Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random ...

BackgroundResearch in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and ...

Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made ...

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75?bp) and ...

... This system is designed to provide a faster and more accurate optical alignment of the pinhole and the device under test. ...

Page 1. Guidance Methods for Accurate In�Flight Alignment of Navy Theatre Wide Missiles 15 May 2001 ... Page 9. In-Flight Alignment Metric � ADOP � ...

Efficient and safe operation of a laser requires precise alignment of the resonator. This paper describes a method for aligning an unstable resonator very accurately with off-axis injection of the alignment beam ultilizing multiple reflections of the Gaussian beam inside the resonator.

ABSTRACT: BACKGROUND: High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most ...

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are ...

... Title : Flat, Straight, Square, Parallel: Laser Alignment Tools Provide a Fast, Accurate Way to Keep Machine Tools in Line for Precision Cutting. ...

A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a part...

This report documents the design and operation of the particle beam alignment system developed for single event upset - Van de Graaff experiments. This system is designed to provide a faster and more accurate optical alignment of the pinhole and the devic...

This work provides a method of mechanical alignment of an array of single mode fibers to an array of optical devices. The technique uses a micromachined metal spring, which captures a vertical, pre- positioned fiber, moves it into accurate alignment, and ...

... Schmoker et al. for the stabilization of bone grafts following partial resection of tumors of the mandible. The technique of ...

and accurately aligned laser assembly that is capable of fast data Processing. producing ultra short pulses at a high repetition rate. It ...

When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts ...

The main peak in the autocorrelation function of bar codes is here utilized as the signal of accurate alignment. Attention is therefore directed to the problem of how to increase the contrast of the main autocorrelation peak above the remaining part of the correlation signal and to the problem concerned with the upper limit that the contrast may attain. To ...

Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global ...

The study purposed to determine if a navigation in total knee arthroplasty (TKA) leads to accurate limb alignment and component position than the conventional technique as measured by full length standing radiographs and to evaluate the correlation between navigation and radiographic measurements. A total of 160 knees underwent navigation (n = 80) or ...

1 Introduction In comparative structural biology studies, analyzing or predicting protein three-dimensional structure often begins with identifying patterns of amino acid substitution via protein sequence alignment. While the evolutionary informationobtained from alignments can provide insights into protein structure, constructing ...

Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the ...

This paper discusses how laser-optic alignment systems can be employed effectively to detect and accurately measure rotary machinery shaft alignment while the machinery is running. These measurements can be used to maintain proper alignment at operating conditions. One of the many significant factors influencing ...

BackgroundAccurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing ...

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions ...

Multiple sequence alignment as a means of comparing DNA, RNA, or amino acid sequences is an essential precondition for various analyses, including structure prediction, modeling binding sites, phylogeny, or function prediction. This range of applications implies a demand for versatile, flexible, and specialized methods to compute accurate ...

The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider. For the reconstruction of charged particles, and their production and their decay vertices, ATLAS is equipped with a sophisticated tracking system, unprecedented in size and complexity. Full exploitation of both the Inner Detector and the muon ...

Interferometrically measured system wavefronts combined with a differential ray-traced lens model are used to determine alignment adjustments to a lens system. This is achieved by minimizing the difference between measured and ray-traced wavefronts by means of a damped least-squares method, without information regarding individual surface shapes or misalignment sources in the ...

A simple and accurate stowage drum and capstan alignment system and method for the Deployable Array Work Group (DAWG) is provided. The system includes a drum reference point fixture for obtaining the drum centerline, a drum sighting assembly and a capstan...

A structural alignment sensor (SAS) was developed for use with large deployable antenna systems for contour measurement and/or active control. The SAS is a laser ranging system using frequency modulation and accurate phase measurement to determine distanc...

Accurate alignment and focus of mirror facets are critical for the integration of concentrators and receivers in many of the low-cost stretched-membrane concentrators currently under development. In this report, the theoretical development of computer sof...

Distributed point-focusing solar concentrators are being developed for dish-Stirling systems and other applications. Many of these concentrators make use of faceted mirrors that have to be accurately aligned. Some of the solar concentrator designs use str...

There are two major goals driving the requirements for alignment and measurement of the detector being designed by the Solenoidal Detector Collaboration (SDC). First is each subsystem's goal of measuring its particular physics data as accurately as possib...

