Control rod housing alignment and repair method

International Nuclear Information System (INIS)

Dixon, R.C.; Deaver, G.A.; Punches, J.R.; Singleton, G.E.; Erbes, J.G.; Offer, H.P.

1992-01-01

This patent describes a method for underwater welding of a control rod drive housing inserted through a stub tube to maintain requisite alignment and elevation of the top of the control rod drive housing to an overlying and corresponding aperture in a core plate as measured by an alignment device which determines the relative elevation and angularity with respect to the aperture. It comprises providing a welding cylinder dependent from the alignment device such that the elevation of the top of the welding cylinder is in a fixed relationship to the alignment device and is gas-proof; pressurizing the welding cylinder with inert welding gas sufficient to maintain the interior of the welding cylinder dry; lowering the welding cylinder through the aperture in the core plate by depending the cylinder with respect to the alignment device, the lowering including lowering through and adjusting the elevation relationship of the welding cylinder to the alignment device such that when the alignment device is in position to measure the elevation and angularity of the new control rod drive housing, the lower distal end of the welding cylinder extends below the upper periphery of the stub where welding is to occur; inserting a new control rod drive housing through the stub tube and positioning the control rod drive housing to a predetermined relationship to the anticipated final position of the control rod drive housing; providing welding implements transversely rotatably mounted interior of the welding cylinder relative to the alignment device such that the welding implements may be accurately positioned for dispensing weldment around the periphery of the top of the stub tube and at the side of the control rod drive housing; measuring the elevation and angularity of the control rod drive housing; and dispensing weldment along the top of the stub tube and at the side of the control rod drive housing

Is there still a role for traditional methods in the management of fractures of the zygomatic complex?

LENUS (Irish Health Repository)

O'Sullivan, S T

2012-02-03

With the introduction of low-profile mini-plating systems, a trend has developed towards open reduction and rigid internal fixation (ORIF) of fractures of the cranio-facial skeleton. The current policy for management of zygomatic fractures in our unit is to attempt primary reduction by traditional methods, and proceed to ORIF in the event of unsatisfactory fracture stability or alignment. Over a one-year period, 109 patients underwent surgical correction of fractures of the zygomatic complex. Standard Gilles\\' elevation was performed in 71 cases, percutaneous elevation in three cases, and ORIF was performed in 35 cases. Mean follow-up was 190 days. One case of persistent infraorbital step and three cases of residual malar flattening were documented in patients who underwent Gilles or percutaneous elevation. Morbidity associated with ORIF was minimal. We conclude that while ORIF of zygomatic fractures may offer better results than traditional methods in the management of complex fractures, traditional methods still have a role to play in less complex fractures.

Quality control methods for linear accelerator radiation and mechanical axes alignment.

Science.gov (United States)

Létourneau, Daniel; Keller, Harald; Becker, Nathan; Amin, Md Nurul; Norrlinger, Bernhard; Jaffray, David A

2018-06-01

The delivery accuracy of highly conformal dose distributions generated using intensity modulation and collimator, gantry, and couch degrees of freedom is directly affected by the quality of the alignment between the radiation beam and the mechanical axes of a linear accelerator. For this purpose, quality control (QC) guidelines recommend a tolerance of ±1 mm for the coincidence of the radiation and mechanical isocenters. Traditional QC methods for assessment of radiation and mechanical axes alignment (based on pointer alignment) are time consuming and complex tasks that provide limited accuracy. In this work, an automated test suite based on an analytical model of the linear accelerator motions was developed to streamline the QC of radiation and mechanical axes alignment. The proposed method used the automated analysis of megavoltage images of two simple task-specific phantoms acquired at different linear accelerator settings to determine the coincidence of the radiation and mechanical isocenters. The sensitivity and accuracy of the test suite were validated by introducing actual misalignments on a linear accelerator between the radiation axis and the mechanical axes using both beam steering and mechanical adjustments of the gantry and couch. The validation demonstrated that the new QC method can detect sub-millimeter misalignment between the radiation axis and the three mechanical axes of rotation. A displacement of the radiation source of 0.2 mm using beam steering parameters was easily detectable with the proposed collimator rotation axis test. Mechanical misalignments of the gantry and couch rotation axes of the same magnitude (0.2 mm) were also detectable using the new gantry and couch rotation axis tests. For the couch rotation axis, the phantom and test design allow detection of both translational and tilt misalignments with the radiation beam axis. For the collimator rotation axis, the test can isolate the misalignment between the beam radiation axis

Automatic Image Alignment and Stitching of Medical Images with Seam Blending

OpenAIRE

Abhinav Kumar; Raja Sekhar Bandaru; B Madhusudan Rao; Saket Kulkarni; Nilesh Ghatpande

2010-01-01

This paper proposes an algorithm which automatically aligns and stitches the component medical images (fluoroscopic) with varying degrees of overlap into a single composite image. The alignment method is based on similarity measure between the component images. As applied here the technique is intensity based rather than feature based. It works well in domains where feature based methods have difficulty, yet more robust than traditional correlation. Component images are stitched together usin...

In-Flight Self-Alignment Method Aided by Geomagnetism for Moving Basement of Guided Munitions

Directory of Open Access Journals (Sweden)

Shuang-biao Zhang

2015-01-01

Full Text Available Due to power-after-launch mode of guided munitions of high rolling speed, initial attitude of munitions cannot be determined accurately, and this makes it difficult for navigation and control system to work effectively and validly. An in-flight self-alignment method aided by geomagnetism that includes a fast in-flight coarse alignment method and an in-flight alignment model based on Kalman theory is proposed in this paper. Firstly a fast in-flight coarse alignment method is developed by using gyros, magnetic sensors, and trajectory angles. Then, an in-flight alignment model is derived by investigation of the measurement errors and attitude errors, which regards attitude errors as state variables and geomagnetic components in navigation frame as observed variables. Finally, fight data of a spinning projectile is used to verify the performance of the in-flight self-alignment method. The satisfying results show that (1 the precision of coarse alignment can attain below 5°; (2 the attitude errors by in-flight alignment model converge to 24′ at early of the latter half of the flight; (3 the in-flight alignment model based on Kalman theory has better adaptability, and show satisfying performance.

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

Directory of Open Access Journals (Sweden)

Patrick D Schloss

Full Text Available Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities. This approach has revealed and introduced questions that were not fully appreciated by those carrying out traditional Sanger sequencing-based methods. These include the effects of alignment quality, the best method of calculating pairwise genetic distances for 16S rRNA genes, whether it is appropriate to filter variable regions, and how the choice of variable region relates to the genetic diversity observed in full-length sequences. I used a diverse collection of 13,501 high-quality full-length sequences to assess each of these questions. First, alignment quality had a significant impact on distance values and downstream analyses. Specifically, the greengenes alignment, which does a poor job of aligning variable regions, predicted higher genetic diversity, richness, and phylogenetic diversity than the SILVA and RDP-based alignments. Second, the effect of different gap treatments in determining pairwise genetic distances was strongly affected by the variation in sequence length for a region; however, the effect of different calculation methods was subtle when determining the sample's richness or phylogenetic diversity for a region. Third, applying a sequence mask to remove variable positions had a profound impact on genetic distances by muting the observed richness and phylogenetic diversity. Finally, the genetic distances calculated for each of the variable regions did a poor job of correlating with the full-length gene. Thus, while it is tempting to apply traditional cutoff levels derived for full-length sequences to these shorter sequences, it is not advisable. Analysis of beta-diversity metrics showed that each of these factors can have a significant impact on the comparison of community membership and structure. Taken together, these results

Proposal for an alignment method of the CLIC linear accelerator - From geodesic networks to the active pre-alignment

International Nuclear Information System (INIS)

Touze, T.

2011-01-01

The compact linear collider (CLIC) is the particle accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nano-metric scale of the CLIC leptons beams, the emittance growth budget is very tight. It induces alignment tolerances on the positions of the CLIC components that have never been achieved before. The last step of the CLIC alignment will be done according to the beam itself. It falls within the competence of the physicists. However, in order to implement the beam-based feedback, a challenging pre-alignment is required: 10 μm at 3σ along a 200 m sliding window. For such a precision, the proposed solution must be compatible with a feedback between the measurement and repositioning systems. The CLIC pre-alignment will have to be active. This thesis does not demonstrate the feasibility of the CLIC active pre-alignment but shows the way to the last developments that have to be done for that purpose. A method is proposed. Based on the management of the Helmert transformations between Euclidean coordinate systems, from the geodetic networks to the metrological measurements, this method is likely to solve the CLIC pre-alignment problem. Large scale facilities have been built and Monte-Carlo simulations have been made in order to validate the mathematical modeling of the measurement systems and of the alignment references. When this is done, it will be possible to extrapolate the modeling to the entire CLIC length. It will be the last step towards the demonstration of the CLIC pre-alignment feasibility. (author)

MEMS Integrated Submount Alignment for Optoelectronics

Science.gov (United States)

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.

A facile method to align carbon nanotubes on polymeric membrane substrate

Science.gov (United States)

Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

2013-01-01

The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

Science.gov (United States)

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

Science.gov (United States)

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

Method and apparatus for improving the alignment of radiographic images

International Nuclear Information System (INIS)

Schuller, P.D.; Hatcher, D.C.; Caelli, T.M.; Eggert, F.M.; Yuzyk, J.

1991-01-01

This invention relates generally to the field of radiology, and has to do particularly with a method and apparatus for improving the alignment of radiographic images taken at different times of the same tissue structure, so that the images can be sequentially shown in aligned condition, whereby changes in the structure can be noted. (author). 10 figs

Getting Your Peaks in Line: A Review of Alignment Methods for NMR Spectral Data

Directory of Open Access Journals (Sweden)

Trung Nghia Vu

2013-04-01

Full Text Available One of the most significant challenges in the comparative analysis of Nuclear Magnetic Resonance (NMR metabolome profiles is the occurrence of shifts between peaks across different spectra, for example caused by fluctuations in pH, temperature, instrument factors and ion content. Proper alignment of spectral peaks is therefore often a crucial preprocessing step prior to downstream quantitative analysis. Various alignment methods have been developed specifically for this purpose. Other methods were originally developed to align other data types (GC, LC, SELDI-MS, etc., but can also be applied to NMR data. This review discusses the available methods, as well as related problems such as reference determination or the evaluation of alignment quality. We present a generic alignment framework that allows for comparison and classification of different alignment approaches according to their algorithmic principles, and we discuss their performance.

Fabrication of Aligned Nanofibers by Manipulated Rotating Drum Method and Studying the Effective Parameters on Fibers Alignment by Image Processing

Directory of Open Access Journals (Sweden)

Zohreh Hadi

2013-01-01

Full Text Available Electrospinning is a known process to produce nanofibers through electrostatic forces. In a typical process, an electrical potential is applied between droplets of polymer solution or melt, held through a syringe needle and a grounded target. In general electrospinning fibers are collected on the grounded target as a random oriented web of nanofiber. Various research projects are attempted to obtain aligned electrospun fibers. This modified electrospinning method can be developed and used in a variety of nanofiber-based applications such as making of nanofibrous scaffolds for tissue engineering. In this study, an effective method has been developed to fabricate aligned nanofibers by manipulation of electrospinning system using two nozzles with opposite charges. Moreover, the effect of some parameters including take-up velocity, applied voltage and polymer solution concentration on alignment of produced nanofibers is investigated. The comparison of fibers alignment was carried out by programming and image processing in MATLAB. It is shown that take-up velocity and polymer solution concentration have significant effect on increasing the fibers alignment. Also, the alignment is increased with applied voltage at first and then, it is decreased. The analytical results and optical microscopic images are clear evidence of showing the maximum alignment of nanofibers obtained at 15% polymer solution concentration with take-up velocity of 600 rpm and 11 kV voltage.

Alignment of the stanford linear collider Arcs

International Nuclear Information System (INIS)

Pitthan, R.; Bell, B.; Friedsam, H.

1987-01-01

The alignment of the Arcs for the Stanford Linear Collider at SLAC has posed problems in accelerator survey and alignment not encountered before. These problems come less from the tight tolerances of 0.1 mm, although reaching such a tight statistically defined accuracy in a controlled manner is difficult enough, but from the absence of a common reference plane for the Arcs. Traditional circular accelerators, including HERA and LEP, have been designed in one plane referenced to local gravity. For the SLC Arcs no such single plane exists. Methods and concepts developed to solve these and other problems, connected with the unique design of SLC, range from the first use of satellites for accelerator alignment, use of electronic laser theodolites for placement of components, computer control of the manual adjustment process, complete automation of the data flow incorporating the most advanced concepts of geodesy, strict separation of survey and alignment, to linear principal component analysis for the final statistical smoothing of the mechanical components

A method to align a bent crystal for channeling experiments by using quasichanneling oscillations

Science.gov (United States)

Sytov, A. I.; Guidi, V.; Tikhomirov, V. V.; Bandiera, L.; Bagli, E.; Germogli, G.; Mazzolari, A.; Romagnoni, M.

2018-04-01

A method to calculate both the bent crystal angle of alignment and radius of curvature by using only one distribution of deflection angles has been developed. The method is based on measuring of the angular position of recently predicted and observed quasichanneling oscillations in the deflection angle distribution and consequent fitting of both the radius and angular alignment by analytic formulae. In this paper this method is applied on the example of simulated angular distributions over a wide range of values of both radius and alignment for electrons. It is carried out through the example of (111) nonequidistant planes though this technique is general and could be applied to any kind of planes. In addition, the method application constraints are also discussed. It is shown by simulations that this method, being in fact a sort of beam diagnostics, allows one in a certain case to increase the crystal alignment accuracy as well as to control precisely the radius of curvature inside an accelerator tube without vacuum breaking. In addition, it speeds up the procedure of crystal alignment in channeling experiments, reducing beamtime consuming.

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

Science.gov (United States)

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.

Accelerating large-scale protein structure alignments with graphics processing units

Directory of Open Access Journals (Sweden)

Pang Bin

2012-02-01

Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

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

Science.gov (United States)

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/.

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

Science.gov (United States)

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

Magnetic Alignment of Pulsed Solenoids Using the Pulsed Wire Method

International Nuclear Information System (INIS)

Arbelaez, D.; Madur, A.; Lipton, T.M.; Waldron, W.L.; Kwan, J.W.

2011-01-01

A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 (micro)m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

Nigeria's Policy of Non-Alignment and Voting in the United Nations ...

African Journals Online (AJOL)

alignment in Nigeria's foreign policy between 1960 and 1965. The tradition that dates from the early 1960s concludes that Nigeria's foreign policy towards the Cold War was independent and non-aligned, and the post-war tradition is that Nigeria ...

Note: A simple image processing based fiducial auto-alignment method for sample registration.

Science.gov (United States)

Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

2015-08-01

A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

Development of a High Precision Edge Alignment System for Touch-Panel Glass Substrates

Directory of Open Access Journals (Sweden)

Hau-Wei Lee

2014-06-01

Full Text Available There are two kinds of alignment systems, marked and unmarked. The glass substrate for touch panels is categorized as an unmarked work piece. Vision based glass substrate alignment (GSA relies on the edge of the glass. Traditional GSA systems compensate first for angular and then for linear error. This reduces alignment accuracy and increases alignment time and edge detection usually takes longer than 10 ms. This study proposes an effortless edge detection method. This method is very simple and can significantly reduce the time taken to detect the edge to about 6 ms using a 1.3 megapixel image. In this study, a floating center idea is used to control the glass substrate on a high precision coplanar XXY alignment stage. According to the method, users can set the rotation center anywhere as long as it is on the working (xy plane. Tolerance prognosis is also considered in this study to help the operator decide if the substrate is usable or should be rejected. The experimental results show alignment repeatability of the x, y, and θ axes to be 1 μm, 1 μm, and 5 arcsec, respectively.

Simple methods of aligning four-circle diffractometers with crystal reflections

Energy Technology Data Exchange (ETDEWEB)

Mitsui, Y [Tokyo Univ. (Japan). Faculty of Pharmaceutical Sciences

1979-08-01

Simple methods of aligning four-circle diffractometers with crystal reflections are devised. They provide the methods to check (1) perpendicularity of chi plane to the incident beam, (2) zero point of 2theta and linearity of focus-chi center-receiving aperture and (3) zero point of chi.

Coordinate alignment of combined measurement systems using a modified common points method

Science.gov (United States)

Zhao, G.; Zhang, P.; Xiao, W.

2018-03-01

The co-ordinate metrology has been extensively researched for its outstanding advantages in measurement range and accuracy. The alignment of different measurement systems is usually achieved by integrating local coordinates via common points before measurement. The alignment errors would accumulate and significantly reduce the global accuracy, thus need to be minimized. In this thesis, a modified common points method (MCPM) is proposed to combine different traceable system errors of the cooperating machines, and optimize the global accuracy by introducing mutual geometric constraints. The geometric constraints, obtained by measuring the common points in individual local coordinate systems, provide the possibility to reduce the local measuring uncertainty whereby enhance the global measuring certainty. A simulation system is developed in Matlab to analyze the feature of MCPM using the Monto-Carlo method. An exemplary setup is constructed to verify the feasibility and efficiency of the proposed method associated with laser tracker and indoor iGPS systems. Experimental results show that MCPM could significantly improve the alignment accuracy.

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

Science.gov (United States)

Quinn, Terrance; Sinkala, Zachariah

2014-01-01

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

A Method for SINS Alignment with Large Initial Misalignment Angles Based on Kalman Filter with Parameters Resetting

Directory of Open Access Journals (Sweden)

Xixiang Liu

2014-01-01

Full Text Available In the initial alignment process of strapdown inertial navigation system (SINS, large initial misalignment angles always bring nonlinear problem, which causes alignment failure when the classical linear error model and standard Kalman filter are used. In this paper, the problem of large misalignment angles in SINS initial alignment is investigated, and the key reason for alignment failure is given as the state covariance from Kalman filter cannot represent the true one during the steady filtering process. According to the analysis, an alignment method for SINS based on multiresetting the state covariance matrix of Kalman filter is designed to deal with large initial misalignment angles, in which classical linear error model and standard Kalman filter are used, but the state covariance matrix should be multireset before the steady process until large misalignment angles are decreased to small ones. The performance of the proposed method is evaluated by simulation and car test, and the results indicate that the proposed method can fulfill initial alignment with large misalignment angles effectively and the alignment accuracy of the proposed method is as precise as that of alignment with small misalignment angles.

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

Science.gov (United States)

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Directory of Open Access Journals (Sweden)

Toh Hiroyuki

2008-04-01

Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

International Nuclear Information System (INIS)

Livingston, Ken

2009-01-01

This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

Energy Technology Data Exchange (ETDEWEB)

Livingston, Ken [Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom)], E-mail: k.livingston@physics.gla.ac.uk

2009-05-21

This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

Science.gov (United States)

Livingston, Ken

2009-05-01

This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

Engaging Students in Traditional and Digital Storytelling to Make Connections between Pedagogy and Children's Experiences

Science.gov (United States)

Lisenbee, Peggy S.; Ford, Carol M.

2018-01-01

Traditional and digital storytelling is a powerful literacy tool which engage students in making connections between pedagogy and academic content. Definitions of traditional and digital storytelling, pedagogical methods aligned with curriculum standards, and examples of literacy centers associated with storytelling in early childhood classrooms…

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

Energy Technology Data Exchange (ETDEWEB)

Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

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 phylogenetic 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.

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

International Nuclear Information System (INIS)

Ovacik, Meric A.; Androulakis, Ioannis P.

2013-01-01

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 phylogenetic 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

Amplitude differences least squares method applied to temporal cardiac beat alignment

International Nuclear Information System (INIS)

Correa, R O; Laciar, E; Valentinuzzi, M E

2007-01-01

High resolution averaged ECG is an important diagnostic technique in post-infarcted and/or chagasic patients with high risk of ventricular tachycardia (VT). It calls for precise determination of the synchronism point (fiducial point) in each beat to be averaged. Cross-correlation (CC) between each detected beat and a reference beat is, by and large, the standard alignment procedure. However, the fiducial point determination is not precise in records contaminated with high levels of noise. Herein, we propose an alignment procedure based on the least squares calculation of the amplitude differences (LSAD) between the ECG samples and a reference or template beat. Both techniques, CC and LSAD, were tested in high resolution ECG's corrupted with white noise and 50 Hz line interference of varying amplitudes (RMS range: 0-100μV). Results point out that LSDA produced a lower alignment error in all contaminated records while in those blurred by power line interference better results were found only within the 0-40 μV range. It is concluded that the proposed method represents a valid alignment alternative

Alignment of the Stanford Linear Collider Arcs: Concepts and results

International Nuclear Information System (INIS)

Pitthan, R.; Bell, B.; Friedsam, H.; Pietryka, M.; Oren, W.; Ruland, R.

1987-02-01

The alignment of the Arcs for the Stanford Linear Collider at SLAC has posed problems in accelerator survey and alignment not encountered before. These problems come less from the tight tolerances of 0.1 mm, although reaching such a tight statistically defined accuracy in a controlled manner is difficult enough, but from the absence of a common reference plane for the Arcs. Traditional circular accelerators, including HERA and LEP, have been designed in one plane referenced to local gravity. For the SLC Arcs no such single plane exists. Methods and concepts developed to solve these and other problems, connected with the unique design of SLC, range from the first use of satellites for accelerator alignment, use of electronic laser theodolites for placement of components, computer control of the manual adjustment process, complete automation of the data flow incorporating the most advanced concepts of geodesy, strict separation of survey and alignment, to linear principal component analysis for the final statistical smoothing of the mechanical components

A comprehensive method for evaluating precision of transfer alignment on a moving base

Science.gov (United States)

Yin, Hongliang; Xu, Bo; Liu, Dezheng

2017-09-01

In this study, we propose the use of the Degree of Alignment (DOA) in engineering applications for evaluating the precision of and identifying the transfer alignment on a moving base. First, we derive the statistical formula on the basis of estimations. Next, we design a scheme for evaluating the transfer alignment on a moving base, for which the attitude error cannot be directly measured. Then, we build a mathematic estimation model and discuss Fixed Point Smoothing (FPS), Returns to Scale (RTS), Inverted Sequence Recursive Estimation (ISRE), and Kalman filter estimation methods, which can be used when evaluating alignment accuracy. Our theoretical calculations and simulated analyses show that the DOA reflects not only the alignment time and accuracy but also differences in the maneuver schemes, and is suitable for use as an integrated evaluation index. Furthermore, all four of these algorithms can be used to identify the transfer alignment and evaluate its accuracy. We recommend RTS in particular for engineering applications. Generalized DOAs should be calculated according to the tactical requirements.

An Automatic High Efficient Method for Dish Concentrator Alignment

Directory of Open Access Journals (Sweden)

Yong Wang

2014-01-01

for the alignment of faceted solar dish concentrator. The isosceles triangle configuration of facet’s footholds determines a fixed relation between light spot displacements and foothold movements, which allows an automatic determination of the amount of adjustments. Tests on a 25 kW Stirling Energy System dish concentrator verify the feasibility, accuracy, and efficiency of our method.

ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

OpenAIRE

Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

2016-01-01

Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was o...

An IMU-to-Body Alignment Method Applied to Human Gait Analysis

Directory of Open Access Journals (Sweden)

Laura Susana Vargas-Valencia

2016-12-01

Full Text Available This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis.

Novel method of aligning ATF-1 coils

International Nuclear Information System (INIS)

Rome, J.A.; Harris, J.H.; Neilson, G.H.; Jernigan, T.C.

1983-08-01

The coils for the Advanced Toroidal Facility (ATF-1) torsatron may be easily aligned before the machine is placed under vacuum. This is done by creating nulls in the magnetic field by energizing the coils in various configurations. All of the nulls in vertical bar B vector vertical bar occur on the z-axis. When the nulls coincide, the coils are properly aligned

A phenomenological study of millennial students and traditional pedagogies.

Science.gov (United States)

Toothaker, Rebecca; Taliaferro, Donna

The Millennial generation comprises the majority of learners in the traditional university setting. Nurse educators identify problems developing teaching strategies in education that undergraduate Millennial nursing students find engaging and meaningful. The purpose of this study was to identify the perception of Millennial students participating in traditional pedagogies and its significant implications for nursing education. This interpretive phenomenological study recorded the lived experiences of Millennial nursing students' experiences in traditional classrooms. One on one interviews with 13 Millennial students were conducted. Data collection and analysis aligned with van Manen's method. There are five themes that emerged from the data: physically present, mentally dislocated; unspoken peer pressure; wanting more from the professors; surface learning; and lack of trust. The essence focuses around the central theme of belonging, while students identified the most significant challenge in a classroom was disengaging professors. Recommendations for faculty to engage nursing students through a method of shared responsibility of educational approach are given. Blended teaching pedagogies that offer traditional and active methods are recommended. Published by Elsevier Inc.

A generalized method for alignment of block copolymer films: solvent vapor annealing with soft shear.

Science.gov (United States)

Qiang, Zhe; Zhang, Yuanzhong; Groff, Jesse A; Cavicchi, Kevin A; Vogt, Bryan D

2014-08-28

One of the key issues associated with the utilization of block copolymer (BCP) thin films in nanoscience and nanotechnology is control of their alignment and orientation over macroscopic dimensions. We have recently reported a method, solvent vapor annealing with soft shear (SVA-SS), for fabricating unidirectional alignment of cylindrical nanostructures. This method is a simple extension of the common SVA process by adhering a flat, crosslinked poly(dimethylsiloxane) (PDMS) pad to the BCP thin film. The impact of processing parameters, including annealing time, solvent removal rate and the physical properties of the PDMS pad, on the quality of alignment quantified by the Herman's orientational factor (S) is systematically examined for a model system of polystyrene-block-polyisoprene-block-polystyrene (SIS). As annealing time increases, the SIS morphology transitions from isotropic rods to highly aligned cylinders. Decreasing the rate of solvent removal, which impacts the shear rate imposed by the contraction of the PDMS, improves the orientation factor of the cylindrical domains; this suggests the nanostructure alignment is primarily induced by contraction of PDMS during solvent removal. Moreover, the physical properties of the PDMS controlled by the crosslink density impact the orientation factor by tuning its swelling extent during SVA-SS and elastic modulus. Decreasing the PDMS crosslink density increases S; this effect appears to be primarily driven by the changes in the solubility of the SVA-SS solvent in the PDMS. With this understanding of the critical processing parameters, SVA-SS has been successfully applied to align a wide variety of BCPs including polystyrene-block-polybutadiene-block-polystyrene (SBS), polystyrene-block-poly(N,N-dimethyl-n-octadecylammonium p-styrenesulfonate) (PS-b-PSS-DMODA), polystyrene-block-polydimethylsiloxane (PS-b-PDMS) and polystyrene-block-poly(2-vinlypyridine) (PS-b-P2VP). These results suggest that SVA-SS is a generalizable

Composite Materials with Magnetically Aligned Carbon Nanoparticles and Methods of Preparation

Science.gov (United States)

Hong, Haiping (Inventor); Peterson, G.P. (Bud) (Inventor); Salem, David R. (Inventor)

2018-01-01

The present invention relates to magnetically aligned carbon nanoparticle composites and methods of preparing the same. The composites comprise carbon nanoparticles, host material, magnetically sensitive nanoparticles and surfactant. The composites may have enhanced mechanical, thermal, and/or electrical properties.

Spent fuel container alignment device and method

Science.gov (United States)

Jones, Stewart D.; Chapek, George V.

1996-01-01

An alignment device is used with a spent fuel shipping container including a plurality of fuel pockets for spent fuel arranged in an annular array and having a rotatable cover including an access opening therein. The alignment device includes a lightweight plate which is installed over the access opening of the cover. A laser device is mounted on the plate so as to emit a laser beam through a laser admittance window in the cover into the container in the direction of a pre-established target associated with a particular fuel pocket. An indexing arrangement on the container provides an indication of the angular position of the rotatable cover when the laser beam produced by the laser is brought into alignment with the target of the associated fuel pocket.

Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

Science.gov (United States)

Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

2018-04-20

The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

Improved image alignment method in application to X-ray images and biological images.

Science.gov (United States)

Wang, Ching-Wei; Chen, Hsiang-Chou

2013-08-01

Alignment of medical images is a vital component of a large number of applications throughout the clinical track of events; not only within clinical diagnostic settings, but prominently so in the area of planning, consummation and evaluation of surgical and radiotherapeutical procedures. However, image registration of medical images is challenging because of variations on data appearance, imaging artifacts and complex data deformation problems. Hence, the aim of this study is to develop a robust image alignment method for medical images. An improved image registration method is proposed, and the method is evaluated with two types of medical data, including biological microscopic tissue images and dental X-ray images and compared with five state-of-the-art image registration techniques. The experimental results show that the presented method consistently performs well on both types of medical images, achieving 88.44 and 88.93% averaged registration accuracies for biological tissue images and X-ray images, respectively, and outperforms the benchmark methods. Based on the Tukey's honestly significant difference test and Fisher's least square difference test tests, the presented method performs significantly better than all existing methods (P ≤ 0.001) for tissue image alignment, and for the X-ray image registration, the proposed method performs significantly better than the two benchmark b-spline approaches (P < 0.001). The software implementation of the presented method and the data used in this study are made publicly available for scientific communities to use (http://www-o.ntust.edu.tw/∼cweiwang/ImprovedImageRegistration/). cweiwang@mail.ntust.edu.tw.

