WorldWideScience

Sample records for barcode scanning system

  1. How do Interruptions Impact Nurses’ Visual Scanning Patterns When Using Barcode Medication Administration Systems?

    Science.gov (United States)

    He, Ze; Marquard, Jenna L.; Henneman, Philip L.

    2014-01-01

    While barcode medication administration (BCMA) systems have the potential to reduce medication errors, they may introduce errors, side effects, and hazards into the medication administration process. Studies of BCMA systems should therefore consider the interrelated nature of health information technology (IT) use and sociotechnical systems. We aimed to understand how the introduction of interruptions into the BCMA process impacts nurses’ visual scanning patterns, a proxy for one component of cognitive processing. We used an eye tracker to record nurses’ visual scanning patterns while administering a medication using BCMA. Nurses either performed the BCMA process in a controlled setting with no interruptions (n=25) or in a real clinical setting with interruptions (n=21). By comparing the visual scanning patterns between the two groups, we found that nurses in the interruptive environment identified less task-related information in a given period of time, and engaged in more information searching than information processing. PMID:25954449

  2. How do interruptions impact nurses' visual scanning patterns when using barcode medication administration systems?

    Science.gov (United States)

    He, Ze; Marquard, Jenna L; Henneman, Philip L

    2014-01-01

    While barcode medication administration (BCMA) systems have the potential to reduce medication errors, they may introduce errors, side effects, and hazards into the medication administration process. Studies of BCMA systems should therefore consider the interrelated nature of health information technology (IT) use and sociotechnical systems. We aimed to understand how the introduction of interruptions into the BCMA process impacts nurses' visual scanning patterns, a proxy for one component of cognitive processing. We used an eye tracker to record nurses' visual scanning patterns while administering a medication using BCMA. Nurses either performed the BCMA process in a controlled setting with no interruptions (n=25) or in a real clinical setting with interruptions (n=21). By comparing the visual scanning patterns between the two groups, we found that nurses in the interruptive environment identified less task-related information in a given period of time, and engaged in more information searching than information processing.

  3. Usability of a barcode scanning system as a means of data entry on a PDA for self-report health outcome questionnaires

    DEFF Research Database (Denmark)

    Boissy, Patrice; Jacobs, Karen; Roy, Serge H

    2006-01-01

    with a text-to-speech synthesizer to collect data electronically from self-report health outcome questionnaires. METHODS: Usability of the system was tested on a sample of 24 community-living older adults (7 men, 17 women) ranging in age from 63 to 93 years. After receiving a brief demonstration on the use......BACKGROUND: Throughout the medical and paramedical professions, self-report health status questionnaires are used to gather patient-reported outcome measures. The objective of this pilot study was to evaluate in individuals over 60 years of age the usability of a PDA-based barcode scanning system...... of the barcode scanner, participants were randomly assigned to complete two sets of 16 questions using the bar code wand scanner for one set and a pen for the other. Usability was assessed using directed interviews with a usability questionnaire and performance-based metrics (task times, errors, sources...

  4. ISBN and QR Barcode Scanning Mobile App for Libraries

    OpenAIRE

    Graham McCarthy; Sally Wilson

    2011-01-01

    This article outlines the development of a mobile application for the Ryerson University Library. The application provides for ISBN barcode scanning that results in a lookup of library copies and services for the book scanned, as well as QR code scanning. Two versions of the application were developed, one for iOS and one for Android. The article includes some details on the free packages used for barcode scanning functionality. Source code for the Ryerson iOS and Android applications are fre...

  5. ISBN and QR Barcode Scanning Mobile App for Libraries

    Directory of Open Access Journals (Sweden)

    Graham McCarthy

    2011-04-01

    Full Text Available This article outlines the development of a mobile application for the Ryerson University Library. The application provides for ISBN barcode scanning that results in a lookup of library copies and services for the book scanned, as well as QR code scanning. Two versions of the application were developed, one for iOS and one for Android. The article includes some details on the free packages used for barcode scanning functionality. Source code for the Ryerson iOS and Android applications are freely available, and instructions are provided on customizing the Ryerson application for use in other library environments. Some statistics on the number of downloads of the Ryerson mobile app by users are included.

  6. Design of Electromagnetic Moving-coil type Voice Coil Motor for Scanning mirror of Barcode reader

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Bu Hyun; Lee, Jeong Woo; Shim, Hyun Ho; Park, Sang Goo [Hanbat National Univ., Daejeon (Korea, Republic of); Lee, Seung Yop [Sogang Univ., Seoul (Korea, Republic of)

    2016-01-15

    A voice coil actuator with moving coil type for scanning mirror system of barcode reader has been developed. The actuator has a simple structure including a magnet, a coil and a pin. The performance of the actuator is analyzed by a linearized theoretical model. And the dynamic performance of the proposed actuator is predicted through motor constant and restoring constant obtained by finite element simulations. The theoretical model was verified by the prototype which has 64 Hz resonance frequency and 60 deg reflecting angle. We also discovered that that 3 V input can make the actuator rotate over 61.8 deg reflecting angle at 50 Hz resonance frequency. The proposed actuator can simplify its driving configuration because of its implementation of open-loop control.

  7. A laboratory information management system for DNA barcoding workflows

    NARCIS (Netherlands)

    Vu, D.; Eberhardt, U.; Szöke, S.; Groenewald, M.; Robert, V.

    2012-01-01

    This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA

  8. Barcode Payment System in Trusted Mobile Devices

    Directory of Open Access Journals (Sweden)

    Vibha Kaw Raina

    2012-11-01

    Full Text Available Mobile payment is an application of mobile commerce which facilitates mobile commerce transactions by providing the mobile customer with a convenient means to pay. Many mobile payment methods have been proposed and implemented like user friendly, customer centric, merchant centric where security concerns are highly addressed. This paper proposes a mobile payment model with barcodes for mobile users to improve mobile user experience in mobile payment. Unlike other existing mobile payment systems, the proposed payment solution provides distinct advantages to support buy-and-sale products and services based on 2D Barcodes. The aim of this work is to integrate a model of payment with the financial services, including payment and banking ones, based on two primary capabilities: the use of computational resources of a trusted mobile device and the establishment of a user controlled channel with the customer’s bank. The proposed architecture is characterized bank-centric, since the bank acts consultatively, informatively and protectively for the end user and it offers flexibility, adaptability and continuous extendibility to open technologies.

  9. A laboratory information management system for DNA barcoding workflows.

    Science.gov (United States)

    Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

    2012-07-01

    This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

  10. Barcode Payment System in Trusted Mobile Devices

    OpenAIRE

    Vibha Kaw Raina

    2012-01-01

    Mobile payment is an application of mobile commerce which facilitates mobile commerce transactions by providing the mobile customer with a convenient means to pay. Many mobile payment methods have been proposed and implemented like user friendly, customer centric, merchant centric where security concerns are highly addressed. This paper proposes a mobile payment model with barcodes for mobile users to improve mobile user experience in mobile payment. Unlike other existing mobile payment syste...

  11. Security Issues for 2D Barcodes Ticketing Systems

    Directory of Open Access Journals (Sweden)

    Cristian Toma

    2011-03-01

    Full Text Available The paper presents a solution for endcoding/decoding access to the subway public transportation systems. First part of the paper is dedicated through section one and two to the most used 2D barcodes used in the market – QR and DataMatrix. The sample for DataMatrix is author propietary and the QR sample is from the QR standard [2]. The section three presents MMS and Digital Rights Management topics used for issuing the 2D barcodes tickets. The second part of the paper, starting with section four shows the architecture of Subway Ticketing Systems and the proposed procedure for the ticket issuing. The conclusions identify trends of the security topics in the public transportation systems.

  12. Cellular barcoding tool for clonal analysis in the hematopoietic system.

    Science.gov (United States)

    Gerrits, Alice; Dykstra, Brad; Kalmykowa, Olga J; Klauke, Karin; Verovskaya, Evgenia; Broekhuis, Mathilde J C; de Haan, Gerald; Bystrykh, Leonid V

    2010-04-01

    Clonal analysis is important for many areas of hematopoietic stem cell research, including in vitro cell expansion, gene therapy, and cancer progression and treatment. A common approach to measure clonality of retrovirally transduced cells is to perform integration site analysis using Southern blotting or polymerase chain reaction-based methods. Although these methods are useful in principle, they generally provide a low-resolution, biased, and incomplete assessment of clonality. To overcome those limitations, we labeled retroviral vectors with random sequence tags or "barcodes." On integration, each vector introduces a unique, identifiable, and heritable mark into the host cell genome, allowing the clonal progeny of each cell to be tracked over time. By coupling the barcoding method to a sequencing-based detection system, we could identify major and minor clones in 2 distinct cell culture systems in vitro and in a long-term transplantation setting. In addition, we demonstrate how clonal analysis can be complemented with transgene expression and integration site analysis. This cellular barcoding tool permits a simple, sensitive assessment of clonality and holds great promise for future gene therapy protocols in humans, and any other applications when clonal tracking is important.

  13. Nurses' Attitudes Toward the Use of the Bar-coding Medication Administration System

    NARCIS (Netherlands)

    S.D. Marini; A. Hasman; H.A.S. Huijer; H. Dimassi

    2010-01-01

    This study determines nurses' attitudes toward bar-coding medication administration system use. Some of the factors underlying the successful use of bar-coding medication administration systems that are viewed as a connotative indicator of users' attitudes were used to gather data that describe the

  14. Accuracy and time requirements of a bar-code inventory system for medical supplies.

    Science.gov (United States)

    Hanson, L B; Weinswig, M H; De Muth, J E

    1988-02-01

    The effects of implementing a bar-code system for issuing medical supplies to nursing units at a university teaching hospital were evaluated. Data on the time required to issue medical supplies to three nursing units at a 480-bed, tertiary-care teaching hospital were collected (1) before the bar-code system was implemented (i.e., when the manual system was in use), (2) one month after implementation, and (3) four months after implementation. At the same times, the accuracy of the central supply perpetual inventory was monitored using 15 selected items. One-way analysis of variance tests were done to determine any significant differences between the bar-code and manual systems. Using the bar-code system took longer than using the manual system because of a significant difference in the time required for order entry into the computer. Multiple-use requirements of the central supply computer system made entering bar-code data a much slower process. There was, however, a significant improvement in the accuracy of the perpetual inventory. Using the bar-code system for issuing medical supplies to the nursing units takes longer than using the manual system. However, the accuracy of the perpetual inventory was significantly improved with the implementation of the bar-code system.

  15. Barcode based localization system in indoor environment

    Directory of Open Access Journals (Sweden)

    Ľubica Ilkovičová

    2014-12-01

    Full Text Available Nowadays, in the era of intelligent buildings, there is a need to create indoornavigation systems, what is steadily a challenge. QR (Quick Response codesprovide accurate localization also in indoor environment, where other navigationtechniques (e.g. GPS are not available. The paper deals with the issues of posi-tioning using QR codes, solved at the Department of Surveying, Faculty of CivilEngineering SUT in Bratislava. Operating principle of QR codes, description ofthe application for positioning in indoor environment based on OS Android forsmartphones are described.

  16. An Analytic Hierarchy Process-based Method to Rank the Critical Success Factors of Implementing a Pharmacy Barcode System.

    Science.gov (United States)

    Alharthi, Hana; Sultana, Nahid; Al-Amoudi, Amjaad; Basudan, Afrah

    2015-01-01

    Pharmacy barcode scanning is used to reduce errors during the medication dispensing process. However, this technology has rarely been used in hospital pharmacies in Saudi Arabia. This article describes the barriers to successful implementation of a barcode scanning system in Saudi Arabia. A literature review was conducted to identify the relevant critical success factors (CSFs) for a successful dispensing barcode system implementation. Twenty-eight pharmacists from a local hospital in Saudi Arabia were interviewed to obtain their perception of these CSFs. In this study, planning (process flow issues and training requirements), resistance (fear of change, communication issues, and negative perceptions about technology), and technology (software, hardware, and vendor support) were identified as the main barriers. The analytic hierarchy process (AHP), one of the most widely used tools for decision making in the presence of multiple criteria, was used to compare and rank these identified CSFs. The results of this study suggest that resistance barriers have a greater impact than planning and technology barriers. In particular, fear of change is the most critical factor, and training is the least critical factor.

  17. Mobile documentation: optimizing technology to do more with less. How the University of Missouri Health System adapted its barcode-scanning system for mobile bedside documentation to enhance the quality and safety of patient care.

    Science.gov (United States)

    Prestigiacomo, Jennifer

    2012-12-01

    When the University of Missouri Health System sought to optimize its bedside documentation work-flows, it chose to enhance its current medication administration devices to allow mobile point-of-care documentation, an innovation that has led to a dramatic advance in speed to documentation of patient data, ultimately improving patient care.

  18. Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN system.

    Directory of Open Access Journals (Sweden)

    Axel Hausmann

    Full Text Available BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN system of BOLD (Barcode of Life Datasystems, a method that supports automated, rapid species delineation and identification. METHODOLOGY/PRINCIPAL FINDINGS: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88% in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93% were found to possess diagnostic barcode sequences at the European level while only three species pairs (3% were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads shared BINs, while specimens from the remaining species (18% were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed

  19. Application of Evolutionary Encryption 2D Barcode Generation Technology in Agricultural Product Quality and Safety Traceability System

    Institute of Scientific and Technical Information of China (English)

    Xiaojun; ZHONG; Zhijie; LAI; Yan; CHEN; Jianxin; QIAN; Xiaocong; HONG; Caiyi; LI

    2014-01-01

    Two-dimensional(2D) barcode technology is an electronic tagging technology based on combination of computer and optical technology. It is an important way of information collection and input. 2D barcode technology has been widely used in various fields of logistics,production automation,and e-commerce,but it also has brought about a series of safety problems. Based on evolutionary encryption technology,this paper improved algorithm of traditional 2D barcode generation,to improve forgery- proof performance of 2D barcode. This algorithm is applied to agricultural products quality and safety traceability system and the results show that it is effective.

  20. Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

    Directory of Open Access Journals (Sweden)

    Kerstin Hoef-Emden

    Full Text Available A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene. In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC, have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

  1. Electrostatic ion beam scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Harper, G.C.; Curtis, W.D.

    1978-04-01

    An electrostatic scanning system has been designed and built to uniformly implant a 1 cm/sup 2/ sample with a charged particle beam. The full angular scan capability for a 2 MeV beam is 0.5 degrees at 6 kV p-p. The design of the system is extremely simple so it is very compact, easy to operate, and has shown very good reliability.

  2. Adaptive CT scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Sampayan, Stephen E.

    2016-11-22

    Apparatus, systems, and methods that provide an X-ray interrogation system having a plurality of stationary X-ray point sources arranged to substantially encircle an area or space to be interrogated. A plurality of stationary detectors are arranged to substantially encircle the area or space to be interrogated, A controller is adapted to control the stationary X-ray point sources to emit X-rays one at a time, and to control the stationary detectors to detect the X-rays emitted by the stationary X-ray point sources.

  3. Identification of crude drugs in the Japanese pharmacopoeia using a DNA barcoding system

    Science.gov (United States)

    Chen, Xiaochen; Xiang, Li; Shi, Linchun; Li, Gang; Yao, Hui; Han, Jianping; Lin, Yulin; Song, Jingyuan; Chen, Shilin

    2017-01-01

    Kampo is the general designation for traditional Japanese herbal medicines, which are recognized as official medicines and listed in the Japanese pharmacopoeia (JP). In most cases, it is difficult to identify the crude drug materials to species level using only traditional identification methods. We report the first online DNA barcode identification system, which includes standard barcode sequences from approximately 95% of the species recorded in the JP (16th edition). This tool provides users with basic information on each crude drug recorded in the JP, DNA barcoding identification of herbal material, and the standard operating procedure (SOP) from sampling to data analysis. ITS2 sequences (psbA-trnH was an alternative when ITS2 could not be amplified) were generated from a total of 576 samples to establish the database. An additional 100 samples (from different medicinal parts, from both single origin and multiple origins and from both retailers and the planting base) were identified using the system. A total of 78% of the test samples were identified as the species listed on their label. This system establishes a model platform for other pharmacopeias from countries like China, Korea, the US and the European Union, for the safe and effective utilization of traditional herbal medicines. PMID:28186159

  4. DPSK-DWT OFDM SYSTEM FOR RELIABLE DATA TRANSMISSION USING BARCODE SYSTEM IN MOBILE DEVICES

    OpenAIRE

    E. Akhila*, K. Ramesh

    2016-01-01

    DPSK-OFDM modulation scheme is implemented in the proposed work to handle the complexity issue in flexible manner for hassle-free data transmission in mobile devices. Barcode scheme has ability to convert the readable form of information into un-understandable form to provide complexity free transmission. Barcode printed on paper has interference free appearance which does not have any leakages while digital barcodes has observed while pixels are leaked into their corresponding black pixels w...

  5. High precision prism scanning system

    Science.gov (United States)

    García-Torales, G.; Flores, J. L.; Muñoz, Roberto X.

    2007-03-01

    Risley prisms are commonly used in continuous scanning manner. Each prism is capable of rotating separately about a common axis at different speeds. Scanning patterns are determined by the ratios of the wedge angles, the speed and direction of rotation of both prisms. The use of this system is conceptually simple. However, mechanical action in most applications becomes a challenge often solved by the design of complex control algorithms. We propose an electronic servomotor system that controls incremental and continuous rotations of the prisms wedges by means of an auto-tuning PID control using a Adaline Neural Network Algorithm, NNA.

  6. Scanning Terahertz Heterodyne Imaging Systems

    Science.gov (United States)

    Siegel, Peter; Dengler, Robert

    2007-01-01

    Scanning terahertz heterodyne imaging systems are now at an early stage of development. In a basic scanning terahertz heterodyne imaging system, (see Figure 1) two far-infrared lasers generate beams denoted the local-oscillator (LO) and signal that differ in frequency by an amount, denoted the intermediate frequency (IF), chosen to suit the application. The LO beam is sent directly to a mixer as one of two inputs. The signal beam is focused to a spot on or in the specimen. After transmission through or reflection from the specimen, the beams are focused to a spot on a terahertz mixer, which extracts the IF outputs. The specimen is mounted on a translation stage, by means of which the focal spot is scanned across the specimen to build up an image.

  7. Genetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  8. The Right Book on the Right Shelf: Missing and Misshelved Books-- How Barcode Scanning Inventories Can Solve the Patrons' Dilemma

    OpenAIRE

    Nixon, Judith M.

    2009-01-01

    After over thirty years of failing to conduct a comprehensive inventory of the book collection at a large liberal arts library, our patrons complained that they could not find one in five books. Study of the problem indicated that in fact 20% of our books were either missing or miss-shelved. This article discusses the investigation of the problem and the impact after five years of conducting an annual inventory by using hand-held devices to gather barcodes and interface these with our catalo...

  9. Developing mobile BIM/2D barcode-based automated facility management system.

    Science.gov (United States)

    Lin, Yu-Cheng; Su, Yu-Chih; Chen, Yen-Pei

    2014-01-01

    Facility management (FM) has become an important topic in research on the operation and maintenance phase. Managing the work of FM effectively is extremely difficult owing to the variety of environments. One of the difficulties is the performance of two-dimensional (2D) graphics when depicting facilities. Building information modeling (BIM) uses precise geometry and relevant data to support the facilities depicted in three-dimensional (3D) object-oriented computer-aided design (CAD). This paper proposes a new and practical methodology with application to FM that uses an integrated 2D barcode and the BIM approach. Using 2D barcode and BIM technologies, this study proposes a mobile automated BIM-based facility management (BIMFM) system for FM staff in the operation and maintenance phase. The mobile automated BIMFM system is then applied in a selected case study of a commercial building project in Taiwan to verify the proposed methodology and demonstrate its effectiveness in FM practice. The combined results demonstrate that a BIMFM-like system can be an effective mobile automated FM tool. The advantage of the mobile automated BIMFM system lies not only in improving FM work efficiency for the FM staff but also in facilitating FM updates and transfers in the BIM environment.

  10. Developing Mobile BIM/2D Barcode-Based Automated Facility Management System

    Directory of Open Access Journals (Sweden)

    Yu-Cheng Lin

    2014-01-01

    Full Text Available Facility management (FM has become an important topic in research on the operation and maintenance phase. Managing the work of FM effectively is extremely difficult owing to the variety of environments. One of the difficulties is the performance of two-dimensional (2D graphics when depicting facilities. Building information modeling (BIM uses precise geometry and relevant data to support the facilities depicted in three-dimensional (3D object-oriented computer-aided design (CAD. This paper proposes a new and practical methodology with application to FM that uses an integrated 2D barcode and the BIM approach. Using 2D barcode and BIM technologies, this study proposes a mobile automated BIM-based facility management (BIMFM system for FM staff in the operation and maintenance phase. The mobile automated BIMFM system is then applied in a selected case study of a commercial building project in Taiwan to verify the proposed methodology and demonstrate its effectiveness in FM practice. The combined results demonstrate that a BIMFM-like system can be an effective mobile automated FM tool. The advantage of the mobile automated BIMFM system lies not only in improving FM work efficiency for the FM staff but also in facilitating FM updates and transfers in the BIM environment.