2D measurement of human joint motion involves analysis of 3D displacements in an observer selected measurement plane. Accurate marker placement and alignment of joint motion plane with the observer plane are difficult. Alignment of the two planes is essen...

Accurate alignment of pencil beam eye shields to protect the lens of the eye may be made easier by means of a simple modification of existing apparatus. This involves drilling a small hole through the center of the shield to isolate the rayline directed to the lens and fabricating a suitable plug for this hole.

In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both ...

Accurate placement of hundreds of focused laser beams on target is necessary to achieve success in the National Ignition Facility (NIF). The current system requirement is {le}7 {mu}rad error in output pointing and {le}1 mm error in focusing. To accommodate several system shots per day, a target alignment system must be able to align ...

MOTIVATION: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new ...

Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual ...

To achieve accurate registration, the transformations which locate the tracking system components with respect to the environment must be known. These transformations relate the base of the tracking system to the virtual world and the tracking system's se...

Image 1: I managed to accurately polar align my mount such that the comet spent an additional ten minutes placed behind the neighbor's air conditioner after ...

7.2.2 GPS Analysis, IVP Determination, Alignment and SINEX. ... accurate connections and their associated variance covariance matrix, and provided an un- ...

Meadowlark Optics, A liquid beam steerer to align accurately laser beams for precise distant measurement (metrology). Pixel Vision, A 20000-frame-per-second ...

Parallax of a thin rotatable glass plate gives accurate compensation of the position of a laser beam used in the outside illumination of a sample in a vacuum system. (Author)

This study aimed to determine limb and component alignment after computer-assisted total knee arthroplasty in 30 patients (32 limbs) with an altered hip center due to a prior hip implant or deformed femoral head. There were no outliers greater than �3� in the postoperative coronal alignment of the limb and the femoral component in relation to the ...

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 ...

The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which ...

Many future mission models require large space (LSS) which have accurate surfaces and/or the capability of being accurately aligned. If ground test approaches which will provide adequate confidence of the structrual performance to the program managers are...

A three-dimensional registration and alignment algorithm was developed to align single photon emission computed tomography examinations and magnetic resonance images. Operators manipulated images interactively with real-time visual feedback, with use of both internal and surface features to achieve accurate ...

Accurate alignment of the electron and ion beams in the RHIC electron cooling solenoids is crucial for well-optimized cooling. Because of the greatly differing rigidities of the electron and ion beams, to achieve the specified alignment accuracy it is required that transverse magnetic fields resulting from imperfections in solenoid ...

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 ...

BackgroundAccurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence ...

A local text alignment algorithm is introduced in this work for synchronizing transcripts. The proposed algorithm can be used for any transcript alignment process where high computational complexity is a concern. Dynamic programming is typically used to align a set of transcripts: however, the computational complexity of dynamic ...

Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is ...

We present two heuristics for speeding up a time series alignment algorithm that is related to dynamic time warping (DTW). In previous work, we developed our multisegment alignment algorithm to answer similarity queries for toxicogenomic time-series data. Our multisegment algorithm returns more accurate alignments ...

This work provides a method of mechanical alignment of an array of single mode fibers to an array of optical devices. The technique uses a micromachined metal spring, which captures a vertical, pre-positioned fiber, moves it into accurate alignment, and holds it for attachment. The spring is fabricated from electroplated nickel, using ...

The design concept and operation performance of a novel alignment system for accurate electron density profile measurement is presented, which has been developed on the basis of the original method for adjusting quantitatively and actively an object field of collection fiber optics to a laser-beam axis. The quantitative expression needed for an appropriate ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue ...

BackgroundProtein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure ...

.e. misalignment of the word CAT. T- Coffee is a progressive alignment with an ability to consider information fromBase categories (CE in Cat1 and 2, CL for Cat3, T-Coffee: a Method for Sequence Alignment 211 #12;Table 1. The effect considering the unweighted average accuracy over the �ve cat- egories (Table 2, Total2) T-Coffee is 9.7 % more

Accurate alignment and focus of mirror facets are critical for the integration of concentrators and receivers in many of the low-cost stretched-membrane concentrators currently under development. In this report, the theoretical development of computer software that traces light rays from a source to a facet of a point-focusing solar concentrator and then ...

