluded images of the COFW data set, without explicit occlusion modeling.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

PubMed

Neuwald, Andrew F

2009-08-01

The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

RAMTaB: Robust Alignment of Multi-Tag Bioimages

PubMed Central

Raza, Shan-e-Ahmed; Humayun, Ahmad; Abouna, Sylvie; Nattkemper, Tim W.; Epstein, David B. A.; Khan, Michael; Rajpoot, Nasir M.

2012-01-01

Background In recent years, new microscopic imaging techniques have evolved to allow us to visualize several different proteins (or other biomolecules) in a visual field. Analysis of protein co-localization becomes viable because molecules can interact only when they are located close to each other. We present a novel approach to align images in a multi-tag fluorescence image stack. The proposed approach is applicable to multi-tag bioimaging systems which (a) acquire fluorescence images by sequential staining and (b) simultaneously capture a phase contrast image corresponding to each of the fluorescence images. To the best of our knowledge, there is no existing method in the literature, which addresses simultaneous registration of multi-tag bioimages and selection of the reference image in order to maximize the overall overlap between the images. Methodology/Principal Findings We employ a block-based method for registration, which yields a confidence measure to indicate the accuracy of our registration results. We derive a shift metric in order to select the Reference Image with Maximal Overlap (RIMO), in turn minimizing the total amount of non-overlapping signal for a given number of tags. Experimental results show that the Robust Alignment of Multi-Tag Bioimages (RAMTaB) framework is robust to variations in contrast and illumination, yields sub-pixel accuracy, and successfully selects the reference image resulting in maximum overlap. The registration results are also shown to significantly improve any follow-up protein co-localization studies. Conclusions For the discovery of protein complexes and of functional protein networks within a cell, alignment of the tag images in a multi-tag fluorescence image stack is a key pre-processing step. The proposed framework is shown to produce accurate alignment results on both real and synthetic data. Our future work will use the aligned multi-channel fluorescence image data for normal and diseased tissue specimens to

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Can CT-based patient-matched instrumentation achieve consistent rotational alignment in knee arthroplasty?

PubMed

Tibesku, C O; Innocenti, B; Wong, P; Salehi, A; Labey, L

2012-02-01

Long-term success of contemporary total knee replacements relies to a large extent on proper implant alignment. This study was undertaken to test whether specimen-matched cutting blocks based on computed axial tomography (CT) scans could provide accurate rotational alignment of the femoral component. CT scans of five fresh frozen full leg cadaver specimens, equipped with infrared reflective markers, were used to produce a specimen-matched femoral cutting block. Using those blocks, the bone cuts were made to implant a bi-compartmental femoral component. Rotational alignment of the components in the horizontal plane was determined using an optical measurement system and compared with all relevant rotational reference axes identified on the CT scans. Average rotational alignment for the bi-compartmental component in the horizontal plane was 1.9° (range 0°-6.3°; standard deviation 2.6°). One specimen that showed the highest deviation from the planned alignment also featured a completely degraded medial articular surface. The CT-based specimen-matched cutting blocks achieved good rotational alignment accuracy except for one specimen with badly damaged cartilage. In such cases, imaging techniques that visualize the cartilage layer might be more suitable to design cutting blocks, as they will provide a better fit and increased surface support.

A phase and frequency alignment protocol for 1H MRSI data of the prostate.

PubMed

Wright, Alan J; Buydens, Lutgarde M C; Heerschap, Arend

2012-05-01

(1)H MRSI of the prostate reveals relative metabolite levels that vary according to the presence or absence of tumour, providing a sensitive method for the identification of patients with cancer. Current interpretations of prostate data rely on quantification algorithms that fit model metabolite resonances to individual voxel spectra and calculate relative levels of metabolites, such as choline, creatine, citrate and polyamines. Statistical pattern recognition techniques can potentially improve the detection of prostate cancer, but these analyses are hampered by artefacts and sources of noise in the data, such as variations in phase and frequency of resonances. Phase and frequency variations may arise as a result of spatial field gradients or local physiological conditions affecting the frequency of resonances, in particular those of citrate. Thus, there are unique challenges in developing a peak alignment algorithm for these data. We have developed a frequency and phase correction algorithm for automatic alignment of the resonances in prostate MRSI spectra. We demonstrate, with a simulated dataset, that alignment can be achieved to a phase standard deviation of 0.095  rad and a frequency standard deviation of 0.68  Hz for the citrate resonances. Three parameters were used to assess the improvement in peak alignment in the MRSI data of five patients: the percentage of variance in all MRSI spectra explained by their first principal component; the signal-to-noise ratio of a spectrum formed by taking the median value of the entire set at each spectral point; and the mean cross-correlation between all pairs of spectra. These parameters showed a greater similarity between spectra in all five datasets and the simulated data, demonstrating improved alignment for phase and frequency in these spectra. This peak alignment program is expected to improve pattern recognition significantly, enabling accurate detection and localisation of prostate cancer with MRSI. Copyright

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoang, Thiem; Lazarian, A.

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

A Comprehensive Two-Dimensional Retention Time Alignment Algorithm To Enhance Chemometric Analysis of Comprehensive Two-Dimensional Separation Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Karisa M.; Wood, Lianna F.; Wright, Bob W.

2005-12-01

A comprehensive two-dimensional (2D) retention time alignment algorithm was developed using a novel indexing scheme. The algorithm is termed comprehensive because it functions to correct the entire chromatogram in both dimensions and it preserves the separation information in both dimensions. Although the algorithm is demonstrated by correcting comprehensive two-dimensional gas chromatography (GC x GC) data, the algorithm is designed to correct shifting in all forms of 2D separations, such as LC x LC, LC x CE, CE x CE, and LC x GC. This 2D alignment algorithm was applied to three different data sets composed of replicate GC x GCmore » separations of (1) three 22-component control mixtures, (2) three gasoline samples, and (3) three diesel samples. The three data sets were collected using slightly different temperature or pressure programs to engender significant retention time shifting in the raw data and then demonstrate subsequent corrections of that shifting upon comprehensive 2D alignment of the data sets. Thirty 12-min GC x GC separations from three 22-component control mixtures were used to evaluate the 2D alignment performance (10 runs/mixture). The average standard deviation of the first column retention time improved 5-fold from 0.020 min (before alignment) to 0.004 min (after alignment). Concurrently, the average standard deviation of second column retention time improved 4-fold from 3.5 ms (before alignment) to 0.8 ms (after alignment). Alignment of the 30 control mixture chromatograms took 20 min. The quantitative integrity of the GC x GC data following 2D alignment was also investigated. The mean integrated signal was determined for all components in the three 22-component mixtures for all 30 replicates. The average percent difference in the integrated signal for each component before and after alignment was 2.6%. Singular value decomposition (SVD) was applied to the 22-component control mixture data before and after alignment to show the restoration

Incorporating evolution of transcription factor binding sites into annotated alignments.

PubMed

Bais, Abha S; Grossmann, Stefen; Vingron, Martin

2007-08-01

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do

Nuclear reactor internals alignment configuration

DOEpatents

Gilmore, Charles B [Greensburg, PA; Singleton, Norman R [Murrysville, PA

2009-11-10

An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

'This is what we got, what would you like?': Aligning and unaligning academic-industry relations.

PubMed

Vedel, Jane Bjørn; Irwin, Alan

2017-06-01

This paper explores academic-industry relations from the perspective of research managers in the pharmaceutical industry. While current policy discourse on academic-industry relations has emphasized the potential of creating stronger alignment between academic research and industrial R&D, scholars have also drawn attention to the fundamental misalignment of the two domains and the inherently problematic aspects of over-close ties. In this paper, we address the articulation of alignment and 'unalignment' in academic-industry relations and explore how industrial participants reflect on their relationship with academic research. The paper draws on a longitudinal study of academic-industry collaboration in a Danish pharmaceutical company, carried out from 2009 to 2011. Focusing on one specific case of collaboration, we show that these industry research managers make sense of academic-industry relations by both aligning and unaligning themselves with academic research. Indeed, at critical stages, and rather than simply serving as an impediment, the process of aligning and unaligning can be an important driver to collaboration. Generally, we propose that focusing on participants' aligning and unaligning stances and efforts holds the promise of developing more nuanced, empirically-based accounts of academic-industry relations.

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

Pairwise Sequence Alignment Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeff Daily, PNNL

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, amore » novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

A Sense of Balance: District Aligns Personalized Learning with School and System Goals

ERIC Educational Resources Information Center

Donsky, Debbie; Witherow, Kathy

2015-01-01

This article addresses the challenge of personalizing learning while also ensuring alignment with system and school improvement plans. Leaders of the York Region District School Board in Ontario knew that what took their high-performing school district from good to great would not take it from great to excellent. The district's early model of…

Antares alignment gimbal positioner

NASA Astrophysics Data System (ADS)

Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, W. C.; Sweatt, W. C.

Antares is a 24-beam 40-TW carbon dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, an wavefront optical path difference, as well as aberration information at both helium neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1 cm cube to a tolerance of 10 micrometers.

Antares Alignment Gimbal Positioner

NASA Astrophysics Data System (ADS)

Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, G. L.; Sweatt, W. C.

1981-12-01

Antares is a 24-beam 40-TW carbon-dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 μm.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Kinematic alignment is a possible alternative to mechanical alignment in total knee arthroplasty.

PubMed

Lee, Yong Seuk; Howell, Stephen M; Won, Ye-Yeon; Lee, O-Sung; Lee, Seung Hoon; Vahedi, Hamed; Teo, Seow Hui

2017-11-01

A systematic review was conducted to answer the following questions: (1) Does kinematically aligned (KA) total knee arthroplasty (TKA) achieve clinical outcomes comparable to those of mechanically aligned (MA) TKA? (2) How do the limb, knee, and component alignments differ between KA and MA TKA? (3) How is joint line orientation angle (JLOA) changed from the native knee in KA TKA compared to that in MA TKA? Nine full-text articles in English that reported the clinical and radiological outcomes of KA TKA were included. Five studies had a control group of patients who underwent MA TKA. Data on patient demographics, clinical scores, and radiological results were extracted. There were two level I, one level II, three level III, and three level IV studies. Six of the nine studies used patient-specific instrumentation, one study used computer navigation, and two studies used manual instrumentation. The clinical outcomes of KA TKA were comparable or superior to those of MA TKA with a minimum 2-year follow-up. Limb and knee alignment in KA TKA was similar to those in MA TKA, and component alignment showed slightly more varus in the tibial component and slightly more valgus in the femoral component. The JLOA in KA TKA was relatively parallel to the floor compared to that in the native knee and not oblique (medial side up and lateral side down) compared to that in MA TKA. The implant survivorship and complication rate of the KA TKA were similar to those of the MA TKA. Similar or better clinical outcomes were produced by using a KA TKA at early-term follow-up and the component alignment differed from that of MA TKA. KA TKA seemed to restore function without catastrophic failure regardless of the alignment category up to midterm follow-up. The JLOA in KA TKA was relatively parallel to the floor similar to the native knee compared to that in MA TKA. The present review of nine published studies suggests that relatively new kinematic alignment is an acceptable and alternative

Standard versus physiologic bone preparation in total knee arthroplasty and the effect on joint space opening.