Dynamic knee alignment and collateral knee laxity and its variations in normal humans

Directory of Open Access Journals (Sweden)

Kamal eDeep

2015-11-01

Full Text Available Alignment of normal, arthritic and replaced human knees is a much debated subject as is the collateral ligamentous laxity. Traditional quantitative values have been challenged. Methods used to measure these are also not without flaws. Authors review the recent literature and a novel method of measurement of these values has been included. This method includes use of computer navigation technique in clinic setting for assessment of the normal or affected knee before the surgery. Computer navigation has been known for achievement of alignment accuracy during knee surgery. Now its use in clinic setting has added to the inventory of measurement methods. Authors dispel the common myth of straight mechanical axis in normal knees and also look at quantification of amount of collateral knee laxity. Based on the scientific studies it has been shown that the mean alignment is in varus in normal knees. It changes from lying non weight bearing position to standing weight bearing position in both coronal and the sagittal planes. It also varies with gender and race. The collateral laxity is also different for males and females. Further studies are needed to define the ideal alignment and collateral laxity which the surgeon should aim for individual knees.

ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods

Directory of Open Access Journals (Sweden)

Luca Levrini

2016-01-01

Full Text Available Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet. At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units; a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet.

ATP Bioluminometers Analysis on the Surfaces of Removable Orthodontic Aligners after the Use of Different Cleaning Methods.

Science.gov (United States)

Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian

2016-01-01

Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet). At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units); a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet.

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

Science.gov (United States)

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were

DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

OpenAIRE

Morgenstern, Burkhard

2004-01-01

DIALIGN is a widely used software tool for multiple DNA and protein sequence alignment. The program combines local and global alignment features and can therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online through Bielefeld Bioinformatics Server (BiBiServ). The downloadable version of the program offers several new program features. To compare the output of different alignment programs, we developed the program AltA...

Pattern recognition in complex activity travel patterns : comparison of Euclidean distance, signal-processing theoretical, and multidimensional sequence alignment methods

NARCIS (Netherlands)

Joh, C.H.; Arentze, T.A.; Timmermans, H.J.P.

2001-01-01

The application of a multidimensional sequence alignment method for classifying activity travel patterns is reported. The method was developed as an alternative to the existing classification methods suggested in the transportation literature. The relevance of the multidimensional sequence alignment

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

Directory of Open Access Journals (Sweden)

Daniels Noah M

2012-10-01

Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

2010-01-01

Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

Relevance of traditional methods of conflict resolution in the justice ...

African Journals Online (AJOL)

The traditional methods of African conflict resolution have long existed and are deeply rooted in the customs and traditions of the peoples of Africa. These methods are geared towards maintaining harmonious and peaceful coexistence in the community. Colonialism introduced the modern justice system, which dominated ...

A Novel Marker Based Method to Teeth Alignment in MRI

Science.gov (United States)

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 Facile Method to Fabricate Anisotropic Hydrogels with Perfectly Aligned Hierarchical Fibrous Structures.

Science.gov (United States)

Mredha, Md Tariful Islam; Guo, Yun Zhou; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

2018-03-01

Natural structural materials (such as tendons and ligaments) are comprised of multiscale hierarchical architectures, with dimensions ranging from nano- to macroscale, which are difficult to mimic synthetically. Here a bioinspired, facile method to fabricate anisotropic hydrogels with perfectly aligned multiscale hierarchical fibrous structures similar to those of tendons and ligaments is reported. The method includes drying a diluted physical hydrogel in air by confining its length direction. During this process, sufficiently high tensile stress is built along the length direction to align the polymer chains and multiscale fibrous structures (from nano- to submicro- to microscale) are spontaneously formed in the bulk material, which are well-retained in the reswollen gel. The method is useful for relatively rigid polymers (such as alginate and cellulose), which are susceptible to mechanical signal. By controlling the drying with or without prestretching, the degree of alignment, size of superstructures, and the strength of supramolecular interactions can be tuned, which sensitively influence the strength and toughness of the hydrogels. The mechanical properties are comparable with those of natural ligaments. This study provides a general strategy for designing hydrogels with highly ordered hierarchical structures, which opens routes for the development of many functional biomimetic materials for biomedical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

Science.gov (United States)

Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

2010-01-01

The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

Ancestral sequence alignment under optimal conditions

Directory of Open Access Journals (Sweden)

Brown Daniel G

2005-11-01

Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

Probabilistic biological network alignment.

Science.gov (United States)

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.

SWAMP+: multiple subsequence alignment using associative massive parallelism

Energy Technology Data Exchange (ETDEWEB)

Steinfadt, Shannon Irene [Los Alamos National Laboratory; Baker, Johnnie W [KENT STATE UNIV.

2010-10-18

A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.

Comparing Traditional and Crowdsourcing Methods for Pretesting Survey Questions

Directory of Open Access Journals (Sweden)

Jennifer Edgar

2016-10-01

Full Text Available Cognitive interviewing is a common method used to evaluate survey questions. This study compares traditional cognitive interviewing methods with crowdsourcing, or “tapping into the collective intelligence of the public to complete a task.” Crowdsourcing may provide researchers with access to a diverse pool of potential participants in a very timely and cost-efficient way. Exploratory work found that crowdsourcing participants, with self-administered data collection, may be a viable alternative, or addition, to traditional pretesting methods. Using three crowdsourcing designs (TryMyUI, Amazon Mechanical Turk, and Facebook, we compared the participant characteristics, costs, and quantity and quality of data with traditional laboratory-based cognitive interviews. Results suggest that crowdsourcing and self-administered protocols may be a viable way to collect survey pretesting information, as participants were able to complete the tasks and provide useful information; however, complex tasks may require the skills of an interviewer to administer unscripted probes.

Initial alignment method for free space optics laser beam

Science.gov (United States)

Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

2016-08-01

The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

Physicochemical characterization of traditional Ghanaian cooking ...

African Journals Online (AJOL)

Traditional vegetable oils derived from Egusi (Citrullus colocynthis) and Werewere ... the FAO/WHO standards for permissible levels of impurity in edible oils. ... to produce Egusi and Werewere oils that are aligned with industry standards.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez

2011-01-01

The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

Improving tibial component coronal alignment during total knee arthroplasty with use of a tibial planing device.

Science.gov (United States)

Patil, Shantanu; D'Lima, Darryl D; Fait, James M; Colwell, Clifford W

2007-02-01

The outcomes of knee arthroplasty have been shown to be affected by component alignment. Intramedullary and extramedullary alignment instrumentation are fairly effective for achieving the desired mean tibial component coronal alignment. However, there are outliers representing >3 degrees of varus or valgus alignment with respect to the anatomic tibial shaft axis. We measured the efficacy of a custom tibial planing device for reducing the outliers in tibial alignment. We designed a tibial planing tool in an effort to improve tibial alignment. In one cohort (100 knees), we used traditional intramedullary alignment instrumentation to make the tibial bone cut. In a second cohort (120 knees), we used intramedullary alignment instrumentation to make the cut and also used a custom tool to check the cut and to correct an inexact cut. Tibial tray alignment relative to the long axis of the tibial shaft was measured in the coronal and sagittal planes on postoperative radiographs. The target coronal alignment was 90 degrees with respect to the tibial shaft axis (with alignment). A total of 100 anteroposterior radiographs and sixty-five lateral radiographs were analyzed for the group that was treated with traditional instrumentation alone, and a total of 120 anteroposterior radiographs and fifty-five lateral radiographs were analyzed for the group that was treated with use of the custom tibial planing device. The mean coronal alignment of the tibial component was 89.5 degrees +/- 2.1 degrees in the group that was treated with traditional instrumentation alone and 89.6 degrees +/- 1.4 degrees in the group that was treated with use of the custom planing device. Although the mean coronal alignment was not significantly different, the number of outliers was substantially reduced when the custom planing device was used. All 120 components that had been aligned with use of the custom planing device were within 3 degrees of the target coronal alignment, compared with only eighty

Sparse alignment for robust tensor learning.

Science.gov (United States)

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.

Modified alignment CGHs for aspheric surface test

Science.gov (United States)

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.

An optimal beam alignment method for large-scale distributed space surveillance radar system

Science.gov (United States)

Huang, Jian; Wang, Dongya; Xia, Shuangzhi

2018-06-01

Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

Teaching-learning: stereoscopic 3D versus Traditional methods in Mexico City.

Science.gov (United States)

Mendoza Oropeza, Laura; Ortiz Sánchez, Ricardo; Ojeda Villagómez, Raúl

2015-01-01

In the UNAM Faculty of Odontology, we use a stereoscopic 3D teaching method that has grown more common in the last year, which makes it important to know whether students can learn better with this strategy. The objective of the study is to know, if the 4th year students of the bachelor's degree in dentistry learn more effectively with the use of stereoscopic 3D than the traditional method in Orthodontics. first, we selected the course topics, to be used for both methods; the traditional method using projection of slides and for the stereoscopic third dimension, with the use of videos in digital stereo projection (seen through "passive" polarized 3D glasses). The main topic was supernumerary teeth, including and diverted from their guide eruption. Afterwards we performed an exam on students, containing 24 items, validated by expert judgment in Orthodontics teaching. The results of the data were compared between the two educational methods for determined effectiveness using the model before and after measurement with the statistical package SPSS 20 version. The results presented for the 9 groups of undergraduates in dentistry, were collected with a total of 218 students for 3D and traditional methods, we found in a traditional method a mean 4.91, SD 1.4752 in the pretest and X=6.96, SD 1.26622, St Error 0.12318 for the posttest. The 3D method had a mean 5.21, SD 1.996779 St Error 0.193036 for the pretest X= 7.82, SD =0.963963, St Error 0.09319 posttest; the analysis of Variance between groups F= 5.60 Prob > 0.0000 and Bartlett's test for equal variances 21.0640 Prob > chi2 = 0.007. These results show that the student's learning in 3D means a significant improvement as compared to the traditional teaching method and having a strong association between the two methods. The findings suggest that the stereoscopic 3D method lead to improved student learning compared to traditional teaching.

Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

International Nuclear Information System (INIS)

Popov, A.G.; Golovnia, O.A.; Protasov, A.V.

2017-01-01

It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 µm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 – 1.2 T to the filling density 2.6 – 3.2×10 3 kg/m 3 . It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×10 3 kg/m 3 , the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with B r ≥1.34 T, H c ≥950 kA/m, (BH) max ≥340 kJ/m 3 , and the degree of alignment exceeding 96% were produced. - Highlights: • The pressless process (PLP) in magnet production is studied. • A new method of the loading of powder in an applied DC magnetic field is suggested. • The method allows achieving higher degree of alignment in moderate magnetic field. • Density of sintered magnets is studied experimentally and via DEM simulation. • Low density is caused by the formation of magnetostatic chains of powder particles.

Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

Energy Technology Data Exchange (ETDEWEB)

Popov, A.G. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation); Golovnia, O.A., E-mail: golovnya@imp.uran.ru [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation); Protasov, A.V. [M.N. Miheev Institute of Metal Physics of Ural Branch of Russian Academy of Sciences, Str. S. Kovalevskoy, 18, 620137 Ekaterinburg (Russian Federation); Institute of Natural Sciences and Mathematics, Ural Federal University, Av. Mira, 19, 620002 Ekaterinburg (Russian Federation)

2017-04-15

It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 µm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 – 1.2 T to the filling density 2.6 – 3.2×10{sup 3} kg/m{sup 3}. It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×10{sup 3} kg/m{sup 3}, the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with B{sub r} ≥1.34 T, H{sub c} ≥950 kA/m, (BH){sub max} ≥340 kJ/m{sup 3}, and the degree of alignment exceeding 96% were produced. - Highlights: • The pressless process (PLP) in magnet production is studied. • A new method of the loading of powder in an applied DC magnetic field is suggested. • The method allows achieving higher degree of alignment in moderate magnetic field. • Density of sintered magnets is studied experimentally and via DEM simulation. • Low density is caused by the formation of magnetostatic chains of powder particles.

A Multi-Objective Method to Align Human Resource Allocation with University Strategy

Science.gov (United States)

Bouillard, Philippe

2016-01-01

Universities are currently under considerable pressure to reach their stakeholders' expectations. Management tools that use strategic plans, key performance indicators and quality assurance methods are increasingly deployed. This paper aims to demonstrate how resource allocation can be aligned with institutional strategic plans with a very simple…

The CMS Muon System Alignment

CERN Document Server

Martinez Ruiz-Del-Arbol, P

2009-01-01

The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

Exploring Non-Traditional Learning Methods in Virtual and Real-World Environments

Science.gov (United States)

Lukman, Rebeka; Krajnc, Majda

2012-01-01

This paper identifies the commonalities and differences within non-traditional learning methods regarding virtual and real-world environments. The non-traditional learning methods in real-world have been introduced within the following courses: Process Balances, Process Calculation, and Process Synthesis, and within the virtual environment through…

Survey Methods, Traditional, Public Opinion Polling

DEFF Research Database (Denmark)

Elmelund-Præstekær, Christian; Hopmann, David Nicolas; Pedersen, Rasmus Tue

2017-01-01

Traditional public opinion polls are surveys in which a random sample of a given population is asked questions about their attitudes, knowledge, or behavior. If conducted properly, the answers from such surveys are approximately representative of the entire population. Traditional public opinion...... polling is typically based on four different methods of data gathering, or combinations hereof: face-to-face, postal surveys, phone surveys, and web surveys. Given that opinion polls are based on a sample, we cannot be sure that the sample reflects public opinion perfectly, however—even if randomness...... is perfect. Moreover, responses may be highly dependent on the contextual information provided with the question. Also, it may be difficult to capture past or complex causes of attitudes or behavior. In short, surveys are a precise way of measuring public opinion, but they do not come without challenges....

Moving beyond Traditional Methods of Survey Validation

Science.gov (United States)

Maul, Andrew

2017-01-01

In his focus article, "Rethinking Traditional Methods of Survey Validation," published in this issue of "Measurement: Interdisciplinary Research and Perspectives," Andrew Maul wrote that it is commonly believed that self-report, survey-based instruments can be used to measure a wide range of psychological attributes, such as…

A Comparison of Soft-Tissue Implanted Markers and Bony Anatomy Alignments for Image-Guided Treatments of Head-and-Neck Cancers

International Nuclear Information System (INIS)

Zeidan, Omar A.; Huddleston, Adam J.; Lee, Choonik; Langen, Katja M.; Kupelian, Patrick A.; Meeks, Sanford L.; Manon, Rafael R.

2010-01-01

Purpose: To compare the geometric alignments of soft-tissue implanted markers to the traditional bony-based alignments in head-and-neck cancers, on the basis of daily image guidance. Dosimetric impact of the two alignment techniques on target coverage is presented. Methods and Materials: A total of 330 retrospective alignments (5 patients) were performed on daily megavoltage computed tomography (MVCT) image sets using both alignment techniques. Intermarker distances were tracked for all fractions to assess marker interfractional stability. Using a deformable image registration algorithm, target cumulative doses were calculated according to generated shifts on daily MVCT image sets. Target D95 was used as a dosimetric endpoint to evaluate each alignment technique. Results: Intermarker distances overall were stable, with a standard deviation of <1.5 mm for all fractions and no observed temporal trends. Differences in shift magnitudes between both alignment techniques were found to be statistically significant, with a maximum observed difference of 8 mm in a given direction. Evaluation of technique-specific dose coverage based on D95 of target clinical target volume and planning target volume shows small differences (within ±5%) compared with the kilovoltage CT plan. Conclusion: The use of daily MVCT imaging demonstrates that implanted markers in oral tongue and soft-palate cancers are stable localization surrogates. Alignments based on implanted markers generate shifts comparable overall to the traditional bony-based alignment, with no observed systematic difference in magnitude or direction. The cumulative dosimetric impact on target clinical target volume and planning target volume coverage was found to be similar, despite large observed differences in daily alignment shifts between the two techniques.

College Students' Perceptions of the Traditional Lecture Method

Science.gov (United States)

Covill, Amy E.

2011-01-01

Fifty-one college students responded to survey questions regarding their perceptions of the traditional lecture method of instruction that they received in a 200-level psychology course. At a time when many professors are being encouraged to use active learning methods instead of lectures, it is important to consider the students' perspective. Do…

RNA Structural Alignments, Part I

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Gorodkin, Jan

2014-01-01

Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

Word aligned bitmap compression method, data structure, and apparatus

Science.gov (United States)

Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

2004-12-14

The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

Physician-Hospital Alignment in Orthopedic Surgery.

Science.gov (United States)

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.

How do we Take Care of Strategic Alignment?

DEFF Research Database (Denmark)

Simonsen, Jesper

1999-01-01

The article reviews the concept of ‘strategic alignment’ and presents the critique by Ciborra in SJIS (Vol. 9, No. 1) entitled “De profundis? Deconstructing the concept of strategic alignment”. We present a design approach that suggests how designers, conducting design projects in a specific orga...... environmental conditions, business strategies, and plans for IT are changing and hence challenge traditional approaches to strategic alignment. The results from the design project are described and related to IS literature and to Ciborra’s article.......The article reviews the concept of ‘strategic alignment’ and presents the critique by Ciborra in SJIS (Vol. 9, No. 1) entitled “De profundis? Deconstructing the concept of strategic alignment”. We present a design approach that suggests how designers, conducting design projects in a specific...... organization, can take care of and ensure that the design of IT is appropriately aligned with the organization’s overall business strategy. We describe a design project using this approach. The project presented took place in a small public organization. Focusing on alignment as part of the design process had...

Injectable Anisotropic Nanocomposite Hydrogels Direct in Situ Growth and Alignment of Myotubes

International Nuclear Information System (INIS)

De France, Kevin J.; Yager, Kevin G.; Chan, Katelyn J. W.; Corbett, Brandon; Cranston, Emily D.; Hoare, Todd

2017-01-01

Here, while injectable in situ cross-linking hydrogels have attracted increasing attention as minimally invasive tissue scaffolds and controlled delivery systems, their inherently disorganized and isotropic network structure limits their utility in engineering oriented biological tissues. Traditional methods to prepare anisotropic hydrogels are not easily translatable to injectable systems given the need for external equipment to direct anisotropic gel fabrication and/or the required use of temperatures or solvents incompatible with biological systems. Herein, we report a new class of injectable nanocomposite hydrogels based on hydrazone cross-linked poly(oligoethylene glycol methacrylate) and magnetically aligned cellulose nanocrystals (CNCs) capable of encapsulating skeletal muscle myoblasts and promoting their differentiation into highly oriented myotubes in situ. CNC alignment occurs on the same time scale as network gelation and remains fixed after the removal of the magnetic field, enabling concurrent CNC orientation and hydrogel injection. The aligned hydrogels show mechanical and swelling profiles that can be rationally modulated by the degree of CNC alignment and can direct myotube alignment both in two- and three-dimensions following coinjection of the myoblasts with the gel precursor components. As such, these hydrogels represent a critical advancement in anisotropic biomimetic scaffolds that can be generated noninvasively in vivo following simple injection.

Metrology and Alignment of Light Weight Grazing Incidence X-Ray Mirrors

Science.gov (United States)

Zhang, William; Content, David; Petre, Robert; Saha, Timo

2000-01-01

Metrology and alignment of light weight X-ray optics have been a challenge for two reasons: (1) that the intrinsic mirror quality and distortions caused by handling can not be easily separated, and (2) the diffraction limits of the visible light become a severe problem at the order of one arc-minute. Traditional methods of using a normal incident pencil or small parallel beam which monitors a tiny fraction of the mirror in question at a given time can not adequately monitor those distortions. We are developing a normal incidence setup that monitors a large fraction, if not the whole, of the mirror at any given time. It will allow us to align thin X-ray mirrors to-an accuracy of a few arc seconds or to a limit dominated by the mirror intrinsic quality.

Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment.

Science.gov (United States)

Cao, Hu; Lu, Yonggang

2017-01-01

With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities. Accordingly, we propose a new flexible protein structure alignment method based on variable-length AFPs. Compared with other methods, the proposed method possesses three main advantages. First, it is based on variable-length AFPs. The length of each AFP is separately determined to maximally represent a local similar structure fragment, which reduces the number of AFPs. Second, it uses local coordinate systems, which simplify the computation at each step of the expansion of AFPs during the AFP identification. Third, it decreases the number of twists by rewarding the situation where nonconsecutive AFPs share the same transformation in the alignment, which is realized by dynamic programming with an improved transition function. The experimental data show that compared with FlexProt, FATCAT, and FlexSnap, the proposed method can achieve comparable results by introducing fewer twists. Meanwhile, it can generate results similar to those of the FATCAT method in much less running time due to the reduced number of AFPs.

Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

Science.gov (United States)

Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

2017-09-01

Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

Alignment for CSR

International Nuclear Information System (INIS)

Wang Shoujin; Man Kaidi; Guo Yizhen; Cai Guozhu; Guo Yuhui

2002-01-01

Cooled Storage Ring of Heavy Ion Research Facility in Lanzhou (HIRFL-CSR) belongs to China great scientific project in China. The alignment for it is very difficult because of very large area and very high accuracy. For the special case in HIRFL-CSR, some new methods and new instruments are used, including the construction of survey control network, the usage of laser tracker, and CSR alignment database system with applications developed to store and analyze data. The author describes the whole procedure of CSR alignment

A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

Science.gov (United States)

Kawata, Masaaki; Sato, Chikara

2007-06-01

In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

libgapmis: extending short-read alignments.

Science.gov (United States)

Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

2013-01-01

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. 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. We present libgapmis, a library for extending pairwise short-read alignments. We

SRF cavity alignment detection method using beam-induced HOM with curved beam orbit

Science.gov (United States)

Hattori, Ayaka; Hayano, Hitoshi

2017-09-01

We have developed a method to obtain mechanical centers of nine cell superconducting radio frequency (SRF) cavities from localized dipole modes, that is one of the higher order modes (HOM) induced by low-energy beams. It is to be noted that low-energy beams, which are used as alignment probes, are easy to bend in fringe fields of accelerator cavities. The estimation of the beam passing orbit is important because only information about the beam positions measured by beam position monitors outside the cavities is available. In this case, the alignment information about the cavities can be obtained by optimizing the parameters of the acceleration components over the beam orbit simulation to consistently represent the position of the beam position monitors measured at every beam sweep. We discuss details of the orbit estimation method, and estimate the mechanical center of the localized modes through experiments performed at the STF accelerator. The mechanical center is determined as (x , y) =(0 . 44 ± 0 . 56 mm , - 1 . 95 ± 0 . 40 mm) . We also discuss the error and the applicable range of this method.

Design of an Image-Servo Mask Alignment System Using Dual CCDs with an XXY Stage

Directory of Open Access Journals (Sweden)

Chih-Jer Lin

2016-02-01

Full Text Available Mask alignment of photolithography technology is used in many applications, such as micro electro mechanical systems’ semiconductor process, printed circuits board, and flat panel display. As the dimensions of the product are getting smaller and smaller, the automatic mask alignment of photolithography is becoming more and more important. The traditional stacked XY-Θz stage is heavy and it has cumulative flatness errors due to its stacked assembly mechanism. The XXY stage has smaller cumulative error due to its coplanar design and it can move faster than the traditional XY-Θz stage. However, the relationship between the XXY stage’s movement and the commands of the three motors is difficult to compute, because the movements of the three motors on the same plane are coupling. Therefore, an artificial neural network is studied to establish a nonlinear mapping from the desired position and orientation of the stage to three motors’ commands. Further, this paper proposes an image-servo automatic mask alignment system, which consists of a coplanar XXY stage, dual GIGA-E CCDs with lens and a programmable automatic controller (PAC. Before preforming the compensation, a self-developed visual-servo provides the positioning information which is obtained from the image processing and pattern recognition according to the specified fiducial marks. To obtain better precision, two methods including the center of gravity method and the generalize Hough Transformation are studied to correct the shift positioning error.

Texture zeros and hierarchical masses from flavour (mis)alignment

Science.gov (United States)

Hollik, W. G.; Saldana-Salazar, U. J.

2018-03-01

We introduce an unconventional interpretation of the fermion mass matrix elements. As the full rotational freedom of the gauge-kinetic terms renders a set of infinite bases called weak bases, basis-dependent structures as mass matrices are unphysical. Matrix invariants, on the other hand, provide a set of basis-independent objects which are of more relevance. We employ one of these invariants to give a new parametrisation of the mass matrices. By virtue of it, one gains control over its implicit implications on several mass matrix structures. The key element is the trace invariant which resembles the equation of a hypersphere with a radius equal to the Frobenius norm of the mass matrix. With the concepts of alignment or misalignment we can identify texture zeros with certain alignments whereas Froggatt-Nielsen structures in the matrix elements are governed by misalignment. This method allows further insights of traditional approaches to the underlying flavour geometry.

Aligning English Language Testing with Curriculum

Science.gov (United States)

Palacio, Marcela; Gaviria, Sandra; Brown, James Dean

2016-01-01

Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia) to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an…

An assessment of existing common traditional methods of water ...

African Journals Online (AJOL)

Classical water purification methods include boiling, filtration, irradiation and the use of chemicals while traditional water purification methods in use are boiling, filtration, sedimentation, long storage and solar radiation. Waterborne diseases are m ore common in the rural communities where potable water supply coverage ...

Geodetic alignment of laser power installations

International Nuclear Information System (INIS)

Shtorm, V.V.; Gostev, A.M.; Drobikov, A.V.

1989-01-01

Main problems occuring in applied geodesy under initial alignment of laser power installation optical channel are considered. Attention is paid to alignment of lens beamguide telescopic pairs and alignment quality control. Methods and means of geodetic measurements under alignment are indicated. Conclusions are made about the degree of working through certain aspects of the problem

Word aligned bitmap compression method, data structure, and apparatus

Energy Technology Data Exchange (ETDEWEB)

Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

2004-12-14

The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

Self-learning computers for surgical planning and prediction of postoperative alignment.

Science.gov (United States)

Lafage, Renaud; Pesenti, Sébastien; Lafage, Virginie; Schwab, Frank J

2018-02-01

In past decades, the role of sagittal alignment has been widely demonstrated in the setting of spinal conditions. As several parameters can be affected, identifying the driver of the deformity is the cornerstone of a successful treatment approach. Despite the importance of restoring sagittal alignment for optimizing outcome, this task remains challenging. Self-learning computers and optimized algorithms are of great interest in spine surgery as in that they facilitate better planning and prediction of postoperative alignment. Nowadays, computer-assisted tools are part of surgeons' daily practice; however, the use of such tools remains to be time-consuming. NARRATIVE REVIEW AND RESULTS: Computer-assisted methods for the prediction of postoperative alignment consist of a three step analysis: identification of anatomical landmark, definition of alignment objectives, and simulation of surgery. Recently, complex rules for the prediction of alignment have been proposed. Even though this kind of work leads to more personalized objectives, the number of parameters involved renders it difficult for clinical use, stressing the importance of developing computer-assisted tools. The evolution of our current technology, including machine learning and other types of advanced algorithms, will provide powerful tools that could be useful in improving surgical outcomes and alignment prediction. These tools can combine different types of advanced technologies, such as image recognition and shape modeling, and using this technique, computer-assisted methods are able to predict spinal shape. The development of powerful computer-assisted methods involves the integration of several sources of information such as radiographic parameters (X-rays, MRI, CT scan, etc.), demographic information, and unusual non-osseous parameters (muscle quality, proprioception, gait analysis data). In using a larger set of data, these methods will aim to mimic what is actually done by spine surgeons, leading

Establishment of 3D culture and induction of osteogenic differentiation of pre-osteoblasts using wet-collected aligned scaffolds

Energy Technology Data Exchange (ETDEWEB)

Ding, Huifen [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Chongqing Affiliated Hospital of Stomatology, Chongqing University of Medical Sciences, Chongqing 400015 (China); Zhong, Junwen [Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China); Xu, Fei; Song, Fangfang; Yin, Miao; Wu, Yanru; Hu, Qiyi [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Wang, Jiawei, E-mail: wangjwei@hotmail.com [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China)

2017-02-01

Aligned fibrous scaffolds have attracted much interest in bone tissue engineering, because they are supposed to induce osteogenic differentiation. For the first time, aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. Moreover, three-dimensional (3D) culture of MC3T3-E1 pre-osteoblasts was established on these fibrous scaffolds. Physicochemical properties of the scaffolds and the behaviour of MC3T3-E1 pre-osteoblasts on the scaffolds were analysed and compared with scaffolds obtained using traditional method. Ethanol bath improved the uniformity and alignment of the fibres and increased the thickness and porosity of the scaffolds. Structures of the fibres were well maintained after immediate crosslinking in ethanol. Cells on the wet-collected scaffolds exhibited more ordered arrangement and elongated morphology as well as faster and deeper infiltration. The ordered infiltration resulted in the establishment of the 3D culture of cells, promoting proliferation and osteogenic differentiation of the pre-osteoblasts. Thus, the wet-collected aligned scaffolds with improved topographical and physicochemical properties presents significant potential application in bone regeneration. - Highlights: • Aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. • Structural properties of the aligned nanofibres were improved. • Three-dimensional culture of MC3T3-E1 pre-osteoblasts was established. • The arrangement, morphology, infiltration, proliferation and osteogenic differentiation of cells were enhanced.