A system for welding fiber optic waveguides is disclosed. The ends of the two fibers to be joined are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45/sup 0/ angle to the optical axis of a stereomicroscope mounted for ...

A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted ...

A technique is described for maintaining the highly precise alignment needed for accurate density profile measurements with the TFTR Thomson scattering system. The method uses the transverse coherence of the fiber bundles in the collection optics to encode the alignment information in the spatial distribution of the scattered light ...

BackgroundLong term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome.MethodA ...

BackgroundGenomic sequence alignment is a powerful method for genome analysis and annotation, as alignments are routinely used to identify functional sites such as genes or regulatory elements. With a growing number of partially or completely sequenced genomes, multiple alignment is playing an increasingly important role in these ...

BackgroundAccurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style structural alignment algorithms cannot efficiently serve for multiple sequences, mostly progressive schemes are used to ...

Precise pre- and postoperative anatomic measurements are necessary to plan, perform, and evaluate total knee arthroplasty (TKA). We evaluated the relationship between radiographic and navigation alignment measurements, identified sources of error in radiographic and navigated alignment assessment, and determined the differences between desired and ...

Abstract. We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwise genome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each ...

A procedure is described for preparing relief alignment marks with precisely degraded quality that are then used to calibrate alignment performance. Alignment degrades with mark quality, eventually failing when the marks are no longer found. Using conventional processes it is difficult to accurately find this ...

We define a �threaded blockset,� which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for �threaded blockset aligner�) builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are ...

National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in ...

National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in ...

This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the ...

Purpose: To evaluate the impact of the number and location of intraprostatic fiducial markers on the accuracy and reproducibility of daily prostate target alignment and to evaluate the migration of such markers. Methods and Materials: Three gold fiducial markers were implanted transrectally under ultrasound guidance near the apex, middle, and base of the prostate in 10 ...

BackgroundIn this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during ...

As the IC product scribe line of logic 90nm (L90) technology shrinks from 80�m to 62?m, the wafer quality (W.Q.), will become weak and less distinguishable during the subsequent ASML scanner stepper's photo mask aligning. Many wafers having photo mask aligning errors will eventually lead to wafer scrapping. In order to improve the photo ...

Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif ...

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple ...

We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints ...

This paper proposes a novel mechanism for the initial alignment of low-cost INS aided by GPS. For low-cost INS, the initial alignment is still a challenging issue because of the high noises from low-cost inertial sensors. In this paper, a two-stage Kalman Filtering mechanism is proposed for the initial alignment of low-cost INS. The ...

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential ...

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential ...

Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background ...

Oct 13, 2004... and starting a long reading with it on a target called "Void. ... During pre -uplink science activities in the early morning, ...

A program was developed to align positron emission tomography images from multiple studies on the same subject. The program allowed alignment of two images with a fineness of one-tenth the width of a pixel. The indications and effects of misalignment were assessed in eight subjects from a placebo-controlled double-blind crossover study on the effects of ...

Droplets of liquid drying on a surface with pinned contact area develop an internal hydrodynamic flow that carries entrained particles to the air-liquid-substrate interface. We use this phenomenon in cylindrical, micrometer-sized droplets of large aspect ratio (more than 1000:1) to align, position, and place individual anisotropic nanostructures such as single-walled carbon ...

The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate ...

Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing methods for multiple sequence ...

Distributed point-focusing solar concentrators are being developed for dish-Stirling systems and other applications. Many of these concentrators make use of faceted mirrors that have to be accurately aligned. Some of the solar concentrator designs use stretched-membrane facets that also require focusing. Accurate mirror ...

A major bottleneck in comparative modeling is the alignment quality; this is especially true for proteins whose distant relationships could be reliably recognized only by recent advances in fold recognition. The best algorithms excel in recognizing distant homologs but often produce incorrect alignments for over 50% of protein pairs in large ...

A major bottleneck in comparative modeling is the alignment quality; this is especially true for proteins whose distant relationships could be reliably recognized only by recent advances in fold recognition. The best algorithms excel in recognizing distant homologs but often produce incorrect alignments for over 50% of protein pairs in large ...

BackgroundSequence 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 ...

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other ...

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other ...

Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new ...

The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic programming using a ...