PubMed

Burkhart, Timothy A; Herman, Benjamin V; Perry, Kevin; Vandekerckhove, Pieter-Jan; Howard, James; Lanting, Brent

2017-11-01

Total knee arthroplasty is an effective treatment for osteoarthritis. Restoration of physiologic varus alignment may restore the native soft tissue tension and improve outcomes. Six paired fresh-frozen knee specimens were used to perform total knee arthroplastys. The left and right sides of were randomly assigned to have either a physiologic alignment cut or a standard of care neutral alignment bony cut prior to the implantation. Loads of 100 and 200N were applied at 0, 30, 60, and 90° of flexion and the magnitude of the medial and lateral compartment distraction was measured. The loads were applied with the knee specimen intact and post arthroplasty. The physiologic alignment had no difference between medial and lateral gaps at either load. With 100N of load the physiologic alignment had a greater gap at 90° than at full extension while the standard alignment had significantly more gap at 60° of flexion than full extension. The physiologic alignment had a significantly greater gap with the implant compared to the intact condition at both loads. The standard alignment had no significant difference in overall gap between the implant and intact condition with any load. Although performing a physiologic aligned TKA resulted in medial-lateral soft tissue balance, the flexion gap was found to have greater magnitude than the intact knee. Notably, a neutral aligned TKA was found to be balanced, but also was found to recreate the intact knee flexion gaps. These results suggest that coronal plane stability can be achieved with physiologic alignment objectives, but the clinician needs to be aware of the potential to have greater laxity than the intact and neutral alignment surgical objectives. Copyright © 2017 Elsevier Ltd. All rights reserved.

What Are School Counselors Expected to Do? Alignment between Professional School Counselor Evaluations and Performance Standards

ERIC Educational Resources Information Center

Nebe, Mary Bayly

2010-01-01

This study examines the alignment between Arizona public high school administrators' expectations of professional school counselors, the "ASCA National Model" (2005), and the instruments used in Arizona to evaluate professional school counselors. Participants included ten principals and assistant principals, and 103 of the 111 public…

Orbit Alignment in Triple Stars

NASA Astrophysics Data System (ADS)

Tokovinin, Andrei

2017-08-01

The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

1993-01-01

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Study of the Reliability of CCSS-Aligned Math Measures (2012 Research Version): Grades 6-8. Technical Report #1312

ERIC Educational Resources Information Center

Anderson, Daniel; Alonzo, Julie; Tindal, Gerald

2012-01-01

In this technical report, we describe the results of a study of mathematics items written to align with the Common Core State Standards (CCSS) in grades 6-8. In each grade, CCSS items were organized into forms, and the reliability of these forms was evaluated along with an experimental form including items aligned with the National Council of…

The Drive towards Sustainable Health Systems Needs an Alignment: Where are the Innovations in Health Systems Planning?

PubMed

Murphy, Gail Tomblin; Birch, Stephen; MacKenzie, Adrian; Rigby, Janet; Purkis, Mary Ellen

2017-01-01

Clarifying the healthcare innovation agenda is critical in order to advance the impact of system innovations. As part of this agenda-setting it is important to address the four conditions within which innovations can enhance system sustainability: 1) the innovation agenda reflects and is aligned with healthcare objectives and policy; 2) planning methodologies for services, workforce and funding are aligned with healthcare objectives and policy; 3) innovations in services are accommodated in systems through innovations in policy, planning and funding; and 4) innovations are systematically monitored and evaluated. In order to illustrate these conditions, the authors present a case study of an evaluation of one Canadian Health Authority's efforts to transform healthcare delivery. This case study reveals that aligning innovations in policy, planning, funding and health services is critical to transforming health systems and that, in the absence of such alignment, sustainable health systems are difficult to achieve.

Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion

PubMed Central

Fernandez, Jose-Jesus; Li, Sam; Bharat, Tanmay A. M.; Agard, David A.

2018-01-01

Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. PMID:29410148

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Standardized Tests as Outcome Measures for Evaluating Instructional Interventions in Mathematics and Science

NASA Astrophysics Data System (ADS)

Sussman, Joshua Michael

psychometric model of alignment grounded in item response modeling generate the results that address the following research question: how do differences between what a test measures and what an intervention teaches influence the results of an evaluation? The simulation derives a functional relationship between alignment, defined as the match between the test and the intervention, and treatment sensitivity, defined as the statistical power for detecting the impact of an intervention. The paper presents a new model of the effect of misalignment on the results of an evaluation and recommendations for outcome measure selection. The third paper documents the educational effectiveness of the Learning Mathematics through Representations (LMR) lesson sequence for students classified as English Learners (ELs). LMR is a research-based curricular unit designed to support upper elementary students' understandings of integers and fractions, areas considered foundational for the development of higher mathematics. The experimental evaluation contains a multilevel analysis of achievement data from two assessments: a standardized test and a researcher-developed assessment. The study coordinates the two sources of research data with a theoretical mechanism of action in order to rigorously document the effectiveness and educational equity of LMR for ELs using multiple sources of information.

Multilevel, Multicomponent Microarchitectures of Vertically-Aligned Carbon Nanotubes for Diverse Applications

DTIC Science & Technology

2011-01-31

Oxide from Synthesis to Proper- ties and to Novel Devices. J. Mater. Chem. 2007, 17, 711– 720. 29. Wang, Z. L. The New Field of Nanopiezotronics...regard, wehave reportedpreviously thepreparation of multicomponent micropatterns of VA- MWNTs interposed with nanoparticles ,17 nonaligned CNTs,18 or VA...aligned arrays on growth substrates, which enabled us to fabricate the CNT nanoelectrode *Address correspondence to lqu@bit.edu.cn, liming.dai

Aligned Layers of Silver Nano-Fibers.

PubMed

Golovin, Andrii B; Stromer, Jeremy; Kreminska, Liubov

2012-02-01

We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

Seamless, axially aligned, fiber tubes, meshes, microbundles and gradient biomaterial constructs

PubMed Central

Elia, Roberto; Firpo, Matthew A.; Kaplan, David L.; Peattie, Robert A.

2012-01-01

A new electrospinning apparatus was developed to generate nanofibrous materials with improved organizational control. The system functions by oscillating the deposition signal (ODS) of multiple collectors, allowing significantly improved nanofiber control by manipulating the electric field which drives the electrospinning process. Other electrospinning techniques designed to impart deposited fiber organizational control, such as rotating mandrels or parallel collector systems, do not generate seamless constructs with high quality alignment in sizes large enough for medical devices. In contrast, the ODS collection system produces deposited fiber networks with highly pure alignment in a variety of forms and sizes, including flat (8 × 8 cm2), tubular (1.3 cm diameter), or rope-like microbundle (45 μm diameter) samples. Additionally, the mechanism of our technique allows for scale-up beyond these dimensions. The ODS collection system produced 81.6 % of fibers aligned within 5° of the axial direction, nearly a four-fold improvement over the rotating mandrel technique. The meshes produced from the 9 % (w/v) fibroin/PEO blend demonstrated significant mechanical anisotropy due to the fiber alignment. In 37 °C PBS, aligned samples produced an ultimate tensile strength of 16.47 ± 1.18 MPa, a Young's modulus of 37.33 MPa, and a yield strength of 7.79 ± 1.13 MPa. The material was 300 % stiffer when extended in the direction of fiber alignment and required 20 times the amount of force to be deformed, compared to aligned meshes extended perpendicular to the fiber direction. The ODS technique could be applied to any electrospinnable polymer to overcome the more limited uniformity and induced mechanical strain of rotating mandrel techniques, and greatly surpasses the limited length of standard parallel collector techniques. PMID:22890517

Importance of orthotic subtalar alignment for development and gait of children with cerebral palsy.

PubMed

Carmick, Judy

2012-01-01

This case report addresses the assumption that ankle and foot orthoses assist children with cerebral palsy. Outcome research reports are not consistent. Clinical observations and research studies suggest that inappropriate fit and design of orthoses may contribute to poor outcomes. In particular, problems occur when the subtalar joint is out of alignment as children often compensate with unwanted movement patterns that affect progress, development, and function. Four cases are presented to demonstrate problems that can occur when ankle-foot or supramalleolar orthoses are not cast in subtalar neutral. Physical therapists can use their clinical observation skills to evaluate the proper fit and alignment of orthoses for children with cerebral palsy.

High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis.

PubMed

Johnson, Kevin J; Wright, Bob W; Jarman, Kristin H; Synovec, Robert E

2003-05-09

A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel profiles obtained using gas chromatography (GC). Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current chemometric techniques to correctly model information that shifts from variable to variable within a dataset. The alignment algorithm developed is shown to increase the efficacy of pattern recognition methods applied to diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retention time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical. Two sets of diesel fuel gas chromatograms were studied using the novel alignment algorithm followed by principal component analysis (PCA). In the first study, retention times for corresponding chromatographic peaks in 60 chromatograms varied by as much as 300 ms between chromatograms before alignment. In the second study of 42 chromatograms, the retention time shifting exhibited was on the order of 10 s between corresponding chromatographic peaks, and required a coarse retention time correction prior to alignment with the algorithm. In both cases, an increase in retention time precision afforded by the algorithm was clearly visible in plots of overlaid chromatograms before and then after applying the retention time alignment algorithm. Using the alignment algorithm, the standard deviation for corresponding peak retention times following alignment was 17 ms throughout a given chromatogram, corresponding to a relative standard deviation of 0.003% at an average retention time of 8 min. This level of retention time precision is a 5-fold improvement over the retention time precision initially provided by a state

Antares alignment gimbal positioner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Day, R.D.; Viswanathan, V.K.; Saxman, A.C.

1981-01-01

Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10more » ..mu..m.« less

Engineering survey planning for the alignment of a particle accelerator: part I. Proposition of an assessment method

NASA Astrophysics Data System (ADS)

Junqueira Leão, Rodrigo; Raffaelo Baldo, Crhistian; Collucci da Costa Reis, Maria Luisa; Alves Trabanco, Jorge Luiz

2018-03-01

The performance of particle accelerators depends highly on the relative alignment between their components. The position and orientation of the magnetic lenses that form the trajectory of the charged beam is kept to micrometric tolerances in a range of hundreds of meters of the length of the machines. Therefore, the alignment problem is fundamentally of a dimensional metrology nature. There is no common way of expressing these tolerances in terms of terminology and alignment concept. The alignment needs for a certain machine is normally given in terms of deviations between the position of any magnet in the accelerator and the fitted line that relates the actual position of the magnets’ assembly. Root mean square errors and standard deviations are normally used interchangeably and measurement uncertainty is often neglected. Although some solutions have been employed successfully in several accelerators, there is no off-the-shelf solution to perform the alignment. Also, each alignment campaign makes use of different measuring instruments to achieve the desired results, which makes the alignment process a complex measurement chain. This paper explores these issues by reviewing the tolerances specified for the alignment of particle accelerators, and proposes a metric to assess the quality of the alignment. The metric has the advantage of fully integrating the measurement uncertainty in the process.