  11. Fungal DNA barcoding.

    Science.gov (United States)

    Xu, Jianping

    2016-11-01

    Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

  12. An Integrated RFID and Barcode Tagged Item Inventory System for Deployment at New Brunswick Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Younkin, James R [ORNL; Kuhn, Michael J [ORNL; Gradle, Colleen [New Brunswick Laboratory, Argonne, IL; Preston, Lynne [U.S. Department of Energy, Office of Health, Safety and Security; Thomas, Brigham B. [ORNL; Laymance, Leesa K [ORNL; Kuziel, Ron [DOE SC - Chicago Office

    2012-01-01

    New Brunswick Laboratory (NBL) has a numerous inventory containing thousands of plutonium and uranium certified reference materials. The current manual inventory process is well established but is a lengthy process which requires significant oversight and double checking to ensure correctness. Oak Ridge National Laboratory has worked with NBL to develop and deploy a new inventory system which utilizes handheld computers with barcode scanners and radio frequency identification (RFID) readers termed the Tagged Item Inventory System (TIIS). Certified reference materials are identified by labels which incorporate RFID tags and barcodes. The label printing process and RFID tag association process are integrated into the main desktop software application. Software on the handheld computers syncs with software on designated desktop machines and the NBL inventory database to provide a seamless inventory process. This process includes: 1) identifying items to be inventoried, 2) downloading the current inventory information to the handheld computer, 3) using the handheld to read item and location labels, and 4) syncing the handheld computer with a designated desktop machine to analyze the results, print reports, etc. The security of this inventory software has been a major concern. Designated roles linked to authenticated logins are used to control access to the desktop software while password protection and badge verification are used to control access to the handheld computers. The overall system design and deployment at NBL will be presented. The performance of the system will also be discussed with respect to a small piece of the overall inventory. Future work includes performing a full inventory at NBL with the Tagged Item Inventory System and comparing performance, cost, and radiation exposures to the current manual inventory process.

  13. Barcode uses and abuses

    Energy Technology Data Exchange (ETDEWEB)

    KEENEN,MARTHA JANE; NUSBAUM,ANNA W.

    2000-05-18

    Barcodes are something that everybody sees every day; so common as to be taken for granted and normally unnoticed. Readable, no one reads them. They are used to allow machines to identify a wide variety of non-electronic, real life objects. Barcode is one of the earliest types of what is now called ``Automatic Identification and Data Capture'' (AIDC), meaning ``data was transmitted into whatever system by something other than typing or hand-writing.'' There are 18 technologies, broken down into six categories--biometrics, electromagnetic, magnetic, optical, Smart Cards, Touch--included in the AIDC concept. Many are used jointly with or as adjuncts to a basic barcode system of some type. All are based on assignment of a unique identifier to the object, usually a number. The uniqueness presumption makes barcode systems very applicable and appropriate to the nuclear information management venue as they inherently comply with the Nuclear Quality Assurance (NQA-1) requirements. Barcode systems belong to the optical category of AIDC. It is very old in usage as these technologies go, having first been patented in 1949. It astonished me, in researching this paper, to find that there are over 250 types of barcode (symbologies), each with its own specialized attributes, though only a few dozen are in active use. The initial uses were in the early 1950s and diversity of use is ever increasing as people find new ways to make this versatile old technology work. To what else could it be applied, in the future? This paper attempts to answer this.

  14. Speckle analysis in laser scanning display system

    Institute of Scientific and Technical Information of China (English)

    Hong Chang; Wei Huang; Fugui Yang; Hai Ming; Jianping Xie

    2009-01-01

    The theory of speckle formation in laser scanning display system is established based on the averaging effect of eye response as laser beam scanning through an eye resolution spot.It is analyzed that speckle reduction can be obtained by averaging states of speckle during scanning.The theoretical results show that a smaller correlation length of screen surface and the narrowing of laser beam in scanning direction can reduce speckle contrast for this system.

  15. A DNA-based registry for all animal species: the barcode index number (BIN system.

    Directory of Open Access Journals (Sweden)

    Sujeevan Ratnasingham

    Full Text Available Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs, these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL and four established (ABGD, CROP, GMYC, jMOTU algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.

  16. QR Codes in the Library: "It's Not Your Mother's Barcode!"

    Science.gov (United States)

    Dobbs, Cheri

    2011-01-01

    Barcode scanning has become more than just fun. Now libraries and businesses are leveraging barcode technology as an innovative tool to market their products and ideas. Developed and popularized in Japan, these Quick Response (QR) or two-dimensional barcodes allow marketers to provide interactive content in an otherwise static environment. In this…

  17. Choosing and using a plant DNA barcode.

    Directory of Open Access Journals (Sweden)

    Peter M Hollingsworth

    Full Text Available The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1 mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

  18. Development of a DNA barcoding system for seagrasses: successful but not simple.

    Directory of Open Access Journals (Sweden)

    Christina Lucas

    Full Text Available Seagrasses, a unique group of submerged flowering plants, profoundly influence the physical, chemical and biological environments of coastal waters through their high primary productivity and nutrient recycling ability. They provide habitat for aquatic life, alter water flow, stabilize the ground and mitigate the impact of nutrient pollution. at the coast region. Although on a global scale seagrasses represent less than 0.1% of the angiosperm taxa, the taxonomical ambiguity in delineating seagrass species is high. Thus, the taxonomy of several genera is unsolved. While seagrasses are capable of performing both, sexual and asexual reproduction, vegetative reproduction is common and sexual progenies are always short lived and epimeral in nature. This makes species differentiation often difficult, especially for non-taxonomists since the flower as a distinct morphological trait is missing. Our goal is to develop a DNA barcoding system assisting also non-taxonomists to identify regional seagrass species. The results will be corroborated by publicly available sequence data. The main focus is on the 14 described seagrass species of India, supplemented with seagrasses from temperate regions. According to the recommendations of the Consortium for the Barcoding of Life (CBOL rbcL and matK were used in this study. After optimization of the DNA extraction method from preserved seagrass material, the respective sequences were amplified from all species analyzed. Tree- and character-based approaches demonstrate that the rbcL sequence fragment is capable of resolving up to family and genus level. Only matK sequences were reliable in resolving species and partially the ecotype level. Additionally, a plastidic gene spacer was included in the analysis to confirm the identification level. Although the analysis of these three loci solved several nodes, a few complexes remained unsolved, even when constructing a combined tree for all three loci. Our approaches

  19. 基于CC2430的无线条码数据采集器的设计%Design of wireless barcode data gathering system based on CC2430

    Institute of Scientific and Technical Information of China (English)

    齐华; 王秋娟; 刘军

    2011-01-01

    介绍了一种利用CC2430实现条码数据无线传输的数据采集系统.该系统利用嵌入式技术、无线通信技术、条码识别技术,以微处理器MCF5249、ZigBee无线传输模块、条码扫描引擎EM3000为核心,解决了以往仓库管理中手工录入信息效率低下的问题,实现了对信息的自动采集、实时传输及分析管理,并具有一体性、机动性、体积小的特点.%This paper introduces a wireless barcode data gathering system which uses CC2430 chip to transmit the barcode information. Design of the system is based on embedded technology, wireless communication technology and barcode recognition technology. The system mainly consists of micro processer unit MCF5249, ZigBee modules and 1D/2D CMOS scan engine EM3000.The traditional low efficiency methods of warehouse management are changed by the system. Information can be recognized,gathered and real-time transmitted by the system. The system is characterized by integration, mobility and small size.

  20. Challenges implementing bar-coded medication administration in the emergency room in comparison to medical surgical units.

    Science.gov (United States)

    Glover, Nancy

    2013-03-01

    Bar-coded medication administration has been successfully implemented and utilized to decrease medication errors at a number of hospitals in recent years. The purpose of this article was to discuss the varying success in utilization of bar-coded medication administration on medical-surgical units and in the emergency department. Utilization reports were analyzed to better understand the challenges between the units. Many factors negatively impacted utilization in the emergency department, including the inability to use bar-coded medication administration for verbal orders or to document medications distributed by the prescribing providers, unique aspects of emergency department nursing workflow, additional steps to chart when using bar-coded medication administration, and alert fatigue. Hardware problems affected all users. Bar-coded medication administration in its current form is more suitable for use on medical-surgical floors than in the emergency department. New solutions should be developed for bar-coded medication administration in the emergency department, keeping in mind requirements to chart medications when there is no order in the system, document medications distributed by prescribing providers, adapt to unpredictable nursing workflow, minimize steps to chart with bar-coded medication administration, limit alerts to those that are clinically meaningful, and choose reliable hardware with adequate bar-code scanning capability.

  1. Laser identification system based on acousto-optical barcode scanner principles

    Science.gov (United States)

    Khansuvarov, Ruslan A.; Korol, Georgy I.; Preslenev, Leonid N.; Bestugin, Aleksandr R.; Paraskun, Arthur S.

    2016-09-01

    The main purpose of the bar code in the modern world is the unique identification of the product, service, or any of their features, so personal and stationary barcode scanners so widely used. One of the important parameters of bar code scanners is their reliability, accuracy of the barcode recognition, response time and performance. Nowadays, the most popular personal barcode scanners contain a mechanical part, which extremely impairs the reliability indices. Group of SUAI engineers has proposed bar code scanner based on laser beam acoustic deflection effect in crystals [RU patent No 156009 issued 4/16/2015] Through the use of an acousto-optic deflector element in barcode scanner described by a group of engineers SUAI, it can be implemented in the manual form factor, and the stationary form factor of a barcode scanner. Being a wave electronic device, an acousto-optic element in the composition of the acousto-optic barcode scanner allows you to clearly establish a mathematical link between the encoded function of the bar code with the accepted input photodetector intensities function that allows you to speak about the great probability of a bar code clear definition. This paper provides a description of the issued patent, the description of the principles of operation based on the mathematical analysis, a description of the layout of the implemented scanner.

  2. DNA barcoding as an effective tool in improving a digital plant identification system: a case study for the area of Mt. Valerio, Trieste (NE Italy.

    Directory of Open Access Journals (Sweden)

    Ilaria Bruni

    Full Text Available BACKGROUND: Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting. DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy. The core barcode markers (plastidial rbcL and matK, plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios. CONCLUSIONS/SIGNIFICANCE: Our results show that the core barcode markers univocally identify most species of our local flora (96%. The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant

  3. Camera Systems Rapidly Scan Large Structures

    Science.gov (United States)

    2013-01-01

    Needing a method to quickly scan large structures like an aircraft wing, Langley Research Center developed the line scanning thermography (LST) system. LST works in tandem with a moving infrared camera to capture how a material responds to changes in temperature. Princeton Junction, New Jersey-based MISTRAS Group Inc. now licenses the technology and uses it in power stations and industrial plants.

  4. The design of laser scanning galvanometer system

    Science.gov (United States)

    Sun, Xiaoling; Zhou, Bin; Xie, Weihao; Zhang, Yuangeng

    2015-02-01

    In this paper, we designed the laser scanning galvanometer system according to our requirements. Based on scanning range of our laser scanning galvanometer system, the design parameters of this system were optimized. During this work, we focused on the design of the f-θ field lens. An optical system of patent lens in the optical manual book, which had three glasses structure, was used in our designs. Combining the aberration theory, the aberration corrections and image quality evaluations were finished using Code V optical design software. An optimum f-θ field lens was designed, which had focal length of 434 mm, pupil diameter of 30 mm, scanning range of 160 mm × 160 mm, and half field angle of 18°×18°. At the last, we studied the influences of temperature changes on our system.

  5. 中药DNA条形码鉴定体系及研究方向%Identification System and Perspective for DNA Barcoding Traditional Chinese Materia Medica

    Institute of Scientific and Technical Information of China (English)

    陈士林; 庞晓慧; 姚辉; 韩建萍; 罗焜

    2011-01-01

    近年来,中药DNA条形码分子鉴定得到快速发展,加快了中药鉴定标准化的进程.通过中药DNA条形码鉴定研究,我国首次提出将ITS2序列作为药用植物鉴定的通用条形码序列,并建立以ITS2为核心、psbA -trnH为补充序列的植物类药材DNA条形码鉴定体系和以COI序列为核心、ITS2为辅助序列的动物类药材DNA条形码鉴定体系,为中药DNA条形码鉴定的发展奠定了坚实基础.本文结合课题组研究工作就构建中药DNA条形码鉴定体系进行了综述,包括中药DNA条形码序列的筛选确定、中药DNA条形码鉴定流程和中药DNA条形码鉴定数据库系统构建,并介绍了中药DNA条形码鉴定的研究方向.%DNA barcoding in Traditional Chinese Materia Medica has developed rapidly in recent years, which accelerates the progress of standardization in identifying Traditional Chinese Materia Medica. Chen et al. First proposed that ITS2 locus can be used as the standard barcode for identifying medicinal plant species based on an extensive study on DNA barcoding in Traditional Chinese Materia Medica. Meanwhile, the systems for barcoding medicinal plants based on a two-locus combination of ITS2+psbA-trnH and for authenticating medicinal animals based on COI+ITS2 have been established, providing a basis for the development of DNA barcoding in Traditional Chinese Materia Medica. In this review, we summarize the establishment of the system for barcoding Traditional Chinese Materia Medica, including the selection and determination of DNA barcodes, the identification process of DNA barcoding in Traditional Chinese Materia Medica and building the database system of DNA barcoding in Traditional Chinese Materia Medica. Moreover, we describe the perspective for further research on DNA barcoding in Traditional Chinese Materia Medica.

  6. Choosing and Using a Plant DNA Barcode

    OpenAIRE

    Hollingsworth, Peter M.; Graham, Sean W.; Little, Damon P.

    2011-01-01

    The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the ...

  7. Scanning tunneling microscope assembly, reactor, and system

    Science.gov (United States)

    Tao, Feng; Salmeron, Miquel; Somorjai, Gabor A

    2014-11-18

    An embodiment of a scanning tunneling microscope (STM) reactor includes a pressure vessel, an STM assembly, and three spring coupling objects. The pressure vessel includes a sealable port, an interior, and an exterior. An embodiment of an STM system includes a vacuum chamber, an STM reactor, and three springs. The three springs couple the STM reactor to the vacuum chamber and are operable to suspend the scanning tunneling microscope reactor within the interior of the vacuum chamber during operation of the STM reactor. An embodiment of an STM assembly includes a coarse displacement arrangement, a piezoelectric fine displacement scanning tube coupled to the coarse displacement arrangement, and a receiver. The piezoelectric fine displacement scanning tube is coupled to the coarse displacement arrangement. The receiver is coupled to the piezoelectric scanning tube and is operable to receive a tip holder, and the tip holder is operable to receive a tip.

  8. ACTD Laser Line Scan System

    Science.gov (United States)

    1997-09-30

    communications with a computer system in the MILVAN. For the ACTD a single board computer dedicated to the EOID Sensor will be inserted into GEM. This... single board computer will provide real time control of the EOID Sensor. Since the bandwidth of the microwave data link is smaller than the data rate of...EOID Sensor image data will be maintained in a circular buffer on the single board computer in GEM. Upon command, full resolution data from any segment

  9. Barcoding poplars (Populus L. from western China.

    Directory of Open Access Journals (Sweden)

    Jianju Feng

    Full Text Available BACKGROUND: Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M, trnG-psbK (G and psbK-psbI (P, and trnH-psbA (H and rbcL (R; the discrimination efficiency of the nuclear ITS (I is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I, and usually discrimination failures occurred among species from sympatric or parapatric areas. CONCLUSIONS/SIGNIFICANCE: In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in

  10. SCANNING VISION SYSTEM FOR VEHICLE NAVIGATION

    OpenAIRE

    O. Sergiyenko

    2012-01-01

    The new model of the scanning vision system for vehicles is offered. The questions of creation, functioning and interaction of the system units and elements are considered. The mathematical apparatus for processing digital information inside the system and for determining distances and an-gle standard in the offered system is worked out. Expected accuracy, functioning speed, range of ac-tion, energy consumption when using the system are determined. The possible areas of the developed automa...

  11. Phased array based ultrasound scanning system development

    Science.gov (United States)

    Sagdiev, R. K.; Denisov, E. S.; Evdokimov, Yu K.; Fazlyyyakhmatov, M. G.; Kashapov, N. F.

    2014-12-01

    Multichannel ultrasound scanning system based on phased arrays development is presented in this paper. Substantiation of system parameters is presented. The description of block diagram and hardware development is presented. The combination of the self-developed receiving and a transmitting units and commercially available FPGA unit and Personal Computer can solve our scientific goals, while providing a relatively low device cost.

  12. SCANNING VISION SYSTEM FOR VEHICLE NAVIGATION

    Directory of Open Access Journals (Sweden)

    O. Sergiyenko

    2012-01-01

    Full Text Available The new model of the scanning vision system for vehicles is offered. The questions of creation, functioning and interaction of the system units and elements are considered. The mathematical apparatus for processing digital information inside the system and for determining distances and an-gle standard in the offered system is worked out. Expected accuracy, functioning speed, range of ac-tion, energy consumption when using the system are determined. The possible areas of the developed automatic navigation system use are offered.

  13. CS-Studio Scan System Parallelization

    Energy Technology Data Exchange (ETDEWEB)

    Kasemir, Kay [ORNL; Pearson, Matthew R [ORNL

    2015-01-01

    For several years, the Control System Studio (CS-Studio) Scan System has successfully automated the operation of beam lines at the Oak Ridge National Laboratory (ORNL) High Flux Isotope Reactor (HFIR) and Spallation Neutron Source (SNS). As it is applied to additional beam lines, we need to support simultaneous adjustments of temperatures or motor positions. While this can be implemented via virtual motors or similar logic inside the Experimental Physics and Industrial Control System (EPICS) Input/Output Controllers (IOCs), doing so requires a priori knowledge of experimenters requirements. By adding support for the parallel control of multiple process variables (PVs) to the Scan System, we can better support ad hoc automation of experiments that benefit from such simultaneous PV adjustments.

  14. DNA barcoding methods for land plants.

    Science.gov (United States)

    Fazekas, Aron J; Kuzmina, Maria L; Newmaster, Steven G; Hollingsworth, Peter M

    2012-01-01

    DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system transitions. Additionally, there are many life-history trait combinations, which combine to reduce the likelihood of a small number of markers effectively tracking plant species boundaries. Recent results, however, from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions trnH-psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extraction protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.

  15. Influence of scanning strategies on the accuracy of digital intraoral scanning systems.

    Science.gov (United States)

    Ender, A; Mehl, A

    2013-01-01

    The digital intraoral impression is a central part in today's CAD/CAM dentistry. With its possibilities, new treatment options for the patient is provided and the prosthetic workflow is accelerated. Nowadays, the major issue with intraoral scanning systems is to gain more accuracy especially for larger scan areas and to simplify clinical handling for the dentist. The aim of this study was to investigate different scanning strategies regardingtheir accuracy with full arch scans in an in-vitro study design. A reference master model was used for the digital impressions with the Lava COS, the Cerec Bluecam and a powderfree intraoral scanning system, Cadent iTero. The trueness and precision of each scanning protocol was measured. Lava COS provides the a trueness of 45.8 microm with the scanning protocol recommended from the manufacturer. A different scanning protocol shows significantly lower accuracy (trueness +/- 90.2 microm). Cerec Bluecam also benefits from an optimal scanning protocol with a trueness of +/- 23.3 microm compared to +/- 52.5 microm with a standard protocol. The powderfree impression system Cadent iTero shows also a high accurate full-arch scan with a trueness of +/- 35.0 microm and a precision of +/- 30.9 microm. With the current intraoral scanning systems, full arch dental impressions are possible with a high accuracy, if adequate scan strategies are used. The powderfree scanning system provides the same level of accuracy compared to scanning systems with surface pretreatment.

  16. Development of an automatic pipeline scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae H.; Lee, Jae C.; Moon, Soon S.; Eom, Heung S.; Choi, Yu R

    1999-11-01

    Pressure pipe inspection in nuclear power plants is one of the mandatory regulation items. Comparing to manual ultrasonic inspection, automatic inspection has the benefits of more accurate and reliable inspection results and reduction of radiation disposal. final object of this project is to develop an automatic pipeline inspection system of pressure pipe welds in nuclear power plants. We developed a pipeline scanning robot with four magnetic wheels and 2-axis manipulator for controlling ultrasonic transducers, and developed the robot control computer which controls the robot to navigate along inspection path exactly. We expect our system can contribute to reduction of inspection time, performance enhancement, and effective management of inspection results. The system developed by this project can be practically used for inspection works after field tests. (author)

  17. Optical analysis of scanning microstereolithography systems

    Science.gov (United States)

    Deshmukh, Suhas P.; Dubey, Shashikant; Gandhi, P. S.

    2006-01-01

    Microstereolithography (MSL) is rapidly developing technique for micro-fabrication. Vector-by-vector scanning MSL has a potential to create true 3D micro-devices as compared to mostly planar (2D-2 1/2 D) devices fabricated by conventional MEMS techniques. Previous literature shows two different scanning methods:(1) Galvanomirror scanning, (2) Photoreactor tank scanning. Galvanomirror scanning technique has higher fabrication speed but poor resolution because of defocusing of laser spot on the resin surface. Photo-reactor tank scanning has higher resolution but produces a wavy structures and limited speed of fabrication. This paper proposes and develops an offaxis lens scanning technique for MSL and carries out optical analysis to compare its performance with the existing techniques mentioned above. The comparison clearly demonstrates improved performance with the proposed offaxis lens scanning technique.

  18. Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes.

    Science.gov (United States)

    Kvist, Sebastian; Oceguera-Figueroa, Alejandro; Siddall, Mark E; Erséus, Christer

    2010-12-01

    Species identifications based on DNA barcoding rely on the correct identity of previously barcoded specimens, but little attention has been given to whether deposited barcodes include correspondence to the species' name-bearing type. The information content associated with COX1 sequences in the two most commonly used repositories of barcodes, GenBank and the Barcode of Life Data System (BOLD), is often insufficient for subsequent evaluation of the robustness of the identification procedure. We argue that DNA barcoding and taxonomy alike will benefit from more information content in the annotations of barcoded specimens as this will allow for validation and re-evaluation of the initial specimen identification. The aim should be to closely connect specimens from which reference barcodes are generated with the holotype through straight-forward taxonomy, and geographical and genetic correlations. Annotated information should also include voucher specimens and collector/identifier information. We examine two case studies based on empirical data, in which barcoding and taxonomy benefit from increased information content. On the basis of data from the first case study, we designate a barcoded neotype of the European medicinal leech, Hirudo medicinalis, on morphological and geographical grounds.