Interconnection blocks: a method for providing reusable, rapid, multiple, aligned and planar microfluidic interconnections

DEFF Research Database (Denmark)

Sabourin, David; Snakenborg, Detlef; Dufva, Hans Martin

2009-01-01

In this paper a method is presented for creating 'interconnection blocks' that are re-usable and provide multiple, aligned and planar microfluidic interconnections. Interconnection blocks made from polydimethylsiloxane allow rapid testing of microfluidic chips and unobstructed microfluidic observ...

Stochastic sampling of the RNA structural alignment space.

Science.gov (United States)

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

2009-07-01

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

Novel method for the production of spin-aligned RI beams in projectile fragmentation reaction with the dispersion matching technique

Energy Technology Data Exchange (ETDEWEB)

Ichikawa, Y., E-mail: yuichikawa@phys.titech.ac.jp [Tokyo Institute of Technology, Department of Physics (Japan); Ueno, H. [RIKEN Nishina Center (Japan); Ishii, Y. [Tokyo Institute of Technology, Department of Physics (Japan); Furukawa, T. [Tokyo Metropolitan University, Department of Physics (Japan); Yoshimi, A. [Okayama University, Research Core for Extreme Quantum World (Japan); Kameda, D.; Watanabe, H.; Aoi, N. [RIKEN Nishina Center (Japan); Asahi, K. [Tokyo Institute of Technology, Department of Physics (Japan); Balabanski, D. L. [Bulgarian Academy of Sciences, Institute for Nuclear Research and Nuclear Energy (Bulgaria); Chevrier, R.; Daugas, J. M. [CEA, DAM, DIF (France); Fukuda, N. [RIKEN Nishina Center (Japan); Georgiev, G. [CSNSM, IN2P3-CNRS, Universite Paris-sud (France); Hayashi, H.; Iijima, H. [Tokyo Institute of Technology, Department of Physics (Japan); Inabe, N. [RIKEN Nishina Center (Japan); Inoue, T. [Tokyo Institute of Technology, Department of Physics (Japan); Ishihara, M.; Kubo, T. [RIKEN Nishina Center (Japan); and others

2013-05-15

A novel method to produce spin-aligned rare-isotope (RI) beam has been developed, that is the two-step projectile fragmentation method with a technique of dispersion matching. The present method was verified in an experiment at the RIKEN RIBF, where an RI beam of {sup 32}Al with spin alignment of 8(1) % was successfully produced from a primary beam of {sup 48}Ca, with {sup 33}Al as an intermediate nucleus. Figure of merit of the present method was found to be improved by a factor larger than 50 compared with a conventional method employing single-step projectile fragmentation.

Thin concentrator photovoltaic module with micro-solar cells which are mounted by self-align method using surface tension of melted solder

Science.gov (United States)

Hayashi, Nobuhiko; Terauchi, Masaharu; Aya, Youichirou; Kanayama, Shutetsu; Nishitani, Hikaru; Nakagawa, Tohru; Takase, Michihiko

2017-09-01

We are developing a thin and lightweight CPV module using small size lens system made from poly methyl methacrylate (PMMA) with a short focal length and micro-solar cells to decrease the transporting and the installing costs of CPV systems. In order to achieve high conversion efficiency in CPV modules using micro-solar cells, the micro-solar cells need to be mounted accurately to the irradiated region of the concentrated sunlight. In this study, we have successfully developed self-align method thanks to the surface tension of the melted solder even utilizing commercially available surface-mounting technology (SMT). Solar cells were self-aligned to the specified positions of the circuit board by this self-align method with accuracy within ±10 µm. We actually fabricated CPV modules using this self-align method and demonstrated high conversion efficiency of our CPV module.

Synthesis and assessment methods for an edge-alignment-free hybrid image

Science.gov (United States)

Sripian, Peeraya; Yamaguchi, Yasushi

2017-07-01

A hybrid image allows multiple image interpretations to be modulated by the viewing distance. It can be constructed on the basis of the multiscale perceptual mechanisms of the human visual system by combining the low and high spatial frequencies of two different images. The hybrid image was introduced as an experimental tool for visual recognition study in terms of spatial frequency perception. To produce a compelling hybrid image, the original hybrid image synthesis method could only use similar shapes of source images that were aligned in the edges. If any two different images can be hybrid, it would be beneficial as a new experimental tool. In addition, there is no measure for the actual perception of spatial frequency, whether a single spatial frequency or both spatial frequencies are perceived from the hybrid stimulus. This paper describes two methods for synthesizing a hybrid image from dissimilar shape images or unaligned images; this hybrid image is known as an "edge-alignment-free hybrid image." A noise-inserted method can be done by intentionally inserting and enhancing noises into the high-frequency image. With this method, the low-frequency blobs are covered with high-frequency noises when viewed up close. A color-inserted method uses complementary color gratings in the background of the high-frequency image to emphasize the high-frequency image when viewed up close, whereas the gratings disappear when viewed from far away. To ascertain that our approach successfully separates the spatial frequency at each viewing distance, we measured this property using our proposed assessment method. Our proposed method allows the experimenter to quantify the probability of perceiving both spatial frequencies and a single spatial frequency in a hybrid image. The experimental results confirmed that our proposed synthesis methods successfully hid the low-frequency image and emphasized the high-frequency image at a close viewing distance. At the same time, the

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

Science.gov (United States)

Anguita, A; García-Remesal, M; de la Iglesia, D; Graf, N; Maojo, V

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional

An alignment-free method to find similarity among protein sequences via the general form of Chou's pseudo amino acid composition.

Science.gov (United States)

Gupta, M K; Niyogi, R; Misra, M

2013-01-01

In this paper, we propose a method to create the 60-dimensional feature vector for protein sequences via the general form of pseudo amino acid composition. The construction of the feature vector is based on the contents of amino acids, total distance of each amino acid from the first amino acid in the protein sequence and the distribution of 20 amino acids. The obtained cosine distance metric (also called the similarity matrix) is used to construct the phylogenetic tree by the neighbour joining method. In order to show the applicability of our approach, we tested it on three proteins: 1) ND5 protein sequences from nine species, 2) ND6 protein sequences from eight species, and 3) 50 coronavirus spike proteins. The results are in agreement with known history and the output from the multiple sequence alignment program ClustalW, which is widely used. We have also compared our phylogenetic results with six other recently proposed alignment-free methods. These comparisons show that our proposed method gives a more consistent biological relationship than the others. In addition, the time complexity is linear and space required is less as compared with other alignment-free methods that use graphical representation. It should be noted that the multiple sequence alignment method has exponential time complexity.

[Applications of mathematical statistics methods on compatibility researches of traditional Chinese medicines formulae].

Science.gov (United States)

Mai, Lan-Yin; Li, Yi-Xuan; Chen, Yong; Xie, Zhen; Li, Jie; Zhong, Ming-Yu

2014-05-01

The compatibility of traditional Chinese medicines (TCMs) formulae containing enormous information, is a complex component system. Applications of mathematical statistics methods on the compatibility researches of traditional Chinese medicines formulae have great significance for promoting the modernization of traditional Chinese medicines and improving clinical efficacies and optimizations of formulae. As a tool for quantitative analysis, data inference and exploring inherent rules of substances, the mathematical statistics method can be used to reveal the working mechanisms of the compatibility of traditional Chinese medicines formulae in qualitatively and quantitatively. By reviewing studies based on the applications of mathematical statistics methods, this paper were summarized from perspective of dosages optimization, efficacies and changes of chemical components as well as the rules of incompatibility and contraindication of formulae, will provide the references for further studying and revealing the working mechanisms and the connotations of traditional Chinese medicines.

Fine-tuning structural RNA alignments in the twilight zone

Directory of Open Access Journals (Sweden)

Schirmer Stefanie

2010-04-01

Full Text Available Abstract Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Reasons for using traditional methods and role of nurses in family planning.

Science.gov (United States)

Yurdakul, Mine; Vural, Gülsen

2002-05-01

The withdrawal method and other traditional methods of contraception are still used in Turkey. Ninety-eight percent of women in Turkey know about modern family planning methods and where to find contraceptives. In fact, only one in every three women uses an effective method. The aim of this descriptive and experimental study was to investigate reasons for using traditional methods and the role of nurses in family planning. The women included in the sample were visited in their homes by nurses and educated for family planning in four sessions. Overall, 53.3% of women were using an effective method. However, 54.3% of women living in the Sirintepe district and 41.6% of women living in the Yenikent district were still using the traditional methods they used before. After the education sessions, the most widely used method was found to be intrauterine device (22.8%) in Sirintepe and condom (25%) in Yenikent. There was a significant difference in family planning methods between these two districts (p < 0.001).

Method to evaluate steering and alignment algorithms for controlling emittance growth

International Nuclear Information System (INIS)

Adolphsen, C.; Raubenheimer, T.

1993-04-01

Future linear colliders will likely use sophisticated beam-based alignment and/or steering algorithms to control the growth of the beam emittance in the linac. In this paper, a mathematical framework is presented which simplifies the evaluation of the effectiveness of these algorithms. As an application, a quad alignment that uses beam data taken with the nominal linac optics, and with a scaled optics, is evaluated in terms of the dispersive emittance growth remaining after alignment

Comparison of traditional physico-chemical methods and molecular ...

African Journals Online (AJOL)

This study was aim to review the efficiency of molecular markers and traditional physico-chemical methods for the identification of basmati rice. The study involved 44 promising varieties of Indica rices collected from geographically distant places and adapted to irrigated and aerobic agro-ecosystems. Quality data for ...

Traditional methods of social control in Afikpo north local ...

African Journals Online (AJOL)

Traditional methods of social control in Afikpo north local government area, Ebonyi state south eastern Nigeria. ... Journal of Religion and Human Relations ... simple percentage was used in presenting and interpreting the quantitative data.

Comparison the Students Satisfaction of Traditional and Integrated Teaching Method in Physiology Course

Directory of Open Access Journals (Sweden)

Keshavarzi Z.

2016-02-01

Full Text Available Aims: Different education methods play crucial roles to improve education quality and students’ satisfaction. In the recent years, medical education highly changes through new education methods. The aim of this study was to compare medical students’ satisfaction in traditional and integrated methods of teaching physiology course. Instrument and Methods: In the descriptive analysis study, fifty 4th semester medical students of Bojnourd University of Medical Sciences were studied in 2015. The subjects were randomly selected based on availability. Data was collected by two researcher-made questionnaires; their validity and reliability were confirmed. Questionnaure 1 was completed by the students after presenting renal and endocrinology topics via traditional and integrated methods. Questionnaire 2 was only completed by the students after presenting the course via integrated method. Data was analyzed by SPSS 16 software using dependent T test. Findings: Mean score of the students’ satisfaction in traditional method (24.80±3.48 was higher than integrated method (22.30±4.03; p<0.0001. In the integrated method, most of the students were agreed and completely agreed on telling stories from daily life (76%, sitting mode in the classroom (48%, an attribution of cell roles to the students (60%, showing movies and animations (76%, using models (84%, and using real animal parts (72% during teaching, as well as expressing clinical items to enhance learning motivations (76%. Conclusion: Favorable satisfaction of the students in traditional lecture method to understand the issues, as well as their acceptance of new and active methods of learning, show effectiveness and efficiency of traditional method and the requirement of its enhancement by the integrated methods. 

Nova laser alignment control system

International Nuclear Information System (INIS)

Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

1984-01-01

Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system

Laser alignment of rotating equipment at PNL

International Nuclear Information System (INIS)

Berndt, R.H.

1994-05-01

Lateral vibration in direct-drive equipment is usually caused by misalignment. Over the years, because of the need to improve on techniques and ways of working more efficiently, various types of alignment methods have evolved. In the beginning, craftsmen used a straight-edge scale across the coupling with a feeler gauge measuring the misalignment error. This is still preferred today for aligning small couplings. The industry has since decided that alignment of large direct-drive equipment needed a more accurate type of instrumentation. Rim and face is another of the first alignment methods and is used on all sizes of equipment. A disadvantage of the rim and face method is that in most cases the coupling has to be disassembled. This can cause alignment problems when the coupling is reassembled. Also, the rim and face method is not fast enough to work satisfactorily on alignment of thermally hot equipment. Another concern is that the coupling has to be manufactured accurately for correct rim and face readings. Reverse dial alignment is an improvement over the rim and face method, and depending on the operator's experience, this method can be very accurate. A good training program along with field experience will bring the operator to a proper level of proficiency for a successful program. A hand-held computer with reverse dial calculations in memory is a must for job efficiency. An advantage over the rim and face method is that the coupling is not disassembled and remains locked together. Reverse dial instrumentation measures from both shaft center lines, rather than the coupling surface so the machining of the coupling during manufacture is not a major concern

Semiautomated improvement of RNA alignments

DEFF Research Database (Denmark)

Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

2007-01-01

connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

Alignment technology and applications of liquid crystal devices

CERN Document Server

Takatoh, Kohki; Hasegawa, Ray; Koden, Mitsushiro; Itoh, Nobuyuki; Hasegawa, Masaki

2005-01-01

Alignment phenomena are characteristic of liquid crystalline materials, and understanding them is critically important in understanding the essential features and behavior of liquid crystals and the performance of Liquid Crystal Devices (LCDs). Furthermore, in LCD production lines, the alignment process is of practical importance. Alignment Technologies and Applications of Liquid Crystal Devices demonstrates both the fundamental and practical aspects of alignment phenomena in liquid crystals. The physical basis of alignment phenomena is first introduced in order to aid the understanding of the various physical phenomena observed in the interface between liquid crystalline materials and alignment layer surfaces. Methods for the characterization of surfaces, which induce the alignment phenomena, and of the alignment layer itself are introduced. These methods are useful for the research of liquid crystalline materials and devices in academic research as well as in industry. In the practical sections, the alignme...

Intravenous catheter training system: computer-based education versus traditional learning methods.

Science.gov (United States)

Engum, Scott A; Jeffries, Pamela; Fisher, Lisa

2003-07-01

Virtual reality simulators allow trainees to practice techniques without consequences, reduce potential risk associated with training, minimize animal use, and help to develop standards and optimize procedures. Current intravenous (IV) catheter placement training methods utilize plastic arms, however, the lack of variability can diminish the educational stimulus for the student. This study compares the effectiveness of an interactive, multimedia, virtual reality computer IV catheter simulator with a traditional laboratory experience of teaching IV venipuncture skills to both nursing and medical students. A randomized, pretest-posttest experimental design was employed. A total of 163 participants, 70 baccalaureate nursing students and 93 third-year medical students beginning their fundamental skills training were recruited. The students ranged in age from 20 to 55 years (mean 25). Fifty-eight percent were female and 68% percent perceived themselves as having average computer skills (25% declaring excellence). The methods of IV catheter education compared included a traditional method of instruction involving a scripted self-study module which involved a 10-minute videotape, instructor demonstration, and hands-on-experience using plastic mannequin arms. The second method involved an interactive multimedia, commercially made computer catheter simulator program utilizing virtual reality (CathSim). The pretest scores were similar between the computer and the traditional laboratory group. There was a significant improvement in cognitive gains, student satisfaction, and documentation of the procedure with the traditional laboratory group compared with the computer catheter simulator group. Both groups were similar in their ability to demonstrate the skill correctly. CONCLUSIONS; This evaluation and assessment was an initial effort to assess new teaching methodologies related to intravenous catheter placement and their effects on student learning outcomes and behaviors

Prevalence of depressive symptoms among medical students taught using problem-based learning versus traditional methods.

Science.gov (United States)

Aragão, José Aderval; Freire, Marianna Ribeiro de Menezes; Nolasco Farias, Lucas Guimarães; Diniz, Sarah Santana; Sant'anna Aragão, Felipe Matheus; Sant'anna Aragão, Iapunira Catarina; Lima, Tarcisio Brandão; Reis, Francisco Prado

2018-06-01

To compare depressive symptoms among medical students taught using problem-based learning (PBL) and the traditional method. Beck's Depression Inventory was applied to 215 medical students. The prevalence of depression was calculated as the number of individuals with depression divided by the total number in the sample from each course, with 95% confidence intervals. The statistical significance level used was 5% (p ≤ .05). Among the 215 students, 52.1% were male and 47.9% were female; and 51.6% were being taught using PBL methodology and 48.4% using traditional methods. The prevalence of depression was 29.73% with PBL and 22.12% with traditional methods. There was higher prevalence among females: 32.8% with PBL and 23.1% with traditional methods. The prevalence of depression with PBL among students up to 21 years of age was 29.4% and among those over 21 years, 32.1%. With traditional methods among students up to 21 years of age, it was 16.7%%, and among those over 21 years, 30.1%. The prevalence of depression with PBL was highest among students in the second semester and with traditional methods, in the eighth. Depressive symptoms were highly prevalent among students taught both with PBL and with traditional methods.

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng

2015-09-09

To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

NGSS-Aligned, K-12 Climate Science Curricula, taught with citizen science and teacher-led inquiry methods

Science.gov (United States)

Zainfeld, S.

2017-12-01

Teacher-led inquiry into student learning is a promising method of formative assessment to gain insight into student achievement. NGSS-aligned K-12 Climate Science curricula taught with citizen science and teacher-led inquiry methods are described, along with results from a scientist-teacher collaboration survey.

Comparison of student success using "atoms first" versus "traditional" curricula

Science.gov (United States)

Hillesheim, Christina S.

The purpose of this study was to investigate the difference between the "atoms first" and the "traditional" curricula. Specifically focusing on which curriculum better aligns to curricular expectations, leads to higher student success when students are grouped together, and when students are differentiated based on several factors. The main difference between the two approaches being the sequence of topics presented in the first semester general chemistry course. This study involves more than 9,500 general chemistry I and II students over 7 semesters with about half of them being taught using the "atoms first" approach. Student success was measured using the American Chemical Society's (ACS) final examination scores and the final letter grades. Alignment to curricular expectations was determined via a qualitative review of textbooks written for each of the approaches. This showed that the "atoms first" approach better aligns to research supported best practices. An analysis of covariance (ANCOVA) was performed to determine if there is a significant difference between the "atoms first" and the "traditional" curricula. The "traditional" approach was found to lead to higher student achievement for both measures of student success in both chemistry I and II courses. Lastly, multiple linear, multinomial logistic, and binary logistic regressions were run using all of the subgroups---gender, race/ethnicity, major, ACT composite, math ACT, overall GPA, and classroom size---as predictor variables to determine if any significant interactions between the curricular methods and the different subgroups existed. Results found that the relationship between gender, GPA, and classroom size groupings significantly impact student achievement in general chemistry. Specifically, the "traditional" approach lead to higher student success compared to the "atoms first" approach for males, females, below average GPA students, above average GPA students, and students in large classroom

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

Alignment performance monitoring for ASML systems

Science.gov (United States)

Chung, Woong-Jae; Temchenko, Vlad; Hauck, Tarja; Schmidt, Sebastian

2006-03-01

In today's semiconductor industry downscaling of the IC design puts a stringent requirement on pattern overlay control. Tighter overlay requirements lead to exceedingly higher rework rates, meaning additional costs to manufacturing. Better alignment control became a target of engineering efforts to decrease rework rate for high-end technologies. Overlay performance is influenced by known parameters such as "Shift, Scaling, Rotation, etc", and unknown parameters defined as "Process Induced Variation", which are difficult to control by means of a process automation system. In reality, this process-induced variation leads to a strong wafer to wafer, or lot to lot variation, which are not easy to detect in the mass-production environment which uses sampling overlay measurements for only several wafers in a lot. An engineering task of finding and correcting a root cause for Process Induced Variations of overlay performance will be greatly simplified if the unknown parameters could be tracked for each wafer. This paper introduces an alignment performance monitoring method based on analysis of automatically generated "AWE" files for ASML scanner systems. Because "AWE" files include alignment results for each aligned wafer, it is possible to use them for monitoring, controlling and correcting the causes of "process induced" overlay performance without requiring extra measurement time. Since "AWE" files include alignment information for different alignment marks, it is also possible to select and optimize the best alignment recipe for each alignment strategy. Several case studies provided in our paper will demonstrate how AWE file analysis can be used to assist engineer in interpreting pattern alignment data. Since implementing our alignment data monitoring method, we were able to achieve significant improvement of alignment and overlay performance without additional overlay measurement time. We also noticed that the rework rate coming from alignment went down and

The alignment of carbon nanotubes: an effective route to extend their excellent properties to macroscopic scale.

Science.gov (United States)

Sun, Xuemei; Chen, Tao; Yang, Zhibin; Peng, Huisheng

2013-02-19

-standing problems from the traditional mechanical rubbing method, which include production of broken debris and structure damage during fabrication and building up electrostatic charge during use. Aligning MWCNTs induces a conformational change in polydiacetylene, which causes the composite fibers to be electrochromatic, a previously unknown reaction in chromatic polymers. Due to their large surface area, flexibility, electrical conductivity, and remarkable electrocatalytic activity, aligned MWCNT films can be used as counter electrodes to produce highly efficient dye-sensitized solar cells. In addition, chemists have developed new electrodes from the aligned MWCNT fibers to make a family of high-performing, wire-shaped dye-sensitized solar cells.

Feature-based Alignment of Volumetric Multi-modal Images

Science.gov (United States)

Toews, Matthew; Zöllei, Lilla; Wells, William M.

2014-01-01

This paper proposes a method for aligning image volumes acquired from different imaging modalities (e.g. MR, CT) based on 3D scale-invariant image features. A novel method for encoding invariant feature geometry and appearance is developed, based on the assumption of locally linear intensity relationships, providing a solution to poor repeatability of feature detection in different image modalities. The encoding method is incorporated into a probabilistic feature-based model for multi-modal image alignment. The model parameters are estimated via a group-wise alignment algorithm, that iteratively alternates between estimating a feature-based model from feature data, then realigning feature data to the model, converging to a stable alignment solution with few pre-processing or pre-alignment requirements. The resulting model can be used to align multi-modal image data with the benefits of invariant feature correspondence: globally optimal solutions, high efficiency and low memory usage. The method is tested on the difficult RIRE data set of CT, T1, T2, PD and MP-RAGE brain images of subjects exhibiting significant inter-subject variability due to pathology. PMID:24683955

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez and Y. Pakhotin

2012-01-01

  A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

Bacterial population in traditional sourdough evaluated by molecular methods

NARCIS (Netherlands)

Randazzo, C.L.; Heilig, G.H.J.; Restuccia, C.; Giudici, P.; Caggia, C.

2005-01-01

Aims: To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Methods and Results: Forty-five LAB isolates were

Traditional acupuncturists and higher education in Britain: the dual, paradoxical impact of biomedical alignment on the holistic view.

Science.gov (United States)

Givati, Assaf; Hatton, Kieron

2015-04-01

Traditional acupuncturists' quest for external legitimacy in Britain involves the standardization of their knowledge bases through the development of training schools and syllabi, formal educational structures, and, since the 1990s, the teaching of undergraduate courses within (or validated by) Higher Education Institutions (HEIs), a process which entails biomedical alignment of the curriculum. However, as holistic discourses were commonly used as a rhetorical strategy by CAM practitioners to distance themselves from biomedicine and as a source of public appeal, this 'mainstreaming' process evoked practitioners' concerns that their holistic claims are being compromised. An additional challenge is being posed by a group of academics and scientists in Britain who launched an attack on CAM courses taught in HEIs, accusing them of being 'unscientific' and 'non-academic' in nature. This paper explores the negotiation of all these challenges during the formalization of traditional acupuncture education in Britain, with a particular focus on the role of HEIs. The in-depth qualitative investigation draws on several data sets: participant observation in a university validated acupuncture course; in-depth interviews; and documentary analysis. The findings show how, as part of the formalization process, acupuncturists in Britain (re)negotiate their holistic, anti-reductionist discourses and claims in relation to contemporary societal, political and cultural forces. Moreover, the teaching and validation of acupuncture courses by HEIs may contribute to broadening acupuncturists' 'holistic awareness' of societal and cultural influences on individuals' and communities' ill-health. This investigation emphasises the dynamic and context-specific (rather than fixed and essentialized) nature of acupuncture practice and knowledge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computer game-based and traditional learning method: a comparison regarding students' knowledge retention.

Science.gov (United States)

Rondon, Silmara; Sassi, Fernanda Chiarion; Furquim de Andrade, Claudia Regina

2013-02-25

Educational computer games are examples of computer-assisted learning objects, representing an educational strategy of growing interest. Given the changes in the digital world over the last decades, students of the current generation expect technology to be used in advancing their learning requiring a need to change traditional passive learning methodologies to an active multisensory experimental learning methodology. The objective of this study was to compare a computer game-based learning method with a traditional learning method, regarding learning gains and knowledge retention, as means of teaching head and neck Anatomy and Physiology to Speech-Language and Hearing pathology undergraduate students. Students were randomized to participate to one of the learning methods and the data analyst was blinded to which method of learning the students had received. Students' prior knowledge (i.e. before undergoing the learning method), short-term knowledge retention and long-term knowledge retention (i.e. six months after undergoing the learning method) were assessed with a multiple choice questionnaire. Students' performance was compared considering the three moments of assessment for both for the mean total score and for separated mean scores for Anatomy questions and for Physiology questions. Students that received the game-based method performed better in the pos-test assessment only when considering the Anatomy questions section. Students that received the traditional lecture performed better in both post-test and long-term post-test when considering the Anatomy and Physiology questions. The game-based learning method is comparable to the traditional learning method in general and in short-term gains, while the traditional lecture still seems to be more effective to improve students' short and long-term knowledge retention.

How often do patients in primary care use the methods of traditional medicine

Directory of Open Access Journals (Sweden)

Petrov-Kiurski Miloranka

2014-01-01

Full Text Available Introduction: Traditional medicine is a comprehensive system of theory and practice, implemented in the prevention, diagnostics and treatment of diseases, which utilizes preparations of vegetable, animal and mineral origin, as well as methods of spiritual therapy Objective: 1. To estimate how many patients in primary care use traditional medicine for diagnostics, treatment and prevention of diseases, and to establish possible differences regarding gender, age and urban or rural location. 2. What methods of traditional medicine are the most often used, and for which diseases and conditions? 3. Why did the subjects opted for this type of treatment, and what was the effect of the therapy? Method: Multicentric research based on interviewing patients in five outpatient health centers in Serbia. As a survey instrument was used a questionnaire with 10 questions. Results: The study included 1157 subjects, 683 women and 474 men, mean age 60.22±14.54, The traditional medicine was used by 83.66% (79.96% males and 86.245% females. Information about the methods of traditional medicine subjects usually received from their friends and acquaintances (54.9% and the media (39.3%. There is no significant difference in the way of obtaining information in relation to gender. Information on the internet was obtained more often in subjects younger than 65 (p=0.000 and in urban population (p=0.000. The same is true for information obtained from doctor or pharmacist (p=0.003. They opted for this method because in their opinion it is less harmful and have less adverse effects (72.8%. This type of treatment patients used for treatment of muscles, bone and joint diseases - 28.5%, diseases of the heart and blood vessels -21,1 %, and for the treatment of pain 19.7%. Patients from rural areas more often used traditional medicine for treatment of cardiovascular diseases (p=0.000. Outcome of treatment was good or satisfactory in 45.3%, moderate in 32%, and in 15.8% effect was

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

Science.gov (United States)

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/.