Precision alignment device

DOEpatents

Jones, Nelson E.

1990-01-01

Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

Updating OSHA Standards Based on National Consensus Standards; Eye and Face Protection. Final rule.

PubMed

2016-03-25

On March 13, 2015, OSHA published in the Federal Register a notice of proposed rulemaking (NPRM) to revise its eye and face protection standards for general industry, shipyard employment, marine terminals, longshoring, and construction by updating the references to national consensus standards approved by the American National Standards Institute (ANSI). OSHA received no significant objections from commenters and therefore is adopting the amendments as proposed. This final rule updates the references in OSHA's eye and face standards to reflect the most recent edition of the ANSI/International Safety Equipment Association (ISEA) eye and face protection standard. It removes the oldest-referenced edition of the same ANSI standard. It also amends other provisions of the construction eye and face protection standard to bring them into alignment with OSHA's general industry and maritime standards.

Implementation of Common Core State Standards: Roles for Advocates

ERIC Educational Resources Information Center

Haycock, Kati

2012-01-01

Forty-six states and the District of Columbia have committed to fully implement the Common Core State Standards (CCSS) by the fall of 2013, and members of the two CCSS-aligned assessment consortia have committed to roll out an aligned assessment the following year. With less than a year until the CCSS must be in place in all classrooms, most…

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Associations of varus thrust and alignment with pain in knee osteoarthritis.

PubMed

Lo, Grace H; Harvey, William F; McAlindon, Timothy E

2012-07-01

To investigate associations of varus thrust and varus static alignment with pain in patients with knee osteoarthritis (OA). This was a cross-sectional study of participants from a randomized controlled trial of vitamin D treatment for knee OA. Participants were video recorded while walking and scored for presence of varus thrust. Static alignment was measured on standard posteroanterior knee radiographs. Pain questions from the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) questionnaire were used to assess symptoms. We calculated means for total WOMAC pain in relation to varus thrust and static varus alignment (i.e., corrected anatomic alignment<178 degrees). Ordinal logistic regressions were performed, with responses on individual WOMAC pain questions as the outcomes and varus thrust and varus alignment as the predictors. There were 82 participants, 60% of whom were female. The mean±SD age was 65.1±8.5 years, and the mean±SD body mass index was 30.2±5.4 kg/m2. The mean total WOMAC pain score was 6.3 versus 3.9, respectively, in those with versus without definite varus thrust (P=0.007) and 5.0 versus 4.2 in those with versus without varus alignment (P=0.36). Odds ratios for pain with walking and standing were 4.7 (95% confidence interval 1.8-11.9) and 5.5 (95% confidence interval 2.2-14.2), respectively, in those with and those without definite varus thrust. There were no significant associations between varus alignment and responses to individual WOMAC pain questions. Sensitivity analyses suggested that varus classified using a more stringent definition might have been associated with pain on walking and standing. In patients with knee OA, varus thrust, and possibly varus static alignment, were associated with pain, specifically during weight-bearing activities. Treatment of varus thrust (e.g., via bracing or gait modification) may lead to improvement of symptoms. Copyright © 2012 by the American College of Rheumatology.

Lexical alignment in triadic communication

PubMed Central

Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

2015-01-01

Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

Challenges of Incorporating Earth and Space Sciences into Curricula Aligned with the Next Generation Science Standards

NASA Astrophysics Data System (ADS)

Wysession, M. E.

2015-12-01

The Next Generation Science Standards present a great opportunity for the increased exposure of contemporary geosciences into the K-12 curricula of most of the countries school. However, the manner by which the NGSS are being adopted by different schools and districts poses several challenges. So far, 13 states and Washington, D.C., have adopted the NGSS in full, accounting for about 30% of the nation's students. In addition, four states (Massachusetts, Oklahoma, South Dakota, and West Virginia), accounting for another 5% of U.S. students, have adopted new state science standards that are adapted from the NGSS, each in different ways. For West Virginia, language concerning climate change has been tempered. For Oklahoma and South Dakota, language concerning climate change has been nearly entirely removed. In addition, there are a large number of independent school districts, accounting for at least and additional 35% of the nation's students, that are in the process of designing curriculum aligned to some degree with the NGSS. These are in states that have either not yet adopted the NGSS or likely will never adopt the NGSS (at a state-wide level). This presents a challenge to the geosciences, because the level of geoscience content will greatly vary, state-to-state and district-to-district. The NGSS present the geosciences with a heavy emphasis on Earth Systems Science, particular as it relates to climate systems and human impacts on systems, but most K-12 teachers have not had exposure to the geosciences in these contexts, and will require significant professional development. In addition, the inclusion of a full year of geoscience content in high school (in addition to a year for middle school), presents another curricular challenge, as most schools have never taught this amount of geoscience to all of its students (the NGSS are designed to have all of its standards taught to all students). The NGSS also emphasizes learning through a set of 8 different practices

Aligning Plasma-Arc Welding Oscillations

NASA Technical Reports Server (NTRS)

Norris, Jeff; Fairley, Mike

1989-01-01

Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

USDA snack food and beverage standards: how big of a stretch for the states?

PubMed

Chriqui, Jamie F; Piekarz, Elizabeth; Chaloupka, Frank J

2014-06-01

The USDA snack food and beverage standards take effect in school year (SY) 2014-2015. Although the USDA standards will provide nationwide requirements, concerns exist about compliance. This study examined whether existing state laws are aligned with the USDA standards to determine whether some states may be better positioned to facilitate compliance. Codified state statutory and regulatory laws effective for SY 2012-2013 for each of the 50 states and the District of Columbia were identified through Boolean keyword searches using the Westlaw and LexisNexis databases. Laws were analyzed for alignment with 18 snack food and beverage provisions contained within the USDA standards. Thirty-eight states had snack food and beverage standards; 33 states' laws exceeded restrictions on foods of minimal nutritional value. Of the 33 states, no states' laws fully met the USDA's standards, 16 states' laws fully met and 10 states' laws partially met at least one USDA provision, and seven states' laws met no USDA provisions. One state's law met 9 of 18 provisions. On average, states met 4 of 18 provisions. States were more likely to meet individual USDA beverage than snack provisions. Implementation and compliance with the USDA standards may be facilitated in states with laws already containing provisions aligned with the USDA standards and may be more difficult in states with fewer or no provisions in alignment, suggesting possible geographic areas for the USDA to target with technical assistance and training efforts and for advocates to work in to facilitate compliance.

Is the aligning prism measured with the Mallett unit correlated with fusional vergence reserves?

PubMed

Conway, Miriam L; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the "aligning prism" needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent?

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

Seeking an Anchorage. Stability and Variability in Tonal Alignment of Rising Prenuclear Pitch Accents in Cypriot Greek.

PubMed

Themistocleous, Charalambos

2016-12-01

Although tonal alignment constitutes a quintessential property of pitch accents, its exact characteristics remain unclear. This study, by exploring the timing of the Cypriot Greek L*+H prenuclear pitch accent, examines the predictions of three hypotheses about tonal alignment: the invariance hypothesis, the segmental anchoring hypothesis, and the segmental anchorage hypothesis. The study reports on two experiments: the first of which manipulates the syllable patterns of the stressed syllable, and the second of which modifies the distance of the L*+H from the following pitch accent. The findings on the alignment of the low tone (L) are illustrative of the segmental anchoring hypothesis predictions: the L persistently aligns inside the onset consonant, a few milliseconds before the stressed vowel. However, the findings on the alignment of the high tone (H) are both intriguing and unexpected: the alignment of the H depends on the number of unstressed syllables that follow the prenuclear pitch accent. The 'wandering' of the H over multiple syllables is extremely rare among languages, and casts doubt on the invariance hypothesis and the segmental anchoring hypothesis, as well as indicating the need for a modified version of the segmental anchorage hypothesis. To address the alignment of the H, we suggest that it aligns within a segmental anchorage-the area that follows the prenuclear pitch accent-in such a way as to protect the paradigmatic contrast between the L*+H prenuclear pitch accent and the L+H* nuclear pitch accent.

A Study of the Alignment of National Standards, State Standards, and Science Assessment.

ERIC Educational Resources Information Center

Burry-Stock, Judith A.; Casebeer, Cindy M.

Educational reform efforts are currently at the top of the nation's agenda. Policymakers are hearing increasing calls from members of the public to improve standardized test scores. These reform calls are a response to the perceived inadequacy of science teaching in our nation. Data were collected from participating states regarding the status of…

Precision alignment device

DOEpatents

Jones, N.E.

1988-03-10

Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

Intraoperative positioning of the hindfoot with the hindfoot alignment guide: a pilot study.

PubMed

Frigg, Arno; Jud, Lukas; Valderrabano, Victor

2014-01-01

In a previous study, intraoperative positioning of the hindfoot by visual means resulted in the wrong varus/valgus position by 8 degrees and a relatively large standard deviation of 8 degrees. Thus, new intraoperative means are needed to improve the precision of hindfoot surgery. We therefore sought a hindfoot alignment guide that would be as simple as the alignment guides used in total knee arthroplasty. A novel hindfoot alignment guide (HA guide) has been developed that projects the mechanical axis from the tibia down to the heel. The HA guide enables the positioning of the hindfoot in the desired varus/valgus position and in plantigrade position in the lateral plane. The HA guide was used intraoperatively from May through November 2011 in 11 complex patients with simultaneous correction of the supramalleolar, tibiotalar, and inframalleolar alignment. Pre- and postoperative Saltzman views were taken and the position was measured. The HA guide significantly improved the intraoperative positioning compared with visual means: The accuracy with the HA guide was 4.5 ± 5.1 degrees (mean ± standard deviation) and without the HA guide 9.4 ± 5.5 degrees (P < .05). In 7 of 11 patients, the preoperative plan was changed because of the HA guide (2 avoided osteotomies, 5 additional osteotomies). The HA guide helped to position the hindfoot intraoperatively with greater precision than visual means. The HA guide was especially useful for multilevel corrections in which the need for and the amount of a simultaneous osteotomy had to be evaluated intraoperatively. Level IV, case series.

Analyzing the Curriculum Alignment of Teachers

ERIC Educational Resources Information Center

Turan-Özpolat, Esen; Bay, Erdal

2017-01-01

The purpose of this research was to analyze the curriculum alignment of teachers in secondary education 5th grade Science course. Alignment levels of teachers in dimensions of acquisition, content, teaching methods and techniques, activity, material and measurement - assessment, and the reasons for their alignment/non-alignment to the curriculum…

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

PubMed

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

GOSSIP: a method for fast and accurate global alignment of protein structures.