  19. Recommendations for Using Barcode in Hospital Process

    Science.gov (United States)

    Hachesu, Peyman Rezaei; Zyaei, Leila; Hassankhani, Hadi

    2016-01-01

    Background: Lack of attention to the proper barcode using leads to lack of use or misuse in the hospitals. The present research aimed to investigate the requirements and barrier for using barcode technology and presenting suggestions to use it. Methods: The research is observational-descriptive. The data was collected using the designed checklist which its validity was assessed. This check list consists of two parts: “Requirements” and “barrier” of using the barcodes. Research community included 10 teaching hospitals and a class of 65 participants included people in the hospitals. The collected data was analyzed using descriptive statistics. Results: Required changes of workflow processes in the hospital and compliance them with the hospital policy are such requirements that had been infringed in the 90 % of hospitals. Prioritization of some hospital processes for barcoding, system integration with Hospital Information system (HIS), training of staff and budgeting are requirements for the successful implementation which had been infringed in the 80% of hospitals. Dissatisfaction with the quality of barcode labels and lacks of adequate scanners both whit the rate of 100 %, and the lack of understanding of the necessary requirements for implementation of barcodes as 80% were the most important barrier. Conclusion: Integrate bar code system with clinical workflow should be considered. Lack of knowledge and understanding toward the infrastructure, inadequate staff training and technologic problems are considered as the greatest barriers. PMID:27482137

  20. Establishing and evaluating bar-code technology in blood sampling system: a model based on human centered human-centered design method.

    Science.gov (United States)

    Chou, Shin-Shang; Yan, Hsiu-Fang; Huang, Hsiu-Ya; Tseng, Kuan-Jui; Kuo, Shu-Chen

    2012-01-01

    This study intended to use a human-centered design study method to develop a bar-code technology in blood sampling process. By using the multilevel analysis to gather the information, the bar-code technology has been constructed to identify the patient's identification, simplify the work process, and prevent medical error rates. A Technology Acceptance Model questionnaire was developed to assess the effectiveness of system and the data of patient's identification and sample errors were collected daily. The average scores of 8 items users' perceived ease of use was 25.21(3.72), 9 items users' perceived usefulness was 28.53(5.00), and 14 items task-technology fit was 52.24(7.09), the rate of patient identification error and samples with order cancelled were down to zero, however, new errors were generated after the new system deployed; which were the position of barcode stickers on the sample tubes. Overall, more than half of nurses (62.5%) were willing to use the new system.

  1. DNA mini-barcodes.

    Science.gov (United States)

    Hajibabaei, Mehrdad; McKenna, Charly

    2012-01-01

    Conventional DNA barcoding uses an approximately 650 bp DNA barcode of the mitochondrial gene COI for species identification in animal groups. Similar size fragments from chloroplast genes have been proposed as barcode markers for plants. While PCR amplification and sequencing of a 650 bp fragment is consistent in freshly collected and well-preserved specimens, it is difficult to obtain a full-length barcode in older museum specimens and samples which have been preserved in formalin or similar DNA-unfriendly preservatives. A comparable issue may prevent effective DNA-based authentication and testing in processed biological materials, such as food products, pharmaceuticals, and nutraceuticals. In these cases, shorter DNA sequences-mini-barcodes-have been robustly recovered and shown to be effective in identifying majority of specimens to a species level. Furthermore, short DNA regions can be utilized via high-throughput sequencing platforms providing an inexpensive and comprehensive means of large-scale species identification. These properties of mini-barcodes, coupled with the availability of standardized and universal primers make mini-barcodes a feasible option for DNA barcode analysis in museum samples and applied diagnostic and environmental biodiversity analysis.

  2. DNA barcoding for plants.

    Science.gov (United States)

    de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte

    2015-01-01

    DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.

  3. Morphostructural analysis of the male reproductive system and DNA barcoding in Balclutha brevis Lindberg 1954 (Homoptera, Cicadellidae).

    Science.gov (United States)

    Vitale, D G M; Viscuso, R; D'Urso, V; Gibilras, S; Sardella, A; Marletta, A; Pappalardo, A M

    2015-12-01

    Balclutha brevis Lindberg 1954 is an allochthonous leafhopper infesting an invasive grass, Pennisetum setaceum, in Sicily and in mainland Europe; therefore, this species could compete with populations of native species, thus contributing to the loss of biodiversity. Considering the ecological implications of B. brevis, investigations on all its biological aspects represent, therefore, a premise for further studies in applied sciences. Based on the lacking ultrastructural data about the reproductive systems of the Auchenorrhyncha, we carried out morphostructural investigations on the male reproductive system of B. brevis. Further, a first report of DNA barcoding analysis (amplification and sequencing of Cytochrome Oxidase I gene) has also been performed to characterize B. brevis compared to other congeneric species. From a morphological point of view, the male reproductive system of B. brevis has an organization comparable to the general anatomical features of most of the Auchenorrhyncha species; however, comparing our data with those concerning the different groups of Cicadomorpha, some considerations are discussed. As for the histological and ultrastructural investigations, our results show a secretory activity of the various examined structures, mainly in the lateral ejaculatory ducts and in the accessory glands. The latter, in particular, show morphostructural differences comparing the distal tract to the proximal one; moreover, the histochemical techniques showed the possible presence of a lipid component in the peculiar cytoplasmic granules found in the gland cells. The significance of these findings in the accessory glands is discussed. Finally, the ultrastructural features found in the seminal vesicles are different from those of the lateral ejaculatory ducts and are indicative of the different roles played by these structures in the organization of the spermatozoa bundles.

  4. New Aspects in Chinese Herb Materials Identification by DNA Barcoding

    OpenAIRE

    Guo, Hui; Siyang JIN; Liu, Han; Zhenyue WANG

    2016-01-01

    The numerous noxious reactions have overwhelming concerning by misusing medicinal plant ingredients. This phenomenon has aroused the worldwide demand over the safe application in pharmaceuticals. DNA barcoding offers a powerful means to complement morphological and chemical processes for distinguishing Chinese medicinal plants. Consequently, a DNA barcoding system should be continuous renewal containing mass information about authentic plant materials and potentially substitutes or adulterant...

  5. System and method for compressive scanning electron microscopy

    Science.gov (United States)

    Reed, Bryan W

    2015-01-13

    A scanning transmission electron microscopy (STEM) system is disclosed. The system may make use of an electron beam scanning system configured to generate a plurality of electron beam scans over substantially an entire sample, with each scan varying in electron-illumination intensity over a course of the scan. A signal acquisition system may be used for obtaining at least one of an image, a diffraction pattern, or a spectrum from the scans, the image, diffraction pattern, or spectrum representing only information from at least one of a select subplurality or linear combination of all pixel locations comprising the image. A dataset may be produced from the information. A subsystem may be used for mathematically analyzing the dataset to predict actual information that would have been produced by each pixel location of the image.

  6. Analysis of data captured by barcode medication administration system using a PDA; aiming at reducing medication errors at point of care in Japanese Red Cross Kochi Hospital.

    Science.gov (United States)

    Akiyama, Masanori; Koshio, Atsushi; Kaihotsu, Nobuyuki

    2010-01-01

    Preventing medication errors by using a barcode administration system has become prevalent in patient safety. Analyses of data captured by bar code systems provide opportunities to understand the actual situation at the point of care. Our study aims at understanding issues of medication safety as well as investigating measures taken to prevent medication accidents, by analyzing data captured by a bar code system and a personal digital assistant (PDA). The barcode administration system named Point-of-Act-System implemented in Japanese Red Cross Kochi Hospital was designed to capture every activity at the bedside. Complete activity data captured by the system, which included injections, treatment and other nursing activity, as well as injection warning data, were used for our analyses. We describe the data and analyze them statistically to find potentially times of risk and to ascertain the relation between busyness and error. The injection warning rate as a whole was 6.1% on average. The results showed there was a negative correlation between the number of injections given and the injection warning rate (-0.48, pmedication safety. A bar code administration system is quite an effective way not only to prevent medication error at point of care, but also to improve patient safety through analyses of data captured by such a system.

  7. 基于条码扫描的便携式拿货提醒设备%Portable Equipment Which is Used for Goods Order Reminding is Based on Barcode Scanning

    Institute of Scientific and Technical Information of China (English)

    赖俊桦; 高维; 朱云来; 孟坚

    2015-01-01

    Barcode technology is mature in the market today, the use of barcode mobile devices also will be quite extensive. A por⁃table device for courier, with the main chip of STC89C52 Single Chip microcontroller, combined with the one-dimensional bar code scanning and GSM SMS module can be used for direct communication with buyers’couriers, it is easy and fast for notifica⁃tion buyers getting goods. The equipment achieves a good access to information, display and processing functions. The equipment includes the following four modules: one-dimensional bar code scanning recognition module, GSM communication module, the central control module and the information display and input module. The buyer’s telephone number stored in the one-dimension⁃al bar code, through the one-dimensional bar code scanning module identification information stored in the bar code, using serial to communicate with the main chip of STC89C52 Single Chip microcontroller, as the same time the information displayed on the LCD module. Internal telephone number will be transferred to the GSM SMS module for sending pre-set message content to buy⁃ers. Message content can be edited. In addition, the product can extract the last digit of the phone number issued to classify the goods.%现今市场条码技术已成熟,条码移动设备也随之快速发展并得到广泛运用。设计以STC89C52单片机作为主控芯片,结合一维条形码扫描和GSM短信发送模块的快递员便携式拿货提醒设备,可用于快递员与买家直接的交流,是一对多方便、快捷的通知买家拿货设备,很好的实现信息的获取、显示和处理等功能。该作品主要包括以下四个模块:一维条码扫描识别模块、GSM通信模块、中央控制模块和信息显示及输入模块。将买家的电话号码存储在一维条码中,通过一维条码扫描模块来识别条码中存储的信息,利用串口和中央主控52单片机进行通信,同时在

  8. Further progress for a fast scanning of nuclear emulsions with Large Angle Scanning System

    Science.gov (United States)

    Alexandrov, A.; Tioukov, V.; Vladymyrov, M.

    2014-02-01

    The LASSO (Large Angle Scanning System for OPERA) is a scanning system designed in the framework of the OPERA experiment as a result of several R&Ds aimed to improve the performance of the European Scanning System (ESS) by increasing the scanning speed, the angular acceptance and the efficiency in microtrack reconstruction. The novel Continuous Motion (CM) scanning approach allows to double the ESS nominal speed without any changes in the hardware set-up. The LASSO modular design makes the system easily adaptable to new hardware. The novel microtrack reconstruction algorithm has been developed to be efficient in both standard Stop&Go (SG) and CM modes, performing a number of corrections during the processing like corrections for vibrations, optical distortions, field of view curvature. As an intermediate step it reconstructs silver grains positions inside emulsion layer to make a transition from 2D images to real 3D traces of a charged particle. This allows the algorithm to have no internal limits on the slope of microtracks being equally efficient on all angles. The LASSO has been used for about one year for mass production scanning of emulsion films of OPERA, Muon Radiography and also of films employed to study nuclear fragmentation of ion beams used in medical physics. More than 50000 cm2 of the emulsion surface have been analyzed during this period.

  9. Determining Lineage Pathways from Cellular Barcoding Experiments

    Directory of Open Access Journals (Sweden)

    Leïla Perié

    2014-02-01

    Full Text Available Cellular barcoding and other single-cell lineage-tracing strategies form experimental methodologies for analysis of in vivo cell fate that have been instrumental in several significant recent discoveries. Due to the highly nonlinear nature of proliferation and differentiation, interrogation of the resulting data for evaluation of potential lineage pathways requires a new quantitative framework complete with appropriate statistical tests. Here, we develop such a framework, illustrating its utility by analyzing data from barcoded multipotent cells of the blood system. This application demonstrates that the data require additional paths beyond those found in the classical model, which leads us to propose that hematopoietic differentiation follows a loss of potential mechanism and to suggest further experiments to test this deduction. Our quantitative framework can evaluate the compatibility of lineage trees with barcoded data from any proliferating and differentiating cell system.

  10. Scanning SQUID microscopy for magnetic flux systems

    CERN Document Server

    Suzuki, J I; Hata, Y

    2003-01-01

    Recently, vortices confined into micro-scale superconductors with shapes like a disk, triangle, square, etc., have attracted much attention because of the quantum phase transition of the self-organized vortex arrangement occurring within such geometrical constraints. Such a transition can be observed using a scanning SQUID microscope with high spatial resolution. We have successfully improved spatial resolution by incorporating a microfabrication technique that reduces both the size of the pick-up coil of the micro DC-SQUID and the standoff distance between the pick-up coil and the sample surface. Using this microscope, we have studied vortex arrangements in micro-scale superconductors made of Nb and YBa sub 2 Cu sub 3 O sub 7 sub - subdelta films with various sizes and geometrical shapes. A peculiar oscillating behavior of diamagnetic magnetization corresponding to the particular vortex state was observed.

  11. Circuit enhances vertical resolution in raster scanning systems

    Science.gov (United States)

    Alsovsky, W. H.; Greenwood, J. R.; Holley, O. M.

    1968-01-01

    Circuit enhances vertical resolution in electron beam, raster scanning systems exhibiting aperture distortion in the vertical direction. A sensitized area /image/ produces a video output when the scan beam nears it, which causes vertical elongation in the reconstructed images of all sensitized areas on the surface.

  12. From Barcode to QR Code Applications

    Directory of Open Access Journals (Sweden)

    László Várallyai

    2012-12-01

    Full Text Available This paper shows the Zsohár Horticulture Company in Nagyrákos, how they want to change their barcode identification system to QR code. They cultivate herbaceous, perpetual decorational plants, rock-garden, flower-bed and swamp perpetuals, decorational grasses and spices. A part of the perpetuals are evergreens, but most of them has special organs - such as onions, thick-, bulbous roots, "winter-proof" buds - so they can survive winter. In the first part of the paper I introduce the different barcode standards, how can it be printed and how can it be read. In the second part of the paper I give details about the quick response code (QR code and the two-dimensional (2D barcode. Third part of this paper illustrates the QR code usability in agriculture focused on the gardening.

  13. DNA barcodes for ecology, evolution, and conservation.

    Science.gov (United States)

    Kress, W John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L

    2015-01-01

    The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed.

  14. A fast DSP-based calorimeter hit scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Sekikawa, S.; Arai, I.; Suzuki, A.; Watanabe, A. [Tsukuba Univ., Ibaraki (Japan). Inst. of Phys.; Kuno, Y. [Department of Physics, National Laboratory for High Energy (KEK), Tsukuba, Ibaraki 305 (Japan); Marlow, D.R.; Mindas, C.R.; Wixted, R.L. [Physics Department, Princeton University, Princeton, NJ (United States)

    1997-08-11

    A custom made digital signal processor (DSP) based system has been developed to scan calorimeter hits read by a 32-channel FASTBUS waveform recorder board. The scanner system identifies hit calorimeter elements by surveying their discriminated outputs. This information is used to generate a list of addresses, which guides the read-out process. The system is described and measurements of the scan times are given. (orig.).

  15. [SCAN system--semi-structured interview based on diagnostic criteria].

    Science.gov (United States)

    Adamowski, Tomasz; Kiejna, Andrzej; Hadryś, Tomasz

    2006-01-01

    This paper presents the main features of contemporary diagnostic systems which are implemented into the SCAN--modern and semi-structured diagnostic interview. The concepts of further development of the classifications, rationale for operationalized diagnostic criteria and for the divisional approach to mental diagnoses will be in focus. The structure and components of SCAN ver. 2.1 (WHO), i.e. Present State Examination--10th edition, Item Group Checklist, Clinical History Schedule, Glossary of Definitions and computer software with the diagnostic algorithm: I-Shell, as well as rules for a reliable use of diagnostic rating scales, will be discussed within the scope of this paper. The materials and training sets necessary for the learning of proper use of the SCAN, especially training sets for SCAN Training Centers and the Reference Manual--a form of guidebook for SCAN shall be introduced. Finally the paper will present evidence that SCAN is an instrument feasible in different cultural settings. Reliability and validity data of SCAN will also be dealt with indicating that SCAN could be widely used in research studies as well as in everyday clinical practice facilitating more detailed diagnostic approach to a patient.

  16. A Multicounter System for Scanning Ultra-Low-Level Radiochromatograms

    DEFF Research Database (Denmark)

    Bøtter-Jensen, Lars; Hansen, Heinz Johs. Max; Theodorsson, P.

    1977-01-01

    A multicounter system consisting of an integrated array of flow counters for the scanning of ultra-low-level radioactivity on paper and thin-layer chromatograms was developed. Experience with routine measurements over a prolonged period has proved the advantages of this system over other systems...

  17. 基于金蝶BOS的条码管理系统设计与实现%Barcode Management System Design and Implementation Based on Kingdee BOS

    Institute of Scientific and Technical Information of China (English)

    王睿; 叶潮流

    2015-01-01

    针对电器销售行业存在的串货、盘点复杂和销售出库异常等问题,引入了条码技术,为每一个商品建立唯一条码。经过对系统需求的分析和数据库的设计,开发了条码管理系统,实现了条码编码、打印和查询等功能。同时,开发了接口程序,实现了与金蝶ERP系统的无缝集成,通过使用PDA数据采集器采集商品信息,实现产品跟踪追溯,帮助企业提高仓库的管理效率。%Regarding the problems of changing products, complex inventory and sales inaccurate in appliance sales industry, introducing barcode technology has realized building a unique barcode for each commodity. After analyzing the system requirements and database design, the study developed the PC and terminal bar code management system to achieve the basic functions of bar code encoding, printing and inquiry. It also developed interface program of Kingdee ERP systems and seamless integration with Kingdee ERP system. The study improved the management efficiency of the enterprise warehouse and products traceability by collecting goods information with the help of PDA data collection.

  18. Barcoded microchips for biomolecular assays.

    Science.gov (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

    2015-01-20

    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  19. DNA barcoding identifies Argentine fishes from marine and brackish waters.

    Directory of Open Access Journals (Sweden)

    Ezequiel Mabragaña

    Full Text Available BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. METHODOLOGY/PRINCIPAL FINDINGS: Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species, and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org. Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125 examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha

  20. Slit scan radiographic system for intermediate size rocket motors

    Science.gov (United States)

    Bernardi, Richard T.; Waters, David D.

    1992-12-01

    The development of slit-scan radiography capability for the NASA Advanced Computed Tomography Inspection System (ACTIS) computed tomography (CT) scanner at MSFC is discussed. This allows for tangential case interface (bondline) inspection at 2 MeV of intermediate-size rocket motors like the Hawk. Motorized mounting fixture hardware was designed, fabricated, installed, and tested on ACTIS. The ACTIS linear array of x-ray detectors was aligned parallel to the tangent line of a horizontal Hawk motor case. A 5 mm thick x-ray fan beam was used. Slit-scan images were produced with continuous rotation of a horizontal Hawk motor. Image features along Hawk motor case interfaces were indicated. A motorized exit cone fixture for ACTIS slit-scan inspection was also provided. The results of this SBIR have shown that slit scanning is an alternative imaging technique for case interface inspection. More data is required to qualify the technique for bondline inspection.

  1. Comparative Geometrical Investigations of Hand-Held Scanning Systems

    Science.gov (United States)

    Kersten, T. P.; Przybilla, H.-J.; Lindstaedt, M.; Tschirschwitz, F.; Misgaiski-Hass, M.

    2016-06-01

    An increasing number of hand-held scanning systems by different manufacturers are becoming available on the market. However, their geometrical performance is little-known to many users. Therefore the Laboratory for Photogrammetry & Laser Scanning of the HafenCity University Hamburg has carried out geometrical accuracy tests with the following systems in co-operation with the Bochum University of Applied Sciences (Laboratory for Photogrammetry) as well as the Humboldt University in Berlin (Institute for Computer Science): DOTProduct DPI-7, Artec Spider, Mantis Vision F5 SR, Kinect v1 + v2, Structure Sensor and Google's Project Tango. In the framework of these comparative investigations geometrically stable reference bodies were used. The appropriate reference data were acquired by measurement with two structured light projection systems (AICON smartSCAN and GOM ATOS I 2M). The comprehensive test results of the different test scenarios are presented and critically discussed in this contribution.

  2. Application Research of QRCode Barcode in Validation of Express Delivery

    Science.gov (United States)

    Liu, Zhihai; Zeng, Qingliang; Wang, Chenglong; Lu, Qing

    The barcode technology has become an important way in the field of information input and identify automatically. With the outstanding features of big storage capacity, secure, rich encoding character set and fast decoding, the two-dimensional(2D) QRcode(Quick Response Barcode) has become an important choice of commerce barcode. The development of wireless communications technology and the popularization and application of mobile device has set the foundation of 2D barcode used in business. In this paper, the characteristics and the compositions of 2D QRcode are described, the secure validation workflows and contents of QRcode in goods express delivery are discussed, the encoding process of QRcode is showed, and the system framework is analyzed and established. At last, the system compositions and functions of each part are discussed.

  3. Mathematical model for light scanning system based on circular laser

    Institute of Scientific and Technical Information of China (English)

    Peiquan Xu; Shun Yao; Fenggui Lu; Xinhua Tang; Wei Zhang

    2005-01-01

    A novel light scanning system based on circular laser trajectory for welding robot is developed. With the help of image processing technique, intelligent laser welding could be realized. According to laser triangulation algorithm and Scheimpflug condition, mathematical model for circular laser vision is built.This scanning system projects circular laser onto welded seams and recovers the depth of the welded seams,escapes from shortcomings of less information, explains ambiguity and single tracking direction inherent in "spot" or "line" type laser trajectory. Three-dimensional (3D) model for welded seams could be recognized after depth recovery. The imaging error is investigated also.

  4. DNA barcoding Bromeliaceae: achievements and pitfalls.

    Directory of Open Access Journals (Sweden)

    Vitor Hugo Maia

    Full Text Available BACKGROUND: DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. METHODOLOGY/PRINCIPAL FINDINGS: It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%. Species paraphyly was a common feature in our sampling. CONCLUSIONS/SIGNIFICANCE: Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to

  5. Illumination Compensation for 2-D Barcode Recognition Basing Morphologic

    Directory of Open Access Journals (Sweden)

    Jian-Hua Li

    2013-04-01

    Full Text Available Improvement of image quality has been highly demanded in digital imaging systems. This study presents a novel illumination normalization approach for 2-D barcode recognition under varying lighting conditions. MMs (Morphological transformations are employed to original images using big scale multiple SEs (structuring elements. Then we make use of entropy to fuse images. The performance of proposed methodology is illustrated through the processing of images with different kinds of 2-D barcodes under different backgrounds. The experimental results show that this approach can process different kinds of 2-D barcodes under varying lighting conditions adaptively. Compared with other conventional methods, our proposed approach does a better job in processing 2-D barcode under non-uniform illumination.