The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called �K*Sync�, in which alignments are generated by dynamic programming using a ...

The laser provides a rapid and accurate method of evaluating machine tool positioning accuracy and slideway alignment; however, the laser is an asset only when used with due respect to the basic principles of metrology. (Author)

Accurate placement of hundreds of focused laser beams on target is necessary to achieve success in the National Ignition Facility (NIF). The current system requirement is (le)7 (mu)rad error in output pointing and (le)1 mm error in focusing. To accommodat...

A three-dimensionally bendable defect bridging plate was first described by Schmoker et al. for the stabilization of bone grafts following partial resection of tumors of the mandible. The technique of plate adaptation and drilling and tapping of the screw...

The report is for use in installing, adjusting and operating the Sferics-Radar Data Converter System. It contains the information necessary to permit accurate testing and alignment of the complete system from sensor to display devices. (Author)

During Centaur launch operations the launch azimuth of the inertial platform's U-accelerometer input axis must be accurately established and maintained. This is accomplished by using an optically closed loop system with a long-range autotheodolite whose l...

for accurate interference pattern align- ment. Indium bumps are deposited on top of the device control nodes

A system and method are provided to accurately track the trajectory of high-speed underwater objects. A number of hoops with means for controlling the buoyancy thereof are aligned on a range in the anticipated path of the high speed projectile. The hoops ...

Free Electron Lasers (FEL) present a unique set of beam parameters to the diagnostics suite. The FEL requires characterization of the full six dimensional phase space of the electron beam at the wiggler and accurate alignment of the electron beam to the o...

Closed circuit television (CCTV) weld targeting systems were developed to provide accurate and repeatable positioning of the electrode of an electronic arc welder with respect to the parts being joined. A sliding mirror electrode holder was developed for ...

Autonomous Shape Model Learning for Object Localization and Recognition Joseph Modayil and Benjamin object recognition and localization. The results are accurate to within sensor precision. I. INTRODUCTION of scans and poses, is useful for both object recognition and localization. The problem of aligning scans

Polarization-Maintaining(PM) optical fiber connector is widely used in various kinds of optic fiber sensors and communication equipments. The alignment of PM fiber polarization axis with the orientation key axis is one of the most important factors determining the extinction ratio of the connector. In order to ensure high accurate ...

We have developed a simple instrument to accurately measure misalignments between a pinhole imaging assembly and the radiation source it is designed to image. Intended for remotely controlled use in the diagnostic canisters employed in underground nuclear...

Purpose: To compare the effectiveness of daily ultrasound (US)- and computed tomography (CT)-guided alignments with an off-line correction protocol using daily bone alignment plus a correction factor for systematic internal prostate displacement (CF{sub ID}). Methods and Materials: Ten prostate cancer patients underwent CT scans three times weekly using an ...

A liquid level system has been installed in the accelerator housing of the PEP storage ring. This instrument spans the entire 2.2 km circumference of the PEP project, and over one hundred readouts provide reference elevations which are used for the accurate alignment of accelerator components. The liquid level has proven to be extremely precise (+-0.10 mm) ...

2D measurement of human joint motion involves analysis of 3D displacements in an observer selected measurement plane. Accurate marker placement and alignment of joint motion plane with the observer plane are difficult. Alignment of the two planes is essential for accurate recording and understanding of the joint ...

A procedure for periodic quality assurance of a video surface imaging system is introduced. AlignRT is a video camera-based patient localization system that captures and compares images of a patient's topography to a DICOM-formatted external contour, then calculates shifts required to accurately reposition the patient. This technical note describes the ...

Methods are disclosed for forming precision, fiber optic interfaces, and a precision, fiber optic interface is disclosed in accordance therewith. An electroformed disk is disclosed to provide fiber alignment, and electrical discharge machining (EDM) is disclosed to provide accurate angular alignment of optical fibers at a planar ...

A versatile x-ray microscope diagnostic has been built to perform target dynamics experiments on the Nova Ten Beam target irradiation facility. This system is based on Wolter's axisymmetric focusing scheme. An alignment system is described which provides for both quick and accurate alignment of the x-ray optic. Results are ...