PubMed

Kifer, I; Nussinov, R; Wolfson, H J

2011-04-01

The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Performance management models for public health: Public Health Accreditation Board/Baldrige connections, alignment, and distinctions.

PubMed

Gorenflo, Grace G; Klater, David M; Mason, Marlene; Russo, Pamela; Rivera, Lillian

2014-01-01

The nationally known Malcolm Baldrige Award for Excellence ("Baldrige program") recognizes outstanding performance management and is specifically cited by the Public Health Accreditation Board (PHAB) as a potential framework for PHAB's requisite performance management system. The authors developed a crosswalk that identifies alignments between the 2 programs and is a highlight of the Quest for Exceptional Performance tool that is intended to help health departments capitalize on the connections between the 2 programs. To provide deeper insight into the most robust connections between the 2 programs. The authors developed a crosswalk by listing the PHAB measures, identifying corresponding Baldrige areas to address, and assigning a rating regarding the strength of the alignment. Subsequently, they generated a matrix with numerical scores reflecting the strength of the PHAB-Baldrige alignments that were then analyzed for frequency and strength of alignment by PHAB domain and by Baldrige category. The tool developers and 3 public health leaders with experience in the Baldrige program contributed to both the design and the analyses. The measures used reflected both the frequency and strength of alignments. Of the 123 alignments identified in the crosswalk, 39 were rated as high, 40 as medium, and 44 as low. The strongest connections were in the areas of performance management, quality improvement, strategic planning, workforce development, assessment and analysis, and customer service. While the areas with the most frequent and strongest connections provide the most useful basis for health departments pursuing Baldrige recognition or using Baldrige criteria as a framework for performance management, all alignments could be considered for both purposes.

A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Alignment of dynamic networks

PubMed Central

Vijayan, V.; Critchlow, D.; Milenković, T.

2017-01-01

Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

Anisotropic Mechanical Properties of Magnetically Aligned Fibrin Gels Measured by Magnetic Resonance Elastography

PubMed Central

Namani, Ravi; Wood, Matthew D.; Sakiyama-Elbert, Shelly E.; Bayly, Philip V.

2009-01-01

The anisotropic mechanical properties of magnetically aligned fibrin gels were measured by magnetic resonance elastography (MRE) and by a standard mechanical test: unconfined compression. Soft anisotropic biomaterials are notoriously difficult to characterize, especially in vivo. MRE is well-suited for efficient, non-invasive, and nondestructive assessment of shear modulus. Direction-dependent differences in shear modulus were found to be statistically significant for gels polymerized at magnetic fields of 11.7T and 4.7T compared to control gels. Mechanical anisotropy was greater in the gels polymerized at the higher magnetic field. These observations were consistent with results from unconfined compression tests. Analysis of confocal microscopy images of gels showed measurable alignment of fibrils in gels polymerized at 11.7T. This study provides direct, quantitative measurements of the anisotropy in mechanical properties that accompanies fibril alignment in fibrin gels. PMID:19656516

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

PubMed Central

Wala, Jeremiah; Beroukhim, Rameen

2017-01-01

Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

Automatic classification of protein structures relying on similarities between alignments

PubMed Central

2012-01-01

Background Identification of protein structural cores requires isolation of sets of proteins all sharing a same subset of structural motifs. In the context of an ever growing number of available 3D protein structures, standard and automatic clustering algorithms require adaptations so as to allow for efficient identification of such sets of proteins. Results When considering a pair of 3D structures, they are stated as similar or not according to the local similarities of their matching substructures in a structural alignment. This binary relation can be represented in a graph of similarities where a node represents a 3D protein structure and an edge states that two 3D protein structures are similar. Therefore, classifying proteins into structural families can be viewed as a graph clustering task. Unfortunately, because such a graph encodes only pairwise similarity information, clustering algorithms may include in the same cluster a subset of 3D structures that do not share a common substructure. In order to overcome this drawback we first define a ternary similarity on a triple of 3D structures as a constraint to be satisfied by the graph of similarities. Such a ternary constraint takes into account similarities between pairwise alignments, so as to ensure that the three involved protein structures do have some common substructure. We propose hereunder a modification algorithm that eliminates edges from the original graph of similarities and gives a reduced graph in which no ternary constraints are violated. Our approach is then first to build a graph of similarities, then to reduce the graph according to the modification algorithm, and finally to apply to the reduced graph a standard graph clustering algorithm. Such method was used for classifying ASTRAL-40 non-redundant protein domains, identifying significant pairwise similarities with Yakusa, a program devised for rapid 3D structure alignments. Conclusions We show that filtering similarities prior to standard

Optimal image alignment with random projections of manifolds: algorithm and geometric analysis.

PubMed

Kokiopoulou, Effrosyni; Kressner, Daniel; Frossard, Pascal

2011-06-01

This paper addresses the problem of image alignment based on random measurements. Image alignment consists of estimating the relative transformation between a query image and a reference image. We consider the specific problem where the query image is provided in compressed form in terms of linear measurements captured by a vision sensor. We cast the alignment problem as a manifold distance minimization problem in the linear subspace defined by the measurements. The transformation manifold that represents synthesis of shift, rotation, and isotropic scaling of the reference image can be given in closed form when the reference pattern is sparsely represented over a parametric dictionary. We show that the objective function can then be decomposed as the difference of two convex functions (DC) in the particular case where the dictionary is built on Gaussian functions. Thus, the optimization problem becomes a DC program, which in turn can be solved globally by a cutting plane method. The quality of the solution is typically affected by the number of random measurements and the condition number of the manifold that describes the transformations of the reference image. We show that the curvature, which is closely related to the condition number, remains bounded in our image alignment problem, which means that the relative transformation between two images can be determined optimally in a reduced subspace.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

PubMed Central

Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

2007-01-01

The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

Aligning Greek-English parallel texts

NASA Astrophysics Data System (ADS)

Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

2015-02-01

In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

Neurient: An Algorithm for Automatic Tracing of Confluent Neuronal Images to Determine Alignment

PubMed Central

Mitchel, J.A.; Martin, I.S.

2013-01-01

A goal of neural tissue engineering is the development and evaluation of materials that guide neuronal growth and alignment. However, the methods available to quantitatively evaluate the response of neurons to guidance materials are limited and/or expensive, and may require manual tracing to be performed by the researcher. We have developed an open source, automated Matlab-based algorithm, building on previously published methods, to trace and quantify alignment of fluorescent images of neurons in culture. The algorithm is divided into three phases, including computation of a lookup table which contains directional information for each image, location of a set of seed points which may lie along neurite centerlines, and tracing neurites starting with each seed point and indexing into the lookup table. This method was used to obtain quantitative alignment data for complex images of densely cultured neurons. Complete automation of tracing allows for unsupervised processing of large numbers of images. Following image processing with our algorithm, available metrics to quantify neurite alignment include angular histograms, percent of neurite segments in a given direction, and mean neurite angle. The alignment information obtained from traced images can be used to compare the response of neurons to a range of conditions. This tracing algorithm is freely available to the scientific community under the name Neurient, and its implementation in Matlab allows a wide range of researchers to use a standardized, open source method to quantitatively evaluate the alignment of dense neuronal cultures. PMID:23384629

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Using Standards To Improve Instruction.

ERIC Educational Resources Information Center

Wilson, Michael; Tienken, Christopher

2002-01-01

Describes a New Jersey program designed to help teachers understand and use state standards and test specifications to improve instruction, without merely teaching to the test, recommending that educators explore the processes of delineation, alignment, and calibration. This ensures that teachers understand the entirety of each subject area and…

Probabilistic biological network alignment.

PubMed

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Alignment telescope for Antares

NASA Astrophysics Data System (ADS)

Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wright, L.

The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since each telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirements as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 (SIGMA)rad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

Alignment Telescope For Antares

NASA Astrophysics Data System (ADS)

Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wrignt, L.

1983-11-01

The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since eacn telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirement as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 prad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

Multiple-level stakeholder engagement in malaria clinical trials: addressing the challenges of conducting clinical research in resource-limited settings.

PubMed

Mtove, George; Kimani, Joshua; Kisinza, William; Makenga, Geofrey; Mangesho, Peter; Duparc, Stephan; Nakalembe, Miriam; Phiri, Kamija S; Orrico, Russell; Rojo, Ricardo; Vandenbroucke, Pol

2018-03-22

Multinational clinical trials are logistically complex and require close coordination between various stakeholders. They must comply with global clinical standards and are accountable to multiple regulatory and ethical bodies. In resource-limited settings, it is challenging to understand how to apply global clinical standards to international, national, and local factors in clinical trials, making multiple-level stakeholder engagement an important element in the successful conduct of these clinical trials. During the planning and implementation of a large multinational clinical trial for intermittent preventive treatment of malaria in pregnancy in resource-limited areas of sub-Saharan Africa, we encountered numerous challenges, which required implementation of a range of engagement measures to ensure compliance with global clinical and regulatory standards. These challenges included coordination with ongoing global malaria efforts, heterogeneity in national regulatory structures, sub-optimal healthcare infrastructure, local practices and beliefs, and perspectives that view healthcare providers with undue trust or suspicion. In addition to engagement with international bodies, such as the World Health Organization, the Malaria in Pregnancy Consortium, the Steve Biko Centre for Bioethics, and the London School of Hygiene and Tropical Medicine, in order to address the challenges just described, Pfizer Inc. and Medicines for Malaria Venture (the "Sponsoring Entities" for these studies) and investigators liaised with national- and district-level stakeholders such as health ministers and regional/local community health workers. Community engagement measures undertaken by investigators included local meetings with community leaders to explain the research aims and answer questions and concerns voiced by the community. The investigators also engaged with family members of prospective trial participants in order to be sensitive to local practices and beliefs. Engagement

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Projected power iteration for network alignment

NASA Astrophysics Data System (ADS)

Onaran, Efe; Villar, Soledad

2017-08-01

The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

Hybrid vehicle motor alignment

DOEpatents

Levin, Michael Benjamin

2001-07-03

A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

Is the Aligning Prism Measured with the Mallett Unit Correlated with Fusional Vergence Reserves?

PubMed Central

Conway, Miriam L.; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

Background The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the “aligning prism” needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Methodology/Principal Findings Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. Conclusions/Significance For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent? PMID:22905174

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

Silicon on insulator self-aligned transistors

DOEpatents

McCarthy, Anthony M.

2003-11-18

A method for fabricating thin-film single-crystal silicon-on-insulator (SOI) self-aligned transistors. Standard processing of silicon substrates is used to fabricate the transistors. Physical spaces, between the source and gate, and the drain and gate, introduced by etching the polysilicon gate material, are used to provide connecting implants (bridges) which allow the transistor to perform normally. After completion of the silicon substrate processing, the silicon wafer is bonded to an insulator (glass) substrate, and the silicon substrate is removed leaving the transistors on the insulator (glass) substrate. Transistors fabricated by this method may be utilized, for example, in flat panel displays, etc.