  6. Moessbauer thermal scan study of a spin crossover system

    Energy Technology Data Exchange (ETDEWEB)

    Zelis, P Mendoza; Pasquevich, G A; Sanchez, F H; Veiga, A; Cabrera, A F [Departamento de Fisica, FCE-UNLP, La Plata (Argentina); Ceolin, M [Instituto de Investigaciones FIsico-Quimicas Teoricas y Aplicadas (UNLP-CONICET), La Plata (Argentina); Coronado-Miralles, E; Monrabal-Capilla, M; Galan-Mascaros, J R, E-mail: pmendoza@fisica.unlp.edu.a [Instituto de Ciencias Moleculares, Universidad de Valencia, Valencia (Spain)

    2010-03-01

    Programmable Velocity equipment was used to perform a Moessbauer Thermal Scans to allow a quasi-continuous temperature study of the magnetic transition between the low-spin and a high-spin configurations in [Fe(Htrz){sub 2}(trz)](BF4) system. The material was studied both in bulk as in nanoparticles sample forms.

  7. A surface refractive index scanning system and method

    DEFF Research Database (Denmark)

    2015-01-01

    The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction, and a s......The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction...... a grating period Λ2 in the longitudinal direction, where the longitudinal direction is orthogonal to the transverse direction. A grating period spacing ΔΛ = Λ1 - Λ2 is finite. Further, the first and second grating periods are chosen to provide optical resonances for light respectively in a first...

  8. Automation and workflow considerations for embedding Digimarc Barcodes at scale

    Science.gov (United States)

    Rodriguez, Tony; Haaga, Don; Calhoon, Sean

    2015-03-01

    The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

  9. DNA barcoding for species identification in the Palmae family.

    Science.gov (United States)

    Naeem, A; Khan, A A; Cheema, H M N; Khan, I A; Buerkert, A

    2014-12-04

    DNA barcoding is a promising tool for species identification at the molecular level. The barcoding system is well established for species differentiation in animals, while it is less common in plants. We evaluated 2 barcoding regions, maturase K (matK) and ribulose bisphosphate carboxylase (rbcL), to compare species of Palmae according to amplification success, discrimination power, and inter- and intra-specific divergence. Both regions appear to have potential to discriminate most species of Palmae, but 2 species, Phoenix dactylifera and Phoenix sylvestris, did not show variation in the nucleotides of the barcode genes. P. sylvestris is said to be the sister species of P. dactilyfera according to its morphological and genetic proximity to the cultivated date palm. Thus, the status of these 2 species needs to be re-evaluated considering more genes as barcodes. Furthermore, rbcL has a higher discrimination power (90%) than matK (66.6%) and can thus be potentially used as a standard barcode to discriminate the species of Palmae.

  10. Research and Application of PMIS Systems Integration and Barcode Warehouse Management System%PMIS系统与条码仓储管理系统融合性研究与应用

    Institute of Scientific and Technical Information of China (English)

    陈宝贵

    2015-01-01

    随着市场竞争的日趋激烈,工程企业的物流环节面临着越来越大的竞争,而仓储作为整个物流、供应链中的重要节点和组成部分,是整个物流系统设计的基础,其规划是否合理会直接影响整个物流系统运作的效率和效益.文章通过对PMIS系统和仓储管理系统详细了解之后,提出了PMIS系统与条码仓储管理系统融合运用的想法.文章从用条码进行仓储管理的可能性、必要性和利用条码进行管理的积极作用和应用效果等方面进行了详细的论述,希望能够推进物流业仓储管理工作的开展.%By after PMIS systems and warehouse management systems to learn more about proposed PMIS systems and barcode warehouse management system combines the use of ideas. In this paper,the possibility of using barcode warehouse management,the need for and use of barcode active role and application of results and other aspects of management were discussed in detail,hoping to promote the development of logistics industry warehouse management.

  11. A Robotic System to Scan and Reproduce Object

    Directory of Open Access Journals (Sweden)

    Cesare Rossi

    2011-01-01

    Full Text Available An application of a robotic system integrated with a vision system is presented. The robot is a 3-axis revolute prototype, while the vision system essentially consists in a laser scanner made up of a camera and a linear laser projector. Both the robotic and the video system were designed and built at DIME (Department of Mechanical Engineering for Energetics, University of Naples Federico II. The presented application essentially consists of a laser scanner that is installed on the robot arm; the scanner scans a 3D surface, and the data are converted in a cloud of points in the robot’s workspace. Then, starting from those points, the end-effector trajectories adopted to replicate the scanned surface are calculated; so, the same robot, by using a tool, can reproduce the scanned object. The software was developed also at the DIME. The adopted tool was a high-speed drill, installed on the last link of the robot arm, with a spherical milling cutter in order to obtain enough accurate surfaces by the data represented by the cloud of points. An algorithm to interpolate the paths and to plan the trajectories was also developed and successfully tested.

  12. Optimum Combined Lenses for Confocal Biochip Scanning System

    Institute of Scientific and Technical Information of China (English)

    黄国亮; 程京; 周玉祥; 冯继宏; 刘诚迅; 金国藩; 邬敏贤; 严瑛白; 张腾飞; 李林

    2002-01-01

    Laboratory-on-a-chip technology has attracted wide interest in recent years, where the sample preparation, bio-chemical reaction, separation, detection and analysis are performed in a small biochip of the size of a fingernail. To obtain a high detection sensitivity of 1 fluors/μm2 (one fluorescence molecule per square micrometer) in biochip scanning systems, the scanning objective lens is required to have a high numerical aperture (>0.5), very small focal spot (3 mm). This study presents the design of optimum combined lenses including scanning objective and fluorescence focal lenses. The scanning objective had a high numerical aperture (NA) of 0.72, a very small focal spot of 1.67 μm, a long back focal length of 3.2 mm, and a high resolving power of 760 lines/mm. The fluorescence focal lenses had an NA of 0.3, a fluorescence focal spot of 16 μm, a long back focal length of 16.7 mm and a resolving power of 590 lines/mm. The phase aberrations of the combined lenses, including the aspherical aberration and the chromatic aberration corresponding to wavelengths of 532, 570, 635, and 670 nm, were well-corrected. The encircled energy diagram of the lenses was within the diffraction limit. The study also included the focal spot diagram, the optical path difference diagram, the transverse ray fan plot, and the modulation transfer function. A confocal biochip scanning system with designed combined lenses was developed and some experiments were conducted on a multi-channel biochip.

  13. Land-Based Mobile Laser Scanning Systems: a Review

    Science.gov (United States)

    Puente, I.; González-Jorge, H.; Arias, P.; Armesto, J.

    2011-09-01

    Mobile mapping has been using various photogrammetric techniques for many years. In recent years, there has been an increase in the number of mobile mapping systems using laser scanners available in the market, partially because of the improvement in GNSS/INS performance for direct georeferencing. In this article, some of the most important land-based mobile laser scanning (MLS) systems are reviewed. Firstly, the main characteristics of MLS systems vs. airborne (ALS) and terrestrial laser scanning (TLS) systems are compared. Secondly, a short overview of the mobile mapping technology is also provided so that the reader can fully grasp the complexity and operation of these devices. As we put forward in this paper, a comparison of different systems is briefly carried out regarding specifications provided by the manufacturers. Focuses on the current research are also addressed with emphasis on the practical applications of these systems. Most of them have been utilized for data collection on road infrastructures or building façades. This article shows that MLS technology is nowadays well established and proven, since the demand has grown to the point that there are several systems suppliers offering their products to satisfy this particular market.

  14. LAND-BASED MOBILE LASER SCANNING SYSTEMS: A REVIEW

    Directory of Open Access Journals (Sweden)

    I. Puente

    2012-09-01

    Full Text Available Mobile mapping has been using various photogrammetric techniques for many years. In recent years, there has been an increase in the number of mobile mapping systems using laser scanners available in the market, partially because of the improvement in GNSS/INS performance for direct georeferencing. In this article, some of the most important land-based mobile laser scanning (MLS systems are reviewed. Firstly, the main characteristics of MLS systems vs. airborne (ALS and terrestrial laser scanning (TLS systems are compared. Secondly, a short overview of the mobile mapping technology is also provided so that the reader can fully grasp the complexity and operation of these devices. As we put forward in this paper, a comparison of different systems is briefly carried out regarding specifications provided by the manufacturers. Focuses on the current research are also addressed with emphasis on the practical applications of these systems. Most of them have been utilized for data collection on road infrastructures or building façades. This article shows that MLS technology is nowadays well established and proven, since the demand has grown to the point that there are several systems suppliers offering their products to satisfy this particular market.

  15. Advancing taxonomy and bioinventories with DNA barcodes

    Science.gov (United States)

    2016-01-01

    We use three examples—field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae—to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the ‘taxonomic impediment’, especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481791

  16. Scanning laser system to determine the corneal shape

    Science.gov (United States)

    Ascanio, Gabriel; Caballero-Ruiz, Alberto; Ruiz-Huerta, Leopoldo; Gonzalez-Cardel, Mario; Diaz-Uribe, Rufino

    2005-07-01

    The development and tests of a scanning system to be used to determine the corneal topography with the laser deflectometry method are presented. In this equipment, a He-Ne laser beam scans the cornea by describing a spiral trajectory generated by two components: radial and angular. The first component is produced by the displacement of a plane mirror moved by a linear pneumatic actuator. The second component is produced by passing the beam through a Dove prism which is rotating by means of a belt drive coupled to a high-speed electric motor. Tests were first performed by analyzing both components independently and then they were characterized by combining the two components. Results are discussed and compared to those of an earlier cited work.

  17. Scanning array radar system for bridge subsurface imaging

    Science.gov (United States)

    Lai, Chieh-Ping; Ren, Yu-Jiun; Yu, Tzu Yang

    2012-04-01

    Early damage detection of bridge has been an important issue for modern civil engineering technique. Existing bridge inspection techniques used by State Department of Transportation (DOT) and County DOT include visual inspection, mechanical sounding, rebound hammer, cover meter, electrical potential measurements, and ultrasonics; other NDE techniques include ground penetrating radar (GPR), radiography, and some experimental types of sensors. Radar technology like GPR has been widely used for the bridge structure detection with a good penetration depth using microwave energy. The system to be presented in this paper is a different type of microwave sensing technology. It is focus on the subsurface detection and trying to find out detail information at subsurface (10 cm) with high resolution radar imaging from a flexible standoff distance. Our radar operating frequency is from 8-12 GHz, which is different from most of the current GPR systems. Scanning array antenna system is designed for adjustable beamwidth, preferable scanning area, and low sidelobe level. From the theoretical analysis and experimental results, it is found that the proposed technique can successfully capture the presence of the near-surface anomaly. This system is part of our Multi- Modal Remote Sensing System (MRSS) and provides good imaging correlations with other MRSS sensors.

  18. Super-resolution for scanning light stimulation systems

    Science.gov (United States)

    Bitzer, L. A.; Neumann, K.; Benson, N.; Schmechel, R.

    2016-09-01

    Super-resolution (SR) is a technique used in digital image processing to overcome the resolution limitation of imaging systems. In this process, a single high resolution image is reconstructed from multiple low resolution images. SR is commonly used for CCD and CMOS (Complementary Metal-Oxide-Semiconductor) sensor images, as well as for medical applications, e.g., magnetic resonance imaging. Here, we demonstrate that super-resolution can be applied with scanning light stimulation (LS) systems, which are common to obtain space-resolved electro-optical parameters of a sample. For our purposes, the Projection Onto Convex Sets (POCS) was chosen and modified to suit the needs of LS systems. To demonstrate the SR adaption, an Optical Beam Induced Current (OBIC) LS system was used. The POCS algorithm was optimized by means of OBIC short circuit current measurements on a multicrystalline solar cell, resulting in a mean square error reduction of up to 61% and improved image quality.

  19. Minimum Detectable Activity for Tomographic Gamma Scanning System

    Energy Technology Data Exchange (ETDEWEB)

    Venkataraman, Ram [Canberra Industries (AREVA BDNM), Meriden, CT (United States); Smith, Susan [Canberra Industries (AREVA BDNM), Meriden, CT (United States); Kirkpatrick, J. M. [Canberra Industries (AREVA BDNM), Meriden, CT (United States); Croft, Stephen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-01-01

    For any radiation measurement system, it is useful to explore and establish the detection limits and a minimum detectable activity (MDA) for the radionuclides of interest, even if the system is to be used at far higher values. The MDA serves as an important figure of merit, and often a system is optimized and configured so that it can meet the MDA requirements of a measurement campaign. The non-destructive assay (NDA) systems based on gamma ray analysis are no exception and well established conventions, such the Currie method, exist for estimating the detection limits and the MDA. However, the Tomographic Gamma Scanning (TGS) technique poses some challenges for the estimation of detection limits and MDAs. The TGS combines high resolution gamma ray spectrometry (HRGS) with low spatial resolution image reconstruction techniques. In non-imaging gamma ray based NDA techniques measured counts in a full energy peak can be used to estimate the activity of a radionuclide, independently of other counting trials. However, in the case of the TGS each “view” is a full spectral grab (each a counting trial), and each scan consists of 150 spectral grabs in the transmission and emission scans per vertical layer of the item. The set of views in a complete scan are then used to solve for the radionuclide activities on a voxel by voxel basis, over 16 layers of a 10x10 voxel grid. Thus, the raw count data are not independent trials any more, but rather constitute input to a matrix solution for the emission image values at the various locations inside the item volume used in the reconstruction. So, the validity of the methods used to estimate MDA for an imaging technique such as TGS warrant a close scrutiny, because the pair-counting concept of Currie is not directly applicable. One can also raise questions as to whether the TGS, along with other image reconstruction techniques which heavily intertwine data, is a suitable method if one expects to measure samples whose activities

  20. Sample heating system for spin-polarized scanning electron microscopy.

    Science.gov (United States)

    Kohashi, Teruo; Motai, Kumi

    2013-08-01

    A sample-heating system for spin-polarized scanning electron microscopy (spin SEM) has been developed and used for microscopic magnetization analysis at temperatures up to 500°C. In this system, a compact ceramic heater and a preheating operation keep the ultra-high vacuum conditions while the sample is heated during spin SEM measurement. Moreover, the secondary-electron collector, which is arranged close to the sample, was modified so that it is not damaged at high temperatures. The system was used to heat a Co(1000) single-crystal sample from room temperature up to 500°C, and the magnetic-domain structures were observed. Changes of the domain structures were observed around 220 and 400°C, and these changes are considered to be due to phase transitions of this sample.

  1. Optoelectronic scanning system upgrade by energy center localization methods

    Science.gov (United States)

    Flores-Fuentes, W.; Sergiyenko, O.; Rodriguez-Quiñonez, J. C.; Rivas-López, M.; Hernández-Balbuena, D.; Básaca-Preciado, L. C.; Lindner, L.; González-Navarro, F. F.

    2016-11-01

    A problem of upgrading an optoelectronic scanning system with digital post-processing of the signal based on adequate methods of energy center localization is considered. An improved dynamic triangulation analysis technique is proposed by an example of industrial infrastructure damage detection. A modification of our previously published method aimed at searching for the energy center of an optoelectronic signal is described. Application of the artificial intelligence algorithm of compensation for the error of determining the angular coordinate in calculating the spatial coordinate through dynamic triangulation is demonstrated. Five energy center localization methods are developed and tested to select the best method. After implementation of these methods, digital compensation for the measurement error, and statistical data analysis, a non-parametric behavior of the data is identified. The Wilcoxon signed rank test is applied to improve the result further. For optical scanning systems, it is necessary to detect a light emitter mounted on the infrastructure being investigated to calculate its spatial coordinate by the energy center localization method.

  2. PSIDD (2): A Prototype Post-Scan Interactive Data Display System for Detailed Analysis of Ultrasonic Scans

    Science.gov (United States)

    Cao, Wei; Roth, Don J.

    1997-01-01

    This article presents the description of PSIDD(2), a post-scan interactive data display system for ultrasonic contact scan and single measurement analysis. PSIDD(2) was developed in conjunction with ASTM standards for ultrasonic velocity and attenuation coefficient contact measurements. This system has been upgraded from its original version PSIDD(1) and improvements are described in this article. PSIDD(2) implements a comparison mode where the display of time domain waveforms and ultrasonic properties versus frequency can be shown for up to five scan points on one plot. This allows the rapid contrasting of sample areas exhibiting different ultrasonic properties as initially indicated by the ultrasonic contact scan image. This improvement plus additional features to be described in the article greatly facilitate material microstructural appraisal.

  3. A DNA barcoding approach in the study of tardigrades

    Directory of Open Access Journals (Sweden)

    Michele Cesari

    2013-05-01

    Full Text Available DNA barcoding is a technique proposed by Hebert and co-workers in 2003 for discriminating species through analysis of a single gene barcode locus. It aims to obtain a better taxonomic resolution than that achieved through morphological studies, and to avoid the decline in taxonomic knowledge. Today DNA barcoding is a global enterprise, and the implementation of the idea has seen a rapid rise (more than 1900 papers published to date on different organisms. Nonetheless, controversy still arises regarding barcoding and taxonomy. It is important to note that DNA barcoding does not focus on building a tree-of-life or on doing DNA taxonomy, even though sometimes it has been used for these purposes. DNA barcoding rather focuses on producing a universal molecular identification key based on strong taxonomic knowledge that should be included in the barcode reference library. In the phylum Tardigrada, DNA barcoding represents a recent approach to species identification and to help in solving taxonomic problems, especially considering the diminutive size of these animals and the paucity of morphological characters useful for taxonomy. In the framework of the MoDNA Project (Morphology and DNA, carried out by our research group in collaboration with several colleagues, we are combining the study of a fragment of the mitochondrial cytochrome c oxidase subunit I gene (cox1 with morphological data, in a wide sense (cuticular structures, chromosomes, data on sex ratio and reproduction, to form an integrative taxonomy approach for tardigrade species identification. We believe that without verified reference sequences from voucher specimens that have been authenticated by qualified taxonomists, there is no reliable library for newly generated sequences with which to be compared. Methods and protocols for standardized results are focused on obtaining tight correspondence between tardigrade morphology (and egg shell morphology, when useful, possibly both light and

  4. Barcoding Fauna Bavarica: 78% of the Neuropterida fauna barcoded!

    Directory of Open Access Journals (Sweden)

    Jérome Morinière

    Full Text Available This publication provides the first comprehensive DNA barcode data set for the Neuropterida of Central Europe, including 80 of the 102 species (78% recorded from Bavaria (Germany and three other species from nearby regions (Austria, France and the UK. Although the 286 specimens analyzed had a heterogeneous conservation history (60% dried; 30% in 80% EtOH; 10% fresh specimens in 95% EtOH, 237 (83% generated a DNA barcode. Eleven species (13% shared a BIN, but three of these taxa could be discriminated through barcodes. Four pairs of closely allied species shared barcodes including Chrysoperla pallida Henry et al., 2002 and C. lucasina Lacroix, 1912; Wesmaelius concinnus (Stephens, 1836 and W. quadrifasciatus (Reuter, 1894; Hemerobius handschini Tjeder, 1957 and H. nitidulus Fabricius, 1777; and H. atrifrons McLachlan, 1868 and H. contumax Tjeder, 1932. Further studies are needed to test the possible synonymy of these species pairs or to determine if other genetic markers permit their discrimination. Our data highlight five cases of potential cryptic diversity within Bavarian Neuropterida: Nineta flava (Scopoli, 1763, Sympherobius pygmaeus (Rambur, 1842, Sisyra nigra (Retzius, 1783, Semidalis aleyrodiformis (Stephens, 1836 and Coniopteryx pygmaea Enderlein, 1906 are each split into two or three BINs. The present DNA barcode library not only allows the identification of adult and larval stages, but also provides valuable information for alpha-taxonomy, and for ecological and evolutionary research.

  5. Barcoding Fauna Bavarica: 78% of the Neuropterida fauna barcoded!

    Science.gov (United States)

    Morinière, Jérome; Hendrich, Lars; Hausmann, Axel; Hebert, Paul; Haszprunar, Gerhard; Gruppe, Axel

    2014-01-01

    This publication provides the first comprehensive DNA barcode data set for the Neuropterida of Central Europe, including 80 of the 102 species (78%) recorded from Bavaria (Germany) and three other species from nearby regions (Austria, France and the UK). Although the 286 specimens analyzed had a heterogeneous conservation history (60% dried; 30% in 80% EtOH; 10% fresh specimens in 95% EtOH), 237 (83%) generated a DNA barcode. Eleven species (13%) shared a BIN, but three of these taxa could be discriminated through barcodes. Four pairs of closely allied species shared barcodes including Chrysoperla pallida Henry et al., 2002 and C. lucasina Lacroix, 1912; Wesmaelius concinnus (Stephens, 1836) and W. quadrifasciatus (Reuter, 1894); Hemerobius handschini Tjeder, 1957 and H. nitidulus Fabricius, 1777; and H. atrifrons McLachlan, 1868 and H. contumax Tjeder, 1932. Further studies are needed to test the possible synonymy of these species pairs or to determine if other genetic markers permit their discrimination. Our data highlight five cases of potential cryptic diversity within Bavarian Neuropterida: Nineta flava (Scopoli, 1763), Sympherobius pygmaeus (Rambur, 1842), Sisyra nigra (Retzius, 1783), Semidalis aleyrodiformis (Stephens, 1836) and Coniopteryx pygmaea Enderlein, 1906 are each split into two or three BINs. The present DNA barcode library not only allows the identification of adult and larval stages, but also provides valuable information for alpha-taxonomy, and for ecological and evolutionary research.