The Qnr proteins belong to the pentapeptide repeat protein family. Despite each pentapeptide repeat unit being an important structural determinant, accurately determining pentapeptide repeat units in the Qnr proteins through sequence-based alignments has been challenging. In the present study, the pentapeptide repeat units of the nine representative Qnr ...

The research is based on a shift control system built on autoreflection scheme. The aim is to examine the possibility of using of the cat's eye reflector for the autocollimating alignment telescopes instead of more common tetrahedral reflectors (e.g. corner cube prism). Zemax simulations were made to study the influence of beam and image deformation (caused by this reflector) ...

The CMS detector has been instrumented with a precise and complex opto-mechanical alignment subsystem that provides a common reference frame between tracker and muon detection systems by means of a net of laser beams. The system allows a continuous and accurate monitoring of the muon chambers positions with respect to the tracker body. Preliminary results ...

This invention relates to a dynamic beam/seam alignment control system for electron beam welds utilizing video apparatus. The system includes automatic control of workpiece illumination, near infrared illumination of the workpiece to limit the range of illumination and camera sensitivity adjustment, curve fitting of seam position data to obtain an accurate ...

Recent progress in the theoretical study of alignment and orientation in atom-atom and ion-atom collisions at intermediate energies is reviewed. Recent systematic studies of the alignment and orientation of electronic charge cloud distributions of excited states resulting from such collisions clearly have provided more detailed information about the ...

A back-reflection Laue camera with three rotation axes and three orthogonal translation axes is described. This camera allows the alignment of large single crystals with a precision of plus or minus 0.25 deg . The degree of single crystallinity of a specimen may be examined. In addition it is possible to accurately mark a crystal for subsequent ...

Accurate chromosome segregation during mitosis and meiosis is essential for cell viability. Two papers in this issue of Cell (Kitajima et�al., 2011; Magidson et�al., 2011) describe chromosome movements during cell division with unprecedented accuracy, revealing previously unrecognized features of chromosome spindle alignment and paving the way to ...

An electrode support which permits accurate alignment and adjustment of the electrode in a plurality of planes and about a plurality of axes in a calutron is described. The support will align the slits in the electrode with the slits of an ionizing chamber so as to provide for the egress of ions. The support comprises an ...

A precision laser aiming system comprises a disrupter tool, a reflector, and a laser fixture. The disrupter tool, the reflector and the laser fixture are configurable for iterative alignment and aiming toward an explosive device threat. The invention enables a disrupter to be quickly and accurately set up, aligned, and aimed in order ...

Accurate measurements of calcite, quartz, and ammonium dihydrogen phosphate (ADP) retarder plates were required as part of a project to measure the characteristics of the solar interior. Important criteria were absolute retardation of multiple-order quartz wave plates, uniformity of retardation of relatively thick calcite and ADP plates, and alignment of ...

Closed circuit television (CCTV) weld targeting systems were developed to provide accurate and repeatable positioning of the electrode of an electronic arc welder with respect to the parts being joined. A sliding mirror electrode holder was developed for use with closed circuit television equipment on existing weld fixturing. A complete motorized CCTV weld ...

-length Stem Fragments Yasuo Tabei a, Koji Tsuda b, Taishin Kin b, Kiyoshi Asai ab a Department-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan, b Computational Biology Research Center, National Institute-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs

Autonomous beam alignment for coherent Doppler lidar requires accurate information about optical misalignment and optical aberrations. A multielement heterodyne detector provides the required information without a loss in overall system performance. The effects of statistical variations from the random backscattered field (speckle field) are determined ...

Traditional alignment systems based on the use of visible light are not practical when opaque materials obstruct the alignment axis. X-ray Alignment Systems (XRA) have been designed specifically to overcome this limitation. XRA systems are analogous to visible light alignment methods, in that they both consist of ...

MOTIVATION: Building an accurate alignment of a large set of distantly-related protein structures is still very challenging. RESULTS: This paper presents a novel method 3DCOMB which can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise ...

BackgroundOne of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to the sensitivity of ...

Target illumination systems for inertial confinement fusion (ICF) experiments require precise alignment of a multitude of mirrors, usually spherically arranged around the ICF target. The mechanical support structure for these mirrors generally consists of a large space frame with many voids. This makes direct alignment or boresighting impossible, since ...