Linking GPS and travel diary data using sequence alignment in a study of children's independent mobility

PubMed Central

2011-01-01

Background Global positioning systems (GPS) are increasingly being used in health research to determine the location of study participants. Combining GPS data with data collected via travel/activity diaries allows researchers to assess where people travel in conjunction with data about trip purpose and accompaniment. However, linking GPS and diary data is problematic and to date the only method has been to match the two datasets manually, which is time consuming and unlikely to be practical for larger data sets. This paper assesses the feasibility of a new sequence alignment method of linking GPS and travel diary data in comparison with the manual matching method. Methods GPS and travel diary data obtained from a study of children's independent mobility were linked using sequence alignment algorithms to test the proof of concept. Travel diaries were assessed for quality by counting the number of errors and inconsistencies in each participant's set of diaries. The success of the sequence alignment method was compared for higher versus lower quality travel diaries, and for accompanied versus unaccompanied trips. Time taken and percentage of trips matched were compared for the sequence alignment method and the manual method. Results The sequence alignment method matched 61.9% of all trips. Higher quality travel diaries were associated with higher match rates in both the sequence alignment and manual matching methods. The sequence alignment method performed almost as well as the manual method and was an order of magnitude faster. However, the sequence alignment method was less successful at fully matching trips and at matching unaccompanied trips. Conclusions Sequence alignment is a promising method of linking GPS and travel diary data in large population datasets, especially if limitations in the trip detection algorithm are addressed. PMID:22142322

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an

Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

ERIC Educational Resources Information Center

Johnson, Lisa M.; Di Paolo, Marianna; Bell, Adrian

2018-01-01

Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research…

Alignment-free inference of hierarchical and reticulate phylogenomic relationships.

PubMed

Bernard, Guillaume; Chan, Cheong Xin; Chan, Yao-Ban; Chua, Xin-Yi; Cong, Yingnan; Hogan, James M; Maetschke, Stefan R; Ragan, Mark A

2017-06-30

We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on k-mers. We reflect on what seems to be successful, and on where further development is needed. © The Author 2017. Published by Oxford University Press.

Validating Coherence Measurements Using Aligned and Unaligned Coherence Functions

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2006-01-01

This paper describes a novel approach based on the use of coherence functions and statistical theory for sensor validation in a harsh environment. By the use of aligned and unaligned coherence functions and statistical theory one can test for sensor degradation, total sensor failure or changes in the signal. This advanced diagnostic approach and the novel data processing methodology discussed provides a single number that conveys this information. This number as calculated with standard statistical procedures for comparing the means of two distributions is compared with results obtained using Yuen's robust statistical method to create confidence intervals. Examination of experimental data from Kulite pressure transducers mounted in a Pratt & Whitney PW4098 combustor using spectrum analysis methods on aligned and unaligned time histories has verified the effectiveness of the proposed method. All the procedures produce good results which demonstrates how robust the technique is.

Jig Aligns Shadow Mask On CCD

NASA Technical Reports Server (NTRS)

Matus, Carlos V.

1989-01-01

Alignment viewed through microscope. Alignment jig positions shadow mask on charge-coupled device (CCD) so metal film deposited on it precisely. Allows CCD package to be inserted and removed without disturbing alignment of mask. Holds CCD packages securely and isolates it electrostatically while providing electrical contact to each of its pins. When alignment jig assembled with CCD, used to move mask under micrometer control.

Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment

PubMed Central

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H.; Timothy Bunnell, H.; Amith, Jonathan D.; García, Rey Castillo

2013-01-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953

Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

PubMed

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

2013-09-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.

40 CFR 59.409 - Addresses of EPA Offices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 6 2012-07-01 2012-07-01 false Addresses of EPA Offices. 59.409... National Volatile Organic Compound Emission Standards for Architectural Coatings § 59.409 Addresses of EPA... manufacturer or importer resides. These areas are indicated in the following list of EPA Regional Offices: EPA...

40 CFR 59.409 - Addresses of EPA Offices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 6 2013-07-01 2013-07-01 false Addresses of EPA Offices. 59.409... National Volatile Organic Compound Emission Standards for Architectural Coatings § 59.409 Addresses of EPA... manufacturer or importer resides. These areas are indicated in the following list of EPA Regional Offices: EPA...

40 CFR 59.409 - Addresses of EPA Offices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 6 2014-07-01 2014-07-01 false Addresses of EPA Offices. 59.409... National Volatile Organic Compound Emission Standards for Architectural Coatings § 59.409 Addresses of EPA... manufacturer or importer resides. These areas are indicated in the following list of EPA Regional Offices: EPA...

Convergence or Divergence: Alignment of Standards, Assessment, and Issues of Diversity.

ERIC Educational Resources Information Center

Carter, Norvella, Ed.

In this report, teacher educators scrutinize the relationships between the standards and assessment movement in education and the United States' increasingly multicultural population. The papers include: "Foreword" (Jacqueline Jordan Irvine); (1) "Diversity and Standards: Defining the Issues" (Norvella P. Carter); (2) "Accountability and…

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

PubMed Central

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

PubMed

Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

2014-08-01

Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis. A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, C.R.; Hammond, R.B.

The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, Charles R.; Hammond, Robert B.

1981-01-01

The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Text-image alignment for historical handwritten documents

NASA Astrophysics Data System (ADS)

Zinger, S.; Nerbonne, J.; Schomaker, L.

2009-01-01

We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

Using partnerships with scientists to enhance teacher capacity to address the NGSS

NASA Astrophysics Data System (ADS)

Pavelsky, T.; Haine, D. B.; Drostin, M.

2013-12-01

Increasingly, scientists are seeking outreach experts to assist with the education and outreach components of their research grants. These experts have the skills and expertise to assist with translating scientific research into lessons and activities that are aligned to the Next Generation Science Standards (NGSS) as well as state standards, are STEM-focused and that address the realities of the K-12 science classroom. Since 2007, the Institute for the Environment (IE) at the University of North Carolina at Chapel Hill has been conducting teacher professional development and high school student science enrichment programs to promote climate literacy. Partnering with scientists to deepen content knowledge and promote engagement with technology and real data has been a successful strategy for cultivating increased climate literacy among teachers and students. In this session, we will share strategies for effectively engaging scientists in K-12 educational activities by providing specific examples of the various ways in which scientists can be integrated into programming and their research translated into relevant classroom activities. Engaging scientists and translating their research into classroom activities is an approach that becomes even more relevant with the advent of the NGSS. The NGSS's Disciplinary Core Ideas (DCIs) that encompass climate literacy can be addressed by partnering with scientists to provide teachers with current content knowledge and technological tools needed to promote integration of relevant science and engineering practices and cross-cutting themes. Here we highlight a successful partnership in which IE science educators collaborated with with a faculty member to develop a lesson for North Carolina teachers introducing them to new research on satellite remote sensing of the water cycle, while also promoting student engagement with local data. The resulting lesson was featured during a two-day, IE-led teacher workshop for 21 North Carolina

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment

PubMed Central

2013-01-01

Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

PubMed

Nagar, Anurag; Hahsler, Michael

2013-01-01

Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to

Synergistic Instance-Level Subspace Alignment for Fine-Grained Sketch-Based Image Retrieval.

PubMed

Li, Ke; Pang, Kaiyue; Song, Yi-Zhe; Hospedales, Timothy M; Xiang, Tao; Zhang, Honggang

2017-08-25

We study the problem of fine-grained sketch-based image retrieval. By performing instance-level (rather than category-level) retrieval, it embodies a timely and practical application, particularly with the ubiquitous availability of touchscreens. Three factors contribute to the challenging nature of the problem: (i) free-hand sketches are inherently abstract and iconic, making visual comparisons with photos difficult, (ii) sketches and photos are in two different visual domains, i.e. black and white lines vs. color pixels, and (iii) fine-grained distinctions are especially challenging when executed across domain and abstraction-level. To address these challenges, we propose to bridge the image-sketch gap both at the high-level via parts and attributes, as well as at the low-level, via introducing a new domain alignment method. More specifically, (i) we contribute a dataset with 304 photos and 912 sketches, where each sketch and image is annotated with its semantic parts and associated part-level attributes. With the help of this dataset, we investigate (ii) how strongly-supervised deformable part-based models can be learned that subsequently enable automatic detection of part-level attributes, and provide pose-aligned sketch-image comparisons. To reduce the sketch-image gap when comparing low-level features, we also (iii) propose a novel method for instance-level domain-alignment, that exploits both subspace and instance-level cues to better align the domains. Finally (iv) these are combined in a matching framework integrating aligned low-level features, mid-level geometric structure and high-level semantic attributes. Extensive experiments conducted on our new dataset demonstrate effectiveness of the proposed method.

Method for alignment of microwires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

2017-01-24

A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

Algorithms for Automatic Alignment of Arrays

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

1996-01-01

Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

MEMS Integrated Submount Alignment for Optoelectronics

NASA Astrophysics Data System (ADS)

Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

2005-02-01

One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae

PubMed Central

Tóth, Annamária; Hausknecht, Anton; Krisai-Greilhuber, Irmgard; Papp, Tamás; Vágvölgyi, Csaba; Nagy, László G.

2013-01-01

Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that – although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching – it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe. PMID:23418526

Cervical Alignment Variations in Different Postures and Predictors of Normal Cervical Kyphosis: A New Understanding.