  6. Hyperspectral imaging system for disease scanning on banana plants

    Science.gov (United States)

    Ochoa, Daniel; Cevallos, Juan; Vargas, German; Criollo, Ronald; Romero, Dennis; Castro, Rodrigo; Bayona, Oswaldo

    2016-05-01

    Black Sigatoka (BS) is a banana plant disease caused by the fungus Mycosphaerella fijiensis. BS symptoms can be observed at late infection stages. By that time, BS has probably spread to other plants. In this paper, we present our current work on building an hyper-spectral (HS) imaging system aimed at in-vivo detection of BS pre-symptomatic responses in banana leaves. The proposed imaging system comprises a motorized stage, a high-sensitivity VIS-NIR camera and an optical spectrograph. To capture images of the banana leaf, the stage's speed and camera's frame rate must be computed to reduce motion blur and to obtain the same resolution along both spatial dimensions of the resulting HS cube. Our continuous leaf scanning approach allows imaging leaves of arbitrary length with minimum frame loss. Once the images are captured, a denoising step is performed to improve HS image quality and spectral profile extraction.

  7. Calibration technology in application of robot-laser scanning system

    Science.gov (United States)

    Ren, YongJie; Yin, ShiBin; Zhu, JiGui

    2012-11-01

    A system composed of laser sensor and 6-DOF industrial robot is proposed to obtain complete three-dimensional (3-D) information of the object surface. Suitable for the different combining ways of laser sensor and robot, a new method to calibrate the position and pose between sensor and robot is presented. By using a standard sphere with known radius as a reference tool, the rotation and translation matrices between the laser sensor and robot are computed, respectively in two steps, so that many unstable factors introduced in conventional optimization methods can be avoided. The experimental results show that the accuracy of the proposed calibration method can be achieved up to 0.062 mm. The calibration method is also implemented into the automated robot scanning system to reconstruct a car door panel.

  8. Numerical Modeling of a Near-Field Scanning Optical System

    Science.gov (United States)

    Kann, Joshua Louis

    A near-field scanning optical (NFO) system utilizes a subwavelength sized aperture to illuminate a sample. The aperture raster scans the sample. During the scan, the aperture is held in proximity to the sample. At each sampling point, the integrated far-zone energy distribution is stored. This collection of data is used to generate an image of the sample's surface. The main advantage of NFO systems is their very high spatial resolution. In this dissertation a hybrid finite-difference-time-domain (FDTD)/angular spectrum code is used to study the electromagnetic and imaging properties of a NFO scanning system. In addition, a finite-difference thermal (FD-thermal) code is used to calculate the thermal properties of a NFO system. Various aperture/sample geometries are studied numerically using both TE and TM polarization within a two-dimensional metallic waveguide that forms the aperture. The spatial properties of the electric field emitted by the aperture with no sample present are greatly influenced by the polarization. In particular, the electric field with TM polarization exhibits sharp peaks near the corners of the aperture, while the field with TE polarization is smooth and peaked at the center of the aperture. For both polarizations, the electric field remains collimated for a distance comparable to the aperture size. The electric field for both polarizations is altered when a dielectric sample is placed in proximity to the aperture. It is shown that the most representative image of the sample's topography is obtained using TE polarization and the resulting total far-zone energy as the sampled data. It is also shown that simpler scalar methods do not accurately predict the imaging behavior of a NFO system. Under certain circumstances the relationship between the sample's topography and the detected image is nearly linear. Under these conditions a system transfer function is calculated. Using the transfer function, it is shown that the spatial resolution of a NFO

  9. DNA barcoding: species delimitation in tree peonies

    Institute of Scientific and Technical Information of China (English)

    ZHANG JinMei; WANG JianXiu; XIA Tao; ZHOU ShiLiang

    2009-01-01

    Delimitations of species are crucial for correct and precise identification of taxa. Unfortunately "spe-cies" is more a subjective than an objective concept in taxonomic practice due to difficulties in re-vealing patterns of infra- or inter-specific variations. Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding. In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies (Paeonia sect. Moutan). We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies. All currently recognized species and majorbvariants have been included in this study. Four chloroplast gene fragments, I.e. ndhF, rps16-trnQ, trnL.F and trnS-G (a total of 5040 characters, 96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment (2093-2197 bp, 279 variable and 148 parsi-mony-informative characters) were used to construct phylogenetic relationships among the taxa. The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P. Decomposita, P. Jishanensis, P. Qiui, and P. Rockii based on morphology. The inconsistencies come from (1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P. Decomposita + P. Rockii, and (2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P. Jishanensis and P. Qiui. The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloro-plast capture event in evolutionary history, as no reproductive barriers exist to prevent inter-specific hybridization. We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies. The variability of chloroplast genes among well

  10. Galvanometer beam-scanning system for laser fiber drawing.

    Science.gov (United States)

    Oehrle, R C

    1979-02-15

    A major difficulty in using a laser to draw optical fibers from a glass preform has been uniformally distributing the laser's energy around the melt zone. Several systems have evolved in recent years, but to date the most successful technique has been the off-axis rotating lens system (RLS). The inability of this device to structure efficiently and dynamically the heat zone longitudinally along the preform has restricted its use to preform of less than 8-mm diameter. A new technique reported here employs two orthogonal mounted mirrors, driven by galvanometers to distribute the laser energy around the preform. This system can be retrofitted into the RLS to replace the rotating lens element. The new system, the galvanometer scanning system (GSS), operates at ten times the rotational speed of the RLS and can instantaneously modify the melt zone. The ability of the GSS to enlarge the melt zone reduces the vaporization rate at the surface of the preform permitting efficient use of higher laser power. Experiments i dicate that fibers can be drawn from significantly larger preforms by using the expanded heat zone provided by the GSS.

  11. [Principles for molecular identification of traditional Chinese materia medica using DNA barcoding].

    Science.gov (United States)

    Chen, Shi-Lin; Yao, Hui; Han, Jian-Ping; Xin, Tian-Yi; Pang, Xiao-Hui; Shi, Lin-Chun; Luo, Kun; Song, Jing-Yuan; Hou, Dian-Yun; Shi, Shang-Mei; Qian, Zhong-Zhi

    2013-01-01

    Since the research of molecular identification of Chinese Materia Medica (CMM) using DNA barcode is rapidly developing and popularizing, the principle of this method is approved to be listed in the Supplement of the Pharmacopoeia of the People's Republic of China. Based on the study on comprehensive samples, the DNA barcoding systems have been established to identify CMM, i.e. ITS2 as a core barcode and psbA-trnH as a complementary locus for identification of planta medica, and COI as a core barcode and ITS2 as a complementary locus for identification of animal medica. This article introduced the principle of molecular identification of CMM using DNA barcoding and its drafting instructions. Furthermore, its application perspective was discussed.

  12. Scanned Image Projection System Employing Intermediate Image Plane

    Science.gov (United States)

    DeJong, Christian Dean (Inventor); Hudman, Joshua M. (Inventor)

    2014-01-01

    In imaging system, a spatial light modulator is configured to produce images by scanning a plurality light beams. A first optical element is configured to cause the plurality of light beams to converge along an optical path defined between the first optical element and the spatial light modulator. A second optical element is disposed between the spatial light modulator and a waveguide. The first optical element and the spatial light modulator are arranged such that an image plane is created between the spatial light modulator and the second optical element. The second optical element is configured to collect the diverging light from the image plane and collimate it. The second optical element then delivers the collimated light to a pupil at an input of the waveguide.

  13. The Emulsion Scanning System of the OPERA experiment

    CERN Document Server

    Juget, F

    2010-01-01

    The OPERA experiment has for goal the direct detection of !μ ! !! oscilla- tion, using an hybrid apparatus composed of electronic detectors and nuclear photographic emulsions. A charged particle crossing an emulsion layer ion- izes the medium along its path leaving a latent image which leads, after de- velopment, to a sequence of aligned grains. Nuclear emulsions are analyzed by means of optical microscopes to reconstruct the 3D particle tracks. The OPERA collaboration has developed a dedicated system to scan a large num- ber of emulsions (surface of about 1000 m2). The achieved resolution is "1 μm and "1 mrad allowing to observe directly the short-lived " particles pro- duced in !!CC interactions.

  14. A Mobile Automated Tomographic Gamma Scanning System - 13231

    Energy Technology Data Exchange (ETDEWEB)

    Kirkpatrick, J.M.; LeBlanc, P.J.; Nakazawa, D.; Petroka, D.L.; Kane Smith, S.; Venkataraman, R.; Villani, M. [Canberra Industries, Inc. 800 Research Parkway, Meriden CT 06450 (United States)

    2013-07-01

    Canberra Industries have recently designed and built a new automated Tomographic Gamma Scanning (TGS) system for mobile deployment. The TGS technique combines high-resolution gamma spectroscopy with low spatial resolution 3-dimensional image reconstruction to provide increased accuracy over traditional approaches for the assay of non-uniform source distributions in low-to medium-density, non-heterogeneous matrices. Originally pioneered by R. Estep at Los Alamos National Laboratory (LANL), the TGS method has been further developed and commercialized by Canberra Industries in recent years. The present system advances the state of the art on several fronts: it is designed to be housed in a standard cargo transport container for ease of transport, allowing waste characterization at multiple facilities under the purview of a single operator. Conveyor feed, drum rotator, and detector and collimator positioning mechanisms operated by programmable logic control (PLC) allow automated batch mode operation. The variable geometry settings can accommodate a wide range of waste packaging, including but not limited to standard 220 liter drums, 380 liter overpack drums, and smaller 20 liter cans. A 20 mCi Eu-152 transmission source provides attenuation corrections for drum matrices up to 1 g/cm{sup 3} in TGS mode; the system can be operated in Segmented Gamma Scanning (SGS) mode to measure higher density drums. To support TGS assays at higher densities, the source shield is sufficient to house an alternate Co-60 transmission source of higher activity, up to 250 mCi. An automated shutter and attenuator assembly is provided for operating the system with a dual intensity transmission source. The system's 1500 kg capacity rotator turntable can handle heavy containers such as concrete lined 380 liter overpack drums. Finally, data acquisition utilizes Canberra's Broad Energy Germanium (BEGE) detector and Lynx MCA, with 32 k channels, providing better than 0.1 ke

  15. Denture bar-coding: An innovative technique in forensic dentistry

    Science.gov (United States)

    Dineshshankar, Janardhanam; Venkateshwaran, Rajendran; Vidhya, J.; Anuradha, R.; Mary, Gold Pealin; Pradeep, R.; Senthileagappan, A. R.

    2015-01-01

    Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews the strengths of bar-coding and how easily it can be used in the routine procedure. PMID:26538876

  16. DNA barcoding, phylogenetic relationships and speciation of snappers (genus Lutjanus)

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.

  17. Denture bar-coding: An innovative technique in forensic dentistry.

    Science.gov (United States)

    Dineshshankar, Janardhanam; Venkateshwaran, Rajendran; Vidhya, J; Anuradha, R; Mary, Gold Pealin; Pradeep, R; Senthileagappan, A R

    2015-08-01

    Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews the strengths of bar-coding and how easily it can be used in the routine procedure.

  18. Statistical Approaches for DNA Barcoding

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Matz, M.

    2006-01-01

    The use of DNA as a tool for species identification has become known as "DNA barcoding" (Floyd et al., 2002; Hebert et al., 2003; Remigio and Hebert, 2003). The basic idea is straightforward: a small amount of DNA is extracted from the specimen, amplified and sequenced. The gene region sequenced...... is chosen so that it is nearly identical among individuals of the same species, but different between species, and therefore its sequence, can serve as an identification tag for the species ("DNA barcode"). By matching the sequence obtained from an unidentified specimen ("query" sequence) to the database...

  19. Plant DNA barcoding: from gene to genome.

    Science.gov (United States)

    Li, Xiwen; Yang, Yang; Henry, Robert J; Rossetto, Maurizio; Wang, Yitao; Chen, Shilin

    2015-02-01

    DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species. Because single-locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole-chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies. While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource-effective and does not yet offer the speed of analysis provided by single-locus barcodes to unspecialized laboratory facilities. Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super-barcode. We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single-locus barcodes and super-barcodes for efficient plant identification. Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels.

  20. Modelling and calibration of the laser beam-scanning triangulation measurement system

    NARCIS (Netherlands)

    Wang, Guoyu; Zheng, Bing; Li, Xin; Houkes, Z.; Regtien, P.P.L.

    2002-01-01

    We present an approach of modelling and calibration of an active laser beam-scanning triangulation measurement system. The system works with the pattern of two-dimensional beam-scanning illumination and one-dimensional slit-scanning detection with a photo-multiplier tube instead of a CCD camera. By

  1. Testing candidate plant barcode regions in the Myristicaceae.

    Science.gov (United States)

    Newmaster, S G; Fazekas, A J; Steeves, R A D; Janovec, J

    2008-05-01

    The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.

  2. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae).

    Science.gov (United States)

    Starr, Julian R; Naczi, Robert F C; Chouinard, Brianna N

    2009-05-01

    We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH-psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best-known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH-psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50-60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0-13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH-psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system

  3. DNA barcoding Chinese medicinal Bupleurum.

    Science.gov (United States)

    Chao, Zhi; Zeng, Weiping; Liao, Jing; Liu, Li; Liang, Zhenbiao; Li, Xiaolei

    2014-11-15

    We tested 4 markers, namely nuclear internal transcribed spacer 2 (ITS2), psbA-trnH, matK, and rbcL, to evaluate these candidate DNA barcodes for distinguishing Bupleuri radix (Chaihu) from its adulterants. 51 plant samples of Bupleurum representing 19 species were collected from different areas in China. Amplification and sequencing were attempted for all the 4 candidate barcode regions, whose validity was assessed in terms of the success rate of PCR amplification and sequencing, differential intra- and inter-specific divergences, DNA barcoding gap and the ability to discriminate species. The results showed that ITS2 had the best performance in identifying Bupleurum with an identification efficiency of 73.68%, which, after combining with psbA-trnH, increased to 83.33%. We further evaluated the efficiency of ITS2 for discriminating the species of Bupleurum using a large database from GenBank, which archived data of 223 samples from 74 species, and ITS2 successfully discriminated 64.13% of the samples at the species level. In conclusion, the ITS2 can serve as a potentially useful barcode for Bupleurum species, with psbA-trnH as a supplementary locus.

  4. Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia.

    Science.gov (United States)

    Yancy, Haile F; Zemlak, Tyler S; Mason, Jacquline A; Washington, Jewell D; Tenge, Bradley J; Nguyen, Ngoc-Lan T; Barnett, James D; Savary, Warren E; Hill, Walter E; Moore, Michelle M; Fry, Frederick S; Randolph, Spring C; Rogers, Patricia L; Hebert, Paul D N

    2008-01-01

    The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/-frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

  5. Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe.

    Science.gov (United States)

    Dinca, Vlad; Zakharov, Evgeny V; Hebert, Paul D N; Vila, Roger

    2011-02-07

    DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.

  6. The hemiptera (insecta of Canada: constructing a reference library of DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Rodger A Gwiazdowski

    Full Text Available DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs, sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD, allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

  7. Challenges in the DNA barcoding of plant material.

    Science.gov (United States)

    Cowan, Robyn S; Fay, Michael F

    2012-01-01

    DNA barcoding, using a short gene sequence from a standardized region of the genome, is a species identification tool which would not only aid species discovery but would also have applications ranging from large-scale biodiversity surveys through to identification of a single fragment of material in forensic contexts. To fulfill this vision a universal, relatively cheap, scalable system needs to be in place. The mitochondrial locus being used for many animal groups and algae is not suitable for use in land plants, and an appropriate alternative is needed.Progress has been made in the selection of two alternative regions for plant DNA barcoding. There are however many challenges in finding a solution that fulfills all the requirements of a successful, universally applicable barcode, and in the short term a pragmatic solution that achieves as much as possible and has payoffs in most areas has been chosen. Research continues in areas ranging from the technicalities of sequencing the regions to data analysis and the potential improvements that may result from the developing technology and data analysis systems.The ultimate success of DNA barcoding as a plant identification tool for all occasions depends on the building of a reference database and it fulfilling the requirements of potential users such that they are able to achieve valid results through its use, that would be more time consuming and costly, and less reliable using other techniques.

  8. DNA barcoding the floras of biodiversity hotspots

    OpenAIRE

    Lahaye, Renaud; van der Bank, Michelle; Bogarin, Diego; Warner, Jorge; Pupulin, Franco; Gigot, Guillaume; Maurin, Olivier; Duthoit, Sylvie; Barraclough, Timothy G.; Savolainen, Vincent

    2008-01-01

    DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern A...

  9. Application of linear systems theory to characterize coherence scanning interferometry

    Science.gov (United States)

    Mandal, Rahul; Palodhi, Kanik; Coupland, Jeremy; Leach, Richard; Mansfield, Daniel

    2012-04-01

    This paper considers coherence scanning interferometry as a linear filtering operation that is characterised by a point spread function in the space domain or equivalently a transfer function in the frequency domain. The applicability of the theory is discussed and the effects of these functions on the measured interferograms, and their influence on the resulting surface measurements, are described. The practical characterisation of coherence scanning interferometers using a spherical reference artefact is then considered and a new method to compensate measurement errors, based on a modified inverse filter, is demonstrated.

  10. Validation of undergraduate clinical data by electronic capture (barcode).

    Science.gov (United States)

    Chadwick, Barbara L; Oliver, Richard G; Gyton, Jane

    2002-03-01

    Assessment of clinical activity is common in dental schools. An audit project to confirm that dental undergraduate clinical activity recorded by electronic data capture is an accurate representation of the clinical case entry is reported. A printout of clinical activity for a period of a week was generated retrospectively and used to identify case notes. Activity recorded in the case notes was compared with the computer printout. All discrepancies were noted. A total of 125 patient files with 270 barcoded items of treatment were retrieved; 29 of 78 (37.1%) paediatric and 23 of 47 (48.9%) orthodontic cases had discrepancies between the case notes and the computer entry. However, some items recorded in the notes do not require barcoding and vice versa. When these were accounted for, only 19 items of treatment appeared in the notes that should have been barcoded, a 7% shortfall in recording of clinical activity. The barcode system is an accurate and reliable way of recording undergraduate clinical activity.

  11. DNA barcoding of Dutch birds

    Directory of Open Access Journals (Sweden)

    Mansour Aliabadian

    2013-12-01

    Full Text Available The mitochondrial cytochrome c-oxidase subunit I (COI can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by >2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorariusat least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present.

  12. DNA Barcoding for Honey Biodiversity

    OpenAIRE

    Alice Valentini; Christian Miquel; Pierre Taberlet

    2010-01-01

    Honey is produced by honeybees from nectar and from secretions of living plants. It reflects the honeybees’ diet and the local plant communities. Honey also shows different plant compositions in different geographical locations. We propose a new method for studying the plant diversity and the geographical origin of honey using a DNA barcoding approach that combines universal primers and massive parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional orig...

  13. 3D Wide FOV Scanning Measurement System Based on Multiline Structured-Light Sensors

    OpenAIRE

    2014-01-01

    Structured-light three-dimensional (3D) vision measurement is currently one of the most common approaches to obtain 3D surface data. However, the existing structured-light scanning measurement systems are primarily constructed on the basis of single sensor, which inevitably generates three obvious problems: limited measurement range, blind measurement area, and low scanning efficiency. To solve these problems, we developed a novel 3D wide FOV scanning measurement system which adopted two mult...

  14. Barcode medication administration work-arounds: a systematic review and implications for nurse executives.

    Science.gov (United States)

    Voshall, Barbara; Piscotty, Ronald; Lawrence, Jeanette; Targosz, Mary

    2013-10-01

    Safe medication administration is necessary to ensure quality healthcare. Barcode medication administration systems were developed to reduce drug administration errors and the related costs and improve patient safety. Work-arounds created by nurses in the execution of the required processes can lead to unintended consequences, including errors. This article provides a systematic review of the literature associated with barcoded medication administration and work-arounds and suggests interventions that should be adopted by nurse executives to ensure medication safety.

  15. An image acquisition system built with a modular frame grabber for scanning electron microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, S. [The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Kapp, O.H. [The Department of Radiology and The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    1995-09-01

    We have built an image acquisition and processing system based on a modular frame grabber board (MFG) for use with scanning (or scanning transmission) electron microscopes. The variable-scan acquisition module of the grabber board provides compatibility with electron microscopes processing various scan speeds, e.g., the very slow scan rate of our mirror-type electron microscope. In addition to the acquisition function, the board provides many image processing capabilities. A special time-base unit was built to synchronize the acquisition system with the scanning system on the electron microscope. A Windows application has been built to operate the MFG as well as manage all functions of the electron microscope. Using this approach we have been able to greatly simplify the task of digital image acquisition as well as creating a powerful and seamless interface to our Windows-based environment. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  16. Angle extended linear MEMS scanning system for 3D laser vision sensor

    Science.gov (United States)

    Pang, Yajun; Zhang, Yinxin; Yang, Huaidong; Zhu, Pan; Gai, Ye; Zhao, Jian; Huang, Zhanhua

    2016-09-01

    Scanning system is often considered as the most important part for 3D laser vision sensor. In this paper, we propose a method for the optical system design of angle extended linear MEMS scanning system, which has features of huge scanning degree, small beam divergence angle and small spot size for 3D laser vision sensor. The principle of design and theoretical formulas are derived strictly. With the help of software ZEMAX, a linear scanning optical system based on MEMS has been designed. Results show that the designed system can extend scanning angle from ±8° to ±26.5° with a divergence angle small than 3.5 mr, and the spot size is reduced for 4.545 times.

  17. 76 FR 34871 - Mobile Barcode Promotion

    Science.gov (United States)

    2011-06-15

    ... 111 Mobile Barcode Promotion AGENCY: Postal Service TM . ACTION: Final rule. SUMMARY: The Postal... ) 709.4 to add a temporary promotion for First-Class Mail cards, letters and flats, and Standard Mail... barcode promotion, and the new mailing standards to implement the promotion. To be eligible,...