This work provides a method of mechanical alignment of an array of single mode fibers to an array of optical devices. The technique uses a micromachined metal spring, which captures a vertical, pre- positioned fiber, moves it into accurate alignment, and holds it for attachment. The spring is fabricated from electroplated mickel, using ...

To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. We present LAGAN, a system for rapid global alignment of two ...

Computational protein structure prediction remains a challenging task in protein bioinformatics. In the recent years, the importance of template-based structure prediction is increasing because of the growing number of protein structures solved by the structural genomics projects. To capitalize the significant efforts and investments paid on the structural genomics projects, it is urgent to ...

The inherently high resolution of imprint lithography has the promise of extending integrated circuit minimum feature sizes down to the 10 nm region. However, the main effort of companies building nanoimprint tools has been directed to the development of robust printing techniques, rather than to alignment. Consequently, no alignment system currently ...

An antenna-coupled detector's directional properties can be verified by measuring its angular radiation pattern. At infrared frequencies, this pattern can be measured by rotating the device while illuminating it with a laser beam. An accurate radiation pattern can be measured only if the device is coaligned with the axis of rotation and the focus of the laser beam. In the ...

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. ...

In chromatography-based metabonomic research, retention time (RT) alignment of chromatographic peaks poses a challenge for the accurate profiling of biomarkers. Although a number of RT alignment software has been reported, the performance of these software packages have not been comprehensively evaluated. This study aimed to evaluate ...

The purpose of the optical distance indicator, or rangefinder, is to set the patient at a certain distance from the radiotherapy source when using either fixed SSD or an isocentric technique. If the distance that is set is not accurate, then the tumor dose calculated using this distance is also incorrect. Unfortunately, an ODI that is not properly aligned ...

-sequence alignment is an important tool in biological research and may be used for a variety of pur- poses ranging Difference (TDD). When the TA tree is topologically more accurate than the HA tree, TDD will be a positive number; if TDD is negative, the HA tree is more accurate that the TA tree. Note that TDD is not itself

A sidereal equation of time is developed which enables equatorial sundials (and armillary spheres) to be employed as accurate nocturnals. An accuracy in the order of one minute can be achieved with such a sundial by simply aligning the gnomon with a bright star from behind the curved dial. This is in contrast to nocturnals which are typically in error by ...

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 ...

This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate ...

Next-generation sequencing technologies have revolutionized genome and transcriptome sequencing. RNA-Seq experiments are able to generate huge amounts of transcriptome sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these technologies are relatively short and error prone. To utilize such reads for transcriptome reconstruction and gene-structure identification, one ...

The CALIPSO LIDAR utilizes a receiver telescope with a narrow Field-of-View (FOV) to reject background light and meet SNR requirements - FOV ? 130 ?rad. To maximize SNR the laser is collimated (divergence ?100 ?rad) and must be aligned to the receiver telescope FOV to within +/- 12 ?rad (allocated). To make accurate LIDAR measurements the receiver/laser ...

One of the major purposes of National Ignition Facility at Lawrence Livermore National Laboratory is to accurately focus 192 high energy laser beams on a nanoscale (mm) fusion target at the precise location and time. The automatic alignment system developed for NIF is used to align the beams in order to achieve the required focusing ...

Empirical studies conducted by maintenance service companies and OEMs, have shown conclusively that misaligned coupled, rotating machinery is the direct cause of 50% or more breakdowns. Shaft misalignment has been difficult to detect, and corrective procedures have been either inadequate, or complicated and time-consuming. The arrival in the early 1980s of the first laser-optical shaft ...

Researchers working with MR observations generally agree that far more information is available in a volume (3D) observation than is considered for diagnosis. The key to the new alignment method is in basing it on available information on surfaces. Using the skin surface is effective a robust algorithm can reliably extract this surface from almost any scan of the head, and a ...

A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following ...

We describe a new, computationally effcient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a ...

The use of cone targets in high intensity laser-plasma experiments has been of recent interest because of their potential use in integrated fast ignition experiments. Simpler experiments provide a good avenue for understanding the underlying physics, however precise control of the alignment along with good pointing accuracy is of crucial importance. While on big laser ...

The use of cone targets in high intensity laser-plasma experiments has been of recent interest because of their potential use in integrated fast ignition experiments. Simpler experiments provide a good avenue for understanding the underlying physics, however precise control of the alignment along with good pointing accuracy is of crucial importance. While on big laser ...