Computer game-based and traditional learning method: a comparison regarding students’ knowledge retention

Directory of Open Access Journals (Sweden)

Rondon Silmara

2013-02-01

Full Text Available Abstract Background Educational computer games are examples of computer-assisted learning objects, representing an educational strategy of growing interest. Given the changes in the digital world over the last decades, students of the current generation expect technology to be used in advancing their learning requiring a need to change traditional passive learning methodologies to an active multisensory experimental learning methodology. The objective of this study was to compare a computer game-based learning method with a traditional learning method, regarding learning gains and knowledge retention, as means of teaching head and neck Anatomy and Physiology to Speech-Language and Hearing pathology undergraduate students. Methods Students were randomized to participate to one of the learning methods and the data analyst was blinded to which method of learning the students had received. Students’ prior knowledge (i.e. before undergoing the learning method, short-term knowledge retention and long-term knowledge retention (i.e. six months after undergoing the learning method were assessed with a multiple choice questionnaire. Students’ performance was compared considering the three moments of assessment for both for the mean total score and for separated mean scores for Anatomy questions and for Physiology questions. Results Students that received the game-based method performed better in the pos-test assessment only when considering the Anatomy questions section. Students that received the traditional lecture performed better in both post-test and long-term post-test when considering the Anatomy and Physiology questions. Conclusions The game-based learning method is comparable to the traditional learning method in general and in short-term gains, while the traditional lecture still seems to be more effective to improve students’ short and long-term knowledge retention.

Analysis of Conflict Centers in Projects Procured with Traditional and Integrated Methods in Nigeria

Directory of Open Access Journals (Sweden)

Martin O. Dada

2012-07-01

Full Text Available Conflicts in any organization can either be functional or dysfunctional and can contribute to or detract from the achievement of organizational or project objectives. This study investigated the frequency and intensity of conflicts, using five conflict centers, on projects executed with either the integrated or traditional method in Nigeria. Questionnaires were administered through purposive and snowballing techniques on 274 projects located in twelve states of Nigeria and Abuja. 94 usable responses were obtained. The collected data were subjected to both descriptive and inferential statistical analysis. In projects procured with traditional methods, conflicts relating to resources for project execution had the greatest frequency, while conflicts around project/client goals had the least frequency. For projects executed with integrated methods, conflicts due to administrative procedures were ranked highest while conflicts due to project/client goals were ranked least. Regarding seriousness of conflict, conflicts due to administrative procedures and resources for project execution were ranked highest respectively for projects procured with traditional and integrated methods. Additionally, in terms of seriousness, personality issues and project/client goals were the least sources of conflict in projects executed with traditional and integrated methods. There were no significant differences in the incidence of conflicts, using the selected conflict centers, between the traditional and integrated procurement methods. There was however significant difference in the intensity or seriousness of conflicts between projects executed with the traditional method and those executed with integrated methods in the following areas: technical issues, administrative matters and personality issues. The study recommends that conscious efforts should be made at teambuilding on projects executed with integrated methods.

Alignment-free phylogeny of whole genomes using underlying subwords

Directory of Open Access Journals (Sweden)

Comin Matteo

2012-12-01

Full Text Available Abstract Background With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment. There are cases where these techniques cannot be applied, for example if two genomes do not share the same set of genes, or if they are not alignable to each other due to low sequence similarity, rearrangements and inversions, or more specifically to their lengths when the organisms belong to different species. For these cases the comparison of complete genomes can be carried out only with ad hoc methods that are usually called alignment-free methods. Methods In this paper we propose a distance function based on subword compositions called Underlying Approach (UA. We prove that the matching statistics, a popular concept in the field of string algorithms able to capture the statistics of common words between two sequences, can be derived from a small set of “independent” subwords, namely the irredundant common subwords. We define a distance-like measure based on these subwords, such that each region of genomes contributes only once, thus avoiding to count shared subwords a multiple number of times. In a nutshell, this filter discards subwords occurring in regions covered by other more significant subwords. Results The Underlying Approach (UA builds a scoring function based on this set of patterns, called underlying. We prove that this set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, we show that the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information. Availability http://www.dei.unipd.it/∼ciompin/main/underlying.html

Identification of the traditional methods of newborn mothers regarding jaundice in Turkey.

Science.gov (United States)

Aydin, Diler; Karaca Ciftci, Esra; Karatas, Hulya

2014-02-01

To detect traditional methods applied for the treatment of newborn jaundice by mothers in Turkey. Traditional methods are generally used in our society. Instead of using medical services, people often use already-known traditional methods to treat the disease. In such cases, the prognosis of the disease generally becomes worse, the treatment period longer and healthcare costs higher, and more medicine is used. A cross-sectional descriptive study. The participants of this study were 229 mothers with newborn babies aged 0-28 days in one university hospital and one public children's hospital in Sanliurfa. The study was conducted between March and May 2012. In this research, the Beliefs and Traditional Methods of Mothers for Jaundice Questionnaire, which was formed by searching the relevant literature, is used as a data collection tool. The data are evaluated by percentage distributions. Mothers apply conventional practices in cases of health problems such as jaundice, and application of these methods is important to mothers. Moreover, mothers reported applying hazardous conventional methods in cases of neonatal jaundice, such as cutting the area between the baby's eyebrows with a blade, cutting the back of the ear and the body and burning the body, which are not applied in different cultures. Education regarding the effects of conventional methods being applied in families should be provided, and the results of this study should serve to guide further studies in assessing the effects of such education. This approach can support beneficial practices involving individual care and prevent the negative health effects of hazardous practices. © 2013 John Wiley & Sons Ltd.

Traditions and Alcohol Use: A Mixed-Methods Analysis

Science.gov (United States)

Castro, Felipe González; Coe, Kathryn

2011-01-01

An integrative mixed-methods analysis examined traditional beliefs as associated with beliefs about self-care during pregnancy and with alcohol abstinence among young adult women from two rural U.S.–Mexico border communities. Quantitative (measured scale) variables and qualitative thematic variables generated from open-ended responses served as within-time predictors of these health-related outcomes. A weaker belief that life is better in big cities was associated with stronger self-care beliefs during pregnancy. Also, a weaker belief that small towns offer tranquil environments was associated with total abstinence from alcohol. Regarding the Hispanic Paradox, these results suggest that a critical appreciation of cultural traditions can be protective, as this avoids stereotypical or idyllic views of urban or rural lifeways, and promotes self-protective beliefs and behaviors. PMID:17967095

Effects of posttreatment skeletal maturity measured with the cervical vertebral maturation method on incisor alignment relapse.

Science.gov (United States)

Fudalej, Piotr; Rothe, Laura E; Bollen, Anne-Marie

2008-08-01

Our aim was to test the hypothesis that relapse of incisor alignment is associated with skeletal maturity at the end of treatment, as assessed with the cervical vertebral maturation (CVM) method. This was a case-control study with information from the postretention database at the University of Washington. Mandibular incisor irregularity (II) at least 10 years out of retention (T3) was used to define the subjects (II >6 mm, relapse group) and the controls (II 0.05). Pretreatment II and postretention time were found to be correlated with long-term incisor stability (P = 0.007 and 0.034, respectively). Sex was not related to relapse (P = 0.33). Maturity of craniofacial structures at the end of treatment evaluated with the CVM method is not associated with long-term stability of incisor alignment.

GapMis: a tool for pairwise sequence alignment with a single gap.

Science.gov (United States)

Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

2013-08-01

Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

Aligning the unalignable: bacteriophage whole genome alignments.

Science.gov (United States)

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).

Note: Non-invasive optical method for rapid determination of alignment degree of oriented nanofibrous layers

Energy Technology Data Exchange (ETDEWEB)

Pokorny, M.; Rebicek, J. [R& D Department, Contipro Biotech s.r.o., 561 02 Dolni Dobrouc (Czech Republic); Klemes, J. [R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic); Kotzianova, A. [R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic); Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno (Czech Republic); Velebny, V. [R& D Department, Contipro Biotech s.r.o., 561 02 Dolni Dobrouc (Czech Republic); R& D Department, Contipro Pharma a.s., 561 02 Dolni Dobrouc (Czech Republic)

2015-10-15

This paper presents a rapid non-destructive method that provides information on the anisotropic internal structure of nanofibrous layers. A laser beam of a wavelength of 632.8 nm is directed at and passes through a nanofibrous layer prepared by electrostatic spinning. Information about the structural arrangement of nanofibers in the layer is directly visible in the form of a diffraction image formed on a projection screen or obtained from measured intensities of the laser beam passing through the sample which are determined by the dependency of the angle of the main direction of polarization of the laser beam on the axis of alignment of nanofibers in the sample. Both optical methods were verified on Polyvinyl alcohol (PVA) nanofibrous layers (fiber diameter of 470 nm) with random, single-axis aligned and crossed structures. The obtained results match the results of commonly used methods which apply the analysis of electron microscope images. The presented simple method not only allows samples to be analysed much more rapidly and without damaging them but it also makes possible the analysis of much larger areas, up to several square millimetres, at the same time.

Note: Non-invasive optical method for rapid determination of alignment degree of oriented nanofibrous layers

International Nuclear Information System (INIS)

Pokorny, M.; Rebicek, J.; Klemes, J.; Kotzianova, A.; Velebny, V.

2015-01-01

This paper presents a rapid non-destructive method that provides information on the anisotropic internal structure of nanofibrous layers. A laser beam of a wavelength of 632.8 nm is directed at and passes through a nanofibrous layer prepared by electrostatic spinning. Information about the structural arrangement of nanofibers in the layer is directly visible in the form of a diffraction image formed on a projection screen or obtained from measured intensities of the laser beam passing through the sample which are determined by the dependency of the angle of the main direction of polarization of the laser beam on the axis of alignment of nanofibers in the sample. Both optical methods were verified on Polyvinyl alcohol (PVA) nanofibrous layers (fiber diameter of 470 nm) with random, single-axis aligned and crossed structures. The obtained results match the results of commonly used methods which apply the analysis of electron microscope images. The presented simple method not only allows samples to be analysed much more rapidly and without damaging them but it also makes possible the analysis of much larger areas, up to several square millimetres, at the same time

[Essential procedure and key methods for survey of traditional knowledge related to Chinese materia medica resources].

Science.gov (United States)

Cheng, Gong; Huang, Lu-qi; Xue, Da-yuan; Zhang, Xiao-bo

2014-12-01

The survey of traditional knowledge related to Chinese materia medica resources is the important component and one of the innovative aspects of the fourth national survey of the Chinese materia medica resources. China has rich traditional knowledge of traditional Chinese medicine (TCM) and the comprehensive investigation of TCM traditional knowledge aims to promote conservation and sustainable use of Chinese materia medica resources. Building upon the field work of pilot investigations, this paper introduces the essential procedures and key methods for conducting the survey of traditional knowledge related to Chinese materia medica resources. The essential procedures are as follows. First is the preparation phrase. It is important to review all relevant literature and provide training to the survey teams so that they have clear understanding of the concept of traditional knowledge and master key survey methods. Second is the field investigation phrase. When conducting field investigations, survey teams should identify the traditional knowledge holders by using the 'snowball method', record the traditional knowledge after obtaining prior informed concerned from the traditional knowledge holders. Researchers should fill out the survey forms provided by the Technical Specification of the Fourth National Survey of Chinese Materia Medica Resources. Researchers should pay particular attention to the scope of traditional knowledge and the method of inheriting the knowledge, which are the key information for traditional knowledge holders and potential users to reach mutual agreed terms to achieve benefit sharing. Third is the data compilation and analysis phrase. Researchers should try to compile and edit the TCM traditional knowledge in accordance with intellectual property rights requirements so that the information collected through the national survey can serve as the basic data for the TCM traditional knowledge database. The key methods of the survey include regional

Aligning English Language Testing With Curriculum

Directory of Open Access Journals (Sweden)

Marcela Palacio

2016-07-01

Full Text Available Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an effort to guarantee the quality of the process of test design. The study included descriptive statistics, item analysis, correlational analyses, reliability estimates, and validity analyses. The results show that the new tests are an excellent addition to the program and an improvement over traditional tests. Implications are discussed and recommendations given for the development of any institutional testing program.

OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

Directory of Open Access Journals (Sweden)

Searle Stephen MJ

2003-10-01

Full Text Available Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. Results The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with http://www.compbio.dundee.ac.uk. Conclusions The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94

Vertically aligned carbon nanotube growth by pulsed laser deposition and thermal chemical vapor deposition methods

International Nuclear Information System (INIS)

Sohn, Jung Inn; Nam, Chunghee; Lee, Seonghoon

2002-01-01

We have grown vertically aligned carbon nanotubes on the various substrates such as a planar p-type Si(1 0 0) wafer, porous Si wafer, SiO 2 , Si 3 N 4 , Al 2 O 3 , and Cr by thermal chemical vapor deposition (CVD) at 800 deg.C, using C 2 H 2 gas as a carbon source and Fe catalyst films deposited by a pulsed laser on the substrates. The Fe films were deposited for 5 min by pulsed laser deposition (PLD). The advantage of Fe deposition by PLD over other deposition methods lies in the superior adhesion of Fe to a Si substrate due to high kinetic energies of the generated Fe species. Scanning electron microscopy (SEM) images show that vertically well-aligned carbon nanotubes are grown on Fe nanoparticles formed from the thermal annealing of the Fe film deposited by PLD on the various substrates. Atomic force microscopy (AFM) images show that the Fe film annealed at 800 deg.C is broken to Fe nanoparticles of 10-50 nm in size. We show that the appropriate density of Fe nanoparticles formed from the thermal annealing of the film deposited by PLD is crucial in growing vertically aligned carbon nanotubes. Using a PLD and a lift-off method, we developed the selective growth of carbon nanotubes on a patterned Fe-coated Si substrate

Multiple network alignment on quantum computers

Science.gov (United States)

Daskin, Anmer; Grama, Ananth; Kais, Sabre

2014-12-01

Comparative analyses of graph-structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given graphs as input, alignment algorithms use topological information to assign a similarity score to each -tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext-Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method and show that it can deliver exponential speedups over conventional (non-quantum) methods.

A New Shape Description Method Using Angular Radial Transform

Science.gov (United States)

Lee, Jong-Min; Kim, Whoi-Yul

Shape is one of the primary low-level image features in content-based image retrieval. In this paper we propose a new shape description method that consists of a rotationally invariant angular radial transform descriptor (IARTD). The IARTD is a feature vector that combines the magnitude and aligned phases of the angular radial transform (ART) coefficients. A phase correction scheme is employed to produce the aligned phase so that the IARTD is invariant to rotation. The distance between two IARTDs is defined by combining differences in the magnitudes and aligned phases. In an experiment using the MPEG-7 shape dataset, the proposed method outperforms existing methods; the average BEP of the proposed method is 57.69%, while the average BEPs of the invariant Zernike moments descriptor and the traditional ART are 41.64% and 36.51%, respectively.

Face Alignment via Regressing Local Binary Features.

Science.gov (United States)

Ren, Shaoqing; Cao, Xudong; Wei, Yichen; Sun, Jian

2016-03-01

This paper presents a highly efficient and accurate regression approach for face alignment. Our approach has two novel components: 1) a set of local binary features and 2) a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. This approach achieves the state-of-the-art results when tested on the most challenging benchmarks to date. Furthermore, because extracting and regressing local binary features are computationally very cheap, our system is much faster than previous methods. It achieves over 3000 frames per second (FPS) on a desktop or 300 FPS on a mobile phone for locating a few dozens of landmarks. We also study a key issue that is important but has received little attention in the previous research, which is the face detector used to initialize alignment. We investigate several face detectors and perform quantitative evaluation on how they affect alignment accuracy. We find that an alignment friendly detector can further greatly boost the accuracy of our alignment method, reducing the error up to 16% relatively. To facilitate practical usage of face detection/alignment methods, we also propose a convenient metric to measure how good a detector is for alignment initialization.

Comparison of Traditional Design Nonlinear Programming Optimization and Stochastic Methods for Structural Design

Science.gov (United States)

Patnaik, Surya N.; Pai, Shantaram S.; Coroneos, Rula M.

2010-01-01

Structural design generated by traditional method, optimization method and the stochastic design concept are compared. In the traditional method, the constraints are manipulated to obtain the design and weight is back calculated. In design optimization, the weight of a structure becomes the merit function with constraints imposed on failure modes and an optimization algorithm is used to generate the solution. Stochastic design concept accounts for uncertainties in loads, material properties, and other parameters and solution is obtained by solving a design optimization problem for a specified reliability. Acceptable solutions were produced by all the three methods. The variation in the weight calculated by the methods was modest. Some variation was noticed in designs calculated by the methods. The variation may be attributed to structural indeterminacy. It is prudent to develop design by all three methods prior to its fabrication. The traditional design method can be improved when the simplified sensitivities of the behavior constraint is used. Such sensitivity can reduce design calculations and may have a potential to unify the traditional and optimization methods. Weight versus reliabilitytraced out an inverted-S-shaped graph. The center of the graph corresponded to mean valued design. A heavy design with weight approaching infinity could be produced for a near-zero rate of failure. Weight can be reduced to a small value for a most failure-prone design. Probabilistic modeling of load and material properties remained a challenge.

Standard test method for verifying the alignment of X-Ray diffraction instrumentation for residual stress measurement

CERN Document Server

American Society for Testing and Materials. Philadelphia

2010-01-01

1.1 This test method covers the preparation and use of a flat stress-free test specimen for the purpose of checking the systematic error caused by instrument misalignment or sample positioning in X-ray diffraction residual stress measurement, or both. 1.2 This test method is applicable to apparatus intended for X-ray diffraction macroscopic residual stress measurement in polycrystalline samples employing measurement of a diffraction peak position in the high-back reflection region, and in which the θ, 2θ, and ψ rotation axes can be made to coincide (see Fig. 1). 1.3 This test method describes the use of iron powder which has been investigated in round-robin studies for the purpose of verifying the alignment of instrumentation intended for stress measurement in ferritic or martensitic steels. To verify instrument alignment prior to stress measurement in other metallic alloys and ceramics, powder having the same or lower diffraction angle as the material to be measured should be prepared in similar fashion...

Alignment of Ion Accelerator for Surface Analysis using Theodolite and Laser Tracker

Energy Technology Data Exchange (ETDEWEB)

Ahn, Tae Sung; Seo, Dong Hyuk; Kim, Dae Il; Kim, Han Sung; Kwon, Hyeok Jung; Cho, Yong Sub [KAERI, Daejeon (Korea, Republic of)

2016-05-15

The method of ion accelerator alignment is used two ways which are a theodolite and laser tracker. For the alignment and maintenance of the proton linear accelerator, the laser tracker is typically used at KOMAC. While the device for alignment by using laser tracker is not installed in all ion accelerator components, it was used in parallel in two methods. In this paper, alignment methods are introduced and the result and comparison of each alignment method are presented. The ion accelerator for surface analysis has aligned using theodolite and laser tracker. The two ways for alignment have advantage as well as weakness. But alignment using laser tracker is stronger than using theodolite. Because it is based on alignment and position data and it is more detailed. Also since the beam distribution is smaller than accelerator component that is direction of beam progress, main component (ex. Magnet, Chamber, Pelletron tank, etc.) alignment using laser tracker is enough to align the ion accelerator.

Vertical periodontal ligament distraction--a new method for aligning ankylosed and displaced canines.

Science.gov (United States)

Wilmes, Benedict; Drescher, Dieter

2009-05-01

In the course of a clinical pilot study we tested the vertical periodontal ligament (V-PDL) distraction as a means of aligning ankylosed upper canines. The objective of this study was to analyze the appropriateness und effectiveness of this method. The ankylosed upper canines of five female patients aged between 16 und 19 years were surgically exposed, luxated, and after a latency period of 5 to 7 days, distracted at a rate of 0.5 mm per day. The installed distractors were borne by the periodontal-mucosa, the periodontal-mucosa and the bone, or by the bone exclusively. We evaluated the distraction distance and time and degree of hard and soft tissue generation present in the region surrounding the distracted teeth. All canines were aligned after a mean distraction period of 43.2 days (+/- 3.6 days). The mean distraction distance was 10.8 mm. Three canines had defects at the cemento-enamel junction, and one canine had to be extracted due to a large defect at the root. Vertical PDL distraction is a minimally-invasive therapy to align ankylosed impacted canines. Even if the long-term prognosis of distracted canines with defects is uncertain, the patient benefits from the vertical PDL distraction because both hard and soft tissues are generated in the vicinity of the distracted canine.

Ingenious method of external fixator use to maintain alignment for nailing a proximal tibial shaft fracture.

Science.gov (United States)

Behera, Prateek; Aggarwal, Sameer; Kumar, Vishal; Kumar Meena, Umesh; Saibaba, Balaji

2015-09-01

Fractures of the tibia are one of the most commonly seen orthopedic injuries. Most of them result from a high velocity trauma. While intramedullary nailing of tibial diaphyseal fractures is considered as the golden standard form of treatment for such cases, many metaphyseal and metaphyseal-diaphyseal junction fractures can also be managed by nailing. Maintenance of alignment of such fractures during surgical procedure is often challenging as the pull of patellar tendon tends to extend the proximal fragment as soon as one flexes the knee for the surgical procedure. Numerous technical modifications have been described in the literature for successfully nailing such fractures including semi extended nailing, use of medial plates and external fixators among others. In this study, it was aimed to report two cases in which we used our ingenious method of applying external fixator for maintaining alignment of the fracture and aiding in the entire process of closed intramedullary nailing of metaphyseal tibial fractures by the conventional method. We were able to get good alignment during and after the closed surgery as observed on post-operative radiographs and believe that further evaluation of this technique may be of help to surgeons who want to avoid other techniques.

The stonehenge technique: a new method of crystal alignment for coherent bremsstrahlung experiments

Science.gov (United States)

Livingston, Kenneth

2005-08-01

In the coherent bremsstrahlung technique a thin diamond crystal oriented correctly in an electron beam can produce photons with a high degree of linear polarization.1 The crystal is mounted on a goniometer to control its orientation and it is necessary to measure the angular offsets a) between the crystal axes and the goniometer axes and b) between the goniometer and the electron beam axis. A method for measuring these offsets and aligning the crystal was developed by Lohman et al, and has been used successfully in Mainz.2 However, recent attempts to investigate new crystals have shown that this approach has limitations which become more serious at higher beam energies where more accurate setting of the crystal angles, which scale with l/Ebeam, is required. (Eg. the recent installation of coherent bremsstrahlung facility at Jlab, with Ebeam = 6 GeV ) This paper describes a new, more general alignment technique, which overcomes these limitations. The technique is based on scans where the horizontal and vertical rotation axes of the goniometer are adjusted in a series of steps to make the normal to the crystal describe a cone of a given angle. For each step in the scan, the photon energy spectrum is measured using a tagging spectrometer, and the offsets between the electron beam and the crystal lattice are inferred from the resulting 2D plot. Using this method, it is possible to align the crystal with the beam quickly, and hence to set any desired orientation of the crystal relative to the beam. This is essential for any experiment requiring linearly polarized photons produced via coherent bremsstrahlung, and is also required for a systematic study of the channeling radiation produced by the electron beam incident on the crystal.

Moving State Marine SINS Initial Alignment Based on High Degree CKF

Directory of Open Access Journals (Sweden)

Yong-Gang Zhang

2014-01-01

Full Text Available A new moving state marine initial alignment method of strap-down inertial navigation system (SINS is proposed based on high-degree cubature Kalman filter (CKF, which can capture higher order Taylor expansion terms of nonlinear alignment model than the existing third-degree CKF, unscented Kalman filter and central difference Kalman filter, and improve the accuracy of initial alignment under large heading misalignment angle condition. Simulation results show the efficiency and advantage of the proposed initial alignment method as compared with existing initial alignment methods for the moving state SINS initial alignment with large heading misalignment angle.

Optical Alignment of the Chromospheric Lyman-Alpha SpectroPolarimeter using Sophisticated Methods to Minimize Activities under Vacuum

Science.gov (United States)

Giono, G.; Katsukawa, Y.; Ishikawa, R.; Narukage, N.; Kano, R.; Kubo, M.; Ishikawa, S.; Bando, T.; Hara, H.; Suematsu, Y.;

An Advanced Electrospinning Method of Fabricating Nanofibrous Patterned Architectures with Controlled Deposition and Desired Alignment

Science.gov (United States)

Rasel, Sheikh Md

We introduce a versatile advanced method of electrospinning for fabricating various kinds of nanofibrous patterns along with desired alignment, controlled amount of deposition and locally variable density into the architectures. In this method, we employed multiple electrodes whose potentials have been altered in milliseconds with the help of microprocessor based control system. Therefore, key success of this method was that the electrical field as well as charge carrying fibers could be switched shortly from one electrode's location to another, as a result, electrospun fibers could be deposited on the designated areas with desired alignment. A wide range of nanofibrous patterned architectures were constructed using proper arrangement of multiple electrodes. By controlling the concurrent activation time of two adjacent electrodes, we demonstrated that amount of fibers going into the pattern can be adjusted and desired alignment in electrospun fibers can be obtained. We also revealed that the deposition density of electrospun fibers in different areas of patterned architectures can be varied. We showed that by controlling the deposition time between two adjacent electrodes, a number of functionally graded patterns can be generated with uniaxial alignment. We also demonstrated that this handy method was capable of producing random, aligned, and multidirectional nanofibrous mats by engaging a number of electrodes and switching them in desired patterns. A comprehensive study using finite element method was carried out to understand the effects of electrical field. Simulation results revealed that electrical field strength alters shortly based on electrode control switch patterns. Nanofibrous polyvinyl alcohol (PVA) scaffolds and its composite reinforced with wollastonite and wood flour were fabricated using rotating drum electrospinning technique. Morphological, mechanical, and thermal, properties were characterized on PVA/wollastonite and PVA/wood flour nanocomposites

Interconnection blocks: a method for providing reusable, rapid, multiple, aligned and planar microfluidic interconnections

International Nuclear Information System (INIS)

Sabourin, D; Snakenborg, D; Dufva, M

2009-01-01

In this paper a method is presented for creating 'interconnection blocks' that are re-usable and provide multiple, aligned and planar microfluidic interconnections. Interconnection blocks made from polydimethylsiloxane allow rapid testing of microfluidic chips and unobstructed microfluidic observation. The interconnection block method is scalable, flexible and supports high interconnection density. The average pressure limit of the interconnection block was near 5.5 bar and all individual results were well above the 2 bar threshold considered applicable to most microfluidic applications

[Application of Delphi method in traditional Chinese medicine clinical research].

Science.gov (United States)

Bi, Ying-fei; Mao, Jing-yuan

2012-03-01

In recent years, Delphi method has been widely applied in traditional Chinese medicine (TCM) clinical research. This article analyzed the present application situation of Delphi method in TCM clinical research, and discussed some problems presented in the choice of evaluation method, classification of observation indexes and selection of survey items. On the basis of present application of Delphi method, the author analyzed the method on questionnaire making, selection of experts, evaluation of observation indexes and selection of survey items. Furthermore, the author summarized the steps of application of Delphi method in TCM clinical research.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields

Energy Technology Data Exchange (ETDEWEB)

Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Guzmán, Orlando [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, DF 09340, México (Mexico); Hernández-Ortiz, Juan P. [Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín (Colombia); Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Pablo, Juan J. de, E-mail: depablo@uchicago.edu [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2015-07-28

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields.

Energy Technology Data Exchange (ETDEWEB)

Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.

2015-07-27

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Plasmon Modes of Vertically Aligned Superlattices

DEFF Research Database (Denmark)

Filonenko, Konstantin; Duggen, Lars; Willatzen, Morten

2017-01-01

By using the Finite Element Method we visualize the modes of vertically aligned superlattice composed of gold and dielectric nanocylinders and investigate the emitter-plasmon interaction in approximation of weak coupling. We find that truncated vertically aligned superlattice can function...

Examining Delivery Method and Infant Feeding Intentions between Women in Traditional and Non-Traditional Prenatal Care.

Science.gov (United States)

Risisky, Deb; Chan, Ronna L; Zigmont, Victoria A; Asghar, Syed Masood; DeGennaro, Nancy

2018-02-01

Introduction The purpose of the study is to evaluate delivery method and breastfeeding initiation in women enrolled in group prenatal care (CenteringPregnancy) and in traditional prenatal care. Methods Data were obtained from medical records of a hospital-based midwifery practice in south central Connecticut that offered both types of prenatal care programs. Medical information from 307 women enrolled in this practice was included in the analysis. Out of the 307, 80 were enrolled in group prenatal care. Socio-demographic, lifestyle, and previous and current obstetrical information from medical records formed the basis of comparison. Bivariate and logistic regression analyses were carried out. Results Women in Centering had fewer planned cesarean sections (1.3 vs. 12.8%) and had a higher breastfeeding initiation (88.7 vs. 80.0%). However, Centering women were found to have a higher portion of unplanned cesarean sections (27.5 vs. 11.0%). Both the unadjusted and the adjusted odds ratios of having a cesarean planned delivery were lower in the group care. Women in Centering had 2.44 (95% CI 1.05, 5.66) times the odds of breastfeeding initiation compared to the odds for women in traditional prenatal care after adjusting for maternal age, smoking status, gestation and race. Discussion CenteringPregnancy can have positive impact for the woman and baby. This program implementation saw lower rates of elective cesarean sections and increased breastfeeding compared to women in traditional care.