  18. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  19. DNA Barcoding Investigations Bring Biology to Life

    Science.gov (United States)

    Musante, Susan

    2010-01-01

    This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

  20. 77 FR 26185 - POSTNET Barcode Discontinuation

    Science.gov (United States)

    2012-05-03

    ... a barcode clear zone on all letters. To maintain focus on the discontinuation of price eligibility... maintain focus on the POSTNET barcode discontinuation, the Postal Service removed the proposal to require... Exceptions are as follows: a. Automation letters. Automation letters do not require an ``AUTO'' marking...

  1. DNA Bar-Coding for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta;

    2013-01-01

    Phytoplasma identi fi cation has proved dif fi cult due to their inability to be maintained in vitro. DNA barcoding is an identi fi cation method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identi fi cat...

  2. Barcoding of soil microarthropods in Kobbefjord

    DEFF Research Database (Denmark)

    Krogh, Paul Henning; Wirta, Helena; Roslin, Tomas

    2013-01-01

    Since it was proposed to identity species by small sequences of DNA with e.g. less than 1000 bp (base pairs) popularized by the term barcode, monitoring of biodiversity has included barcoding (Hebert et al. 2003, Hogg and Hebert 2004 and Rougerie et al. 2009). It is now a rapidly increasing...

  3. Reducing field distortion for galvanometer scanning system using a vision system

    Science.gov (United States)

    Ortega Delgado, Moises Alberto; Lasagni, Andrés Fabián

    2016-11-01

    Laser galvanometer scanning systems are well-established devices for material processing, medical imaging and laser projection. Besides all the advantages of these devices like high resolution, repeatability and processing velocity, they are always affected by field distortions. Different pre-compensating techniques using iterative marking and measuring methods are applied in order to reduce such field distortions and increase in some extends the accuracy of the scanning systems. High-tech devices, temperature control systems and self-adjusting galvanometers are some expensive possibilities for reducing these deviations. This contribution presents a method for reducing field distortions using a coaxially coupled vision device and a self-designed calibration plate; this avoids, among others, the necessity of repetitive marking and measuring phases.

  4. Control electronics for a multi-laser/multi-detector scanning system

    Science.gov (United States)

    Kennedy, W.

    1980-01-01

    The Mars Rover Laser Scanning system uses a precision laser pointing mechanism, a photodetector array, and the concept of triangulation to perform three dimensional scene analysis. The system is used for real time terrain sensing and vision. The Multi-Laser/Multi-Detector laser scanning system is controlled by a digital device called the ML/MD controller. A next generation laser scanning system, based on the Level 2 controller, is microprocessor based. The new controller capabilities far exceed those of the ML/MD device. The first draft circuit details and general software structure are presented.

  5. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market.

    Science.gov (United States)

    Mishra, Priyanka; Kumar, Amit; Nagireddy, Akshitha; Mani, Daya N; Shukla, Ashutosh K; Tiwari, Rakesh; Sundaresan, Velusamy

    2016-01-01

    The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.

  6. [Locality identification of Chinese medicinal plant Scutellaria baicalensis (Lamiaceae) population-level DNA barcoding].

    Science.gov (United States)

    Zhang, Bin; Yuan, Qingjun; Huang, Luqi; Liu, Xiaoguang; Li, Xiaoming; Lin, Shufang; Chen, Meilan; Ge, Xiaoguang

    2012-04-01

    Scutellaria baicalensis is an important traditional Chinese medicine and Scutellaria flavonoids have received worldwide attention in recent years. It is the basis of controlling quality of S. baicalensis to develop a reliable genetic marker system used to identify locality of origin. Because of the characteristics of maternal inherited and high-rate of evolution, the cpDNA intergenic spacer can effectively elucidate the degree of genetic variation in different areas of the same species (populations), which can be used as the population-level DNA barcoding to locality identify. In this study, we have used the molecular phylogeography analysis for the three cpDNA intergenic spacers atpB-rbcL, trnL-trnF and psbA-trnH of 17 wild populations from different localities, which reveals the 20 haplotypes, including 13 polymorphic sites and constitutes a shallow gene tree. The authers have divided the haplotypes of S. baicalensis into three grades of population-level DNA barcoding according to the frequence and geographic distribution: 3 highest-frequency haplotypes as area-population-level DNA barcoding, 3 haplotypes were mainly shared by 2-3 adjacent populations as region-population-level DNA barcoding, and there are also 8 unique-population haplotypes as unique-population-level DNA barcoding. The result of this study reveals that population-level DNA barcoding is a reliable genetic marker used to locality identify of S. baicalensis.

  7. With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast.

    Science.gov (United States)

    Borges, Luísa M S; Hollatz, Claudia; Lobo, Jorge; Cunha, Ana M; Vilela, Ana P; Calado, Gonçalo; Coelho, Rita; Costa, Ana C; Ferreira, Maria S G; Costa, Maria H; Costa, Filipe O

    2016-02-15

    The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.

  8. Construction of a New Molecular Barcode for Discriminating Plants and Animals with a Close Genetic Relationship

    Institute of Scientific and Technical Information of China (English)

    HUANG Li; ZHAO Xiao-feng; ZHU Yi-peng; DONG Heng; XU Ning-ying; CAO Jia-shu

    2013-01-01

    DNA barcodes have been proposed as a shortcut to provide species identification and as a way to accelerate the discovery of new species. A number of candidate gene regions have been suggested as possible barcodes for animals and plants, but for the identification of recently diverged species and/or varieties with only a few genetic differences it has been reported to be problematic in some cases. This study selected widely cultivated cruciferous vegetables as the primary samples, after failure of discrimination of each species using current DNA barcodes, we performed the fluorescent amplified fragment length polymorphism (F-AFLP) and successfully discriminated each species, subspecies, variety and their cultivar in 74 samples. Then the non-qualitative results obtained from F-AFLP were transformed into two-dimensional barcodes image file of each cultivar via the PDF417 software. This method was also successfully applied to the discrimination of 17 Chinese indigenous pig breeds. The barcode we constructed which greatly reduces the information storage space is genotypes-specific, and can be conveniently decoded into the original data and thereby be conveniently shared and referred to. We believe that it is possible to construct a new data sharing molecular barcode system that could discriminate the subspecies, varieties, cultivars and even individuals with close genetic relationships.

  9. Evaluation of anthropometric accuracy and reliability using different three-dimensional scanning systems

    NARCIS (Netherlands)

    Fourie, Zacharias; Damstra, Janalt; Gerrits, Peter O.; Ren, Yijin

    2011-01-01

    The aim of this study was to evaluate the accuracy and reliability of standard anthropometric linear measurements made with three different three-dimensional scanning systems namely laser surface scanning (Minolta Vivid 900), cone beam computed tomography (CBCT), 3D stereo-photogrammetry (Di3D syste

  10. Denture identification using unique identification authority of India barcode

    Directory of Open Access Journals (Sweden)

    Sudhindra Mahoorkar

    2013-01-01

    Full Text Available Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient′s unique identification number and barcode printed in the patient′s Aadhaar card issued by Unique Identification Authority of India (UIDAI are used as denture markers. This article describes a simple, quick, and economical method for identification of individual.

  11. Two-axis polydimethylsiloxane-based electromagnetic microelectromechanical system scanning mirror for optical coherence tomography

    Science.gov (United States)

    Kim, Sehui; Lee, Changho; Kim, Jin Young; Kim, Jeehyun; Lim, Geunbae; Kim, Chulhong

    2016-10-01

    Compact size and fast imaging abilities are key requirements for the clinical implementation of an optical coherence tomography (OCT) system. Among the various small-sized technology, a microelectromechanical system (MEMS) scanning mirror is widely used in a miniaturized OCT system. However, the complexities of conventional MEMS fabrication processes and relatively high costs have restricted fast clinical translation and commercialization of the OCT systems. To resolve these problems, we developed a two-axis polydimethylsiloxane (PDMS)-based MEMS (2A-PDMS-MEMS) scanning mirror through simple processes with low costs. It had a small size of 15×15×15 mm3, was fast, and had a wide scanning range at a low voltage. The AC/DC responses were measured to evaluate the performance of the 2A-PDMS-MEMS scanning mirror. The maximum scanning angles were measured as ±16.6 deg and ±11.6 deg along the X and Y axes, respectively, and the corresponding field of view was 29.8 mm×20.5 mm with an optical focal length of 50 mm. The resonance frequencies were 82 and 57 Hz along the X and Y axes, respectively. Finally, in vivo B-scan and volumetric OCT images of human fingertips and palms were successfully acquired using the developed SD-OCT system based on the 2A-PDMS-MEMS scanning mirror.

  12. DNA barcoding amphibians and reptiles.

    Science.gov (United States)

    Vences, Miguel; Nagy, Zoltán T; Sonet, Gontran; Verheyen, Erik

    2012-01-01

    Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.

  13. A DNA barcode for land plants

    OpenAIRE

    Hollingsworth, Peter M.; Forrest, Laura L.; Spouge, John L; Hajibabaei, Mehrdad; Ratnasingham,Sujeevan; van der Bank, Michelle; Chase, Mark W.; Cowan, Robyn S.; Erickson, David L.; Fazekas, Aron J.; Graham, Sean W.; James, Karen E.; Kim, Ki-Joong; Kress, W. John; Schneider, Harald

    2009-01-01

    DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quali...

  14. Scanning SQUID microscope system for geological samples: system integration and initial evaluation

    Science.gov (United States)

    Oda, Hirokuni; Kawai, Jun; Miyamoto, Masakazu; Miyagi, Isoji; Sato, Masahiko; Noguchi, Atsushi; Yamamoto, Yuhji; Fujihira, Jun-ichi; Natsuhara, Nobuyoshi; Aramaki, Yoshiyasu; Masuda, Takashige; Xuan, Chuang

    2016-11-01

    We have developed a high-resolution scanning superconducting quantum interference device (SQUID) microscope for imaging the magnetic field of geological samples at room temperature. In this paper, we provide details about the scanning SQUID microscope system, including the magnetically shielded box (MSB), the XYZ stage, data acquisition by the system, and initial evaluation of the system. The background noise in a two-layered PC permalloy MSB is approximately 40-50 pT. The long-term drift of the system is approximately ≥1 nT, which can be reduced by drift correction for each measurement line. The stroke of the XYZ stage is 100 mm × 100 mm with an accuracy of 10 µm, which was confirmed by laser interferometry. A SQUID chip has a pick-up area of 200 μm × 200 μm with an inner hole of 30 μm × 30 μm. The sensitivity is 722.6 nT/V. The flux-locked loop has four gains, i.e., ×1, ×10, ×100, and ×500. An analog-to-digital converter allows analog voltage input in the range of about ±7.5 V in 0.6-mV steps. The maximum dynamic range is approximately ±5400 nT, and the minimum digitizable magnetic field is 0.9 pT. The sensor-to-sample distance is measured with a precision line current, which gives the minimum of 200 µm. Considering the size of pick-up coil, sensor-to-sample distance, and the accuracy of XYZ stage, spacial resolution of the system is 200 µm. We developed the software used to measure the sensor-to-sample distance with line scan data, and the software to acquire data and control the XYZ stage for scanning. We also demonstrate the registration of the magnetic image relative to the optical image by using a pair of point sources placed on the corners of a sample holder outside of a thin section placed in the middle of the sample holder. Considering the minimum noise estimate of the current system, the theoretical detection limit of a single magnetic dipole is 1 × 10-14 Am2. The new instrument is a powerful tool that could be used in various

  15. Design and construction of a fine drive system for scanning optical elements

    Science.gov (United States)

    Golnabi, H.; Jafari, R.

    2008-09-01

    The design and operation of a simple mechanical drive system, which is able to perform a fine course of angular motion, are reported. The system consists of a lead screw, a drive nut, sine bar legs, and an output shaft that can scan the optical holder mount. With a stepper motor coupled to the lead screw and interfaced to a PC, it is possible to control the scanning operation. When a 800 step/turn motor is used, it is possible to have an angular resolution of about 0.5 mdegree for a dynamic range of about 23°. The reproducibility of the results is about 0.22% for the scan angle and the hysteresis effect of the system is in the range of 1.71%. For a total scan of 51,200 steps, a scan angle of about 23.3° is acheived. The fitted line to the experimental results shows that scan angle changes linearly with the scan length. With good precision in system construction and careful alignment, the overall nonlinearity can be less than 1%.

  16. Hierarchical, Three-Dimensional Measurement System for Crime Scene Scanning.

    Science.gov (United States)

    Marcin, Adamczyk; Maciej, Sieniło; Robert, Sitnik; Adam, Woźniak

    2017-02-02

    We present a new generation of three-dimensional (3D) measuring systems, developed for the process of crime scene documentation. This measuring system facilitates the preparation of more insightful, complete, and objective documentation for crime scenes. Our system reflects the actual requirements for hierarchical documentation, and it consists of three independent 3D scanners: a laser scanner for overall measurements, a situational structured light scanner for more minute measurements, and a detailed structured light scanner for the most detailed parts of tscene. Each scanner has its own spatial resolution, of 2.0, 0.3, and 0.05 mm, respectively. The results of interviews we have conducted with technicians indicate that our developed 3D measuring system has significant potential to become a useful tool for forensic technicians. To ensure the maximum compatibility of our measuring system with the standards that regulate the documentation process, we have also performed a metrological validation and designated the maximum permissible length measurement error EMPE for each structured light scanner. In this study, we present additional results regarding documentation processes conducted during crime scene inspections and a training session.

  17. Low-power portable scanning imaging ladar system

    Science.gov (United States)

    Pyburn, Dana; Leon, Roberto; Haji-Saeed, B.; Sengupta, Sandip K.; Testorf, Markus; Kierstead, John; Khoury, Jehad; Woods, Charles L.; Lorenzo, Joseph

    2003-08-01

    We propose and are in the process of progressively implementing an improved architecture for a laser based system to acquire intensity and range images of hard targets in real-time. The system design emphasizes the use of low power laser sources in conjunction with optical preamplification of target return signals to maintain eye safety without incurring the associated performance penalty. The design leverages advanced fiber optic component technology developed for the commercial market to achieve compactness and low power consumption without the high costs and long lead times associated with custom military devices. All important system parameters are designed to be configured in the field, by the user, in software, allowing for adaptive reconfiguration for different missions and targets. Recently we have started our transition from the initial test bed, using a laser in the visible wavelength, into the final system with a 1550nm diode laser. Currently we are able to acquire and display 3-D false-color and gray-scale images, in the laboratory, at moderate frame rates in real-time. Commercial off-the-shelf data acquisition and signal processing software on a desktop computer equipped with commercial acquisition hardware is utilized. Significant improvements in both range and spatial resolution are expected in the near future.

  18. Performances of the scanning system for the CNAO center of oncological hadron therapy

    Energy Technology Data Exchange (ETDEWEB)

    Giordanengo, S., E-mail: giordane@to.infn.i [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Donetti, M. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); CNAO - Centro Nazionale di Adroterapia Oncologica Foundation, Milano (Italy); Marchetto, F. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Ansarinejad, A. [Department of Physics, University of Torino, Torino (Italy); Attili, A. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Bourhaleb, F. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Department of Physics, University of Torino, Torino (Italy); Burini, F. [OCEM SpA, Bologna (Italy); Cirio, R. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Department of Physics, University of Torino, Torino (Italy); Fabbricatore, P. [INFN - Istituto Nazionale di Fisica Nucleare, Genova (Italy); Voelker, F. [CERN, Geneve (Switzerland); Garella, M.A. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Incurvati, M. [OCEM SpA, Bologna (Italy); Monaco, V. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Department of Physics, University of Torino, Torino (Italy); Pardo, J. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Peroni, C.; Russo, G.; Sacchi, R. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy); Department of Physics, University of Torino, Torino (Italy); Taddia, G. [OCEM SpA, Bologna (Italy); Zampieri, A. [INFN - Istituto Nazionale di Fisica Nucleare, Torino (Italy)

    2010-02-01

    In hadron therapy one of the most advanced methods for beam delivery is the active scanning technique which uses fast scanning magnets to drive a narrow particle beam across the target. The Centro Nazionale di Adroterapia Oncologica (CNAO) will treat tumours with this technique. The CNAO scanning system includes two identical dipole magnets for horizontal and vertical beam deflection, each one connected to a fast power supply. The dose delivery system exploits a set of monitor chambers to measure the fluence and position of the beam and drives the beam during the treatment by controlling the sequence of currents set by the power supplies. A test of the dynamic performance of the scanning system has been performed using a Hall probe to measure the field inside the magnet and the results are presented in this paper.

  19. Performances of the scanning system for the CNAO center of oncological hadron therapy

    CERN Document Server

    Giordanengo, S; Attili, A; Pardo, J; Russo, G; Taddia, G; Monaco, V; Garella, M A; Zampieri, A; Fabbricatore, P; Cirio, R; Voelker, F; Sacchi, R; Bourhaleb, F; Marchetto, F; Burini, F; Incurvati, M; Ansarinejad, A; Peroni, C

    2010-01-01

    In hadron therapy one of the most advanced methods for beam delivery is the active scanning technique which uses fast scanning magnets to drive a narrow particle beam across the target. The Centro Nazionale di Adroterapia Oncologica (CNAO) will treat tumours with this technique. The CNAO scanning system includes two identical dipole magnets for horizontal and vertical beam deflection, each one connected to a fast power supply. The dose delivery system exploits a set of monitor chambers to measure the fluence and position of the beam and drives the beam during the treatment by controlling the sequence of currents set by the power supplies. A test of the dynamic performance of the scanning system has been performed using a Hall probe to measure the field inside the magnet and the results are presented in this paper. (C) 2009 Elsevier B.V. All rights reserved.

  20. Development of a Mixed Scanning Interactive System for Decision Support.

    Science.gov (United States)

    1984-07-01

    0542 IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBEN ETIca , VOL SMC-10, NO. 12, DBCDMER 1980 891 REFERENCES The options assumed available to the...nore gen - and decision support is strong; consequently there erally determining the set P2 9H x n, where (7’, is much motivation to seek an approach...1. 8 -h* a. o" 6*81t & aS t hSO.418 bal-.. 0) * 11. $500 $750 3 1.0 .5 3/S 5-1000.0 A - $0 IS) C.-. SiLaiata 6 Decisin treefor ~ Fig. 3. Gen . probi

  1. DNA barcoding of the Lemnaceae, a family of aquatic monocots

    Directory of Open Access Journals (Sweden)

    Wang Wenqin

    2010-09-01

    Full Text Available Abstract Background Members of the aquatic monocot family Lemnaceae (commonly called duckweeds represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants. Results We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree. Conclusions Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.

  2. DNA Barcoding for Minor Crops and Food Traceability

    Directory of Open Access Journals (Sweden)

    Andrea Galimberti

    2014-01-01

    Full Text Available This outlook paper addresses the problem of the traceability of minor crops. These kinds of cultivations consist in a large number of plants locally distributed with a modest production in terms of cultivated acreage and quantity of final product. Because of globalization, the diffusion of minor crops is increasing due to their benefit for human health or their use as food supplements. Such a phenomenon implies a major risk for species substitution or uncontrolled admixture of manufactured plant products with severe consequences for the health of consumers. The need for a reliable identification system is therefore essential to evaluate the quality and provenance of minor agricultural products. DNA-based techniques can help in achieving this mission. In particular, the DNA barcoding approach has gained a role of primary importance thanks to its universality and versatility. Here, we present the advantages in the use of DNA barcoding for the characterization and traceability of minor crops based on our previous or ongoing studies at the ZooPlantLab (Milan, Italy. We also discuss how DNA barcoding may potentially be transferred from the laboratory to the food supply chain, from field to table.

  3. DNA barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera.

    Directory of Open Access Journals (Sweden)

    Robert G Foottit

    Full Text Available BACKGROUND: Many studies have shown the suitability of sequence variation in the 5' region of the mitochondrial cytochrome c oxidase I (COI gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. METHODOLOGY/PRINCIPAL FINDINGS: Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%. CONCLUSIONS/SIGNIFICANCE: This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage.

  4. DNA Barcoding for Honey Biodiversity

    Directory of Open Access Journals (Sweden)

    Alice Valentini

    2010-04-01

    Full Text Available Honey is produced by honeybees from nectar and from secretions of living plants. It reflects the honeybees’ diet and the local plant communities. Honey also shows different plant compositions in different geographical locations. We propose a new method for studying the plant diversity and the geographical origin of honey using a DNA barcoding approach that combines universal primers and massive parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional origin and one composed of a worldwide mix of different honeys. We demonstrate that the method proposed here is fast, simple to implement, more robust than classical methods, and therefore suitable for analyzing plant diversity in honey.

  5. 3D Wide FOV Scanning Measurement System Based on Multiline Structured-Light Sensors

    Directory of Open Access Journals (Sweden)

    He Gao

    2014-03-01

    Full Text Available Structured-light three-dimensional (3D vision measurement is currently one of the most common approaches to obtain 3D surface data. However, the existing structured-light scanning measurement systems are primarily constructed on the basis of single sensor, which inevitably generates three obvious problems: limited measurement range, blind measurement area, and low scanning efficiency. To solve these problems, we developed a novel 3D wide FOV scanning measurement system which adopted two multiline structured-light sensors. Each sensor is composed of a digital CCD camera and three line-structured-light projectors. During the measurement process, the measured object is scanned by the two sensors from two different angles at a certain speed. Consequently, the measurement range is expanded and the blind measurement area is reduced. More importantly, since six light stripes are simultaneously projected on the object surface, the scanning efficiency is greatly improved. The Multiline Structured-light Sensors Scanning Measurement System (MSSS is calibrated on site by a 2D pattern. The experimental results show that the RMS errors of the system for calibration and measurement are less than 0.092 mm and 0.168 mm, respectively, which proves that the MSSS is applicable for obtaining 3D object surface with high efficiency and accuracy.