PubMed

Hey, Hwee Weng Dennis; Lau, Eugene Tze-Chun; Wong, Gordon Chengyuan; Tan, Kimberly-Anne; Liu, Gabriel Ka-Po; Wong, Hee-Kit

2017-11-01

Comparative study of prospectively collected radiographic data. To predict physiological alignment of the cervical spine and study its morphology in different postures. There is increasing evidence that normal cervical spinal alignment may vary from lordosis to neutral to kyphosis, or form S-shaped or reverse S-shaped curves. Standing, erect sitting, and natural sitting whole-spine radiographs were obtained from 26 consecutive patients without cervical spine pathology. Sagittal vertical axis (SVA), global cervical lordosis, lower cervical alignment C4-T1, C0-C2 angle, T1 slope, C0-C7 SVA and C2-7SVA, SVA, thoracic kyphosis, thoracolumbar junctional angle, lumbar lordosis, sacral slope, pelvic tilt, and pelvic incidence were measured. Statistical analysis was performed to elucidate differences in cervical alignment for all postures. Predictive values of T1 slope and SVA for cervical kyphosis were evaluated. Most patients (73.0%) do not have lordotic cervical alignment (C2-C7) upon standing (mean -0.6, standard deviation 11.1°). Lordosis increases significantly when transitioning from standing to erect sitting, as well as from erect to natural sitting (mean -17.2, standard deviation 12.1°). Transition from standing to natural sitting also produces concomitant increases in SVA (-8.8-65.2 mm) and T1-slope (17.4°-30.2°). T1 slope and SVA measured during standing significantly predicts angular cervical spine alignment in the same position. SVA < 10 mm significantly predicts C4-C7 kyphosis (P < 0.001), and to a lesser extent, C2-C7 kyphosis (P = 0.02). T1 slope <20° is both predictive of C2-C7 and C4-7 kyphosis (P = 0.001 and P = 0.023, respectively). For global cervical Cobb angle, T1 slope seems to be a more significant predictor of kyphosis than SVA (odds ratio 17.33, P = 0.001 vs odds ratio 11.67, P = 0.02, respectively). The cervical spine has variable normal morphology. Key determinants of its alignment include SVA and T1 slope

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

PubMed

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Alignment of World Language Standards and Assessments: A Multiple Case Study

ERIC Educational Resources Information Center

Kaplan, Carolyn Shemwell

2016-01-01

Previous research has examined world language classroom-based assessment practices as well as the impact of the Standards for Foreign Language Learning in the 21st Century (National Standards in Foreign Language Education Project, 1999) on practice. However, the extent to which K-12 teachers' assessment practices reflect national and state…

A Novel Marker Based Method to Teeth Alignment in MRI

NASA Astrophysics Data System (ADS)

Luukinen, Jean-Marc; Aalto, Daniel; Malinen, Jarmo; Niikuni, Naoko; Saunavaara, Jani; Jääsaari, Päivi; Ojalammi, Antti; Parkkola, Riitta; Soukka, Tero; Happonen, Risto-Pekka

2018-04-01

Magnetic resonance imaging (MRI) can precisely capture the anatomy of the vocal tract. However, the crowns of teeth are not visible in standard MRI scans. In this study, a marker-based teeth alignment method is presented and evaluated. Ten patients undergoing orthognathic surgery were enrolled. Supraglottal airways were imaged preoperatively using structural MRI. MRI visible markers were developed, and they were attached to maxillary teeth and corresponding locations on the dental casts. Repeated measurements of intermarker distances in MRI and in a replica model was compared using linear regression analysis. Dental cast MRI and corresponding caliper measurements did not differ significantly. In contrast, the marker locations in vivo differed somewhat from the dental cast measurements likely due to marker placement inaccuracies. The markers were clearly visible in MRI and allowed for dental models to be aligned to head and neck MRI scans.

A Note on Standard Deviation and Standard Error

ERIC Educational Resources Information Center

Hassani, Hossein; Ghodsi, Mansoureh; Howell, Gareth

2010-01-01

Many students confuse the standard deviation and standard error of the mean and are unsure which, if either, to use in presenting data. In this article, we endeavour to address these questions and cover some related ambiguities about these quantities.

A Framework for Aligning Needs, Abilities and Affordances to Inform Design and Practice of Educational Technologies

ERIC Educational Resources Information Center

Antonenko, Pavlo D.; Dawson, Kara; Sahay, Shilpa

2017-01-01

This paper addresses the need for enhancing our awareness of user-centered design in educational technology through a more explicit and systematic alignment between the needs of educational technology users (learners and educators) and the affordances provided by the technology. First, we define the term "affordance" and discuss it from…

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

Questioning Points and Percentages: Standards-Based Grading (SBG) in Higher Education

ERIC Educational Resources Information Center

Buckmiller, Tom; Peters, Randal; Kruse, Jerrid

2017-01-01

Despite its growing use at the K-12 level, standards-based grading (alignment of grading to course standards) has been comparatively neglected in higher education. College students are often confronted with grading practices that reflect subjective, non-standardized formats incorporating a blend of academic and non-academic components. This case…

Non-Standard Orthography and Non-Standard Speech.

ERIC Educational Resources Information Center

Jaffe, Alexandra

2000-01-01

Provides a framework of key issues surrounding the non-standard orthographic representation of non-standard language varieties. The following topics are addressed: the selective nature of orthographic choice; relational an contrastive meaning of orthographic conventions; interplay of sameness and difference in use of orthography to make claims on…

Heuristics for multiobjective multiple sequence alignment.

PubMed

Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

2016-07-15

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

NASA Astrophysics Data System (ADS)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, Y; Crane, C; Krishnan, S

Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near themore » tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.« less

Alignment and Distortion-Free Integration of Lightweight Mirrors into Meta-Shells for High-Resolution Astronomical X-Ray Optics

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Zhang, William W.; Schofield, Mark J.; Numata, Ai; Mazzarella, James R.; Saha, Timo T.; Biskach, Michael P.; McCelland, Ryan S.; Niemeyer, Jason; Sharpe, Marton V.;

On-command on/off switching of progenitor cell and cancer cell polarized motility and aligned morphology via a cytocompatible shape memory polymer scaffold.

PubMed

Wang, Jing; Quach, Andy; Brasch, Megan E; Turner, Christopher E; Henderson, James H

2017-09-01

In vitro biomaterial models have enabled advances in understanding the role of extracellular matrix (ECM) architecture in the control of cell motility and polarity. Most models are, however, static and cannot mimic dynamic aspects of in vivo ECM remodeling and function. To address this limitation, we present an electrospun shape memory polymer scaffold that can change fiber alignment on command under cytocompatible conditions. Cellular response was studied using the human fibrosarcoma cell line HT-1080 and the murine mesenchymal stem cell line C3H/10T1/2. The results demonstrate successful on-command on/off switching of cell polarized motility and alignment. Decrease in fiber alignment causes a change from polarized motility along the direction of fiber alignment to non-polarized motility and from aligned to unaligned morphology, while increase in fiber alignment causes a change from non-polarized to polarized motility along the direction of fiber alignment and from unaligned to aligned morphology. In addition, the findings are consistent with the hypothesis that increased fiber alignment causes increased cell velocity, while decreased fiber alignment causes decreased cell velocity. On-command on/off switching of cell polarized motility and alignment is anticipated to enable new study of directed cell motility in tumor metastasis, in cell homing, and in tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

SIM Lite: Ground Alignment of the Instrument

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-01-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

SIM Lite: ground alignment of the instrument

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-07-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

The development of alignment turning system for precision len cells

NASA Astrophysics Data System (ADS)

Huang, Chien-Yao; Ho, Cheng-Fang; Wang, Jung-Hsing; Chung, Chien-Kai; Chen, Jun-Cheng; Chang, Keng-Shou; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

2017-08-01

In general, the drop-in and cell-mounted assembly are used for standard and high performance optical system respectively. The optical performance is limited by the residual centration error and position accuracy of the conventional assembly. Recently, the poker chip assembly with high precision lens barrels that can overcome the limitation of conventional assembly is widely applied to ultra-high performance optical system. ITRC also develops the poker chip assembly solution for high numerical aperture objective lenses and lithography projection lenses. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module including a non-contact displacement sensor and an autocollimator can measure centration errors of the top and the bottom surface of a lens respectively. The alignment module comprising tilt and translation stages can align the optical axis of the lens to the rotating axis of the vertical lathe. The key specifications of the ATS are maximum lens diameter, 400mm, and radial and axial runout of the rotary table < 2 μm. The cutting performances of the ATS are surface roughness Ra < 1 μm, flatness < 2 μm, and parallelism < 5 μm. After measurement, alignment and turning processes on our ATS, the centration error of a lens cell with 200mm in diameter can be controlled in 10 arcsec. This paper also presents the thermal expansion of the hydrostatic rotating table. A poker chip assembly lens cell with three sub-cells is accomplished with average transmission centration error in 12.45 arcsec by fresh technicians. The results show that ATS can achieve high assembly efficiency for precision optical systems.

Image alignment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dowell, Larry Jonathan

Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishingmore » features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.« less

An analysis of the New York State Earth Science Curriculum with respect to standards, classroom practices, and the Regents Examination

NASA Astrophysics Data System (ADS)

Contino, Julie Anna

In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. In New York State, standards are provided to the teachers who then create individual curricula that will lead to student success on the state assessment. This mixed methods study presents an analysis of the alignment between the National Science Education Standards (NSES), New York State Physical Setting/Earth Science Core Curriculum (Core Curriculum), and New York State Earth Science Regents Examination (Regents)---the sources teachers use for creating Earth Science curricula in New York State. The NSES were found to have a 49% overlap with the Core Curriculum and a 27% overlap with the Regents. The Core Curriculum and Regents, represented by matrices consisting of performance indicators and cognitive demands, were compared using the Porter alignment index. The alignment was 0.35, categorized as slightly aligned, due to the different emphases on cognitive levels (the Core Curriculum focused on Understand and Apply while the Regents focused on Apply followed by Understand and Remember). Additionally, a purposeful sample of experienced and innovative teachers were surveyed and interviewed to gain insight on how NYS Earth Science teachers organize their scope and sequences, align their lessons with the Core Curriculum, establish internal lesson coherence, and prepare their students for the Regents Exam. Teachers' scope and sequences were well-aligned with the Core Curriculum and Regents but misalignment was found between their lessons and the Core Curriculum as well as between the stated objectives for their students and evaluation of those objectives. Based on the findings, it is suggested that the NSES be revised and the Core Curriculum updated to include quantifiable emphasis on the major understandings such as percentage of time, as well as an emphasis on alignment principles. Teacher professional development focused on alignment issues

MUSE optical alignment procedure

NASA Astrophysics Data System (ADS)

Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

2012-09-01

MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

California Diploma Project Technical Report II: Alignment Study--Alignment Study of the Health Sciences and Medical Technology Draft Standards and California's Exit Level Common Core State Standards

ERIC Educational Resources Information Center

McGaughy, Charis; de Gonzalez, Alicia

2012-01-01

The California Department of Education is in the process of revising the Career and Technical Education (CTE) Model Curriculum Standards. The Educational Policy Improvement Center (EPIC) conducted an investigation of the draft version of the Health Sciences and Medical Technology Standards (Health Science). The purpose of the study is to…

System alignment using the Talbot effect

NASA Astrophysics Data System (ADS)

Chevallier, Raymond; Le Falher, Eric; Heggarty, Kevin

1990-08-01

The Talbot effect is utilized to correct an alignment problem related to a neural network used for image recognition, which required the alignment of a spatial light modulator (SLM) with the input module. A mathematical model which employs the Fresnel diffraction theory is presented to describe the method. The calculation of the diffracted amplitude describes the wavefront sphericity and the original object transmittance function in order to qualify the lateral shift of the Talbot image. Another explanation is set forth in terms of plane-wave illumination in the neural network. Using a Fourier series and by describing planes where all the harmonics are in phase, the reconstruction of Talbot images is explained. The alignment is effective when the lenslet array is aligned on the even Talbot images of the SLM pixels and the incident wave is a plane wave. The alignment is evaluated in terms of source and periodicity errors, tilt of the incident plane waves, and finite object dimensions. The effects of the error sources are concluded to be negligible, the lenslet array is shown to be successfully aligned with the SLM, and other alignment applications are shown to be possible.