Efficient alignment-free DNA barcode analytics.

Science.gov (United States)

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.

Alignment at the ESRF

International Nuclear Information System (INIS)

Martin, D.; Levet, N.; Gatta, G.

1999-01-01

The ESRF Survey and Alignment group is responsible for the installation, control and periodic realignment of the accelerators and experiments which produce high quality x-rays used by scientists from Europe and around the world. Alignment tolerances are typically less than one millimetre and often in the order of several micrometers. The group is composed of one engineer, five highly trained survey technicians, one electronic and one computer technician. This team is fortified during peak periods by technicians from an external survey company. First an overview and comparative study of the main large-scale survey instrumentation and methods used by the group is made. Secondly a discussion of long term deformation on the ESRF site is presented. This is followed by presentation of the methods used in the realignment of the various machines. Two important aspects of our work, beamline and front-end alignment, and the so-called machine exotic devices are briefly discussed. Finally, the ESRF calibration bench is presented. (authors)

A cross-species alignment tool (CAT)

DEFF Research Database (Denmark)

Li, Heng; Guan, Liang; Liu, Tao

2007-01-01

BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...... sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...... at http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT...

Warping methods for spectroscopic and chromatographic signal alignment: A tutorial

Energy Technology Data Exchange (ETDEWEB)

Bloemberg, Tom G., E-mail: T.Bloemberg@science.ru.nl [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Radboud University Nijmegen, Education Institute for Molecular Sciences, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Gerretzen, Jan; Lunshof, Anton [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Wehrens, Ron [Centre for Research and Innovation, Fondazione Edmund Mach, Via E. Mach, 1, 38010 San Michele all’Adige, TN (Italy); Buydens, Lutgarde M.C. [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands)

2013-06-05

Highlights: •The concepts of warping and alignment are introduced. •The most important warping methods are critically reviewed and explained. •Reference selection, evaluation and place of warping in preprocessing are discussed. •Some pitfalls, especially for LC–MS and similar data, are addressed. •Examples are provided, together with programming scripts to rework and extend them. -- Abstract: Warping methods are an important class of methods that can correct for misalignments in (a.o.) chemical measurements. Their use in preprocessing of chromatographic, spectroscopic and spectrometric data has grown rapidly over the last decade. This tutorial review aims to give a critical introduction to the most important warping methods, the place of warping in preprocessing and current views on the related matters of reference selection, optimization, and evaluation. Some pitfalls in warping, notably for liquid chromatography–mass spectrometry (LC–MS) data and similar, will be discussed. Examples will be given of the application of a number of freely available warping methods to a nuclear magnetic resonance (NMR) spectroscopic dataset and a chromatographic dataset. As part of the Supporting Information, we provide a number of programming scripts in Matlab and R, allowing the reader to work the extended examples in detail and to reproduce the figures in this paper.

The linear collider alignment and survey (LiCAS) project

International Nuclear Information System (INIS)

Bingham, Richard; Botcherby, Edward; Coe, Paul; Grzelak, Grzegorz; Mitra, Ankush; Reichold, Armin; Prenting, Johannes

2003-01-01

For the next generation of Linear Colliders (LC) the precision alignment of accelerator components will be critical. The DESY applied geodesy group has developed the concept of an automated 'survey train'. The train runs along the accelerator wall measuring the 3D position of a set of equispaced reference markers. This reference structure is then used to align the accelerator components. The LiCAS group is developing a measurement system for the survey train. It will use a combination of Laser Straightness Monitors (SM) and Frequency Scanning Interferometry (FSI). FSI is an interferometric length measurement technique originally developed for the online alignment of the ATLAS Inner Detector. This novel combination of optical techniques is expected to overcome the limitations of traditional open air survey. The authors describe the LiCAS project, the measurement systems and their integration into the survey train. The technical parameters and constraints will be mentioned. There will also be brief discussion of the second phase of the project to allow on-line monitoring of the LC alignment. (author)

Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

Directory of Open Access Journals (Sweden)

Hazelhurst Scott

2010-03-01

Full Text Available Abstract Background Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution. Results A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution, which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions. Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the

Using structure to explore the sequence alignment space of remote homologs.

Science.gov (United States)

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Angular momentum alignment in molecular beam scattering

International Nuclear Information System (INIS)

Treffers, M.A.

1985-01-01

It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na 2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

Aligning English Language Testing With Curriculum

OpenAIRE

Marcela Palacio; Sandra Gaviria; James Dean Brown

2016-01-01

Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia) to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an effort to guarantee the quality of the process of test design. The study included descriptive statistics, item analysis, correlational analyses, reliab...

AlignMe—a membrane protein sequence alignment web server

Science.gov (United States)

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

Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

Energy Technology Data Exchange (ETDEWEB)

Frazier, Shane D.; Srubar, Wil V., E-mail: wsrubar@colorado.edu

2016-05-01

Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm{sup 3}) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

International Nuclear Information System (INIS)

Frazier, Shane D.; Srubar, Wil V.

2016-01-01

Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm"3) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

How accurate is anatomic limb alignment in predicting mechanical limb alignment after total knee arthroplasty?

Science.gov (United States)

Lee, Seung Ah; Choi, Sang-Hee; Chang, Moon Jong

2015-10-27

Anatomic limb alignment often differs from mechanical limb alignment after total knee arthroplasty (TKA). We sought to assess the accuracy, specificity, and sensitivity for each of three commonly used ranges for anatomic limb alignment (3-9°, 5-10° and 2-10°) in predicting an acceptable range (neutral ± 3°) for mechanical limb alignment after TKA. We also assessed whether the accuracy of anatomic limb alignment was affected by anatomic variation. This retrospective study included 314 primary TKAs. The alignment of the limb was measured with both anatomic and mechanical methods of measurement. We also measured anatomic variation, including the femoral bowing angle, tibial bowing angle, and neck-shaft angle of the femur. All angles were measured on the same full-length standing anteroposterior radiographs. The accuracy, specificity, and sensitivity for each range of anatomic limb alignment were calculated and compared using mechanical limb alignment as the reference standard. The associations between the accuracy of anatomic limb alignment and anatomic variation were also determined. The range of 2-10° for anatomic limb alignment showed the highest accuracy, but it was only 73 % (3-9°, 65 %; 5-10°, 67 %). The specificity of the 2-10° range was 81 %, which was higher than that of the other ranges (3-9°, 69 %; 5-10°, 67 %). However, the sensitivity of the 2-10° range to predict varus malalignment was only 16 % (3-9°, 35 %; 5-10°, 68 %). In addition, the sensitivity of the 2-10° range to predict valgus malalignment was only 43 % (3-9°, 71 %; 5-10°, 43 %). The accuracy of anatomical limb alignment was lower for knees with greater femoral (odds ratio = 1.2) and tibial (odds ratio = 1.2) bowing. Anatomic limb alignment did not accurately predict mechanical limb alignment after TKA, and its accuracy was affected by anatomic variation. Thus, alignment after TKA should be assessed by measuring mechanical alignment rather than anatomic

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

DEFF Research Database (Denmark)

Nielsen, Morten; Lund, Ole

2009-01-01

this binding event. RESULTS: Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data...

Reliability studies of diagnostic methods in Indian traditional Ayurveda medicine

DEFF Research Database (Denmark)

Kurande, Vrinda Hitendra; Waagepetersen, Rasmus; Toft, Egon

2013-01-01

as prakriti classification), method development (pulse diagnosis), quality assurance for diagnosis and treatment and in the conduct of clinical studies. Several reliability studies are conducted in western medicine. The investigation of the reliability of traditional Chinese, Japanese and Sasang medicine...

GraphAlignment: Bayesian pairwise alignment of biological networks

Directory of Open Access Journals (Sweden)

Kolář Michal

2012-11-01

Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

Using structure to explore the sequence alignment space of remote homologs.

Directory of Open Access Journals (Sweden)

Andrew Kuziemko

2011-10-01

Full Text Available Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Accelerator and transport line survey and alignment

International Nuclear Information System (INIS)

Ruland, R.E.

1991-10-01

This paper summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are introduced and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations. Various approaches to smoothing used at major laboratories are discussed. 47 refs., 19 figs., 1 tab

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

Science.gov (United States)

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.

Perspective for applying traditional and inovative teaching and learning methods to nurses continuing education

OpenAIRE

Bendinskaitė, Irmina

2015-01-01

Bendinskaitė I. Perspective for applying traditional and innovative teaching and learning methods to nurse’s continuing education, magister thesis / supervisor Assoc. Prof. O. Riklikienė; Departament of Nursing and Care, Faculty of Nursing, Lithuanian University of Health Sciences. – Kaunas, 2015, – p. 92 The purpose of this study was to investigate traditional and innovative teaching and learning methods perspective to nurse’s continuing education. Material and methods. In a period fro...

Development of the laser alignment system with PSD used for shaft calibration

Science.gov (United States)

Jiao, Guohua; Li, Yulin; Hu, Baowen

2006-02-01

Shaft calibration is an important technique during installation and maintenance of a rotating machine. It requires unique and high-precision measurement instruments with calculation capability, and relies on experience on heavy, high-speed, or high-temperature machines. A high-precision laser alignment system has been designed using PSD (Position Sensing Detector) to change traditional manual way of shaft calibration and to make the measurement easier and more accurate. The system is comprised of two small measuring units (Laser transmitter and detector) and a hand operated control unit or a PC. Such a laser alignment system has been used in some actual shaft alignment with offset resolution 1.5μm and angular resolution 0.1°.

The ethics of improving African traditional medical practice: scientific or African traditional research methods?

Science.gov (United States)

Nyika, Aceme

2009-11-01

The disease burden in Africa, which is relatively very large compared with developed countries, has been attributed to various factors that include poverty, food shortages, inadequate access to health care and unaffordability of Western medicines to the majority of African populations. Although for 'old diseases' knowledge about the right African traditional medicines to treat or cure the diseases has been passed from generation to generation, knowledge about traditional medicines to treat newly emerging diseases has to be generated in one way or another. In addition, the existing traditional medicines have to be continuously improved, which is also the case with Western scientific medicines. Whereas one school of thought supports the idea of improving medicines, be they traditional or Western, through scientific research, an opposing school of thought argues that subjecting African traditional medicines to scientific research would be tantamount to some form of colonization and imperialism. This paper argues that continuing to use African traditional medicines for old and new diseases without making concerted efforts to improve their efficacy and safety is unethical since the disease burden affecting Africa may continue to rise in spite of the availability and accessibility of the traditional medicines. Most importantly, the paper commends efforts being made in some African countries to improve African traditional medicine through a combination of different mechanisms that include the controversial approach of scientific research on traditional medicines.

Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods

Directory of Open Access Journals (Sweden)

Levrini L

2015-12-01

Full Text Available Luca Levrini, Francesca Novara, Silvia Margherini, Camilla Tenconi, Mario Raspanti Department of Surgical and Morphological Sciences, Dental Hygiene School, Research Centre Cranio Facial Disease and Medicine, University of Insubria, Varese, Italy Background: Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. Purpose: The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Methods: Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1 running water (control condition; 2 effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3 brushing alone (with a toothbrush and toothpaste. At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. Results: The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. Conclusion: On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental

Efficacy of traditional maize (Zea mays L.) seed storage methods in ...

African Journals Online (AJOL)

Efficacy of traditional maize (Zea mays L.) seed storage methods in western Kenya. ... PROMOTING ACCESS TO AFRICAN RESEARCH. AFRICAN JOURNALS ONLINE (AJOL) ... African Journal of Food, Agriculture, Nutrition and Development.

Facile method to align crystalline needles composed of organic ...

Indian Academy of Sciences (India)

2017-09-23

Sep 23, 2017 ... (using self-assembly) used for the purpose, its disadvantage is that a larger amount of the material dissolves in the solution than what ... Working hypothesis for aligning crystalline needles .... using a home-made equipment.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G.Gomez.

Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

Statistical alignment: computational properties, homology testing and goodness-of-fit

DEFF Research Database (Denmark)

Hein, J; Wiuf, Carsten; Møller, Martin

2000-01-01

The model of insertions and deletions in biological sequences, first formulated by Thorne, Kishino, and Felsenstein in 1991 (the TKF91 model), provides a basis for performing alignment within a statistical framework. Here we investigate this model.Firstly, we show how to accelerate the statistical...... alignment algorithms several orders of magnitude. The main innovations are to confine likelihood calculations to a band close to the similarity based alignment, to get good initial guesses of the evolutionary parameters and to apply an efficient numerical optimisation algorithm for finding the maximum...... analysis.Secondly, we propose a new homology test based on this model, where homology means that an ancestor to a sequence pair can be found finitely far back in time. This test has statistical advantages relative to the traditional shuffle test for proteins.Finally, we describe a goodness-of-fit test...

Optimal Nonlinear Filter for INS Alignment

Institute of Scientific and Technical Information of China (English)

赵瑞; 顾启泰

2002-01-01

All the methods to handle the inertial navigation system (INS) alignment were sub-optimal in the past. In this paper, particle filtering (PF) as an optimal method is used for solving the problem of INS alignment. A sub-optimal two-step filtering algorithm is presented to improve the real-time performance of PF. The approach combines particle filtering with Kalman filtering (KF). Simulation results illustrate the superior performance of these approaches when compared with extended Kalman filtering (EKF).

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

Science.gov (United States)

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.

Some Alignment Considerations for the Next Linear Collider

International Nuclear Information System (INIS)

Ruland, R

2004-01-01

Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued

Multiple Whole Genome Alignments Without a Reference Organism

Energy Technology Data Exchange (ETDEWEB)

Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

2009-01-16

Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

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

Directory of Open Access Journals (Sweden)

Claros M Gonzalo

2010-06-01

Full Text Available Abstract 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

Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

International Nuclear Information System (INIS)

Bree, Michael; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade

2016-01-01

The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

Energy Technology Data Exchange (ETDEWEB)

Bree, Michael, E-mail: michael.bree@lightsource.ca; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade [Canadian Light Source Inc., 44 Innovation Blvd, Saskatoon, SK S7N 2V3 Canada (Canada)

2016-07-27

The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

Improvement in the traditional processing method and nutritional quality of traditional extruded cassava-based snack (modified Ajogun).

Science.gov (United States)

Obadina, Adewale O; Oyewole, Olusola B; Williams, Oluwasolabomi E

2013-07-01

This study was carried out to investigate and improve the traditional processing method and nutritional quality of the traditional cassava snack (Ajogun). Cassava root (Manihot esculenta Crantz L.) of TME 419 variety was processed into mash (40% moisture content). The cassava mash was mixed into different blends to produce fried traditional "Ajogun", fried and baked extrudates (modified Ajogun) as snacks. These products were analyzed to determine the proximate composition including carbohydrate, fat, protein, fiber, ash, and moisture contents and functional properties such as bulk density. The results obtained for the moisture, fat, protein, and ash contents showed significant difference (P extrudates. However, there was no significant difference (P > 0.05) in the carbohydrate and fiber contents between the three samples. There was no significant difference (P > 0.05) in the bulk density of the snacks. Also, sensory evaluation was carried out on the cassava-based snacks using the 9-point hedonic scale to determine the degree of acceptability. Results obtained showed significant difference (P extrudates and control sample in terms of appearance, taste, flavor, color, aroma, texture, and overall acceptability. The highest acceptability level of the product was at 8.04 for the control sample (traditional Ajogun). This study has shown that "Ajogun", which is a lesser known cassava product, is rich in protein and fat.

Comparison of Traditional Versus Evidence-Based Journal Club Formats

Directory of Open Access Journals (Sweden)

Kathleen Packard, PharmD, MS, BCPS

2011-01-01

Full Text Available AbstractPurpose: The objective of the study was to compare a traditionally structured journal club with an evidence based structured journal club during an advanced clinical pharmacy rotation and to determine the best utilization that aligns with recent changes to the pharmacy school accreditation standards.Methods: The study included 21 students who completed journal club utilizing the traditional journal club format and 24 students who utilized an evidence based journal club format. Background characteristics, student reported beliefs, and mean critical evaluation skills scores were evaluated and compared in each group.Results: There were no statistically significant differences between the two cohorts in mean overall percentage grade for the activity. Students in the traditional cohort received significantly higher grades for the Study Analysis and Critique section (90.97 + 12.18 versus 81.25 + 11.18, P=0.01 as well as for the Preparedness section (96.11 + 8.03 versus 85.0 + 17.13, P=0.002. Students in the evidence based cohort received statistically superior grades for the Presentation Skills section (96.43 + 6.39 versus 82.47 + 14.12, P=0.0004.Conclusion: An evidence based journal club is a reasonable and effective alternative to the traditionally structured journal club when the primary objective is to assist students in understanding evidence based concepts and to apply current literature to clinical practice.

Traditional transformations and transmedial affirmations: Blurring the boundaries of Sherlockian fan practices

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Ashley D. Polasek

2017-03-01

Full Text Available The modes of discourse employed by fans of Sherlock Holmes represent both affirmational and transformational impulses. As the fan community has grown and diversified, tensions have arisen between Sherlockians who prefer to utilize traditional frameworks dating back to the early practices of the Baker Street Irregulars in the 1930s and '40s and those who operate primarily in virtual spaces and utilize 21st-century digital platforms as frameworks for their discourse. Because the demographics of affirmational fans tend to align with those of fans preferring traditional frameworks, and conversely, the demographics of transformational fans tend to align with those of fans preferring transmedial frameworks, the styles of engagement often become conflated with the impulses driving the discourse itself. By first examining these tensions and then utilizing case studies that illustrate the four combinations of frameworks and modes of discourse—traditional-affirmational, transmedial-affirmational, traditional-transformational, and transmedial-transformational—I seek to complicate the boundaries that appear to divide the larger Sherlock Holmes fan community. I will demonstrate that the twin fannish impulses to affirm the text and transform it have operated not at odds but in parallel throughout the history of the fandom.

The analysis of the accuracy of the wheel alignment inspection method on the side-slip plate stand

Science.gov (United States)

Gajek, A.; Strzępek, P.

2016-09-01

The article presents the theoretical basis and the results of the examination of the wheel alignment inspection method on the slide slip plate stand. It is obligatory test during periodic technical inspection of the vehicle. The measurement is executed in the dynamic conditions. The dependence between the lateral displacement of the plate and toe-in of the tested wheels has been shown. If the diameter of the wheel rim is known then the value of the toe-in can be calculated. The comparison of the toe-in measurements on the plate stand and on the four heads device for the wheel alignment inspection has been carried out. The accuracy of the measurements and the influence of the conditions of the tests on the plate stand (the way of passing through the plate) were estimated. The conclusions about the accuracy of this method are presented.

Deep learning versus traditional machine learning methods for aggregated energy demand prediction

NARCIS (Netherlands)

Paterakis, N.G.; Mocanu, E.; Gibescu, M.; Stappers, B.; van Alst, W.

2018-01-01

In this paper the more advanced, in comparison with traditional machine learning approaches, deep learning methods are explored with the purpose of accurately predicting the aggregated energy consumption. Despite the fact that a wide range of machine learning methods have been applied to

MUON DETECTORS: ALIGNMENT

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G.Gomez

2010-01-01

The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

FACT. Bokeh alignment for Cherenkov telescopes

Energy Technology Data Exchange (ETDEWEB)

Mueller, Sebastian Achim [ETH Zurich (Switzerland); Buss, Jens [TU Dortmund (Germany)

2016-07-01

Imaging Atmospheric Cherenkov Telescopes (IACTs) need fast and large imaging optics to map the faint Cherenkov light emitted in cosmic ray air showers onto their image sensors. Segmented reflectors are inexpensive, lightweight and offer good image quality. However, alignment of the mirror facets remains a challenge. A good alignment is crucial in IACT observations to separate gamma rays from hadronic cosmic rays. We present a simple, yet extendable method, to align segmented reflectors using their Bokeh. Bokeh alignment does not need a star or good weather nights but can be done anytime, even during the day. Bokeh alignment optimizes the facet orientations by comparing the segmented reflector's Bokeh to a predefined template. The Bokeh is observed using the out of focus image of a nearby point like light source in a distance of about ten times the focal lengths. We introduce Bokeh alignment on segmented reflectors and present its use on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on Canary Island La Palma, as well as on the Cherenkov Telescope Array (CTA) Medium Size Telescope (MST) prototype in Berlin Adlershof.

Traditional oral health beliefs and practices of Bulang people in Yunnan, China.

Science.gov (United States)

Zhang, Shinan; Lo, Edward C M; Chu, Chun-Hung

2018-02-01

The aim of the present study was to explore traditional oral health beliefs among the Bulang ethnic minority group in China. Eighteen village leaders, chiefs, elders, and seniors in Yunnan, China were assigned to three focus groups for discussion of traditional oral health beliefs. The discussions were led by a facilitator. Transcripts were made, and data were extracted. The focus group discussions on traditional oral health beliefs addressed three themes: (a) the perception of oral health; (b) the impact of healthy teeth (oral health), in that healthy teeth essentially have an impact on physical health, emotions, and social status; and (c) toothache management, which was regarded as tooth decay (dental caries). Blackening teeth was a pain relief method. Blackened teeth were reported to be part of ethnic identity, and considered esthetically pleasing. It also indicated the marital status of women. Some Bulang people believed that healthy dentition has no spacing, pain, or functioning problems. Well-aligned dentition was associated with higher social status. Toothaches were considered to be caused by tooth worms. Consulting a monk was another way to manage a toothache. Tooth blackening was considered traditional, and effective for caries prevention. © 2017 John Wiley & Sons Australia, Ltd.

A Fast and Specific Alignment Method for Minisatellite Maps

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Eric Rivals

2006-01-01

Full Text Available Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length (i.e., in number of copies of minisatellites proved useful in population genetics.Motivation: In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications.Results: We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1 human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases.Availability: Software is available at http://atgc.lirmm.fr/ms_align/

Mango: multiple alignment with N gapped oligos.

Science.gov (United States)

Zhang, Zefeng; Lin, Hao; Li, Ming

2008-06-01

Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

Gender preference between traditional and PowerPoint methods of teaching gross anatomy.

Science.gov (United States)

Nuhu, Saleh; Adamu, Lawan Hassan; Buba, Mohammed Alhaji; Garba, Sani Hyedima; Dalori, Babagana Mohammed; Yusuf, Ashiru Hassan

2018-01-01

Teaching and learning process is increasingly metamorphosing from the traditional chalk and talk to the modern dynamism in the information and communication technology. Medical education is no exception to this dynamism more especially in the teaching of gross anatomy, which serves as one of the bases of understanding the human structure. This study was conducted to determine the gender preference of preclinical medical students on the use of traditional (chalk and talk) and PowerPoint presentation in the teaching of gross anatomy. This was cross-sectional and prospective study, which was conducted among preclinical medical students in the University of Maiduguri, Nigeria. Using simple random techniques, a questionnaire was circulated among 280 medical students, where 247 students filled the questionnaire appropriately. The data obtained was analyzed using SPSS version 20 (IBM Corporation, Armonk, NY, USA) to find the method preferred by the students among other things. Majority of the preclinical medical students in the University of Maiduguri preferred PowerPoint method in the teaching of gross anatomy over the conventional methods. The Cronbach alpha value of 0.76 was obtained which is an acceptable level of internal consistency. A statistically significant association was found between gender and preferred method of lecture delivery on the clarity of lecture content where females prefer the conventional method of lecture delivery whereas males prefer the PowerPoint method, On the reproducibility of text and diagram, females prefer PowerPoint method of teaching gross anatomy while males prefer the conventional method of teaching gross anatomy. There are gender preferences with regard to clarity of lecture contents and reproducibility of text and diagram. It was also revealed from this study that majority of the preclinical medical students in the University of Maiduguri prefer PowerPoint presentation over the traditional chalk and talk method in most of the

Cryo-EM image alignment based on nonuniform fast Fourier transform

International Nuclear Information System (INIS)

Yang Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis

Cryo-EM image alignment based on nonuniform fast Fourier transform.

Science.gov (United States)

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

MANGO: a new approach to multiple sequence alignment.

Science.gov (United States)

Zhang, Zefeng; Lin, Hao; Li, Ming

2007-01-01

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

Traditional and New methods for the Preparation of Diazocarbonyl Compounds

Directory of Open Access Journals (Sweden)

ANTONIO C.B. BURTOLOSO

2018-04-01

Full Text Available ABSTRACT For many years diazocarbonyl compounds have been studied due to their versatility and usability in many chemical transformations. In this review, we summarize the traditional methods to prepare these compounds as well as the new methods and recent improvements in experimental procedures. Moreover, emergence of continuous flow techniques has allowed safer and environmentally friendly procedures for the handling of diazomethane and diazo compounds and will also be a topic in this review.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Shrushrita Sharma

Full Text Available 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.

CORAL: aligning conserved core regions across domain families.

Science.gov (United States)

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.

DNAAlignEditor: DNA alignment editor tool

Directory of Open Access Journals (Sweden)

Guill Katherine E

2008-03-01

Full Text Available Abstract 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.

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

Science.gov (United States)

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

Science.gov (United States)

Kuznetsov, Igor B; McDuffie, Michael

2015-05-07

Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities. PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach. PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

VOLATILE CONSTITUENTS OF GINGER OIL PREPARED ACCORDING TO IRANIAN TRADITIONAL MEDICINE AND CONVENTIONAL METHOD: A COMPARATIVE STUDY.

Science.gov (United States)

Shirooye, Pantea; Mokaberinejad, Roshanak; Ara, Leila; Hamzeloo-Moghadam, Maryam

2016-01-01

Herbal medicines formulated as oils were believed to possess more powerful effects than their original plants in Iranian Traditional Medicine (ITM). One of the popular oils suggested for treatment of various indications was ginger oil. In the present study, to suggest a more convenient method of oil preparation (compared to the traditional method), ginger oil has been prepared according to both the traditional and conventional maceration methods and the volatile oil constituents have been compared. Ginger oil was obtained in sesame oil according to both the traditional way and the conventional (maceration) methods. The volatile oil of dried ginger and both oils were obtained by hydro-distillation and analyzed by gas chromatography/mass spectroscopy. Fifty five, fifty nine and fifty one components consisting 94 %, 94 % and 98 % of the total compounds were identified in the volatile oil of ginger, traditional and conventional oils, respectively. The most dominant compounds of the traditional and conventional oils were almost similar; however they were different from ginger essential oil which has also been to possess limited amounts of anti-inflammatory components. It was concluded that ginger oil could be prepared through maceration method and used for indications mentioned in ITM.

A method for optical ground station reduce alignment error in satellite-ground quantum experiments

Science.gov (United States)

He, Dong; Wang, Qiang; Zhou, Jian-Wei; Song, Zhi-Jun; Zhong, Dai-Jun; Jiang, Yu; Liu, Wan-Sheng; Huang, Yong-Mei

2018-03-01

A satellite dedicated for quantum science experiments, has been developed and successfully launched from Jiuquan, China, on August 16, 2016. Two new optical ground stations (OGSs) were built to cooperate with the satellite to complete satellite-ground quantum experiments. OGS corrected its pointing direction by satellite trajectory error to coarse tracking system and uplink beacon sight, therefore fine tracking CCD and uplink beacon optical axis alignment accuracy was to ensure that beacon could cover the quantum satellite in all time when it passed the OGSs. Unfortunately, when we tested specifications of the OGSs, due to the coarse tracking optical system was commercial telescopes, the change of position of the target in the coarse CCD was up to 600μrad along with the change of elevation angle. In this paper, a method of reduce alignment error between beacon beam and fine tracking CCD is proposed. Firstly, OGS fitted the curve of target positions in coarse CCD along with the change of elevation angle. Secondly, OGS fitted the curve of hexapod secondary mirror positions along with the change of elevation angle. Thirdly, when tracking satellite, the fine tracking error unloaded on the real-time zero point position of coarse CCD which computed by the firstly calibration data. Simultaneously the positions of the hexapod secondary mirror were adjusted by the secondly calibration data. Finally the experiment result is proposed. Results show that the alignment error is less than 50μrad.

Interference Alignment-based Precoding and User Selection with Limited Feedback in Two-cell Downlink Multi-user MIMO Systems

Directory of Open Access Journals (Sweden)

Yin Zhu

2016-05-01

Full Text Available Interference alignment (IA is a new approach to address interference in modern multiple-input multiple-out (MIMO cellular networks in which interference is an important factor that limits the system throughput. System throughput in most IA implementation schemes is significantly improved only with perfect channel state information and in a high signal-to-noise ratio (SNR region. Designing a simple IA scheme for the system with limited feedback and investigating system performance at a low-to-medium SNR region is important and practical. This paper proposed a precoding and user selection scheme based on partial interference alignment in two-cell downlink multi-user MIMO systems under limited feedback. This scheme aligned inter-cell interference to a predefined direction by designing user’s receive antenna combining vectors. A modified singular value decomposition (SVD-based beamforming method and a corresponding user-selection algorithm were proposed for the system with low rate limited feedback to improve sum rate performance. Simulation results show that the proposed scheme achieves a higher sum rate than traditional schemes without IA. The modified SVD-based beamforming scheme is also superior to the traditional zero-forcing beamforming scheme in low-rate limited feedback systems. The proposed partial IA scheme does not need to collaborate between transmitters and joint design between the transmitter and the users. The scheme can be implemented with low feedback overhead in current MIMO cellular networks.