  6. Handheld Thermoacoustic Scanning System Based on a Linear-array Transducer.

    Science.gov (United States)

    Ji, Zhong; Ding, Wenzheng; Ye, Fanghao; Lou, Cunguang

    2016-07-01

    To receive the information necessary for imaging, traditional microwave-induced thermoacoustic imaging systems (MITISs) use a type of circular-scanning mode using single or arc detectors. However, the use of MITISs for body scanning is complicated by restrictions in space and imaging time. A linear-array detector, the most widely used transducer in medical ultrasound imaging systems for body scanning, is a possible alternative to MITISs for scanning biological tissues, such as from the breast or limbs. In this paper, a handheld MITIS, based on a linear-array detector and a multiple data acquisition system, is described, and the capacity of the system is explored experimentally. First, the vertical and lateral resolution of the system is discussed. Next, real-time imaging of a moving object, obtained with an image capture rate of 20 frame/s, is described. Finally, a phantom experiment is detailed, investigating the overall imaging capability. The results show that this system achieves rapid scanning with a large field of view. The system has the obvious advantages of being handheld, not using coupled fluids, and achieving real-time imaging with a large field of view, which make this MITIS more suitable for clinical applications.

  7. Reliability of the TekScan MatScan® system for the measurement of postural stability in older people with rheumatoid arthritis

    OpenAIRE

    Brenton-Rule Angela; Mattock Joshua; Carroll Matthew; Dalbeth Nicola; Bassett Sandra; Menz Hylton B; Rome Keith

    2012-01-01

    Abstract Background Postural stability can be measured in clinical and research settings using portable plantar pressure systems. People with rheumatoid arthritis (RA) have decreased postural stability compared to non-RA populations and impaired postural stability is associated with falls in people with RA. The purpose of this study was therefore to investigate the reliability of the TekScan MatScan® system in assessing postural stability in people with RA. Methods Twenty three participants w...

  8. Design and verification of the miniature optical system for small object surface profile fast scanning

    Science.gov (United States)

    Chi, Sheng; Lee, Shu-Sheng; Huang, Jen, Jen-Yu; Lai, Ti-Yu; Jan, Chia-Ming; Hu, Po-Chi

    2016-04-01

    As the progress of optical technologies, different commercial 3D surface contour scanners are on the market nowadays. Most of them are used for reconstructing the surface profile of mold or mechanical objects which are larger than 50 mm×50 mm× 50 mm, and the scanning system size is about 300 mm×300 mm×100 mm. There are seldom optical systems commercialized for surface profile fast scanning for small object size less than 10 mm×10 mm×10 mm. Therefore, a miniature optical system has been designed and developed in this research work for this purpose. Since the most used scanning method of such system is line scan technology, we have developed pseudo-phase shifting digital projection technology by adopting projecting fringes and phase reconstruction method. A projector was used to project a digital fringe patterns on the object, and the fringes intensity images of the reference plane and of the sample object were recorded by a CMOS camera. The phase difference between the plane and object can be calculated from the fringes images, and the surface profile of the object was reconstructed by using the phase differences. The traditional phase shifting method was accomplished by using PZT actuator or precisely controlled motor to adjust the light source or grating and this is one of the limitations for high speed scanning. Compared with the traditional optical setup, we utilized a micro projector to project the digital fringe patterns on the sample. This diminished the phase shifting processing time and the controlled phase differences between the shifted phases become more precise. Besides, the optical path design based on a portable device scanning system was used to minimize the size and reduce the number of the system components. A screwdriver section about 7mm×5mm×5mm has been scanned and its surface profile was successfully restored. The experimental results showed that the measurement area of our system can be smaller than 10mm×10mm, the precision reached to

  9. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.

    Science.gov (United States)

    Hajibabaei, Mehrdad; Shokralla, Shadi; Zhou, Xin; Singer, Gregory A C; Baird, Donald J

    2011-04-13

    Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding

  10. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

    Science.gov (United States)

    Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

    2012-01-01

    Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

  11. 3D cavity detection technique and its application based on cavity auto scanning laser system

    Institute of Scientific and Technical Information of China (English)

    LIU Xi-ling; LI Xi-bing; LI Fa-ben; ZHAO Guo-yan; QIN Yu-hui

    2008-01-01

    Ground constructions and mines are severely threatened by underground cavities especially those unsafe or inaccessible ones. Safe and precise cavity detection is vital for reasonable cavity evaluation and disposal. The conventional cavity detection methods and their limitation were analyzed. Those methods cannot form 3D model of underground cavity which is used for instructing the cavity disposal; and their precisions in detection are always greatly affected by the geological circumstance. The importance of 3D cavity detection in metal mine for safe exploitation was pointed out; and the 3D cavity laser detection method and its principle were introduced. A cavity auto scanning laser system was recommended to actualize the cavity 3D detection after comparing with the other laser detection systems. Four boreholes were chosen to verify the validity of the cavity auto scanning laser system. The results show that the cavity auto scanning laser system is very suitable for underground 3D cavity detection, especially for those inaccessible ones.

  12. Georeferenced scanning system to estimate the leaf wall area in tree crops.

    Science.gov (United States)

    del-Moral-Martínez, Ignacio; Arnó, Jaume; Escolà, Alexandre; Sanz, Ricardo; Masip-Vilalta, Joan; Company-Messa, Joaquim; Rosell-Polo, Joan R

    2015-04-10

    This paper presents the use of a terrestrial light detection and ranging (LiDAR) system to scan the vegetation of tree crops to estimate the so-called pixelated leaf wall area (PLWA). Scanning rows laterally and considering only the half-canopy vegetation to the line of the trunks, PLWA refers to the vertical projected area without gaps detected by LiDAR. As defined, PLWA may be different depending on the side from which the LiDAR is applied. The system is completed by a real-time kinematic global positioning system (RTK-GPS) sensor and an inertial measurement unit (IMU) sensor for positioning. At the end, a total leaf wall area (LWA) is computed and assigned to the X, Y position of each vertical scan. The final value of the area depends on the distance between two consecutive scans (or horizontal resolution), as well as the number of intercepted points within each scan, since PLWA is only computed when the laser beam detects vegetation. To verify system performance, tests were conducted related to the georeferencing task and synchronization problems between GPS time and central processing unit (CPU) time. Despite this, the overall accuracy of the system is generally acceptable. The Leaf Area Index (LAI) can then be estimated using PLWA as an explanatory variable in appropriate linear regression models.

  13. Georeferenced Scanning System to Estimate the Leaf Wall Area in Tree Crops

    Directory of Open Access Journals (Sweden)

    Ignacio del-Moral-Martínez

    2015-04-01

    Full Text Available This paper presents the use of a terrestrial light detection and ranging (LiDAR system to scan the vegetation of tree crops to estimate the so-called pixelated leaf wall area (PLWA. Scanning rows laterally and considering only the half-canopy vegetation to the line of the trunks, PLWA refers to the vertical projected area without gaps detected by LiDAR. As defined, PLWA may be different depending on the side from which the LiDAR is applied. The system is completed by a real-time kinematic global positioning system (RTK-GPS sensor and an inertial measurement unit (IMU sensor for positioning. At the end, a total leaf wall area (LWA is computed and assigned to the X, Y position of each vertical scan. The final value of the area depends on the distance between two consecutive scans (or horizontal resolution, as well as the number of intercepted points within each scan, since PLWA is only computed when the laser beam detects vegetation. To verify system performance, tests were conducted related to the georeferencing task and synchronization problems between GPS time and central processing unit (CPU time. Despite this, the overall accuracy of the system is generally acceptable. The Leaf Area Index (LAI can then be estimated using PLWA as an explanatory variable in appropriate linear regression models.

  14. DNA barcoding of Dalbergia spp. from Western Ghats in India

    Directory of Open Access Journals (Sweden)

    R. M. Bhagwat

    2011-01-01

    Full Text Available (Abstract selected from presentation in National Conference on Biodiversity of Medicinal and Aromatic Plants: Collection, Characterization and Utilization, held at Anand, India during November 24-25, 2010   The Western Ghats (WG in India are well known for their rich and unique assemblage of flora and fauna, and are amongst the 25 biodiversity hotspots identified in the world. Dalbergia (family: Fabaceae is an important member of the WG flora; valued for decorative and often fragrant wood (rosewood, African blackwood, sisu and is rich in aromatic oils. There is taxonomic confusion with respect to several Dalbergia species as these often have more than one species names. Hence, the size of the Dalbergia genus remains disputed. DNA barcoding is modern biotechnological tool which can distinguish among species that look alike. It is also useful in medicinal formulations to identify adulterants. Although DNA barcoding is well established ly accepted barcode is still lacking in plants. Hence, the main objective of this study is to develop a unique barcode for quick, accurate and reliable species identification using the Dalbergia genus as a model system. Leaf samples from 15 accessions each, belonging to six validated Dalbergia species (D. melanoxylon, D. candenatensis, D. rubiginosa, D. latifolia, D. volubilis and D. paniculata were collected from different locations in WG and DNA extractions have been carried out from these as well as characterized herbaria samples. Total 37 primer pairs specific to several chloroplast genes (matK, rpoC, rpoB, rbcL, accD, ndhJ, ycf5 and trnH-psbA as well as the nuclear genes were evaluated in the samples and 16 of these have been standardized for the six Dalbergia species. We are currently targeting the DNA sequences corresponding to matK, rpoc, rpoB, rbcl, trnH-psbA and nuclear ITS. Based on the preliminary sequence data, the resolution of the species differentiation using the rpoB and rbcL genes individually was

  15. Recommendations for the design and the installation of large laser scanning microscopy systems

    Science.gov (United States)

    Helm, P. Johannes

    2012-03-01

    Laser Scanning Microscopy (LSM) has since the inventions of the Confocal Scanning Laser Microscope (CLSM) and the Multi Photon Laser Scanning Microscope (MPLSM) developed into an essential tool in contemporary life science and material science. The market provides an increasing number of turn-key and hands-off commercial LSM systems, un-problematic to purchase, set up and integrate even into minor research groups. However, the successful definition, financing, acquisition, installation and effective use of one or more large laser scanning microscopy systems, possibly of core facility character, often requires major efforts by senior staff members of large academic or industrial units. Here, a set of recommendations is presented, which are helpful during the process of establishing large systems for confocal or non-linear laser scanning microscopy as an effective operational resource in the scientific or industrial production process. Besides the description of technical difficulties and possible pitfalls, the article also illuminates some seemingly "less scientific" processes, i.e. the definition of specific laboratory demands, advertisement of the intention to purchase one or more large systems, evaluation of quotations, establishment of contracts and preparation of the local environment and laboratory infrastructure.

  16. Multi-frequency AOM for multi-beam laser scanning exposure system

    Science.gov (United States)

    Shinada, Hidetoshi

    2016-10-01

    Digital printing systems recorded on films or computer to plates (CTPs) have been required to improve their productivity and image quality. Under the circumstance, a printing technology of the multi-beam laser scanning for the drum capstan system, which is almost the same as optics configuration as the flat bed system, was developed using a newly developed multi-frequency acousto-optic modulator (AOM) as a key device instead of ultra-fast scanning devices toward a main scan direction. The multi-frequency AOM was developed with phased array-type transducers, achieving a wider bandwidth of over 160 MHz. The design consisted of a simultaneous three beams generation with interlace scan to avoid the beat effect by adjacent Doppler-shifted beams, which consequently attained the fastest recording speed of 5.0 mm/s compared with 2.0-3.0 mm/s of existing systems in those days. Furthermore, a couple of critical parameters of the multi-frequency AOM are studied, for example, a treatment of third-order intermodulation and also beat effect in connection with photosensitive media. As a result, the necessity of interlaces scanning to obtain good image quality without beat effect and also to allow a lower laser power to apply is proposed.

  17. Generating barcoded libraries for multiplex high-throughput sequencing.

    Science.gov (United States)

    Knapp, Michael; Stiller, Mathias; Meyer, Matthias

    2012-01-01

    Molecular barcoding is an essential tool to use the high throughput of next generation sequencing platforms optimally in studies involving more than one sample. Various barcoding strategies allow for the incorporation of short recognition sequences (barcodes) into sequencing libraries, either by ligation or polymerase chain reaction (PCR). Here, we present two approaches optimized for generating barcoded sequencing libraries from low copy number extracts and amplification products typical of ancient DNA studies.

  18. The correction of vibration in frequency scanning interferometry based absolute distance measurement system for dynamic measurements

    Science.gov (United States)

    Lu, Cheng; Liu, Guodong; Liu, Bingguo; Chen, Fengdong; Zhuang, Zhitao; Xu, Xinke; Gan, Yu

    2015-10-01

    Absolute distance measurement systems are of significant interest in the field of metrology, which could improve the manufacturing efficiency and accuracy of large assemblies in fields such as aircraft construction, automotive engineering, and the production of modern windmill blades. Frequency scanning interferometry demonstrates noticeable advantages as an absolute distance measurement system which has a high precision and doesn't depend on a cooperative target. In this paper , the influence of inevitable vibration in the frequency scanning interferometry based absolute distance measurement system is analyzed. The distance spectrum is broadened as the existence of Doppler effect caused by vibration, which will bring in a measurement error more than 103 times bigger than the changes of optical path difference. In order to decrease the influence of vibration, the changes of the optical path difference are monitored by a frequency stabilized laser, which runs parallel to the frequency scanning interferometry. The experiment has verified the effectiveness of this method.

  19. Innovative Gamma Ray Spectrometer Detection Systems for Conducting Scanning Surveys on Challenging Terrain - 13583

    Energy Technology Data Exchange (ETDEWEB)

    Palladino, Carl; Mason, Bryan; Engle, Matt; LeVangie, James [The Palladino Company, Inc., 720 Fillmore St., San Francisco, CA 94117 (United States); Dempsey, Gregg [United States Environmental Protection Agency, P.O. Box 98517, Las Vegas, NV 89193-8517 (United States); Klemovich, Ron [HydroGeoLogic, Inc., 6340 Glenwood, Suite 200, Building No. 7, Overland Park, KS 66202 (United States)

    2013-07-01

    The Santa Susana Field Laboratory located near Simi Valley, California was investigated to determine the nature and extent of gamma radiation anomalies. The primary objective was to conduct gamma scanning surveys over 100 percent of the approximately 1,906,000 square meters (471 acre) project site with the most sensitive detection system possible. The site had challenging topography that was not conducive to traditional gamma scanning detection systems. Terrain slope varied from horizontal to 48 degrees and the ground surface ranged from flat, grassy meadows to steep, rocky hillsides. In addition, the site was home to many protected endangered plant and animal species, and archaeologically significant sites that required minimal to no disturbance of the ground surface. Therefore, four innovative and unique gamma ray spectrometer detection systems were designed and constructed to successfully conduct gamma scanning surveys of approximately 1,076,000 square meters (266 acres) of the site. (authors)

  20. DNA barcoding:species delimitation in tree peonies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Delimitations of species are crucial for correct and precise identification of taxa.Unfortunately "spe-cies" is more a subjective than an objective concept in taxonomic practice due to difficulties in revealing patterns of infra-or inter-specific variations.Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding.In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies(Paeonia sect.Moutan).We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies.All currently recognized species and major variants have been included in this study.Four chloroplast gene fragments,i.e.ndhF,rps16-trnQ,trnL-F and trnS-G(a total of 5040 characters,96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment(2093?2197 bp,279 variable and 148 parsi-mony-informative characters) were used to construct phylogenetic relationships among the taxa.The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P.decomposita,P.jishanensis,P.qiui,and P.rockii based on morphology.The inconsistencies come from(1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P.decomposita + P.rockii,and(2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P.jishanensis and P.qiui.The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloro-plast capture event in evolutionary history,as no reproductive barriers exist to prevent inter-specific hybridization.We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies.The variability of chloroplast genes among well-defined species or population systems of a

  1. DNA Barcode Analysis of Thrips (Thysanoptera Diversity in Pakistan Reveals Cryptic Species Complexes.

    Directory of Open Access Journals (Sweden)

    Romana Iftikhar

    Full Text Available Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27% at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%. BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci, and one predatory thrips (Aeolothrips intermedius showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

  2. Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers

    Directory of Open Access Journals (Sweden)

    Oh Hyun-Woo

    2010-07-01

    Full Text Available Abstract Background DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Results Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1 to produce a cocktail which generated a barcode amplicon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to amplify with standard primers. Conclusions A cocktail of two tRNA-W forward primers coupled with a standard reverse primer amplifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the amplification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.

  3. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    Institute of Scientific and Technical Information of China (English)

    Changku Sun; Li Tao; Peng Wang; Li He

    2006-01-01

    @@ A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  4. Initial Tests and Accuracy Assesment of a Compact Mobile Laser Scanning System

    Science.gov (United States)

    Julge, K.; Ellmann, A.; Vajakas, T.; Kolka, R.

    2016-06-01

    Mobile laser scanning (MLS) is a faster and cost-effective alternative to static laser scanning, even though there is a slight trade-off in accuracy. This contribution describes a compact mobile laser scanning system mounted on a vehicle. The technical parameters of the used system components, i.e. a small LIDAR sensor Velodyne VLP-16 and a dual antenna GNSS/INS system Advanced Navigation Spatial Dual, are reviewed, along with the integration of these components for spatial data acquisition. Calculation principles of 3D coordinates from the real-time data of all the involved sensors are discussed. The field tests were carried out in a controlled environment of a parking lot and at different velocities. Experiments were carried out to test the ability of the GNSS/INS system to cope with difficult conditions, e.g. sudden movements due to cornering or swerving. The accuracy of the resulting MLS point cloud is evaluated with respect to high-accuracy static terrestrial laser scanning data. Problems regarding combining LIDAR, GNSS and INS sensors are outlined, as well as the initial accuracy assessments. Initial tests revealed errors related to insufficient quality of inertial data and a need for the trajectory post-processing calculations. Although this study was carried out while the system was mounted on a car, there is potential for operating the system on an unmanned aerial vehicle, all-terrain vehicle or in a backpack mode due to its relatively compact size.

  5. Experimental underwater scanning imaging system using pulsed blue-green lasers

    Science.gov (United States)

    Wang, Lei; Xu, Zhi-yong; Zhang, Qi-heng; Wang, Hua-chuang; Yu, Xue-gang; Nie, Rui-jie

    2011-06-01

    A new, simple and compact experimental laser scanning imaging system is introduced for underwater imaging, and the characteristics of the system are analyzed in this paper. The system consists of the illuminator, optical scanning system, optical receiving system, narrow band filters, high-sensitivity gated image sensor, synchronous control and data acquisition system and power supply and cooling system. The illuminator is a lump-pumped, Q-switched, frequency doubled Nd:YAG pulsed laser operating at 532 nm with a frequency of 50 Hz. The receiver is a self-made gated intensified charge coupled device (ICCD). As a result, gated super Gen-II image intensifier and PAL format charge-coupled device (CCD) camera are assembled to meet the requirements. The coupling gated ICCD has a sensitivity of approximated 10-5lx, and the minimum gate width can reach to 40 ns. And a set of scanning structure which only uses one mirror is used in the experimental system. In addition, the performance parameters are listed. Finally, the detection capabilities of the imaging system are theoretically analyzed in typical seawater. The analysis indicates that the detection depth of the system can reach to 16 m in the clear seawater.

  6. Design and performance of a practical variable-temperature scanning tunneling potentiometry system.

    Science.gov (United States)

    Rozler, M; Beasley, M R

    2008-07-01

    We have constructed a scanning tunneling potentiometry system capable of simultaneously mapping the transport-related electrochemical potential of a biased sample along with its surface topography. Combining a novel sample biasing technique with a continuous current-nulling feedback scheme pushes the noise performance of the measurement to its fundamental limit--the Johnson noise of the scanning tunneling microscope (STM) tunnel junction. The resulting 130 nV voltage sensitivity allows us to spatially resolve local potentials at scales down to 2 nm, while maintaining angstrom scale STM imaging, all at scan sizes of up to 15 microm. A millimeter-range two-dimensional coarse positioning stage and the ability to operate from liquid helium to room temperature with a fast turn-around time greatly expand the versatility of the instrument. By performing studies of several model systems, we discuss the implications of various types of surface morphology for potentiometric measurements.

  7. 条码系统在企业ERP系统中的应用研究%Application of Barcode System in the Enterprise ERP System

    Institute of Scientific and Technical Information of China (English)

    陈玉娟; 杨淑梅; 王一兵

    2016-01-01

    With the development of enterprise information construction, the resource management in military enterprises should rely on ERP application platform, ERP system and bar code system and other enterprise application systems are combined with the depth, improve enterprise management level and production and research capacity. This paper analyzes the current situation of enterprise ERP, expounds the concept of bar code technology, and discusses the application of bar code technology in enterprise ERP, production, quality management, after sales module.%随着企业信息化建设的发展,军工企业的资源管理应凭借ERP应用平台,将ERP系统与条码系统以及企业其他应用系统深度结合,提高企业管理水平和生产科研能力。文章分析了企业ERP现状,阐述了条码技术概念,探讨条码技术在企业ERP、生产、质量管理、售后模块中的具体应用。

  8. Design of Dual Axis Laser Scanning Diameter Measuring Gauge System with PID Co

    Institute of Scientific and Technical Information of China (English)

    LI Xin-qiu; LI Zhi-wei; LIU Da-jiang

    2009-01-01

    Dual axis laser scanning diameter measuring gauge system(DALSDMGS)with PID controller,which can be used for online non-contact diameter measuring and control on the hose,wire and rod production line,is introduced.The measure principle and implementation of this system are also presented.A PID control module with PID parameters tuning is included in the measuring and control system,which functions as a PID automatic controller of the diameter.

  9. Plant DNA barcoding in China

    Institute of Scientific and Technical Information of China (English)

    De-Zhu LI; Jian-Quan LIU; Zhi-Duan CHEN; Hong WANG; Xue-Jun GE; Shi-Liang ZHOU; Lian-Ming GAO; Cheng-Xin FU; Shi-Lin CHEN

    2011-01-01

    @@ Identification is the keystone of biology (Bell, 1986).However, to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English, Chinese, or other living languages.In addition, the identification cues vary greatly between different taxonomical groups.Even for the taxonomists with long training and experience, it is difficult to remember all specific terms for a given group, e.g., Orchidaceae or Poaceae, without help of floristic books or monographs.It takes much time and effort to train a taxonomist, at a time when fewer and fewer young students are interested in this "classical" and "out-of-style", but extremely important, discipline.Many students elect to learn the more "advanced'' and "modem" biological disciples like molecular biology and biochemistry.Thus, in China and therest of the world, taxonomists are themselves becoming "endangered".The rise of the DNA barcoding is expected to mitigate, at least in part, this dilemma.