Aberration caused by the errors of alignment and adjustment in reflecting telescope

NASA Astrophysics Data System (ADS)

Tan, Hui-Song

The 2-mirror Cassegrain geometry has firmly become a standard tool for modern astronomical research. The alignment and adjustment of aplanatic (RC) Cassegrain telescope is therefore by far the most important aspect. The errors that arise in telescope through maladjustment are discussed and the aberrations are calculated for the 2.4 m telescope which will be mounted at Gaomeigu.

System and method for 2D workpiece alignment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

2015-07-14

A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

ISLLC/ELCC Standards Implementation: Do Educational Administration Faculty Practice What They Preach?

ERIC Educational Resources Information Center

Machado, Crystal

2012-01-01

Both the 1996 Interstate School Leadership Licensure Consortium (ISLLC) standards and the 2002 Educational Leadership Constituent Council (ELCC) standards, adopted by preparation programs nationwide have a strong emphasis on democratic ideals. By aligning their programs with these standards education administration faculty have taken a step in the…

40 CFR 59.512 - Addresses of EPA regional offices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... (CONTINUED) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.512 Addresses of EPA..., Air Pesticides and Toxics, Management Division, Atlanta Federal Center, 61 Forsyth Street, SW...

40 CFR 59.512 - Addresses of EPA regional offices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... (CONTINUED) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.512 Addresses of EPA..., Air Pesticides and Toxics, Management Division, Atlanta Federal Center, 61 Forsyth Street, SW...

40 CFR 59.512 - Addresses of EPA regional offices.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.512 Addresses of EPA..., Air Pesticides and Toxics, Management Division, Atlanta Federal Center, 61 Forsyth Street, SW...

40 CFR 59.512 - Addresses of EPA regional offices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (CONTINUED) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.512 Addresses of EPA..., Air Pesticides and Toxics, Management Division, Atlanta Federal Center, 61 Forsyth Street, SW...

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

Leadership in Nursing Homes: Directors of Nursing Aligning Practice With Regulations.

PubMed

Siegel, Elena O; Bettega, Kristen; Bakerjian, Debra; Sikma, Suzanne

2018-06-01

Nursing homes use team nursing, with minimal RN presence, leaving the majority of direct care to licensed practical/vocational nurses (LPNs/LVNs) and unlicensed assistive personnel (UAP), including medication aides. The current article describes challenges faced by nursing home directors of nursing (DONs) leading and managing a team nursing approach, including consideration of scope of practice, delegation and supervision regulations, and related policy implications. A secondary data analysis was performed of qualitative data from a study to develop and test DON guidelines for delegation in nursing home practice. A convenience sample (N = 29) of current or previous DONs and other nursing home leaders with knowledge and expertise in the DON role participated in in-depth, guided interviews. The findings highlight a core concern to nursing licensure policy and regulation: knowledge and practice gaps related to scope of practice and delegation and supervision among DONs, RNs, and LPNs/LVNs, as well as administrators, and the role of nursing leaders in supporting appropriate delegation practices. The findings offer directions for research and practice in addressing challenges in aligning team nursing practices with regulatory standards as well as the related gaps in knowledge among DONs, administrators, and nursing staff. [Journal of Gerontological Nursing, 44(6), 10-14.]. Copyright 2018, SLACK Incorporated.

Motorized Beam Alignment of a Commercial X-ray Diffractometer

NASA Technical Reports Server (NTRS)

Van Zandt, Noah R.; Myers, James F.; Rogers, Richard B

2013-01-01

X-ray diffraction (XRD) is a powerful analysis method that allows researchers to noninvasively probe the crystalline structure of a material. This includes the ability to determine the crystalline phases present, quantify surface residual stresses, and measure the distribution of crystallographic orientations. The Structures and Materials Division at the NASA Glenn Research Center (GRC) heavily uses the on-site XRD lab to characterize advanced metal alloys, ceramics, and polymers. One of the x-ray diffractometers in the XRD lab (Bruker D8 Discover) uses three different x-ray tubes (Cu, Cr, and Mn) for optimal performance over numerous material types and various experimental techniques. This requires that the tubes be switched out and aligned between experiments. This alignment maximizes the x-ray tube s output through an iterative process involving four set screws. However, the output of the x-ray tube cannot be monitored during the adjustment process due to standard radiation safety engineering controls that prevent exposure to the x-ray beam when the diffractometer doors are open. Therefore, the adjustment process is a very tedious series of blind adjustments, each followed by measurement of the output beam using a PIN diode after the enclosure doors are shut. This process can take up to 4 hr to perform. This technical memorandum documents an in-house project to motorize this alignment process. Unlike a human, motors are not harmed by x-ray radiation of the energy range used in this instrument. Therefore, using motors to adjust the set screws will allow the researcher to monitor the x-ray tube s output while making interactive adjustments from outside the diffractometer. The motorized alignment system consists of four motors, a motor controller, and a hand-held user interface module. Our goal was to reduce the alignment time to less than 30 min. The time available was the 10-week span of the Lewis' Educational and Research Collaborative Internship Project (LERCIP

RF Jitter Modulation Alignment Sensing

NASA Astrophysics Data System (ADS)

Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

2017-01-01

We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

Fixture for aligning motor assembly

DOEpatents

Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

2009-12-08

An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

Vane segment support and alignment device

DOEpatents

McLaurin, Leroy Dixon; Sizemore, John Derek

1999-01-01

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position.

A comparison of radiographic anatomic axis knee alignment measurements and cross-sectional associations with knee osteoarthritis.

PubMed

Goulston, L M; Sanchez-Santos, M T; D'Angelo, S; Leyland, K M; Hart, D J; Spector, T D; Cooper, C; Dennison, E M; Hunter, D; Arden, N K

2016-04-01

Malalignment is associated with knee osteoarthritis (KOA), however, the optimal anatomic axis (AA) knee alignment measurement on a standard limb radiograph (SLR) is unknown. This study compares one-point (1P) and two-point (2P) AA methods using three knee joint centre locations and examines cross-sectional associations with symptomatic radiographic knee osteoarthritis (SRKOA), radiographic knee osteoarthritis (RKOA) and knee pain. AA alignment was measured six different ways using the KneeMorf software on 1058 SLRs from 584 women in the Chingford Study. Cross-sectional associations with principal outcome SRKOA combined with greatest reproducibility determined the optimal 1P and 2P AA method. Appropriate varus/neutral/valgus alignment categories were established using logistic regression with generalised estimating equation models fitted with restricted cubic spline function. The tibial plateau centre displayed greatest reproducibility and associations with SRKOA. As mean 1P and 2P values differed by >2°, new alignment categories were generated for 1P: varus <178°, neutral 178-182°, valgus >182° and for 2P methods: varus <180°, neutral 180-185°, valgus >185°. Varus vs neutral alignment was associated with a near 2-fold increase in SRKOA and RKOA, and valgus vs neutral for RKOA using 2P method. Nonsignificant associations were seen for 1P method for SRKOA, RKOA and knee pain. AA alignment was associated with SRKOA and the tibial plateau centre had the strongest association. Differences in AA alignment when 1P vs 2P methods were compared indicated bespoke alignment categories were necessary. Further replication and validation with mechanical axis alignment comparison is required. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

A comparison of radiographic anatomic axis knee alignment measurements and cross-sectional associations with knee osteoarthritis

PubMed Central

Goulston, L.M.; Sanchez-Santos, M.T.; D'Angelo, S.; Leyland, K.M.; Hart, D.J.; Spector, T.D.; Cooper, C.; Dennison, E.M.; Hunter, D.; Arden, N.K.

2016-01-01

Summary Objective Malalignment is associated with knee osteoarthritis (KOA), however, the optimal anatomic axis (AA) knee alignment measurement on a standard limb radiograph (SLR) is unknown. This study compares one-point (1P) and two-point (2P) AA methods using three knee joint centre locations and examines cross-sectional associations with symptomatic radiographic knee osteoarthritis (SRKOA), radiographic knee osteoarthritis (RKOA) and knee pain. Methods AA alignment was measured six different ways using the KneeMorf software on 1058 SLRs from 584 women in the Chingford Study. Cross-sectional associations with principal outcome SRKOA combined with greatest reproducibility determined the optimal 1P and 2P AA method. Appropriate varus/neutral/valgus alignment categories were established using logistic regression with generalised estimating equation models fitted with restricted cubic spline function. Results The tibial plateau centre displayed greatest reproducibility and associations with SRKOA. As mean 1P and 2P values differed by >2°, new alignment categories were generated for 1P: varus <178°, neutral 178–182°, valgus >182° and for 2P methods: varus <180°, neutral 180–185°, valgus >185°. Varus vs neutral alignment was associated with a near 2-fold increase in SRKOA and RKOA, and valgus vs neutral for RKOA using 2P method. Nonsignificant associations were seen for 1P method for SRKOA, RKOA and knee pain. Conclusions AA alignment was associated with SRKOA and the tibial plateau centre had the strongest association. Differences in AA alignment when 1P vs 2P methods were compared indicated bespoke alignment categories were necessary. Further replication and validation with mechanical axis alignment comparison is required. PMID:26700504

76 FR 52737 - Oil and Natural Gas Sector: New Source Performance Standards and National Emission Standards for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-23

...This action announces how the EPA proposes to address the reviews of the new source performance standards for volatile organic compound and sulfur dioxide emissions from natural gas processing plants. We are proposing to add to the source category list any oil and gas operation not covered by the current listing. This action also includes proposed amendments to the existing new source performance standards for volatile organic compounds from natural gas processing plants and proposed standards for operations that are not covered by the existing new source performance standards. In addition, this action proposes how the EPA will address the residual risk and technology review conducted for the oil and natural gas production and natural gas transmission and storage national emission standards for hazardous air pollutants. This action further proposes standards for emission sources within these two source categories that are not currently addressed, as well as amendments to improve aspects of these national emission standards for hazardous air pollutants related to applicability and implementation. Finally, this action addresses provisions in these new source performance standards and national emission standards for hazardous air pollutants related to emissions during periods of startup, shutdown and malfunction.

Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.

PubMed

Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

2014-08-01

Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. Copyright © 2013 Elsevier B.V. All rights reserved.

How Engineering Standards Are Interpreted and Translated for Middle School

ERIC Educational Resources Information Center

Judson, Eugene; Ernzen, John; Krause, Stephen; Middleton, James A.; Culbertson, Robert J.

2016-01-01

In this exploratory study we examined the alignment of Next Generation Science Standards (NGSS) middle school engineering design standards with lesson ideas from middle school teachers, science education faculty, and engineering faculty (4-6 members per group). Respondents were prompted to provide plain language interpretations of two middle…

Conceptual Acrobatics: Talking about Assessment Standards in the Transparency Era

ERIC Educational Resources Information Center

Hudson, Jane; Bloxham, Sue; den Outer, Birgit; Price, Margaret

2017-01-01

Since their introduction in the 1990s, explicit standards documents have pervaded higher education assessment--success likely linked to their compatibility with constructive alignment and quality assurance regimes. Researchers, however, criticise that such documents are based on a misconception of standards as explicit and absolute, when in fact…

Sparse alignment for robust tensor learning.