Helical coil alignment in the advanced toroidal facility

International Nuclear Information System (INIS)

Taylor, D.J.; Cole, M.J.; Johnson, R.L.; Nelson, B.E.; Warwick, J.E.; Whitson, J.C.

1985-01-01

This paper presents a brief overview of the helical coil design concept, detailed descriptions of the method for installation and alignment, and discussions of segment installation and alignment equipment. Alignment is accomplished by optical methods using electronic theodolites connected to a microcomputer to form a coordinate measurement system. The coordinate measurement system is described in detail, along with target selection and fixturing for manipulation of the helical coil segments during installation. In addition, software is described including vendor-supplied software used in the coordinate measurement system and in-house-developed software used to calibrate segment and positioning fixture motion. 2 refs., 8 figs

[Discussion on ideological concept implied in traditional reinforcing and reducing method of acupuncture].

Science.gov (United States)

Li, Suyun; Zhao, Jingsheng

2017-11-12

The forming and development of traditional reinforcing and reducing method of acupuncture was rooted in traditional culture of China, and was based on the ancients' special understanding of nature, life and diseases, therefore its principle and methods were inevitably influenced by philosophy culture and medicine concept at that time. With deep study on Inner Canon of Huangdi and representative reinforcing and reducing method of acupuncture, the implied ideological concept, including contradiction view and profit-loss view in ancient dialectic, yin-yang balance theory, concept of life flow, monophyletic theory of qi , theory of existence of disease-evil, yin - yang astrology theory, theory of inter-promotion of five elements, were summarized and analyzed. The clarified and systematic understanding on guiding ideology of reinforcing and reducing method of acupuncture could significantly promote the understanding on principle, method, content and manipulation.

Automatic alignment of radionuclide images

International Nuclear Information System (INIS)

Barber, D.C.

1982-01-01

The variability of the position, dimensions and orientation of a radionuclide image within the field of view of a gamma camera hampers attempts to analyse the image numerically. This paper describes a method of using a set of training images of a particular type, in this case right lateral brain images, to define the likely variations in the position, dimensions and orientation for that type of image and to provide alignment data for a program that automatically aligns new images of the specified type to a standard position, size and orientation. Examples are given of the use of this method on three types of radionuclide image. (author)

Liquid crystallinity driven highly aligned large graphene oxide composites

Energy Technology Data Exchange (ETDEWEB)

Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong [Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701 (Korea, Republic of); Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701 (Korea, Republic of); Kim, Sang Ouk, E-mail: sangouk.kim@kaist.ac.kr [Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701 (Korea, Republic of); Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701 (Korea, Republic of)

2015-04-15

Graphene is an emerging graphitic carbon materials, consisting of sp{sup 2} hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented within flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites.

Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods.

Science.gov (United States)

Levrini, Luca; Novara, Francesca; Margherini, Silvia; Tenconi, Camilla; Raspanti, Mario

2015-01-01

Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1) running water (control condition); 2) effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3) brushing alone (with a toothbrush and toothpaste). At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental hygienists should strongly advise patients wearing orthodontic aligners to clean them using a combination of brushing and commercially available tablets for cleaning oral appliances.

Functional alignments and self-tests for tilted and decentered optics

International Nuclear Information System (INIS)

Bauke, W.; Cross, E.W.

1983-01-01

The alignment of tilted and decentered optics is ordinarily difficult, because such optics have neither simple alignment points amenable to ordinary boresight methods, nor a simple alignment theory. Several different alignment examples which provide insight into a practical universal approach to all such systems are explored. The examples detailed are segments of the Antares Laser Fusion Project's optical train

Bacterial population in traditional sourdough evaluated by molecular methods.

Science.gov (United States)

Randazzo, C L; Heilig, H; Restuccia, C; Giudici, P; Caggia, C

2005-01-01

To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Forty-five LAB isolates were identified both by phenotypic and molecular methods. The restriction fragment length polymorphism and 16S ribosomal DNA gene sequencing gave evidence of a variety of species with the dominance of Lactobacillus sanfranciscensis and Lactobacillus pentosus, in all sourdoughs tested. Culture-independent method, such as denaturing gradient gel electrophoresis (DGGE) of the V6-V8 regions of the 16S rDNA, was applied for microbial community fingerprint. The DGGE profiles revealed the dominance of L. sanfranciscensis species. In addition, Lactobacillus-specific primers were used to amplify the V1-V3 regions of the 16S rDNA. DGGE profiles flourished the dominance of L. sanfranciscensis and Lactobacillus fermentum in the traditional sourdoughs, and revealed that the closely related species Lactobacillus kimchii and Lactobacillus alimentarius were not discriminated. Lactobacillus-specific PCR-DGGE analysis is a rapid tool for rapid detection of Lactobacillus species in artisanal sourdough. This study reports a characterization of Lactobacillus isolates from artisanal sourdoughs and highlights the value of DGGE approach to detect uncultivable Lactobacillus species.

System and method for aligning heliostats of a solar power tower

Science.gov (United States)

Convery, Mark R.

2013-01-01

Disclosed is a solar power tower heliostat alignment system and method that includes a solar power tower with a focal area, a plurality of heliostats that each reflect sunlight towards the focal area of the solar power tower, an off-focal area location substantially close to the focal area of the solar power tower, a communication link between the off-focal area location and a misaligned heliostat, and a processor that interprets the communication between the off-focal area location and the misaligned heliostat to identify the misaligned heliostat from the plurality of heliostats and that determines a correction for the identified misaligned heliostat to realign the misaligned heliostat to reflect sunlight towards the focal area of the solar power tower.

Using traditional methods and indigenous technologies for coping with climate variability

NARCIS (Netherlands)

Stigter, C.J.; Zheng Dawei,; Onyewotu, L.O.Z.; Mei Xurong,

2005-01-01

In agrometeorology and management of meteorology related natural resources, many traditional methods and indigenous technologies are still in use or being revived for managing low external inputs sustainable agriculture (LEISA) under conditions of climate variability. This paper starts with the

Discriminative Shape Alignment

DEFF Research Database (Denmark)

Loog, M.; de Bruijne, M.

2009-01-01

, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...

Do new wipe materials outperform traditional lead dust cleaning methods?

Science.gov (United States)

Lewis, Roger D; Ong, Kee Hean; Emo, Brett; Kennedy, Jason; Brown, Christopher A; Condoor, Sridhar; Thummalakunta, Laxmi

2012-01-01

Government guidelines have traditionally recommended the use of wet mopping, sponging, or vacuuming for removal of lead-contaminated dust from hard surfaces in homes. The emergence of new technologies, such as the electrostatic dry cloth and wet disposable clothes used on mopheads, for removal of dust provides an opportunity to evaluate their ability to remove lead compared with more established methods. The purpose of this study was to determine if relative differences exist between two new and two older methods for removal of lead-contaminated dust (LCD) from three wood surfaces that were characterized by different roughness or texture. Standard leaded dust, coefficient of friction was performed for each wipe material. Analysis of variance was used to evaluate the surface and cleaning methods. There were significant interactions between cleaning method and surface types, p = 0.007. Cleaning method was found be a significant factor in removal of lead, p coefficient of friction, significantly different among the three wipes, is likely to influence the cleaning action. Cleaning method appears to be more important than texture in LCD removal from hard surfaces. There are some small but important factors in cleaning LCD from hard surfaces, including the limits of a Swiffer mop to conform to curved surfaces and the efficiency of the wetted shop towel and vacuuming for cleaning all surface textures. The mean percentage reduction in lead dust achieved by the traditional methods (vacuuming and wet wiping) was greater and more consistent compared to the new methods (electrostatic dry cloth and wet Swiffer mop). Vacuuming and wet wiping achieved lead reductions of 92% ± 4% and 91%, ± 4%, respectively, while the electrostatic dry cloth and wet Swiffer mops achieved lead reductions of only 89 ± 8% and  81 ± 17%, respectively.

Alignment of non-covalent interactions at protein-protein interfaces.

Directory of Open Access Journals (Sweden)

Hongbo Zhu

Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

Islamic geometric patterns their historical development and traditional methods of construction

CERN Document Server

Bonner, Jay

2017-01-01

The main focus of this unique book is an in-depth examination of the polygonal technique; the primary method used by master artists of the past in creating Islamic geometric patterns. The author details the design methodology responsible for this all-but-lost art form and presents evidence for its use from the historical record, both of which are vital contributions to the understanding of this ornamental tradition. Additionally, the author examines the historical development of Islamic geometric patterns, the significance of geometric design within the broader context of Islamic ornament as a whole, the formative role that geometry plays throughout the Islamic ornamental arts (including calligraphy, the floral idiom, dome decoration, geometric patterns, and more), and the underexamined question of pattern classification. Featuring over 600 beautiful color images, Islamic Geometric Patterns: Their Historical Development and Traditional Methods of Construction is a valuable addition to the literature of Islam...

Alignment of the HERA-B RICH optical system with data

International Nuclear Information System (INIS)

Gorisek, A.; Krizan, P.; Korpar, S.; Staric, M.

1999-01-01

We present a method for alignment of the mirror segments in the Ring Image Cherenkov Counter of the HERA-B spectrometer. The method will use recorded data, and was tested by using simulated events. The study shows that the mirrors can be aligned accurately enough to make the corresponding error in Cherenkov angle measurement negligible compared to other contributions. The mirrors are aligned relative to one mirror segment which can be chosen arbitrarily

Multiple sequence alignment accuracy and phylogenetic inference.

Science.gov (United States)

Ogden, T Heath; Rosenberg, Michael S

2006-04-01

Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

Research on localization and alignment technology for transfer cask

Energy Technology Data Exchange (ETDEWEB)

Wang, Jingchuan, E-mail: jchwang@sjtu.edu.cn [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China); Yang, Ming; Chen, Weidong [Department of Automation, Shanghai Jiao Tong University, Shanghai (China); Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai (China)

2015-10-15

Highlights: • A method for the alignment between TB and HCB based on localizability is proposed. • A localization method based on the localizability estimation is proposed to realize the cask's localization accurately and ensures the transfer cask's accurate docking in the front of the window of Tokmak Building. • The experimental results show that the proposed algorithm works well in the indoor simulation environment. This system will be test in EAST of China. - Abstract: According to the long length characteristics of transfer cask compared to the environment space between Tokmak Building (TB) and HCB (Hot Cell Building), this paper proposes an autonomous localization and alignment method for the internal components transportation and replacement. A localization method based on the localizability estimation is used to realize the cask's localization and navigation accurately. Once the cask arrives at the front of the TB window, the position and attitude measurement system is used to detect the relative alignment error between the seal door of pallet and the window of TB real-time. The alignment between seal door and TB window could be realized based on this offset. The simulation experiment based on the real model is designed according to the real TB situation. The experiment results show that the proposed localization and alignment method can be used for transfer cask.

Alignment between galaxies and large-scale structure

International Nuclear Information System (INIS)

Faltenbacher, A.; Li Cheng; White, Simon D. M.; Jing, Yi-Peng; Mao Shude; Wang Jie

2009-01-01

Based on the Sloan Digital Sky Survey DR6 (SDSS) and the Millennium Simulation (MS), we investigate the alignment between galaxies and large-scale structure. For this purpose, we develop two new statistical tools, namely the alignment correlation function and the cos(2θ)-statistic. The former is a two-dimensional extension of the traditional two-point correlation function and the latter is related to the ellipticity correlation function used for cosmic shear measurements. Both are based on the cross correlation between a sample of galaxies with orientations and a reference sample which represents the large-scale structure. We apply the new statistics to the SDSS galaxy catalog. The alignment correlation function reveals an overabundance of reference galaxies along the major axes of red, luminous (L ∼ * ) galaxies out to projected separations of 60 h- 1 Mpc. The signal increases with central galaxy luminosity. No alignment signal is detected for blue galaxies. The cos(2θ)-statistic yields very similar results. Starting from a MS semi-analytic galaxy catalog, we assign an orientation to each red, luminous and central galaxy, based on that of the central region of the host halo (with size similar to that of the stellar galaxy). As an alternative, we use the orientation of the host halo itself. We find a mean projected misalignment between a halo and its central region of ∼ 25 deg. The misalignment decreases slightly with increasing luminosity of the central galaxy. Using the orientations and luminosities of the semi-analytic galaxies, we repeat our alignment analysis on mock surveys of the MS. Agreement with the SDSS results is good if the central orientations are used. Predictions using the halo orientations as proxies for central galaxy orientations overestimate the observed alignment by more than a factor of 2. Finally, the large volume of the MS allows us to generate a two-dimensional map of the alignment correlation function, which shows the reference

A new correlation based alignment technique for use in electron tomography

International Nuclear Information System (INIS)

Jones, S.D.; Härting, M.

2013-01-01

In this paper we present a new correlation based method for the alignment of a single axis tilt series. Rather than performing the pairwise correlation procedure with the central image as the starting point, the method presented here calculates the optimal starting position within the tilt series and proceeds towards both ends. The starting position is determined by maximisation of a viability function, J, which rewards cumulative series correlation and penalises both cumulative series shift and distance from the centre of the image series. - Highlights: • Pairwise correlation based alignment is investigated as a function of seed position. • It is shown that the convention of using the central image as the seed is not optimal. • A function is proposed which improves alignment by finding the optimal seed position. • The method is found to produce alignment with lower residual scores with the phantom data. • Superior alignment is produced vs the standard method with the experimental data

XUV ionization of aligned molecules

Energy Technology Data Exchange (ETDEWEB)

Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

2011-11-15

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

XUV ionization of aligned molecules

International Nuclear Information System (INIS)

Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

2011-01-01

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO 2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

Science.gov (United States)

Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

2008-04-01

The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

Developing Employability Skills in Information System Graduates: Traditional vs. Innovative Teaching Methods

Science.gov (United States)

Osmani, Mohamad; Hindi, Nitham M.; Weerakkody, Vishanth

2018-01-01

It is widely acknowledged that traditional teaching methods such as lectures, textbooks and case study techniques on their own are not adequate to improving the most in-demand employability skills for graduates. The aim of this article is to explore the potential impact that novel learning and teaching methods can have on improving the…

Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

Institute of Scientific and Technical Information of China (English)

ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

2001-01-01

Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Z. Szillasi and G. Gomez.

2013-01-01

When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

Modeling electrical conductivities of nanocomposites with aligned carbon nanotubes

International Nuclear Information System (INIS)

Bao, W S; Meguid, S A; Zhu, Z H; Meguid, M J

2011-01-01

We have developed an improved three-dimensional (3D) percolation model to investigate the effect of the alignment of carbon nanotubes (CNTs) on the electrical conductivity of nanocomposites. In this model, both intrinsic and contact resistances are considered, and a new method of resistor network recognition that employs periodically connective paths is developed. This method leads to a reduction in the size effect of the representative cuboid in our Monte Carlo simulations. With this new technique, we were able to effectively analyze the effects of the CNT alignment upon the electrical conductivity of nanocomposites. Our model predicted that the peak value of the conductivity occurs for partially aligned rather than perfectly aligned CNTs. It has also identified the value of the peak and the corresponding alignment for different volume fractions of CNTs. Our model works well for both multi-wall CNTs (MWCNTs) and single-wall CNTs (SWCNTs), and the numerical results show a quantitative agreement with existing experimental observations.

Comparison of traditional and interactive teaching methods in a UK emergency department.

Science.gov (United States)

Armstrong, Peter; Elliott, Tim; Ronald, Julie; Paterson, Brodie

2009-12-01

Didactic teaching remains a core component of undergraduate education, but developing computer assisted learning (CAL) packages may provide useful alternatives. We compared the effectiveness of interactive multimedia-based tutorials with traditional, lecture-based models for teaching arterial blood gas interpretation to fourth year medical students. Participants were randomized to complete a tutorial in either lecture or multimedia format containing identical content. Upon completion, students answered five multiple choice questions assessing post-tutorial knowledge, and provided feedback on their allocated learning method. Marks revealed no significant difference between either group. All lecture candidates rated their teaching as good, compared with 89% of the CAL group. All CAL users found multiple choice questions assessment useful, compared with 83% of lecture participants. Both groups highlighted the importance of interaction. CAL complements other teaching methods, but should be seen as an adjunct to, rather than a replacement for, traditional methods, thus offering students a blended learning environment.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez and J. Pivarski

2011-01-01

Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

MUON DETECTORS: ALIGNMENT

CERN Multimedia

Gervasio Gomez

The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

Device and method for traditional chinese medicine diagnosis using radioactive tracer method

Energy Technology Data Exchange (ETDEWEB)

Wu, Shanling; Shen, Miaohe

1997-05-29

Disclosed is a device and method for traditional chinese medicine diagnosis using radioactive-tracer method. At least two nuclear radiation probes are arranged apart along the channels to detect the changing with time and on space of the intensity of radioactivity of the nuclear radioactive tracer which has been injected into the body in the channel position. The detected signals are amplified by amplifiers, and the outputs of the amplifiers are applied to data processing means which monitor the whole detecting process in real time and analyse and process the detected information about the changing of the intensity of radioactivity with time and on space indicating the operating of vital energy and blood, and obtain state parameters about operating of vital energy and blood in the body which is then output through data output means. (author) figs.

Heuristics for multiobjective multiple sequence alignment.

Science.gov (United States)

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

THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

CERN Document Server

Marti i Garcia, Salvador; The ATLAS collaboration

2018-01-01

The alignment of the ATLAS Inner Detector is performed with a track-based alignment algorithm. Its goal is to provide an accurate description of the detector geometry such that track parameters are accurately determined and free from biases. Its software implementation is modular and configurable, with a clear separation of the alignment algorithm from the detector system specifics and the database handling. The alignment must cope with the rapid movements of the detector as well as with the slow drift of the different mechanical units. Prompt alignment constants are derived for every run at the calibration stage. These sets of constants are then dynamically split from the beginning of the run in many chunks, allowing to describe the tracker geometry as it evolves with time. The alignment of the Inner Detector is validated and improved by studying resonance decays (Z and J/psi to mu+mu-), as well as using information from the calorimeter system with the E/p method with electrons. A detailed study of these res...

FACT. Normalized and asynchronous mirror alignment for Cherenkov telescopes

Energy Technology Data Exchange (ETDEWEB)

Mueller, Sebastian Achim [ETH Zurich (Switzerland); Buss, Jens [TU Dortmund (Germany)

2016-07-01

Imaging Atmospheric Cherenkov Telescopes (IACTs) need fast and large imaging optics to map the faint Cherenkov light emitted in cosmic ray air showers onto their image sensors. Segmented reflectors are inexpensive, lightweight and offer good image quality. However, alignment of the mirror facets remains a challenge. A good alignment is crucial in IACT observations to separate gamma rays from hadronic cosmic rays. We present a star tracking alignment method which is not restricted to clear nights. It normalizes the mirror facet reflections to be independent of the reference star or the cloud coverage. It records asynchronously of the telescope drive which makes the method easy to integrate in existing telescopes. It can be combined with remote facet actuation, but it does not need one to work. Furthermore, it can reconstruct all individual mirror facet point spread functions. We present the method and alignment results on the First Geiger-mode Photo Diode Avalanche Cherenkov Telescope (FACT) on the Canary Island of La Palma, Spain.

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

Energy Technology Data Exchange (ETDEWEB)

Suh, Y; Crane, C; Krishnan, S; Das, P; Koay, E; Beddar, S [UT MD Anderson Cancer Center, Houston, TX (United States)

2015-06-15

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 the 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.

THE APPARATUS FOR ALIGNMENT OF THE PHOTOMETRIC LAMP FILAMENT

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V. A. Dlugunovich

2015-01-01

Full Text Available During photometric measurements involving the use of photometric lamps it is necessary that the filament of lamp takes a strictly predetermined position with respect to the photodetector and the optical axis of the photometric setup. The errors in positioning of alignment filament with respect to the optical axis of the measuring system lead to increase the uncertainty of measurement of the photometric characteristics of the light sources. A typical method for alignment of filament of photometric lamps is based on the use a diopter tubes (telescopes. Using this method, the mounting of filament to the required position is carried out by successive approximations, which requires special concentration and a lot of time. The aim of this work is to develop an apparatus for alignment which allows simultaneous alignment of the filament of lamps in two mutually perpendicular planes. The method and apparatus for alignment of the photometric lamp filament during measurements of the photometric characteristics of light sources based on two digital video cameras is described in this paper. The apparatus allows to simultaneously displaying the image of lamps filament on the computer screen in two mutually perpendicular planes. The apparatus eliminates a large number of functional units requiring elementwise alignment and reduces the time required to carry out the alignment. The apparatus also provides the imaging of lamps filament with opaque coated on the bulb. The apparatus is used at the National standard of light intensity and illuminance units of the Republic of Belarus. 

BarraCUDA - a fast short read sequence aligner using graphics processing units

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Klus Petr

2012-01-01

Full Text Available Abstract Background With the maturation of next-generation DNA sequencing (NGS technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU, extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net

BarraCUDA - a fast short read sequence aligner using graphics processing units

LENUS (Irish Health Repository)

Klus, Petr

2012-01-13

Abstract Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http:\\/\\/seqbarracuda.sf.net

Isotope-selective ionization using four-pulse alignment

International Nuclear Information System (INIS)

Akagi, Hiroshi; Kasajima, Tatsuya; Kumada, Takayuki; Itakura, Ryuji; Yokoyama, Atsushi; Hasegawa, Hirokazu; Ohshima, Yasuhiro

2013-01-01

We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14 N 2 and 15 N 2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

Improving Nursing Students' Learning Outcomes in Fundamentals of Nursing Course through Combination of Traditional and e-Learning Methods.

Science.gov (United States)

Sheikhaboumasoudi, Rouhollah; Bagheri, Maryam; Hosseini, Sayed Abbas; Ashouri, Elaheh; Elahi, Nasrin

2018-01-01

Fundamentals of nursing course are prerequisite to providing comprehensive nursing care. Despite development of technology on nursing education, effectiveness of using e-learning methods in fundamentals of nursing course is unclear in clinical skills laboratory for nursing students. The aim of this study was to compare the effect of blended learning (combining e-learning with traditional learning methods) with traditional learning alone on nursing students' scores. A two-group post-test experimental study was administered from February 2014 to February 2015. Two groups of nursing students who were taking the fundamentals of nursing course in Iran were compared. Sixty nursing students were selected as control group (just traditional learning methods) and experimental group (combining e-learning with traditional learning methods) for two consecutive semesters. Both groups participated in Objective Structured Clinical Examination (OSCE) and were evaluated in the same way using a prepared checklist and questionnaire of satisfaction. Statistical analysis was conducted through SPSS software version 16. Findings of this study reflected that mean of midterm (t = 2.00, p = 0.04) and final score (t = 2.50, p = 0.01) of the intervention group (combining e-learning with traditional learning methods) were significantly higher than the control group (traditional learning methods). The satisfaction of male students in intervention group was higher than in females (t = 2.60, p = 0.01). Based on the findings, this study suggests that the use of combining traditional learning methods with e-learning methods such as applying educational website and interactive online resources for fundamentals of nursing course instruction can be an effective supplement for improving nursing students' clinical skills.

BFAST: an alignment tool for large scale genome resequencing.

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Nils Homer

2009-11-01

Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

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Yiran Huang

Full Text Available 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.

The Use Potential of Traditional Building Materials for the Realization of Structures by Modern Methods of Construction

Science.gov (United States)

Spišáková, Marcela; Mačková, Daniela

2015-11-01

The sustainable building has taken off in recent years with many investors looking for new and different methods of construction. The traditional building materials can be made out of natural materials, while others can help to lower energy costs of the occupant once built. Regardless of what the goal of the investor is, traditional building materials and their use is on the rise. The submitted paper provides an overview of natural building materials and possible modern building systems using these construction materials. Based on the questionnaire survey is defined the use potential of traditional building materials for the realization of the construction by methods of modern constructions and then are determined the drivers and barriers of traditional materials through using modern methods of construction. Considering the analysis of the achieved results, we can identify the gaps in the construction market in Slovakia and also to assess the perception of potential investors in the field of traditional building materials use, which is the purpose of submitted paper.

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

Science.gov (United States)

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.

Alignment of the eight beams Octal 82 laser

International Nuclear Information System (INIS)

Josse, Michel.

1982-10-01

The OCTAL 82 laser facility is a Neodymium glass laser system, recently put in operation at Limeil, France. It is designed to create high energy light beams during very short periods of time in the nanosecond range and shorter, in order to irradiate and compress microscopic fusion targets to extremely high densities. The alignment is undertaken in two stages, each using a telescope with vidicon detectors connected to a real time computer named ''CENTROIDE'' which displays the digitized image on a color TV screen. First, a refracting telescope is used to inject the front-end beam into the preamplifier assembly and to align all its optical components. Second, a reflecting telescope and ten insertable mirrors are used to align the eight individual power chains and the beam splitter arrays. The alignment method works with a manually controlled closed loop which is the most flexible approach that can meet our dual objectives of reliability and accuracy. The over all alignment of OCTAL 82 was first completed in may 1982 and since that time only minor routine realignments have been made, thereby proving the feasibility of the method

Software alignment of the LHCb inner tracker sensors

Energy Technology Data Exchange (ETDEWEB)

Maciuc, Florin

2009-04-20

This work uses the Millepede linear alignment method, which is essentially a {chi}{sup 2} minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate {chi}{sup 2} model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from {chi}{sup 2} function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

Software alignment of the LHCb inner tracker sensors

International Nuclear Information System (INIS)

Maciuc, Florin

2009-01-01

This work uses the Millepede linear alignment method, which is essentially a χ 2 minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate χ 2 model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from χ 2 function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

Software alignment of the LHCb inner tracker sensors

Energy Technology Data Exchange (ETDEWEB)

Maciuc, Florin

2009-04-20

This work uses the Millepede linear alignment method, which is essentially a {chi}{sup 2} minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate {chi}{sup 2} model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from {chi}{sup 2} function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

Enterprise strategic alignment method: a cross-disciplinary capability-driven approach

NARCIS (Netherlands)

Aldea, Adina

2017-01-01

The environment of organisations is changing more rapidly in the recent years, which makes it increasingly more difficult to stay competitive. Organisations need to ensure that when they make transformations, they focus on maintaining or improving their strategic alignment. However, the current

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

Precision alignment and calibration of optical systems using computer generated holograms

Science.gov (United States)

Coyle, Laura Elizabeth

As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the

Open bite treatment using clear aligners.

Science.gov (United States)

Guarneri, Maria Paola; Oliverio, Teresa; Silvestre, Ivana; Lombardo, Luca; Siciliani, Giuseppe

2013-09-01

A 35-year-old female patient with dentoalveolar open bite of 4 mm, molar Class I malocclusion, centered midlines, moderate crowding, and labial inclination of the lower incisor was treated with clear aligners to reduce protrusion and close the anterior open bite. The result showed that clear aligners were an effective method with which to correct this malocclusion. The treatment was complete after 18 months. The patient was satisfied with her new appearance and function.

Wet etch methods for InAs nanowire patterning and self-aligned electrical contacts

Science.gov (United States)

Fülöp, G.; d'Hollosy, S.; Hofstetter, L.; Baumgartner, A.; Nygård, J.; Schönenberger, C.; Csonka, S.

2016-05-01

Advanced synthesis of semiconductor nanowires (NWs) enables their application in diverse fields, notably in chemical and electrical sensing, photovoltaics, or quantum electronic devices. In particular, indium arsenide (InAs) NWs are an ideal platform for quantum devices, e.g. they may host topological Majorana states. While the synthesis has been continously perfected, only a few techniques have been developed to tailor individual NWs after growth. Here we present three wet chemical etch methods for the post-growth morphological engineering of InAs NWs on the sub-100 nm scale. The first two methods allow the formation of self-aligned electrical contacts to etched NWs, while the third method results in conical shaped NW profiles ideal for creating smooth electrical potential gradients and shallow barriers. Low temperature experiments show that NWs with etched segments have stable transport characteristics and can serve as building blocks of quantum electronic devices. As an example we report the formation of a single electrically stable quantum dot between two etched NW segments.

The determinants of traditional medicine use in Northern Tanzania: a mixed-methods study.