The use of cone targets in high intensity laser-plasma experiments has been of recent interest because of their potential use in integrated fast ignition experiments. Simpler experiments provide a good avenue for understanding the underlying physics, however precise control of the alignment along with good pointing accuracy is of crucial importance. While on big laser ...

There are many filtering methods that can be used for the initial alignment of an integrated inertial navigation system. This paper discussed the use of GPS, but focused on two kinds of filters for the initial alignment of an integrated strapdown inertial navigation system (SINS). One method is based on the Kalman filter (KF), and the other is based on the ...

The KEK Accelerator Test Facility (ATF) damping ring is a prototype low emittance source for the NLC/JLC linear collider. To achieve the goal normalized vertical emittance {gamma}{var_epsilon}{sub {gamma}} = 20 nm-rad, magnet placement accuracy better than 30 mm must be achieved. Accurate beam-based alignment (BBA) is required. The ATF arc optics uses a ...

The KEK Accelerator Test Facility (ATF) damping ring is a prototype low emittance source for the NLC/JLC linear collider. To achieve the goal normalized vertical emittance {gamma}{var_epsilon}{sub y} = 20 nm-rad, magnet placement accuracy better than 30 mm must be achieved. Accurate beam-based alignment (BBA) is required. The ATF arc optics uses a FOBO ...

Fabrication of slapper type detonator cables requires bonding of a thin barrel over a bridge. Location of the barrel hole with respect to the bridge is critical: the barrel hole must be centered over the bridge uniform spacing on each side. An alignment fixture which permits rapid adjustment of the barrel position with respect to the bridge is described. The barrel is ...

Proper alignment of a needle template and ultrasound software grid is required to accurately deliver permanent prostate seed implants optimized using pretreatment volume studies. Correct alignment may also reduce tissue edema, morbidity, and the time and labor required to deliver permanent prostate seed implants. A technique has been ...

Multigigahertz flexible electronics are attractive and have broad applications. A gate-after-source/drain fabrication process using preselectively doped single-crystal silicon nanomembranes (SiNM) is an effective approach to realizing high device speed. However, further downscaling this approach has become difficult in lithography alignment. In this full paper, a local ...

A portable spectrometer prototype is built to study wavelength calibration for flat-field grating spectrometers. An accurate calibration method called parameter fitting is presented. Both optical and structural parameters of the spectrometer are included in the wavelength calibration model, which accurately describes the relationship between wavelength and ...

A measuring system is disclosed for surveying and very accurately positioning objects with respect to a reference line. A principal use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. ...

A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. ...

A measuring system is disclosed for surveying and very accurately positioning objects with respect to a reference line. A principal use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. ...

BackgroundMultiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms.Methodology/Principal FindingsWe describe a new method to align two or more genomes that have undergone rearrangements due to ...

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 ...

BackgroundSequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In particular, an alignment for homologous sequences with low sequence similarity is not in satisfactory ...

This paper presents a backside-to-frontside alignment technique for the backside processing of Si wafers. Integrated MEMS components like BiCMOS-embedded RF-MEMS switches require accurate (1-2?m) alignment. We demonstrate an alignment technique providing overlay values of less than 500 nm by using a backside ...

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. ...

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. ...

The National Ignition Facility in Livermore, California, completed it's commissioning milestone on March 10, 2009 when it fired all 192 beams at a combined energy of 1.1 MJ at 351nm. Subsequently, a target shot series from August through December of 2009 culminated in scale ignition target design experiments up to 1.2 MJ in the National Ignition Campaign. Preparations are underway through the ...

Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric obstruction model (Zweckstetter and Bax, 2000). A simple extension of this model is described that results in improved predictions for both the ...

Retention time shifts badly impair qualitative or quantitative results of chemometric analyses when entire chromatographic data are used. Hence, chromatograms should be aligned to perform further analysis. Being inspired and motivated by this purpose, a practical and handy peak alignment method (alignDE) is proposed, implemented in ...

Most threading methods predict the structure of a protein using only a single template. Due to the increasing number of solved structures, a protein without solved structure is very likely to have more than one similar template structures. Therefore, a natural question to ask is if we can improve modeling accuracy using multiple templates. This article describes a new multiple-template threading ...