PubMed

Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

2014-10-01

Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.

ALIGNING JIG

DOEpatents

Culver, J.S.; Tunnell, W.C.

1958-08-01

A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

A cadaveric investigation into the demographic and bony alignment properties associated with osteoarthritis of the patellofemoral joint.

PubMed

Weinberg, Douglas S; Tucker, Braden J; Drain, Joseph P; Wang, David M; Gilmore, Allison; Liu, Raymond W

2016-06-01

Patellofemoral joint osteoarthritis is common, although circumstances dictating its evolution and pathogenesis remain unclear. Advances in surgical technique have improved the ability to modify long-bone alignment in the coronal, sagittal, and axial planes. However, to our knowledge, there is no significant long-term data available in regard to the relationship between anatomic alignment parameters most amenable to surgical modification and patellofemoral joint osteoarthritis. Five-hundred and seventy-one cadaveric skeletons were obtained from the Hamann-Todd osteological collection. Mechanical lateral distal femoral angle, medial proximal tibial angle, tibial slope, femoral version, tibial torsion, the position of the tibial tubercle relative to the width of the tibial plateau, trochlear depth, and patellar size were measured using validated techniques. A previously published grading system for patellofemoral joint arthritis was used to quantify macroscopic signs of degenerative joint disease. Increasing age (standardized beta 0.532, p<0.001), female gender (standardized beta 0.201, p=0.002), and decreasing mechanical lateral distal femoral angle (standardized beta -0.128, p=0.025) were independent correlates of increased patellofemoral joint osteoarthritis. A relatively more laterally positioned tibial tubercle trended towards predicting patellofemoral joint osteoarthritis (standardized beta 0.080, p=0.089). These findings confirm that patellofemoral joint osteoarthritis is strongly associated with increasing age and female gender. Valgus alignment of the distal femur, a relatively more lateral location of the tibial tubercle, and a shallower trochlear grove appear to have modest effects on the development of patellofemoral joint osteoarthritis. Copyright © 2016 Elsevier B.V. All rights reserved.

Pope John Paul II and the neurological standard for the determination of death: A critical analysis of his address to the Transplantation Society

PubMed Central

2017-01-01

The introduction of the “brain death” criterion constitutes a significant paradigm shift in the determination of death. The perception of the public at large is that the Catholic Church has formally endorsed this neurological standard. However, a critical reading of the only magisterial document on this subject, Pope John Paul II’s 2000 address, shows that the pope’s acceptance of the neurological criterion is conditional in that it entails a twofold requirement. It requires that certain medical presuppositions of the neurological standard are fulfilled, and that its philosophical premise coheres with the Church’s teaching on the body-soul union. This article demonstrates that the medical presuppositions are not fulfilled, and that the doctrine of the brain as the central somatic integrator of the body does not cohere either with the current holistic understanding of the human organism or with the Church’s Thomistic doctrine of the soul as the form of the body. Summary The concept of “brain death” (the neurological basis for legally declaring a person dead) has caused much controversy since its inception. In this regard, it has been generally perceived that the Catholic Church has officially affirmed the “brain death” criterion. The address of Pope John Paul II in 2000 shows, however, that he only gave it a conditional acceptance, one which requires that several medical and philosophical presuppositions of the “brain death” standard be fulfilled. This article demonstrates, taking into consideration both the empirical evidence and the Church’s Thomistic anthropology, that the presuppositions have not been fulfilled. PMID:28698708

Vane segment support and alignment device

DOEpatents

McLaurin, L.D.; Sizemore, J.D.

1999-07-13

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.

Vane segment support and alignment device

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLaurin, L.D.; Sizemore, J.D.

1999-07-13

A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pinmore » is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.« less

Docking alignment system

NASA Technical Reports Server (NTRS)

Monford, Leo G. (Inventor)

1990-01-01

Improved techniques are provided for alignment of two objects. The present invention is particularly suited for three-dimensional translation and three-dimensional rotational alignment of objects in outer space. A camera 18 is fixedly mounted to one object, such as a remote manipulator arm 10 of the spacecraft, while the planar reflective surface 30 is fixed to the other object, such as a grapple fixture 20. A monitor 50 displays in real-time images from the camera, such that the monitor displays both the reflected image of the camera and visible markings on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm 10 manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

Optics Alignment Panel

NASA Technical Reports Server (NTRS)

Schroeder, Daniel J.

1992-01-01

The Optics Alignment Panel (OAP) was commissioned by the HST Science Working Group to determine the optimum alignment of the OTA optics. The goal was to find the position of the secondary mirror (SM) for which there is no coma or astigmatism in the camera images due to misaligned optics, either tilt or decenter. The despace position was reviewed of the SM and the optimum focus was sought. The results of these efforts are as follows: (1) the best estimate of the aligned position of the SM in the notation of HDOS is (DZ,DY,TZ,TY) = (+248 microns, +8 microns, +53 arcsec, -79 arcsec), and (2) the best focus, defined to be that despace which maximizes the fractional energy at 486 nm in a 0.1 arcsec radius of a stellar image, is 12.2 mm beyond paraxial focus. The data leading to these conclusions, and the estimated uncertainties in the final results, are presented.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

Well-pump alignment system

DOEpatents

Drumheller, Douglas S.

1998-01-01

An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

Silicon Alignment Pins: An Easy Way to Realize a Wafer-to-Wafer Alignment

NASA Technical Reports Server (NTRS)

Jung-Kubiak, Cecile; Reck, Theodore J.; Lin, Robert H.; Peralta, Alejandro; Gill, John J.; Lee, Choonsup; Siles, Jose; Toda, Risaku; Chattopadhyay, Goutam; Cooper, Ken B.;

HSA: a heuristic splice alignment tool.

PubMed

Bu, Jingde; Chi, Xuebin; Jin, Zhong

2013-01-01

RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.

Theory of grain alignment in molecular clouds

NASA Technical Reports Server (NTRS)

Roberge, Wayne G.

1993-01-01

Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Self-aligning biaxial load frame

DOEpatents

Ward, Michael B.; Epstein, Jonathan S.; Lloyd, W. Randolph

1994-01-01

An self-aligning biaxial loading apparatus for use in testing the strength of specimens while maintaining a constant specimen centroid during the loading operation. The self-aligning biaxial loading apparatus consists of a load frame and two load assemblies for imparting two independent perpendicular forces upon a test specimen. The constant test specimen centroid is maintained by providing elements for linear motion of the load frame relative to a fixed crosshead, and by alignment and linear motion elements of one load assembly relative to the load frame.

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

106-17 Telemetry Standards Chapter 1

DTIC Science & Technology

2017-07-01

Telemetry Standards , RCC Standard 106-17 Chapter 1, July 2017 1-1 CHAPTER 1 Introduction The Telemetry Standards address the here-to-date...generally devoted to a different element of the telemetry system or process . Chapters 21 through 28 address the topic of network telemetry. These...Commonly used terms are defined in standard reference glossaries and dictionaries. Definitions of terms with special applications are included when

The Greatest Learning Return on Your Pedagogical Investment: Alignment, Assessment or In-Class Instruction?

PubMed

Holt, Emily A; Young, Craig; Keetch, Jared; Larsen, Skylar; Mollner, Brayden

2015-01-01

Critical thinking is often considered an essential learning outcome of institutions in higher education. Previous work has proposed three pedagogical strategies to address this goal: more active, student-centered in-class instruction, assessments which contain higher-order cognitive questions, and greater alignment within a classroom (i.e., high agreement of the cognitive level of learning objectives, assessments, and in-class instruction). Our goals were to determine which of these factors, individually or the interactions therein, contributed most to improvements in university students' critical thinking. We assessed students' higher-order cognitive skills in introductory non-majors biology courses the first and last week of instruction. For each of the fifteen sections observed, we also measured the cognitive level of assessments and learning objectives, evaluated the learner-centeredness of each classroom, and calculated an alignment score for each class. The best model to explain improvements in students' high-order cognitive skills contained the measure of learner-centeredness of the class and pre-quiz scores as a covariate. The cognitive level of assessments, learning objectives, nor alignment explained improvements in students' critical thinking. In accordance with much of the current literature, our findings support that more student-centered classes had greater improvements in student learning. However, more research is needed to clarify the role of assessment and alignment in student learning.

The Greatest Learning Return on Your Pedagogical Investment: Alignment, Assessment or In-Class Instruction?

PubMed Central

Holt, Emily A.; Young, Craig; Keetch, Jared; Larsen, Skylar; Mollner, Brayden

2015-01-01

Critical thinking is often considered an essential learning outcome of institutions in higher education. Previous work has proposed three pedagogical strategies to address this goal: more active, student-centered in-class instruction, assessments which contain higher-order cognitive questions, and greater alignment within a classroom (i.e., high agreement of the cognitive level of learning objectives, assessments, and in-class instruction). Our goals were to determine which of these factors, individually or the interactions therein, contributed most to improvements in university students’ critical thinking. We assessed students’ higher-order cognitive skills in introductory non-majors biology courses the first and last week of instruction. For each of the fifteen sections observed, we also measured the cognitive level of assessments and learning objectives, evaluated the learner-centeredness of each classroom, and calculated an alignment score for each class. The best model to explain improvements in students’ high-order cognitive skills contained the measure of learner-centeredness of the class and pre-quiz scores as a covariate. The cognitive level of assessments, learning objectives, nor alignment explained improvements in students’ critical thinking. In accordance with much of the current literature, our findings support that more student-centered classes had greater improvements in student learning. However, more research is needed to clarify the role of assessment and alignment in student learning. PMID:26340659

Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

NASA Astrophysics Data System (ADS)

Lieberman, J. E.; Cheatham, M.; Varanka, D.

2015-12-01

similarities in either sense. Our study serves both to determine the limits of standard methods for aligning spatial ontologies and to suggest new methods of calculating similarity axioms that take into account semantic, spatial, and cognitive criteria relevant to fitness for relevant usage scenarios.

MICA: Multiple interval-based curve alignment

NASA Astrophysics Data System (ADS)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

Factors Associated with Alignment between Teacher Survey Reports and Classroom Observation Ratings of Mathematics Instruction

ERIC Educational Resources Information Center

Kaufman, Julia Heath; Stein, Mary Kay; Junker, Brian

2016-01-01

We investigated the alignment between a teacher survey self-report measure and classroom observation measure of ambitious mathematics instructional practice among teachers in two urban school districts using two different standards-based mathematics curricula. Survey reports suggested mild differences in teachers' instructional practices between…

Well-pump alignment system

DOEpatents