Directory of Open Access Journals (Sweden)

John W Stanifer

Full Text Available Traditional medicines are an important part of healthcare in sub-Saharan Africa, and building successful disease treatment programs that are sensitive to traditional medicine practices will require an understanding of their current use and roles, including from a biomedical perspective. Therefore, we conducted a mixed-method study in Northern Tanzania in order to characterize the extent of and reasons for the use of traditional medicines among the general population so that we can better inform public health efforts in the region.Between December 2013 and June 2014 in Kilimanjaro, Tanzania, we conducted 5 focus group discussions and 27 in-depth interviews of key informants. The data from these sessions were analyzed using an inductive framework method with cultural insider-outsider coding. From these results, we developed a structured survey designed to test different aspects of traditional medicine use and administered it to a random sample of 655 adults from the community. The results were triangulated to explore converging and diverging themes.Most structured survey participants (68% reported knowing someone who frequently used traditional medicines, and the majority (56% reported using them themselves in the previous year. The most common uses were for symptomatic ailments (42%, chronic diseases (15%, reproductive problems (11%, and malaria/febrile illnesses (11%. We identified five major determinants for traditional medicine use in Northern Tanzania: biomedical healthcare delivery, credibility of traditional practices, strong cultural identities, individual health status, and disease understanding.In order to better formulate effective local disease management programs that are sensitive to TM practices, we described the determinants of TM use. Additionally, we found TM use to be high in Northern Tanzania and that its use is not limited to lower-income areas or rural settings. After symptomatic ailments, chronic diseases were reported as

A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.

Science.gov (United States)

Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L

2018-05-16

During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Directory of Open Access Journals (Sweden)

Kierzynka Michal

2011-05-01

Full Text Available Abstract Background 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. Results 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. Conclusions 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.

Pattern analysis of aligned nanowires in a microchannel

International Nuclear Information System (INIS)

Jeon, Young Jin; Kang, Hyun Wook; Ko, Seung Hwan; Sung, Hyung Jin

2013-01-01

An image processing method for evaluating the quality of nanowire alignment in a microchannel is described. A solution containing nanowires flowing into a microchannel will tend to deposit the nanowires on the bottom surface of the channel via near-wall shear flows. The deposited nanowires generally form complex directional structures along the direction of flow, and the physical properties of these structures depend on the structural morphology, including the alignment quality. A quantitative analysis approach to characterizing the nanowire alignment is needed to estimate the useful features of the nanowire structures. This analysis consists of several image processing methods, including ridge detection, texton analysis and autocorrelation function (ACF) calculation. The ridge detection method improved the ACF by extracting nanowire frames 1–2 pixels in width. Dilation filters were introduced to permit a comparison of the ACF results calculated from different images, regardless of the nanowire orientation. An ACF based on the FFT was then calculated over a square interrogation window. The alignment angle probability distribution was obtained using texton analysis. Monte Carlo simulations of artificially generated images were carried out, and the new algorithm was applied to images collected using two types of microscopy. (paper)

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

Science.gov (United States)

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

Web-based versus traditional lecture: are they equally effective as a flexible bronchoscopy teaching method?

OpenAIRE

Sterse Mata, Caio Augusto [UNIFESP; Ota, Luiz Hirotoshi [UNIFESP; Suzuki, Iunis [UNIFESP; Telles, Adriana [UNIFESP; Miotto, Andre [UNIFESP; Leao, Luiz Eduardo Villaca [UNIFESP

2012-01-01

This study compares the traditional live lecture to a web-based approach in the teaching of bronchoscopy and evaluates the positive and negative aspects of both methods. We developed a web-based bronchoscopy curriculum, which integrates texts, images and animations. It was applied to first-year interns, who were later administered a multiple-choice test. Another group of eight first-year interns received the traditional teaching method and the same test. the two groups were compared using the...

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

2012-01-01

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.

2012-01-26

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

Oriented Edge-Based Feature Descriptor for Multi-Sensor Image Alignment and Enhancement

Directory of Open Access Journals (Sweden)

Myung-Ho Ju

2013-10-01

Full Text Available In this paper, we present an efficient image alignment and enhancement method for multi-sensor images. The shape of the object captured in a multi-sensor images can be determined by comparing variability of contrast using corresponding edges across multi-sensor image. Using this cue, we construct a robust feature descriptor based on the magnitudes of the oriented edges. Our proposed method enables fast image alignment by identifying matching features in multi-sensor images. We enhance the aligned multi-sensor images through the fusion of the salient regions from each image. The results of stitching the multi-sensor images and their enhancement demonstrate that our proposed method can align and enhance multi-sensor images more efficiently than previous methods.

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

Directory of Open Access Journals (Sweden)

Lund Ole

2009-09-01

Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.

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

Science.gov (United States)

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.

Dynamic evaluation method of lower limbs joint alignment (MADAAMI for dancers during the plié

Directory of Open Access Journals (Sweden)

Kaanda Nabilla Souza Gontijo

Full Text Available Abstract In classical ballet, the joint misalignments during the plié can generate various injuries. To evaluate potential misalignments during the plié the aim of this study was to present a method for dynamic evaluation of lower limb alignment articulation (called MADAAMI. MADAAMI was validated by 12 experts, and for the evaluation of its reproducibility and for agreement with 3D kinematics, 20 dancers were assessed using a video recording of their plié. For statistical analysis we used the Kappa coefficient (k (p 0.40 and C > 80%, and it is a suitable and valid method for use by the same examiner.

Traditional methods v. new technologies – dilemmas for dietary assessment in large-scale nutrition surveys and studies

DEFF Research Database (Denmark)

Amoutzopoulos, B.; Steer, T.; Roberts, C.

2018-01-01

assessment in population surveys’, was held at the 9th International Conference on Diet and Activity Methods (ICDAM9), Brisbane, September 2015. Despite respondent and researcher burden, traditional methods have been most commonly used in nutrition surveys. However, dietary assessment technologies offer...... of traditional dietary assessment methods (food records, FFQ, 24 h recalls, diet history with interviewer-assisted data collection) v. new technology-based dietary assessment methods (web-based and mobile device applications). The panel discussion ‘Traditional methods v. new technologies: dilemmas for dietary......The aim of the present paper is to summarise current and future applications of dietary assessment technologies in nutrition surveys in developed countries. It includes the discussion of key points and highlights of subsequent developments from a panel discussion to address strengths and weaknesses...

Electron re-scattering from aligned linear molecules using the R-matrix method

International Nuclear Information System (INIS)

Harvey, A G; Tennyson, J

2009-01-01

Electron re-scattering in a strong laser field provides an important probe of molecular structure and processes. The laser field drives the ionization of the molecule, followed by acceleration and subsequent recollision of the electron with the parent molecular ion, the scattered electrons carry information about the nuclear geometry and electronic states of the molecular ion. It is advantageous in strong field experiments to work with aligned molecules, which introduces extra physics compared to the standard gas-phase, electron-molecule scattering problem. The formalism for scattering from oriented linear molecules is presented and applied to H 2 and CO 2 . Differential cross sections are presented for (re-)scattering by these systems concentrating on the most common, linear alignment. In H 2 these cross sections show significant angular structure which, particularly for a scattering angle of 90 deg., are predicted to vary significantly between re-collisions stimulated by an even or an odd number of photons. In CO 2 these cross sections are zero indicating the necessity of using non-parallel alignment with this molecule.

Comparing the Effects of Objective Structured Assessment of Technical Skills (OSATS) and Traditional Method on Learning of Students.

Science.gov (United States)

Mansoorian, Mohammad Reza; Hosseiny, Marzeih Sadat; Khosravan, Shahla; Alami, Ali; Alaviani, Mehri

2015-06-01

Despite the benefits of the objective structured assessment of technical skills (OSATS) and it appropriateness for evaluating clinical abilities of nursing students , few studies are available on the application of this method in nursing education. The purpose of this study was to compare the effect of using OSATS and traditional methods on the students' learning. We also aimed to signify students' views about these two methods and their views about the scores they received in these methods in a medical emergency course. A quasi-experimental study was performed on 45 first semester students in nursing and medical emergencies passing a course on fundamentals of practice. The students were selected by a census method and evaluated by both the OSATS and traditional methods. Data collection was performed using checklists prepared based on the 'text book of nursing procedures checklists' published by Iranian nursing organization and a questionnaire containing learning rate and students' estimation of their received scores. Descriptive statistics as well as paired t-test and independent samples t-test were used in data analysis. The mean of students' score in OSATS was significantly higher than their mean score in traditional method (P = 0.01). Moreover, the mean of self-evaluation score after the traditional method was relatively the same as the score the students received in the exam. However, the mean of self-evaluation score after the OSATS was relatively lower than the scores the students received in the OSATS exam. Most students believed that OSATS can evaluate a wide range of students' knowledge and skills compared to traditional method. Results of this study indicated the better effect of OSATS on learning and its relative superiority in precise assessment of clinical skills compared with the traditional evaluation method. Therefore, we recommend using this method in evaluation of students in practical courses.

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

Science.gov (United States)

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

Operational auditing versus traditional method: A comparative investigation

Directory of Open Access Journals (Sweden)

Reza Tehrani

2013-06-01

Full Text Available Operational auditing is one of the management consultancy services whose significance is on the rise day by day. This approach is, clearly, a systematic and methodical process used to evaluate economic savings of financial processes in organizations and the results of the evaluations are reported to interested people along with some comments to improve operational processes. Accordingly, it appears that the proper employment of the existing rationale in operational auditing can be a significant step towards the improvement of financial efficiency in Iranian public and private banking sector. This paper studies the effects of operational auditing on the improvement of economic saving of financial processes in Iranian private banks compared with traditional approaches where the operations are based on financial statements. The population of this survey includes 15 private and public Iranian banks and the proposed study selects 78 branches, randomly. The Cronbach alpha was used to test the reliability a questionnaire employed to collect the needed data in this study. The results obtained by SPSS Software indicated that the reliability of the instrumentsanged between 0.752 and 0.867, suggesting an acceptable level of the reliability for the questionnaire. Besides, content validity was used to confirm the validity of the instrument. The results of the study indicated that the operational auditing as a useful approach influencing the financial efficiency of public and private banks has significantly transformed the traditional thinking in the field of management auditing. The operational auditing has a number of significant advantages including a better method of controlling financial operations within Iranian banks, efficient planning in the future, facilitating efficient, appropriate, and accurate management decision making, and sound evaluation of managers’ financial operations.

Optimization methods of pulse-to-pulse alignment using femtosecond pulse laser based on temporal coherence function for practical distance measurement

Science.gov (United States)

Liu, Yang; Yang, Linghui; Guo, Yin; Lin, Jiarui; Cui, Pengfei; Zhu, Jigui

2018-02-01

An interferometer technique based on temporal coherence function of femtosecond pulses is demonstrated for practical distance measurement. Here, the pulse-to-pulse alignment is analyzed for large delay distance measurement. Firstly, a temporal coherence function model between two femtosecond pulses is developed in the time domain for the dispersive unbalanced Michelson interferometer. Then, according to this model, the fringes analysis and the envelope extraction process are discussed. Meanwhile, optimization methods of pulse-to-pulse alignment for practical long distance measurement are presented. The order of the curve fitting and the selection of points for envelope extraction are analyzed. Furthermore, an averaging method based on the symmetry of the coherence function is demonstrated. Finally, the performance of the proposed methods is evaluated in the absolute distance measurement of 20 μ m with path length difference of 9 m. The improvement of standard deviation in experimental results shows that these approaches have the potential for practical distance measurement.

Validation and prediction of traditional Chinese physical operation on spinal disease using multiple deformation models.

Science.gov (United States)

Pan, Lei; Yang, Xubo; Gu, Lixu; Lu, Wenlong; Fang, Min

2011-03-01

Traditional Chinese medical massage is a physical manipulation that achieves satisfactory results on spinal diseases, according to its advocates. However, the method relies on an expert's experience. Accurate analysis and simulation of massage are essential for validation of traditional Chinese physical treatment. The objective of this study is to provide analysis and simulation that can reproducibly verify and predict treatment efficacy. An improved physical multi-deformation model for simulating human cervical spine is proposed. First, the human spine, which includes muscle, vertebrae and inter- vertebral disks, are segmented and reconstructed from clinical CT and MR images. Homogeneous landmark registration is employed to align the spine models before and after the massage manipulation. Central line mass spring and contact FEM deformation models are used to individually evaluate spinal anatomy variations. The response of the human spine during the massage process is simulated based on specific clinical cases. Ten sets of patient data, including muscle-force relationships, displacement of vertebrae, strain and stress distribution on inter-vertebral disks were collected, including the pre-operation, post-operation and the 3-month follow-up. The simulation results demonstrate that traditional Chinese massage could significantly affect and treat most mild spinal disease. A new method that simulates a traditional Chinese medical massage operation on the human spine may be a useful tool to scientifically validate and predict treatment efficacy.

The Use Potential of Traditional Building Materials for the Realization of Structures by Modern Methods of Construction

Directory of Open Access Journals (Sweden)

Spišáková Marcela

2015-11-01

Full Text Available The sustainable building has taken off in recent years with many investors looking for new and different methods of construction. The traditional building materials can be made out of natural materials, while others can help to lower energy costs of the occupant once built. Regardless of what the goal of the investor is, traditional building materials and their use is on the rise. The submitted paper provides an overview of natural building materials and possible modern building systems using these construction materials. Based on the questionnaire survey is defined the use potential of traditional building materials for the realization of the construction by methods of modern constructions and then are determined the drivers and barriers of traditional materials through using modern methods of construction. Considering the analysis of the achieved results, we can identify the gaps in the construction market in Slovakia and also to assess the perception of potential investors in the field of traditional building materials use, which is the purpose of submitted paper.

Implementation of a Parallel Protein Structure Alignment Service on Cloud

Directory of Open Access Journals (Sweden)

Che-Lun Hung

2013-01-01

Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

Efficient and robust model-to-image alignment using 3D scale-invariant features.

Science.gov (United States)

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Measuring the distance between multiple sequence alignments.

Science.gov (United States)

Blackburne, Benjamin P; Whelan, Simon

2012-02-15

Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

DEFF Research Database (Denmark)

Wernersson, Rasmus; Pedersen, Anders Gorm

2003-01-01

The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

Science.gov (United States)

Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

2016-07-01

It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. © 2016 Wiley Periodicals, Inc.

A novel classification method for aid decision of traditional Chinese patent medicines for stroke treatment.

Science.gov (United States)

Zhao, Yufeng; Liu, Bo; He, Liyun; Bai, Wenjing; Yu, Xueyun; Cao, Xinyu; Luo, Lin; Rong, Peijing; Zhao, Yuxue; Li, Guozheng; Liu, Baoyan

2017-09-01

Traditional Chinese patent medicines are widely used to treat stroke because it has good efficacy in the clinical environment. However, because of the lack of knowledge on traditional Chinese patent medicines, many Western physicians, who are accountable for the majority of clinical prescriptions for such medicine, are confused with the use of traditional Chinese patent medicines. Therefore, the aid-decision method is critical and necessary to help Western physicians rationally use traditional Chinese patent medicines. In this paper, Manifold Ranking is employed to develop the aid-decision model of traditional Chinese patent medicines for stroke treatment. First, 115 stroke patients from three hospitals are recruited in the cross-sectional survey. Simultaneously, traditional Chinese physicians determine the traditional Chinese patent medicines appropriate for each patient. Second, particular indicators are explored to characterize the population feature of traditional Chinese patent medicines for stroke treatment. Moreover, these particular indicators can be easily obtained byWestern physicians and are feasible for widespread clinical application in the future. Third, the aid-decision model of traditional Chinese patent medicines for stroke treatment is constructed based on Manifold Ranking. Experimental results reveal that traditional Chinese patent medicines can be differentiated. Moreover, the proposed model can obtain high accuracy of aid decision.

Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

Science.gov (United States)

Guzzi, Pietro Hiram; Milenković, Tijana

2017-01-05

Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A comparative study of traditional lecture methods and interactive lecture methods in introductory geology courses for non-science majors at the college level

Science.gov (United States)

Hundley, Stacey A.

In recent years there has been a national call for reform in undergraduate science education. The goal of this reform movement in science education is to develop ways to improve undergraduate student learning with an emphasis on developing more effective teaching practices. Introductory science courses at the college level are generally taught using a traditional lecture format. Recent studies have shown incorporating active learning strategies within the traditional lecture classroom has positive effects on student outcomes. This study focuses on incorporating interactive teaching methods into the traditional lecture classroom to enhance student learning for non-science majors enrolled in introductory geology courses at a private university. Students' experience and instructional preferences regarding introductory geology courses were identified from survey data analysis. The information gained from responses to the questionnaire was utilized to develop an interactive lecture introductory geology course for non-science majors. Student outcomes were examined in introductory geology courses based on two teaching methods: interactive lecture and traditional lecture. There were no significant statistical differences between the groups based on the student outcomes and teaching methods. Incorporating interactive lecture methods did not statistically improve student outcomes when compared to traditional lecture teaching methods. However, the responses to the survey revealed students have a preference for introductory geology courses taught with lecture and instructor-led discussions and students prefer to work independently or in small groups. The results of this study are useful to individuals who teach introductory geology courses and individuals who teach introductory science courses for non-science majors at the college level.

Peak alignment and robust principal component analysis of gas chromatograms of fatty acid methyl esters and volatiles

DEFF Research Database (Denmark)

Frosch, Stina; Jørgensen, Bo

2007-01-01

. The ability of robust algorithms to deal with outlier problems, including both sample-wise and element-wise outliers, and the advantages and drawbacks of two robust PCA methods, robust PCA (ROBPCA) and robust singular value decomposition when analysing these GC data were investigated. The results show...... that the usage of ROPCA is advantageous, compared with traditional PCA, when analysing the entire profile of chromatographic data in cases of sub-optimally aligned data. It also demonstrates how choosing the most robust PCA (sample or element-wise) depends on the type of outliers present in the data set....

A simple method for fabrication of electrospun fibers with controlled degree of alignment having potential for nerve regeneration applications

Energy Technology Data Exchange (ETDEWEB)

Vimal, Sunil Kumar; Ahamad, Nadim; Katti, Dhirendra S., E-mail: dsk@iitk.ac.in

2016-06-01

In peripheral nerve injuries where direct suturing of nerve endings is not feasible, nerve regeneration has been facilitated through the use of artificially aligned fibrous scaffolds that provide directional growth of neurons to bridge the gap. The degree of fiber alignment is crucial and can impact the directionality of cells in a fibrous scaffold. While there have been multiple approaches that have been used for controlling fiber alignment, however, they have been associated with a compromised control on other properties, such as diameter, morphology, curvature, and topology of fibers. Therefore, the present study demonstrates a modified electrospinning set-up, that enabled fabrication of electrospun fibers with controlled degree of alignment from non-aligned (NA), moderately aligned (MA, 75%) to highly aligned (HA, 95%) sub-micron fibers while keeping other physical properties unchanged. The results demonstrate that the aligned fibers (MA and HA) facilitated directional growth of human astrocytoma cells (U373), wherein the aspect ratio of cells was found to increase with an increase in degree of fibers alignment. In contrast to NA and MA fibers, the HA fibers showed improved contact guidance to U373 cells that was demonstrated by a significantly higher cell aspect ratio and nuclear aspect ratio. In conclusion, the present study demonstrated a modified electrospinning setup to fabricate differentially aligned fibrous scaffolds with the HA fibers showing potential for use in neural tissue engineering. - Highlights: • Modified electrospinning set-up for fabrication of fibers with controlled alignment • Three parameter-based control on the degree of alignment of fibers • The aligned fibers enhanced cell elongation and cell-cell contact. • The aligned fibers show potential for use in nerve regeneration.

Traditional and robust vector selection methods for use with similarity based models

International Nuclear Information System (INIS)

Hines, J. W.; Garvey, D. R.

2006-01-01

Vector selection, or instance selection as it is often called in the data mining literature, performs a critical task in the development of nonparametric, similarity based models. Nonparametric, similarity based modeling (SBM) is a form of 'lazy learning' which constructs a local model 'on the fly' by comparing a query vector to historical, training vectors. For large training sets the creation of local models may become cumbersome, since each training vector must be compared to the query vector. To alleviate this computational burden, varying forms of training vector sampling may be employed with the goal of selecting a subset of the training data such that the samples are representative of the underlying process. This paper describes one such SBM, namely auto-associative kernel regression (AAKR), and presents five traditional vector selection methods and one robust vector selection method that may be used to select prototype vectors from a larger data set in model training. The five traditional vector selection methods considered are min-max, vector ordering, combination min-max and vector ordering, fuzzy c-means clustering, and Adeli-Hung clustering. Each method is described in detail and compared using artificially generated data and data collected from the steam system of an operating nuclear power plant. (authors)

Reduce conflicts in traditional merariq traditions through the long tradition of the tribal people of sasak lombok

Science.gov (United States)

Sarmini; Nadiroh, Ulin; Saeun Fahmi, Muhammad

2018-01-01

Marriage is a container for framing the inner-to-heart relationship, the bond of love and affection between a man and woman to nurture a joy of happiness. This study aims to find out how the process and stages in traditional merariq traditions in the Sasak people, conflicts arising from merariq traditions, and reduce conflict through the tradition of selabar. The method used in this research is qualitative analysis method. In the process, merariq tradition is done by kidnapping the bride without the knowledge of the parents or the family of the women. There are several stages that must be passed by the bride and groom in the tradition merariq, namely: besejati, nyelabar, bait wali, sorong serah dan nyongkolang. Conflict that often arises, for internal family, merariq often become a place of coercion against the female family. For society, merariq impact on disruption of harmony of social life. In order to reduce the conflicts done selabar tradition, the tragedy is regarded as an alternative problem solving in the form of negotiations between the bride and groom’s family and the bride-to-be relating to ajikrame and pisuke transactions.

Principles of alignment of multibeam lasers for thermonuclear purposes

International Nuclear Information System (INIS)

Basovy, N.G.; Ol'shevskii, Y.N.; Belyan, V.F.

1980-01-01

The concrete object of the investigation is the alignment of the high-power 12-channel ''Del'fin'' neodymium-glass laser facilaity. The objects of the alignment are the optical channel of the laser installation, the system for pointing and focusing the laser radiation on the target, the system for positioning the target in the focal volume, and the system for monitoring the optical quality of the elements of the laser installation and laser beams and also the conditions of the target irradiation in the vacuum chamber. The list of requirements that must be satisfied by the alignment beams, the possible sources of alignment beams, the makeup of the apparatus, and the methods of aligning the laser facility are considered. The principles and the actual systems of automatic alignment of the optical elements are described, as are the operating models of the automatized units. The problem of simulating the working laser beams by the alignment beams and the possibility of automatizing the control of the spatial and angular characteristics of the laser radiation are discussed. The system for controlling the alignment processes by means of a laser is considered, as it also a scheme for incorporating the automatized alignment subsystem in the overall system for the automation of the ''Del'fin'' facility

Application of Improved 5th-Cubature Kalman Filter in Initial Strapdown Inertial Navigation System Alignment for Large Misalignment Angles.

Science.gov (United States)

Wang, Wei; Chen, Xiyuan

2018-02-23

In view of the fact the accuracy of the third-degree Cubature Kalman Filter (CKF) used for initial alignment under large misalignment angle conditions is insufficient, an improved fifth-degree CKF algorithm is proposed in this paper. In order to make full use of the innovation on filtering, the innovation covariance matrix is calculated recursively by an innovative sequence with an exponent fading factor. Then a new adaptive error covariance matrix scaling algorithm is proposed. The Singular Value Decomposition (SVD) method is used for improving the numerical stability of the fifth-degree CKF in this paper. In order to avoid the overshoot caused by excessive scaling of error covariance matrix during the convergence stage, the scaling scheme is terminated when the gradient of azimuth reaches the maximum. The experimental results show that the improved algorithm has better alignment accuracy with large misalignment angles than the traditional algorithm.

MUON DETECTORS: ALIGNMENT

CERN Multimedia

S. Szillasi

2013-01-01

The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

Science.gov (United States)

Lee, Hui Sun; Im, Wonpil

2013-01-01

Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

Association between traditional oral hygiene methods with tooth wear, gingival bleeding, and recession: A descriptive cross-sectional study.

Science.gov (United States)

Shah, Naseem; Mathur, Vijay Prakash; Jain, Veena; Logani, Ajay

2018-01-01

Oral hygiene maintenance is crucial for prevention of various oral diseases. Oral hygiene practices across the country vary largely and people in peri-urban and rural areas use traditional methods of oral hygiene like powders, bark, oil and salt etc. Their effect on oral soft and hard tissues need to be studied to understand their beneficial and/ or harmful effects on maintenance of oral hygiene and prevention or causation of oral diseases. This study aimed to assess the plaque-cleaning efficacy, gingival bleeding, recession and tooth wear with different traditional oral hygiene methods as compared to use of toothpaste-toothbrush, the most accepted method of oral hygiene practice. Hospital based cross sectional analytical study. Results: Total 1062 traditional oral hygiene method users were compared with same number of toothpaste-brush users. The maximum number in the former group used tooth powder (76%) as compared to other indigenous methods, such as use of bark of trees etc and out of tooth powder users; almost 75% reported using red toothpowder. The plaque scores and gingival bleeding & recession were found to be more in traditional oral hygiene method users. The toothwear was also more severe among the toothpowder users. Traditional methods were found to be inferior in plaque control as was documented by increased bleeding and gingival recession. Its effect on hard tissues of teeth was very damaging with higher tooth wear scores on all surfaces.

Alignment of the MSGC barrel support structure

International Nuclear Information System (INIS)

Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala; Antti, Onnela

1999-01-01

The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

Alignment of the MSGC barrel support structure

Energy Technology Data Exchange (ETDEWEB)

Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala [HIP, Helsinki Institute of Physics, CERN/EP, Geneva (Switzerland); Antti, Onnela [CERN, Conseil Europeen pour la recherche nucleaire, Laboratoire europeen pour la physique des particules, Geneve (Switzerland)

1999-07-01

The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

Directory of Open Access Journals (Sweden)

Sadreyev Ruslan I

2004-08-01

Full Text Available Abstract Background Profile-based analysis of multiple sequence alignments (MSA allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1 MSA position and a set of predicted residue frequencies, and (2 between two MSA positions. These problems are important for (i evaluation and optimization of methods predicting residue occurrence at protein positions; (ii detection of potentially misaligned regions in automatically produced alignments and their further refinement; and (iii detection of sites that determine functional or structural specificity in two related families. Results For problems (1 and (2, we propose analytical estimates of P-value and apply them to the detection of significant positional dissimilarities in various experimental situations. (a We compare structure-based predictions of residue propensities at a protein position to the actual residue frequencies in the MSA of homologs. (b We evaluate our method by the ability to detect erroneous position matches produced by an automatic sequence aligner. (c We compare MSA positions that correspond to residues aligned by automatic structure aligners. (d We compare MSA positions that are aligned by high-quality manual superposition of structures. Detected dissimilarities reveal shortcomings of the automatic methods for residue frequency prediction and alignment construction. For the high-quality structural alignments, the dissimilarities suggest sites of potential functional or structural importance. Conclusion The proposed computational method is of significant potential value for the analysis of protein families.

Relevance-based evaluation of alignment approaches: The OAEI2007 food task revisited

NARCIS (Netherlands)

Hage, W.R. van; Kolb, H.; Schreiber, G.

2008-01-01

Current state-of-the-art ontology-alignment evaluation methods are based on the assumption that alignment relations come in two flavors: correct and incorrect. Some alignment systems find more correct mappings than others and hence, by this assumption, they perform better. In practical applications

Alignment-free genome tree inference by learning group-specific distance metrics.

Science.gov (United States)

Patil, Kaustubh R; McHardy, Alice C

2013-01-01

Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.

Alignment of the drift tube detector at the neutrino oscillation experiment OPERA; Alignment des Driftroehrendetektors am Neutrino-Oszillationsexperiment OPERA

Energy Technology Data Exchange (ETDEWEB)

Goellnitz, Christoph

2012-09-15

The present thesis was composed during the course of the OPERA experiment, which aims to give a direct evidence for neutrino oscillations in the channel {nu}{sub {mu}} {yields} {nu}{sub {tau}}. The OPERA detector is designed to observe the appearance of tau neutrinos in an originally pure muon neutrino beam, the CNGS beam. As important part of the detector the precision tracker (PT), a drift tube detector, consists of 9504 drift tubes in 198 modules. In this thesis, several parts of the slow control of the PT are developed and implemented to ensure operation during data taking over several years. The main part is the geometric calibration, the alignment of the detector. The alignment procedure contains both hardware and software parts, the software methods are developed and applied. Using straight particle tracks, the detector components are geometrically corrected. A special challenge for the alignment for the PT is the fact that at this kind of low-rate experiment only a small number of particle tracks is available. With software-based corrections of the module rotation, a systematic error of 0.2 mrad has been attained, for corrections of translation, a systematic error of 32 {mu}m is reached. For the alignment between two adjacent PT walls, the statistical error is less than 8 {mu}m. All results of the position monitoring system are considered. All developed methods are tested with Monte Carlo simulations. The detector requirements ({Delta}p/p {<=} 0.25 below 25 GeV) are met. The analysis of the momentum measurement for high energies above 25 GeV demonstrates the resulting improvement. The mean momentum is falling significantly using the new alignment values. The significance of the detector alignment becomes most evident in the analysis of cosmic particles. The muon charge ratio R{sub {mu}} is expected not to be angular dependent. The {chi}{sup 2} probability of the measured distribution improves up to 58%. The muon charge ratio was also investigated in

MaxAlign: maximizing usable data in an alignment

DEFF Research Database (Denmark)

Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

2007-01-01

Align. 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. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

Identification of some Fusarium species from selected crop seeds using traditional method and BIO-PCR

Directory of Open Access Journals (Sweden)

Tomasz Kulik

2012-12-01

Full Text Available We identified a species level of the fungal cultures isolated from selected crop seeds using traditional method and BIO-PCR. The use of BIO-PCR did not correspond completely to the morphological analyses. Both methods showed increased infection with F. poae in winter wheat seed sample originated from north Poland. Fungal culture No 40 (isolated from faba bean and identified with traditional method as mixed culture with F. culmorum and F. graminearum did not produce expected product after PCR reaction with species specific primers OPT18F470, OPT18R470. However, the use of additional primers Fc01F, Fc01R allowed for reliable identification of F. culmorum in the culture.

Aligning for Innovation - Alignment Strategy to Drive Innovation

Science.gov (United States)

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.

Rethinking traditional methods for measuring intellectual capital.

Science.gov (United States)

Corso, John A

2007-01-01

Historically, approaches to measuring intellectual capital have included both conventional accounting-based measures, such as variants of the market-to-book ratio, and more progressive measures, such as the measurement of intangible assets found in approaches such as the Balanced Scorecard and Human Resource Accounting. As greater emphasis is placed on intellectual capital and its various aspects in the continually growing service and knowledge economy, the use of assessment instruments to inventory the alignment, balance, and variety of intellectual capacities and metrics that assess the effectiveness of succession planning may represent new directions in which organizations can head in the measurement of this important construct.

Electric field-induced astrocyte alignment directs neurite outgrowth.

Science.gov (United States)

Alexander, John K; Fuss, Babette; Colello, Raymond J

2006-05-01

The extension and directionality of neurite outgrowth are key to achieving successful target connections during both CNS development and during the re-establishment of connections lost after neural trauma. The degree of axonal elongation depends, in large part, on the spatial arrangement of astrocytic processes rich in growth-promoting proteins. Because astrocytes in culture align their processes on exposure to an electrical field of physiological strength, we sought to determine the extent to which aligned astrocytes affect neurite outgrowth. To this end, dorsal root ganglia cells were seeded onto cultured rat astrocytes that were pre-aligned by exposure to an electric field of physiological strength (500 mV mm(-1)). Using confocal microscopy and digital image analysis, we found that neurite outgrowth at 24 hours and at 48 hours is enhanced significantly and directed consistently along the aligned astrocyte processes. Moreover, this directed neurite outgrowth is maintained when grown on fixed, aligned astrocytes. Collectively, these results indicate that endogenous electric fields present within the developing CNS might act to align astrocyte processes, which can promote and direct neurite growth. Furthermore, these results demonstrate a simple method to produce an aligned cellular substrate, which might be used to direct regenerating neurites.

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests.

Science.gov (United States)

Lee, Ping-Shin; Gan, Han Ming; Clements, Gopalasamy Reuben; Wilson, John-James

2016-11-01

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.

Survey and alignment of high energy physics accelerators and transport lines

International Nuclear Information System (INIS)

Ruland, R.E.

1992-11-01

This talk summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are revisited and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step by step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations

Generation and Detection of Alignments in Gabor Patterns

Directory of Open Access Journals (Sweden)

Samy Blusseau

2016-11-01

Full Text Available This paper presents a method to be used in psychophysical experiments to compare directly visual perception to an a contrario algorithm, on a straight patterns detection task. The method is composed of two parts. The first part consists in building a stimulus, namely an array of oriented elements, in which an alignment is present with variable salience. The second part focuses on a detection algorithm, based on the a contrario theory, which is designed to predict which alignment will be considered as the most salient in a given stimulus.

A Composite Model of Wound Segmentation Based on Traditional Methods and Deep Neural Networks

Directory of Open Access Journals (Sweden)

Fangzhao Li

2018-01-01

Full Text Available Wound segmentation plays an important supporting role in the wound observation and wound healing. Current methods of image segmentation include those based on traditional process of image and those based on deep neural networks. The traditional methods use the artificial image features to complete the task without large amounts of labeled data. Meanwhile, the methods based on deep neural networks can extract the image features effectively without the artificial design, but lots of training data are required. Combined with the advantages of them, this paper presents a composite model of wound segmentation. The model uses the skin with wound detection algorithm we designed in the paper to highlight image features. Then, the preprocessed images are segmented by deep neural networks. And semantic corrections are applied to the segmentation results at last. The model shows a good performance in our experiment.

An Aural Learning Project: Assimilating Jazz Education Methods for Traditional Applied Pedagogy

Science.gov (United States)

Gamso, Nancy M.

2011-01-01

The Aural Learning Project (ALP) was developed to incorporate jazz method components into the author's classical practice and her applied woodwind lesson curriculum. The primary objective was to place a more focused pedagogical emphasis on listening and hearing than is traditionally used in the classical applied curriculum. The components of the…

Study on the traditional pattern retrieval method of minorities in Gansu province

Science.gov (United States)

Zheng, Gang; Wang, Beizhan; Sun, Yuchun; Xu, Jin

2018-03-01

The traditional patterns of ethnic minorities in gansu province are ethnic arts with strong ethnic characteristics. It is the crystallization of the hard work and wisdom of minority nationalities in gansu province. Unique traditional patterns of ethnic minorities in Gansu province with rich ethnic folk arts, is the crystallization of geographical environment in Gansu minority diligence and wisdom. By using the Surf feature point identification algorithm, the feature point extractor in OpenCV is used to extract the feature points. And the feature points are applied to compare the pattern features to find patterns similar to the artistic features. The application of this method can quickly or efficiently extract pattern information in a database.

Hardware Accelerated Sequence Alignment with Traceback

Directory of Open Access Journals (Sweden)

Scott Lloyd

2009-01-01

in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

Control rod housing alignment

International Nuclear Information System (INIS)

Dixon, R.C.; Deaver, G.A.; Punches, J.R.; Singleton, G.E.; Erbes, J.G.; Offer, H.P.

1990-01-01

This patent describes a process for measuring the vertical alignment between a hole in a core plate and the top of a corresponding control rod drive housing within a boiling water reactor. It comprises: providing an alignment apparatus. The alignment apparatus including a lower end for fitting to the top of the control rod drive housing; an upper end for fitting to the aperture in the core plate, and a leveling means attached to the alignment apparatus to read out the difference in angularity with respect to gravity, and alignment pin registering means for registering to the alignment pin on the core plate; lowering the alignment device on a depending support through a lattice position in the top guide through the hole in the core plate down into registered contact with the top of the control rod drive housing; registering the upper end to the sides of the hole in the core plate; registering the alignment pin registering means to an alignment pin on the core plate to impart to the alignment device the required angularity; and reading out the angle of the control rod drive housing with respect to the hole in the core plate through the leveling devices whereby the angularity of the top of the control rod drive housing with respect to the hole in the core plate can be determined

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

Directory of Open Access Journals (Sweden)

Lee DT

2007-02-01

Full Text Available Abstract Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.

High precision optical fiber alignment using tube laser bending

NARCIS (Netherlands)

Folkersma, Ger; Römer, Gerardus Richardus, Bernardus, Engelina; Brouwer, Dannis Michel; Herder, Justus Laurens

2016-01-01

In this paper, we present a method to align optical fibers within 0.2 μm of the optimal position, using tube laser bending and in situ measuring of the coupling efficiency. For near-UV wavelengths, passive alignment of the fibers with respect to the waveguides on photonic integrated circuit chips

MUON DETECTORS: ALIGNMENT

CERN Multimedia

G. Gomez

2012-01-01

  A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

Laser beam alignment and profilometry using diagnostic fluorescent safety mirrors

Science.gov (United States)

Lizotte, Todd E.

2011-03-01

There are a wide range of laser beam delivery systems in use for various purposes; including industrial and medical applications. Virtually all such beam delivery systems for practical purposes employ optical systems comprised of mirrors and lenses to shape, focus and guide the laser beam down to the material being processed. The goal of the laser beam delivery is to set the optimum parameters and to "fold" the beam path to reduce the mechanical length of the optical system, thereby allowing a physically compact system. In many cases, even a compact system can incorporate upwards of six mirrors and a comparable number of lenses all needing alignment so they are collinear. One of the major requirements for use of such systems in industry is a method of safe alignment. The alignment process requires that the aligner determine where the beam strikes each element. The aligner should also preferably be able to determine the shape or pattern of the laser beam at that point and its relative power. These alignments are further compounded in that the laser beams generated are not visible to the unaided human eye. Such beams are also often of relatively high power levels, and are thereby a significant hazard to the eyes of the aligner. Obvious an invisible beam makes it nearly impossible to align laser system without some form of optical assistance. The predominant method of visually aligning the laser beam delivery is the use of thermal paper, paper cards or fluorescing card material. The use of paper products which have limited power handling capability or coated plastics can produce significant debris and contaminants within the beam line that ultimately damage the optics. The use of the cards can also create significant laser light scatter jeopardizing the safety of the person aligning the system. This paper covers a new safety mirror design for use with at various UV and Near IR wavelengths (193 nm to 1064 nm) within laser beam delivery systems and how its use can

Magnet-assisted device-level alignment for the fabrication of membrane-sandwiched polydimethylsiloxane microfluidic devices

International Nuclear Information System (INIS)

Lu, J-C; Liao, W-H; Tung, Y-C

2012-01-01

Polydimethylsiloxane (PDMS) microfluidic device is one of the most essential techniques that advance microfluidics research in recent decades. PDMS is broadly exploited to construct microfluidic devices due to its unique and advantageous material properties. To realize more functionalities, PDMS microfluidic devices with multi-layer architectures, especially those with sandwiched membranes, have been developed for various applications. However, existing alignment methods for device fabrication are mainly based on manual observations, which are time consuming, inaccurate and inconsistent. This paper develops a magnet-assisted alignment method to enhance device-level alignment accuracy and precision without complicated fabrication processes. In the developed alignment method, magnets are embedded into PDMS layers at the corners of the device. The paired magnets are arranged in symmetric positions at each PDMS layer, and the magnetic attraction force automatically pulls the PDMS layers into the aligned position during assembly. This paper also applies the method to construct a practical microfluidic device, a tunable chaotic micromixer. The results demonstrate the successful operation of the device without failure, which suggests the accurate alignment and reliable bonding achieved by the method. Consequently, the fabrication method developed in this paper is promising to be exploited to construct various membrane-sandwiched PDMS microfluidic devices with more integrated functionalities to advance microfluidics research. (paper)

Simulation of beamline alignment operations

International Nuclear Information System (INIS)

Annese, C; Miller, M G.

1999-01-01

The CORBA-based Simulator was a Laboratory Directed Research and Development (LDRD) project that applied simulation techniques to explore critical questions about distributed control systems. The simulator project used a three-prong approach that studied object-oriented distribution tools, computer network modeling, and simulation of key control system scenarios. The National Ignition Facility's (NIF) optical alignment system was modeled to study control system operations. The alignment of NIF's 192 beamlines is a large complex operation involving more than 100 computer systems and 8000 mechanized devices. The alignment process is defined by a detailed set of procedures; however, many of the steps are deterministic. The alignment steps for a poorly aligned component are similar to that of a nearly aligned component; however, additional operations/iterations are required to complete the process. Thus, the same alignment operations will require variable amounts of time to perform depending on the current alignment condition as well as other factors. Simulation of the alignment process is necessary to understand beamline alignment time requirements and how shared resources such as the Output Sensor and Target Alignment Sensor effect alignment efficiency. The simulation has provided alignment time estimates and other results based on documented alignment procedures and alignment experience gained in the laboratory. Computer communication time, mechanical hardware actuation times, image processing algorithm execution times, etc. have been experimentally determined and incorporated into the model. Previous analysis of alignment operations utilized average implementation times for all alignment operations. Resource sharing becomes rather simple to model when only average values are used. The time required to actually implement the many individual alignment operations will be quite dynamic. The simulation model estimates the time to complete an operation using

Precision alignment of permanent-magnet drift tubes

International Nuclear Information System (INIS)

Liska, D.J.; Dauelsberg, L.B.; Spalek, G.

1986-01-01

The Lawrence Berkeley National Laboratory (LBNL) technique of drift-tube alignment has been resurrected at Los Alamos for the precision alignment of 1-cm-bore drift tubes that carry high-gradient rare-earth-cobalt quadrupole. Because the quadrupole cannot be switched off, this technique is not applicable to a drift-tube assembly, but tests indicate that individual magnetic centers can be detected with a precision of +- 0.003 mm. Methods of transferring this information to machined alignment flats on the sides of the drift-tube body are discussed. With measurements of drift tubes designed for a 100-mA. 425-MHz drift-tube linac, we have detected offsets between the geometric and magnetic axes of up to +- 0.05 mm following final assembly and welding. This degree of offset is serious if not accommodated, because it represents the entire alignment tolerance for the 40-cell tank. The measurement equipment and technique are described

Prediction of molecular alignment of nucleic acids in aligned media

International Nuclear Information System (INIS)

Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

2006-01-01

We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Directory of Open Access Journals (Sweden)

Emanuel Santos

Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Science.gov (United States)

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

On the generation of coastline-following grids for ocean models—trade-off between orthogonality and alignment to coastlines

Science.gov (United States)

Liu, Xiaonan; Ma, Jialiang; Xu, Shiming; Wang, Bin

2017-08-01

Regional ocean models usually utilize orthogonal curvilinear grids that are fit to the coastline of the modeled regions. While the orthogonality of the grid is required from the perspective of the numerical algorithms, the alignment to the irregular coastlines improves the characterization of the land-sea distribution and the ocean simulation. In this article, we carry out fractal analysis of two representative coastal regions and discuss the trade-offs between the orthogonality and coastline alignment during the grid generation of these regions. A new grid generation method based on Schwarz-Christoffel conformal mappings is proposed, with automatic coastal boundary retrieval algorithm that generates resolution dependent boundary for grid generation and alleviates the human efforts involved in traditional methods. We show that for the southeastern Pacific region, the coastline is smooth with low fractal dimension and there exists effective trade-off with a coastline boundary that adjusts to the desired grid resolution. On the contrary, there is no effective trade-off for southeast China seas where the coastline is of higher fractal dimension, and a coarser coastline boundary is recommended for better orthogonality with little loss in coastline alignment. Further numerical study of coastal trapped Kelvin waves for the typical regions demonstrate that the new coastline-fitting grids achieve smaller error in numerical dispersion and higher accuracy. Through analysis, we conclude that for grid generation for regional ocean modeling, modelers should bring into consideration of the multi-scale fractal characteristics of the coastline.

Alignment of the ALICE Inner Tracking System with cosmic-ray tracks

CERN Document Server

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Zbroszczyk, H; Zelnicek, P; Zenin, A; Zepeda, A; Zgura, I; Zhalov, M; Zhang, X; Zhou, D; Zhou, S; Zhu, J; Zichichi, A; Zinchenko, A; Zinovjev, G; Zinovjev, M; Zoccarato, Y; Zychácek, V

2010-01-01

ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 micron in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10^5 charged tracks from cosmic rays that h...

Spatial Visualization Learning in Engineering: Traditional Methods vs. a Web-Based Tool

Science.gov (United States)

Pedrosa, Carlos Melgosa; Barbero, Basilio Ramos; Miguel, Arturo Román

2014-01-01

This study compares an interactive learning manager for graphic engineering to develop spatial vision (ILMAGE_SV) to traditional methods. ILMAGE_SV is an asynchronous web-based learning tool that allows the manipulation of objects with a 3D viewer, self-evaluation, and continuous assessment. In addition, student learning may be monitored, which…

Spatio-temporal alignment of pedobarographic image sequences.

Science.gov (United States)

Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

2011-07-01

This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P alignment of pedobarographic image data, since previous methods can only be applied on static images.

A comparison of radiographic anatomic axis knee alignment measurements and cross-sectional associations with knee osteoarthritis

Science.gov (United States)

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 182° and for 2P methods: varus 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

A Practical Guide to Multi-image Alignment

OpenAIRE

Aguerrebere, Cecilia; Delbracio, Mauricio; Bartesaghi, Alberto; Sapiro, Guillermo

2018-01-01

Multi-image alignment, bringing a group of images into common register, is an ubiquitous problem and the first step of many applications in a wide variety of domains. As a result, a great amount of effort is being invested in developing efficient multi-image alignment algorithms. Little has been done, however, to answer fundamental practical questions such as: what is the comparative performance of existing methods? is there still room for improvement? under which conditions should one techni...

A new prosthetic alignment device to read and record prosthesis alignment data.

Science.gov (United States)

Pirouzi, Gholamhossein; Abu Osman, Noor Azuan; Ali, Sadeeq; Davoodi Makinejad, Majid

2017-12-01

Prosthetic alignment is an essential process to rehabilitate patients with amputations. This study presents, for the first time, an invented device to read and record prosthesis alignment data. The digital device consists of seven main parts: the trigger, internal shaft, shell, sensor adjustment button, digital display, sliding shell, and tip. The alignment data were read and recorded by the user or a computer to replicate prosthesis adjustment for future use or examine the sequence of changes in alignment and its effect on the posture of the patient. Alignment data were recorded at the anterior/posterior and medial/lateral positions for five patients. Results show the high level of confidence to record alignment data and replicate adjustments. Therefore, the device helps patients readjust their prosthesis by themselves, or prosthetists to perform adjustment for patients and analyze the effects of malalignment.

Synthesis and electroconductivity of epoxy/aligned CNTs composites

Energy Technology Data Exchange (ETDEWEB)

Chechenin, N.G., E-mail: chechenin@sinp.msu.ru [Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow, Leninskie Gory 1/2, 119234 (Russian Federation); Chernykh, P.N.; Vorobyeva, E.A.; Timofeev, O.S. [Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow, Leninskie Gory 1/2, 119234 (Russian Federation)

2013-06-15

An efficient method is described of growing of vertically aligned carbon nanotubes (VANTs) densely packed on a large area with uniform height up to 1 mm. The method is based on injection of active solution of ferrocene in cyclohexane into reactor during the growth process. We also describe a method of ER/VANTs composite preparation based on infiltration of epoxy resin (ER) liquid monomer into arrays of the VANTs forest with polymerization followed. Further on we describe a press-and-draw method to reorient VANTs into horizontally aligned carbon nanotubes (HANTs) in the liquid composite precursor. The electrical conductivities up to 0.6 S/cm in ER/VANTs and up to 0.85 S/cm in ER/HANTs are obtained.

Synthesis and electroconductivity of epoxy/aligned CNTs composites

International Nuclear Information System (INIS)

Chechenin, N.G.; Chernykh, P.N.; Vorobyeva, E.A.; Timofeev, O.S.

2013-01-01

An efficient method is described of growing of vertically aligned carbon nanotubes (VANTs) densely packed on a large area with uniform height up to 1 mm. The method is based on injection of active solution of ferrocene in cyclohexane into reactor during the growth process. We also describe a method of ER/VANTs composite preparation based on infiltration of epoxy resin (ER) liquid monomer into arrays of the VANTs forest with polymerization followed. Further on we describe a press-and-draw method to reorient VANTs into horizontally aligned carbon nanotubes (HANTs) in the liquid composite precursor. The electrical conductivities up to 0.6 S/cm in ER/VANTs and up to 0.85 S/cm in ER/HANTs are obtained.

Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

Science.gov (United States)

Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

2014-01-01

Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

A unified model for transfer alignment at random misalignment angles based on second-order EKF

International Nuclear Information System (INIS)

Cui, Xiao; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo; Mei, Chunbo

2017-01-01

In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles. (paper)

A unified model for transfer alignment at random misalignment angles based on second-order EKF

Science.gov (United States)

Cui, Xiao; Mei, Chunbo; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo

2017-04-01

In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles.

Markov random field based automatic image alignment for electron tomography.

Science.gov (United States)

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

High anisotropy of flow-aligned bicellar membrane systems

KAUST Repository

Kogan, Maxim

2013-10-01

In recent years, multi-lipid bicellar systems have emerged as promising membrane models. The fast orientational diffusion and magnetic alignability made these systems very attractive for NMR investigations. However, their alignment was so far achieved with a strong magnetic field, which limited their use with other methods that require macroscopic orientation. Recently, it was shown that bicelles could be aligned also by shear flow in a Couette flow cell, making it applicable to structural and biophysical studies by polarized light spectroscopy. Considering the sensitivity of this lipid system to small variations in composition and physicochemical parameters, efficient use of such a flow-cell method with coupled techniques will critically depend on the detailed understanding of how the lipid systems behave under flow conditions. In the present study we have characterized the flow alignment behavior of the commonly used dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine (DMPC/DHPC) bicelle system, for various temperatures, lipid compositions, and lipid concentrations. We conclude that at optimal flow conditions the selected bicellar systems can produce the most efficient flow alignment out of any lipid systems used so far. The highest degree of orientation of DMPC/DHPC samples is noticed in a narrow temperature interval, at a practical temperature around 25 C, most likely in the phase transition region characterized by maximum sample viscosity. The change of macroscopic orientation factor as function of the above conditions is now described in detail. The increase in macroscopic alignment observed for bicelles will most likely allow recording of higher resolution spectra on membrane systems, which provide deeper structural insight and analysis into properties of biomolecules interacting with solution phase lipid membranes. © 2013 Elsevier Ireland Ltd.

A rank-based sequence aligner with applications in phylogenetic analysis.

Directory of Open Access Journals (Sweden)

Liviu P Dinu

Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

Preparation and Characterization of Highly Aligned Carbon Nanotubes/Polyacrylonitrile Composite Nanofibers

Directory of Open Access Journals (Sweden)

Yanhua Song

2017-01-01

Full Text Available In the electrospinning process, a modified parallel electrode method (MPEM, conducted by placing a positively charged ring between the needle and the parallel electrode collector, was used to fabricate highly aligned carbon nanotubes/polyacrylonitrile (CNTs/PAN composite nanofibers. Characterizations of the samples—such as morphology, the degree of alignment, and mechanical and conductive properties—were investigated by a combination of scanning electron microscopy (SEM, transmission electron microscopy (TEM, universal testing machine, high-resistance meter, and other methods. The results showed the MPEM could improve the alignment and uniformity of electrospun CNTs/PAN composite nanofibers, and enhance their mechanical and conductive properties. This meant the successful preparation of highly aligned CNT-reinforced PAN nanofibers with enhanced physical properties, suggesting their potential application in appliances and communication areas.

Effects of variable attachment shapes and aligner material on aligner retention.

Science.gov (United States)

Dasy, Hiltrud; Dasy, Andreas; Asatrian, Greg; Rózsa, Noémi; Lee, Hao-Fu; Kwak, Jin Hee

2015-11-01

To evaluate the retention of four types of aligners on a dental arch with various attachments. For this study, three casts were manufactured, two of which contained attachments (ellipsoid and beveled), and one without any attachments to serve as a control. Four types of aligners were thermoformed: Clear-Aligner (CA)-soft, CA-medium, and CA-hard, with various thicknesses, and Essix ACE. Measurements of vertical displacement force during aligner removal were performed with the Gabo Qualimeter Eplexor. Means and standard deviations were next compared between different aligner thicknesses and attachment shapes. CA-soft, CA-medium, and CA-hard did not present a significant increase in retention, except when used in the presence of attachments. Additionally, CA-medium and CA-hard required significantly more force for removal. Essix ACE demonstrated a significant decrease in retention when used with ellipsoid attachments. The force value for Essix ACE removal from the cast with beveled attachments was comparable to that of CA-medium. Forces for aligner removal from the model without attachments showed a linear trend. Essix ACE did not show a continuous increase in retention for each model. Overall, ellipsoid attachments did not present a significant change in retention. In contrast, beveled attachments improved retention. Ellipsoid attachments had no significant influence on the force required for aligner removal and hence on aligner retention. Essix ACE showed significantly less retention than CA-hard on the models with attachments. Furthermore, beveled attachments were observed to increase retention significantly, compared with ellipsoid attachments and when using no attachments.

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

Science.gov (United States)

Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

2014-06-10

Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Science.gov (United States)

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

Aligning Mathematical Tasks to the Common Core Standards for Mathematical Practice

OpenAIRE

Johnson, Raymond

2016-01-01

How do algebra teachers align mathematical tasks to the CCSSM Standards of Mathematical Practice? Using methods of design-based implementation research, we identified difficulties of alignment to practices and developed strategies identifying high-quality tasks.

Using lexical and logical methods for the alignment of medical terminologies

NARCIS (Netherlands)

Klein, Michel; Aleksovski, Zharko

2005-01-01

Standardized medical terminologies are often used for the registration of patient data. In several situations there is a need to align these terminologies to other terminologies. Even when the terminologies cover the same domain, this is often a non-trivial task. The task is even more complicated

Assembly and alignment method for optimized spatial resolution of off-axis three-mirror fore optics of hyperspectral imager.

Science.gov (United States)

Kim, Youngsoo; Hong, Jinsuk; Choi, Byungin; Lee, Jong-Ung; Kim, Yeonsoo; Kim, Hyunsook

2017-08-21

A fore optics for the hyperspectral spectrometer is designed, manufactured, assembled, and aligned. The optics has a telecentric off-axis three-mirror configuration with a field of view wider than 14 degrees and an f-number as small as 2.3. The primary mirror (M1) and the secondary mirror (M2) are axially symmetric aspheric surfaces to minimize the sensitivity. The tertiary mirror (M3) is a decentered aspheric surface to minimize the coma and astigmatism aberration. The M2 also has a hole for the slit to maintain the optical performance while maximizing the telecentricity. To ensure the spatial resolution performance of the optical system, an alignment procedure is established to assemble and align the entrance slit of the spectrometer to the rear end of the fore optics. It has a great advantage to confirm and maintain the alignment integrity of the fore optics module throughout the alignment procedure. To perform the alignment procedure successfully, the precision movement control requirements are calculated and applied. As a result, the alignment goal of the RMS wave front error (WFE) to be smaller than 90 nm at all fields is achieved.

Separating intrinsic alignment and galaxy-galaxy lensing

International Nuclear Information System (INIS)

Blazek, Jonathan; Seljak, Uroš; Mandelbaum, Rachel; Nakajima, Reiko

2012-01-01

The coherent physical alignment of galaxies is an important systematic for gravitational lensing studies as well as a probe of the physical mechanisms involved in galaxy formation and evolution. We develop a formalism for treating this intrinsic alignment (IA) in the context of galaxy-galaxy lensing and present an improved method for measuring IA contamination, which can arise when sources physically associated with the lens are placed behind the lens due to photometric redshift scatter. We apply the technique to recent Sloan Digital Sky Survey (SDSS) measurements of Luminous Red Galaxy lenses and typical ( ∼ L * ) source galaxies with photometric redshifts selected from the SDSS imaging data. Compared to previous measurements, this method has the advantage of being fully self-consistent in its treatment of the IA and lensing signals, solving for the two simultaneously. We find an IA signal consistent with zero, placing tight constraints on both the magnitude of the IA effect and its potential contamination to the lensing signal. While these constraints depend on source selection and redshift quality, the method can be applied to any measurement that uses photometric redshifts. We obtain a model-independent upper-limit of roughly 10% IA contamination for projected separations of r p ≈ 0.1–10 h −1 Mpc. With more stringent photo-z cuts and reasonable assumptions about the physics of intrinsic alignments, this upper limit is reduced to 1–2%. These limits are well below the statistical error of the current lensing measurements. Our results suggest that IA will not present intractable challenges to the next generation of galaxy-galaxy lensing experiments, and the methods presented here should continue to aid in our understanding of alignment processes and in the removal of IA from the lensing signal

Spatiotemporal alignment of in utero BOLD-MRI series.

Science.gov (United States)

Turk, Esra Abaci; Luo, Jie; Gagoski, Borjan; Pascau, Javier; Bibbo, Carolina; Robinson, Julian N; Grant, P Ellen; Adalsteinsson, Elfar; Golland, Polina; Malpica, Norberto

2017-08-01

To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412. © 2017 International Society for Magnetic Resonance in Medicine.

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

Science.gov (United States)

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

Mask alignment system for semiconductor processing

Science.gov (United States)

Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

2017-02-14

A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.