  10. Confirming Hypoderma tarandi (Diptera: Oestridae) human ophthalmomyiasis by larval DNA barcoding.

    Science.gov (United States)

    Rukke, Bjørn Arne; Cholidis, Symira; Johnsen, Arild; Ottesen, Preben

    2014-06-01

    DNA barcoding is a practical tool for species identification, when morphological classification of an organism is difficult. Herein we describe the utilisation of this technique in a case of ophthalmomyiasis interna. A 12-year-old boy was infested during a summer holiday in northern Norway, while visiting an area populated with reindeer. Following medical examination, a Diptera larva was surgically removed from the boy's eye and tentatively identified from its morphological traits as Hypoderma tarandi (L.) (Diptera: Oestridae). Ultimately, DNA barcoding confirmed this impression. The larval cytochrome c oxidase subunit 1 (COI) DNA sequence was matched with both profiles of five adult H. tarandi from the same region where the boy was infested, and other established profiles of H. tarandi in the Barcode of Life Data Systems (BOLD) identification engine.

  11. DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae).

    Science.gov (United States)

    Park, D-S; Suh, S-J; Hebert, P D N; Oh, H-W; Hong, K-J

    2011-08-01

    Although DNA barcode coverage has grown rapidly for many insect orders, there are some groups, such as scale insects, where sequence recovery has been difficult. However, using a recently developed primer set, we recovered barcode records from 373 specimens, providing coverage for 75 species from 31 genera in two families. Overall success was >90% for mealybugs and >80% for armored scale species. The G·C content was very low in most species, averaging just 16.3%. Sequence divergences (K2P) between congeneric species averaged 10.7%, while intra-specific divergences averaged 0.97%. However, the latter value was inflated by high intra-specific divergence in nine taxa, cases that may indicate species overlooked by current taxonomic treatments. Our study establishes the feasibility of developing a comprehensive barcode library for scale insects and indicates that its construction will both create an effective system for identifying scale insects and reveal taxonomic situations worthy of deeper analysis.

  12. Influence of scanning system and dentist's level of training in the accuracy of digital impressions

    Science.gov (United States)

    Hategan, Simona; Gabor, Alin; Zaharia, Cristian; Sinescu, Cosmin; Negrutiu, Meda Lavinia; Jivanescu, Anca

    2016-03-01

    Background: The principal aim of our study was to evaluate digital impressions, taken with spray powder and powderfree scan systems, in order to determine the influence of the dentist's commitment to training as a critical factor regarding quality. Material and method: Two digital intraoral impression systems from the same manufacture (Sirona) : Apollo DI and CEREC Omnicam, were used to scan 16 crown preparations on teeth on a typodont maxillary model. Because an Apollo Di intraoral camera is a powder system, an adhesive was applied before using the powder spray. Three groups were used to scan the crown preparations in order to determine coating thickness homogeneity. One group consisted of senior year dental students, a second consisted of prosthodontics residents, and the third consisted of prosthodontics specialists. The same procedure was applied with a CEREC Omnicam intraoral camera, which is a powder-free system. By using the two systems software parameters we were able to determine the scanning precision. Results: Homogeneity scores for Apollo Di regarding the spray layer was significantly thinner for all dental surfaces in the first group, while the second group had thinner coatings for buccal and distal surfaces. For the third group, the crown preparations were coated more homogeneously than the first two groups. The powder-free system CEREC Omnicam can, to a degree, mask the lack of experience in direct optical impressions by avoiding the poor quality coating, which can lead to defective marginal adaptation of definitive restoration. Conclusions: The dentist's lack of experience can be mitigated, and partially avoided, by using powder-free systems. At the same time, the dentist can give more time towards learning how to integrate computerized fabricated restoration into the practice. The commitment to training is a critical factor in the successful integration of the technology. In addition, scanning marginal preparation details needs time in order to

  13. Design of 220 GHz electronically scanned reflectarrays for confocal imaging systems

    Science.gov (United States)

    Hedden, Abigail S.; Dietlein, Charles R.; Wikner, David A.

    2012-09-01

    The authors analyze properties of a 220 GHz imaging system that uses a scanned reflectarray to perform electronic beam scanning of a confocal imager for applications including imaging meter-sized fields of view at 50 m standoff. Designs incorporating reflectarrays with confocal imagers have not been examined previously at these frequencies. We examine tradeoffs between array size, overall system size, and number of achievable image pixels resulting in a realistic architecture capable of meeting the needs of our application. Impacts to imaging performance are assessed through encircled energy calculations, beam pointing accuracy, and examining the number and intensity of quantization lobes that appear over the scan ranges of interest. Over the desired scan range, arrays with 1 and 2-bit phase quantization showed similar array main beam energy efficiencies. Two-bit phase quantization is advantageous in terms of pointing angle error, resulting in errors of at most 15% of the diffraction-limited beam size. However, both phase quantization cases considered resulted in spurious returns over the scan range of interest and other array layouts should be examined to eliminate potential imaging artifacts.

  14. Short barcodes for next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Katharina Mir

    Full Text Available We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters. We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.

  15. Short barcodes for next generation sequencing.

    Science.gov (United States)

    Mir, Katharina; Neuhaus, Klaus; Bossert, Martin; Schober, Steffen

    2013-01-01

    We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.

  16. A Charge-Coupled Device CCD line-scan system for road luminance measurement.

    NARCIS (Netherlands)

    Schreuder, D.A.

    1996-01-01

    The problems involved in measuring road luminance are discussed and a new measuring system described which is based on a line-scan Charge Coupled Device (CCD) configuration. It is designed for the assessment of average road surface luminance and degree of non-uniformity of road lighting. Additionall

  17. Organizations as Information Processing Systems. Environmental Characteristics, Company Performance, and Chief Executive Scanning: An Empirical Study.

    Science.gov (United States)

    1986-04-01

    Environmental sectors also differ in their pePV𔃻...., .’,.porte:,: e for or),n.ini at i ionI performance ( Aaker , 1983). Importance is related t,) the notion of...your company’s external environment. . % 30 Re f e rences Aaker , David A., "Organizing a Strategic inturmatLou Scanning System," % California

  18. Stripping chronopotentiometry at scanned deposition potential (SSCP). Part 5. Features of multi-metal systems

    NARCIS (Netherlands)

    Town, R.M.; Leeuwen, van H.P.

    2004-01-01

    This paper considers the mutual effects of metals on each other in scanned deposition potential stripping chronopotentiometry measurements (SSCP) on multi-metal systems. As compared to stripping voltammetry, depletive SSCP displays a certain resistance to the impact of intermetallic compounds, while

  19. DNA Barcoding on Bacteria: A Review

    Directory of Open Access Journals (Sweden)

    D. E. Lebonah

    2014-01-01

    Full Text Available Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.

  20. DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica.

    Science.gov (United States)

    Janzen, Daniel H; Hallwachs, Winnie

    2016-09-01

    The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

  1. Nanoelectrical probing with multiprobe SPM Systems compatible with scanning electron microscopes

    Science.gov (United States)

    Lewis, Aaron; Ignatov, Andrey; Taha, Hesham; Zhinoviev, Oleg; Komissar, Anatoly; Krol, Alexander; Lewis, David

    2011-03-01

    A scanning electron microscope compatible platform that permits multiprobe atomic force microscopy based nanoelectrical characterization will be described. To achieve such multiple parameter nanocharacterization with scanning electron microscope compatibility involves a number of innovations both in instrument and probe design. This presentation will focus on how these advances were achieved and the results obtained with such instrumentation on electrical nano-characterization and electrical nano-manipulation. The advances include: 1. Specialized scanners; 2. An ultrasensitive feedback mechanism based on tuning forks with no optical feedback interference that can induce carriers in semiconductor devices; and 3. Unique probes compatible with multiprobe geometries in which the probe tips can be brought into physical contact with one another. Experiments will be described with such systems that will include multiprobe electrical measurements with metal and glass coated coaxial nanowires of platinum. This combination of scanning electron microscopes integrated with multiprobe instrumentation allows for important applications not available today in the field of semiconductor processing technology.

  2. A Laser Line Auto-Scanning System for Underwater 3D Reconstruction.

    Science.gov (United States)

    Chi, Shukai; Xie, Zexiao; Chen, Wenzhu

    2016-09-20

    In this study, a laser line auto-scanning system was designed to perform underwater close-range 3D reconstructions with high accuracy and resolution. The system changes the laser plane direction with a galvanometer to perform automatic scanning and obtain continuous laser strips for underwater 3D reconstruction. The system parameters were calibrated with the homography constraints between the target plane and image plane. A cost function was defined to optimize the galvanometer's rotating axis equation. Compensation was carried out for the refraction of the incident and emitted light at the interface. The accuracy and the spatial measurement capability of the system were tested and analyzed with standard balls under laboratory underwater conditions, and the 3D surface reconstruction for a sealing cover of an underwater instrument was proved to be satisfactory.

  3. A Laser Line Auto-Scanning System for Underwater 3D Reconstruction

    Directory of Open Access Journals (Sweden)

    Shukai Chi

    2016-09-01

    Full Text Available In this study, a laser line auto-scanning system was designed to perform underwater close-range 3D reconstructions with high accuracy and resolution. The system changes the laser plane direction with a galvanometer to perform automatic scanning and obtain continuous laser strips for underwater 3D reconstruction. The system parameters were calibrated with the homography constraints between the target plane and image plane. A cost function was defined to optimize the galvanometer’s rotating axis equation. Compensation was carried out for the refraction of the incident and emitted light at the interface. The accuracy and the spatial measurement capability of the system were tested and analyzed with standard balls under laboratory underwater conditions, and the 3D surface reconstruction for a sealing cover of an underwater instrument was proved to be satisfactory.

  4. Scanning tunneling spectroscopy on heavy-fermion systems; Rastertunnelspektroskopie an Schwere-Fermionen-Systemen

    Energy Technology Data Exchange (ETDEWEB)

    Ernst, Stefan

    2011-06-24

    in the framework of this thesis different heavy-fermion systems were studied by means of scanning tunneling microscopy and spectroscopy. In the experiment two main topics existed. On the one hand the heavy-fermion superconductivity in the compounds CeCu{sub 2}Si{sub 2}, CeCoIn{sub 5}, and on the other hand the Kondo effect in the Kondo-lattice system YbRh{sub 2}Si{sub 2}.

  5. Histometric data obtained by in vivo confocal laser scanning microscopy in patients with systemic sclerosis

    Directory of Open Access Journals (Sweden)

    Altmeyer Peter

    2002-08-01

    Full Text Available Abstract Background It would be a benefit if time-saving, non-invasive methods could give hints for diagnosing systemic sclerosis. To investigate the skin of patients with systemic sclerosis using confocal laser scanning microscopy in vivo and to develop histometric parameters to describe characteristic cutaneous changes of systemic sclerosis observed by this new technique, we conducted an exploratory study. Materials and Methods Fifteen patients with systemic sclerosis treated with extracorporal photopheresis were compared with 15 healthy volunteers and 10 patients with other disorders also treated with extracorporal photopheresis. All subjects were investigated using confocal laser scanning microscopy in vivo. Results Micromorphologic characteristics of skin of patients with systemic sclerosis and measuring parameters for melanisation, epidermal hypotrophy, and fibrosis for dislocation of capillaries by collagen deposits in the papillary dermis were evaluated. An interesting finding was an increased thickness of the tissue in the dermal papillae superior to the first dermal papilla vessel. It was also possible to reproduce characteristic histologic features by confocal laser scanning microscopy in vivo. Histometric parameters for fibrosis and vascular features developed in this study showed significant differences in patients with systemic sclerosis compared to controls. Conclusions Although the predominant histopathological features in systemic sclerosis are findings of the reticular dermis and the subcutis, and in histopathological investigation the epidermis seems to remain unaffected by the disease, we have demonstrate some characteristic differences in the epidermis and papillary dermis by confocal laser scanning microscopy in vivo. Some of them have not been described so far. However, to use this technique as a tool for diagnosis and/or staging of systemic sclerosis, further studies are needed investigating the sensitivity and

  6. Assessment of mangroves from Goa, west coast India using DNA barcode.

    Science.gov (United States)

    Saddhe, Ankush Ashok; Jamdade, Rahul Arvind; Kumar, Kundan

    2016-01-01

    Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.

  7. Reliability of the TekScan MatScan® system for the measurement of postural stability in older people with rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Brenton-Rule Angela

    2012-08-01

    Full Text Available Abstract Background Postural stability can be measured in clinical and research settings using portable plantar pressure systems. People with rheumatoid arthritis (RA have decreased postural stability compared to non-RA populations and impaired postural stability is associated with falls in people with RA. The purpose of this study was therefore to investigate the reliability of the TekScan MatScan® system in assessing postural stability in people with RA. Methods Twenty three participants with RA, mean (SD age 69.74 (10.1 years, were assessed in barefoot double-limb quiet standing, with eyes open and eyes closed, for antero-posterior and medio-lateral postural sway values. Three repetitions, at a sampling frequency of 40 Hz, were recorded for each test condition to obtain a mean value. Measurements were repeated one hour later. Intraclass correlation coefficients (ICC with 95% confidence intervals (CI were calculated to determine between-session reliability. Measurement error was assessed through the calculation of the standard error of the measurement (SEM and the smallest real difference (SRD. Results The system displayed good to excellent reliability for antero-posterior and medio-lateral sway, with eyes open and closed, as indicated by ICC values ranging from 0.84 to 0.92. Measurement error, as evidenced by the SEM, ranged from 1.27 to 2.35 mm. The degree of change required to exceed the expected trial to trial variability was relatively high, compared to mean values, with SRD ranging from 3.08 to 5.71 mm. Conclusions The portability and ease of use of the TekScan MatScan® makes it a useful tool for the measurement of postural stability in clinical and research settings. The TekScan MatScan® system can reliably measure double-limb quiet standing in older people, aged 60 to 80 years, with RA.

  8. Cytochrome c oxidase I primers for corbiculate bees: DNA barcode and mini-barcode.

    Science.gov (United States)

    Françoso, E; Arias, M C

    2013-09-01

    Bees (Apidae), of which there are more than 19 900 species, are extremely important for ecosystem services and economic purposes, so taxon identity is a major concern. The goal of this study was to optimize the DNA barcode technique based on the Cytochrome c oxidase (COI) mitochondrial gene region. This approach has previously been shown to be useful in resolving taxonomic inconsistencies and for species identification when morphological data are poor. Specifically, we designed and tested new primers and standardized PCR conditions to amplify the barcode region for bees, focusing on the corbiculate Apids. In addition, primers were designed to amplify small COI amplicons and tested with pinned specimens. Short barcode sequences were easily obtained for some Bombus century-old museum specimens and shown to be useful as mini-barcodes. The new primers and PCR conditions established in this study proved to be successful for the amplification of the barcode region for all species tested, regardless of the conditions of tissue preservation. We saw no evidence of Wolbachia or numts amplification by these primers, and so we suggest that these new primers are of broad value for corbiculate bee identification through DNA barcode.

  9. A system level boundary scan controller board for VME applications [to CERN experiments

    CERN Document Server

    Cardoso, N; Da Silva, J C

    2000-01-01

    This work is the result of a collaboration between INESC and LIP in the CMS experiment being conducted at CERN. The collaboration addresses the application of boundary scan test at system level namely the development of a VME boundary scan controller (BSC) board prototype and the corresponding software. This prototype uses the MTM bus existing in the VME64* backplane to apply the 1149.1 test vectors to a system composed of nineteen boards, called here units under test (UUTs). A top-down approach is used to describe our work. The paper begins with some insights about the experiment being conducted at CERN, proceed with system level considerations concerning our work and with some details about the BSC board. The results obtained so far and the proposed work is reviewed in the end of this contribution. (11 refs).

  10. Design and Experiment of PZT Network-based Structural Health Monitoring Scanning System

    Institute of Scientific and Technical Information of China (English)

    Qiu Lei; Yuan Shenfang; Wang Qiang; Sun Yajie; Yang Weiwei

    2009-01-01

    The active Lamb wave and piezoelectric transducer (PZT)-based structural health monitoring (SHM) technology is a kind of efficient approach to estimate the health state of aircraft structure. In practical applications, PZT networks are needed to monitor large scale structures. Scanning many of the different PZT actuator-sensor channels within these PZT networks to achieve on-line SHM task is important. Based on a peripheral component interconnect extensions for instrumentation (PXI) platform, an active Lamb wave and PZT network-based integrated multi-channel scanning system (PXI-ISS) is developed for the purpose of practical applications of SHM, which is compact and portable, and can scan large numbers of actuator-sensor channels and perform damage assessing automatically. A PXI-based 4 channels gain-programmable charge amplifier, an external scanning module with 276 actuator-sensor channels and integrated SHM software are proposed and discussed in detail. The experimental research on a carbon fiber composite wing box of an unmanned aerial vehicle (UAV) for verifying the functions of the PXI-ISS is mainly discussed, including the design of PZTs layer, the method of excitation frequency selection, functional test of damage imaging, stability test of the PXI-ISS, and the loading effect on signals. The experimental results have verified the stability and damage functions of this system.

  11. Beam characteristics in two different proton uniform scanning systems: A side-by-side comparison

    Energy Technology Data Exchange (ETDEWEB)

    Nichiporov, Dmitri; Hsi Wen; Farr, Jonathan [Indiana University Integrated Science and Accelerator Technology Hall, 2401 Milo B. Sampson Lane, Bloomington, Indiana 47408 (United States); ProCure Treatment Centers, Inc., 420 North Walnut Street, Bloomington, Indiana 47401 (United States); Westdeutsches Protonentherapiezentrum, Hufelandstr. 55, Essen, NRW 45147 (Germany)

    2012-05-15

    Purpose: To compare clinically relevant dosimetric characteristics of proton therapy fields produced by two uniform scanning systems that have a number of similar hardware components but employ different techniques of beam spreading. Methods: This work compares two technologically distinct systems implementing a method of uniform scanning and layer stacking that has been developed independently at Indiana University (IU) and by Ion Beam Applications, S. A. (IBA). Clinically relevant dosimetric characteristics of fields produced by these systems are studied, such as beam range control, peak-to-entrance ratio (PER), lateral penumbra, field flatness, effective source position, precision of dose delivery at different gantry angles, etc. Results: Under comparable conditions, both systems controlled beam range with an accuracy of 0.5 mm and a precision of 0.1 mm. Compared to IBA, the IU system produced pristine peaks with a slightly higher PER (3.23 and 3.45, respectively) and smaller, symmetrical, lateral in-air penumbra of 1 mm compared to about 1.9/2.4 mm in the inplane/crossplane (IP/CP) directions for IBA. Large field flatness results in the IP/CP directions were similar: 3.0/2.4% for IU and 2.9/2.4% for IBA. The IU system featured a longer virtual source-to-isocenter position, which was the same for the IP and CP directions (237 cm), as opposed to 212/192 cm (IP/CP) for IBA. Dose delivery precision at different gantry angles was higher in the IBA system (0.5%) than in the IU system (1%). Conclusions: Each of the two uniform scanning systems considered in this work shows some attractive performance characteristics while having other features that can be further improved. Overall, radiation field characteristics of both systems meet their clinical specifications and show comparable results. Most of the differences observed between the two systems are clinically insignificant.

  12. Reliability of the TekScan MatScan® system for the measurement of plantar forces and pressures during barefoot level walking in healthy adults

    Directory of Open Access Journals (Sweden)

    Munteanu Shannon E

    2010-06-01

    Full Text Available Abstract Background Plantar pressure systems are increasingly being used to evaluate foot function in both research settings and in clinical practice. The purpose of this study was to investigate the reliability of the TekScan MatScan® system in assessing plantar forces and pressures during barefoot level walking. Methods Thirty participants were assessed for the reliability of measurements taken one week apart for the variables maximum force, peak pressure and average pressure. The following seven regions of the foot were investigated; heel, midfoot, 3rd-5th metatarsophalangeal joint, 2nd metatarsophalangeal joint, 1st metatarsophalangeal joint, hallux and the lesser toes. Results Reliability was assessed using both the mean and the median values of three repeated trials. The system displayed moderate to good reliability of mean and median calculations for the three analysed variables across all seven regions, as indicated by intra-class correlation coefficients ranging from 0.44 to 0.95 for the mean and 0.54 to 0.97 for the median, and coefficients of variation ranging from 5 to 20% for the mean and 3 to 23% for the median. Selecting the median value of three repeated trials yielded slightly more reliable results than the mean. Conclusions These findings indicate that the TekScan MatScan® system demonstrates generally moderate to good reliability.

  13. Universal COI primers for DNA barcoding amphibians.

    Science.gov (United States)

    Che, Jing; Chen, Hong-Man; Yang, Jun-Xiao; Jin, Jie-Qiong; Jiang, Ke; Yuan, Zhi-Yong; Murphy, Robert W; Zhang, Ya-Ping

    2012-03-01

    DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.

  14. DNA barcoding of clinically relevant Cunninghamella species

    NARCIS (Netherlands)

    Yu, Jin; Walther, G; Van Diepeningen, A D; Gerrits Van Den Ende, A H G; Li, Ruo-Yu; Moussa, T A A; Almaghrabi, O A; De Hoog, G S

    2015-01-01

    Mucormycosis caused, in part, by representatives of the genus Cunninghamella is a severe infection with high mortality in patients with impaired immunity. Several species have been described in the literature as etiologic agents. A DNA barcoding study using ITS rDNA and tef-1α provided concordance o

  15. Evaluation of a Backpack-Mounted 3D Mobile Scanning System

    Directory of Open Access Journals (Sweden)

    Helge A. Lauterbach

    2015-10-01

    Full Text Available Recently, several backpack-mounted systems, also known as personal laser scanning systems, have been developed. They consist of laser scanners or cameras that are carried by a human operator to acquire measurements of the environment while walking. These systems were first designed to overcome the challenges of mapping indoor environments with doors and stairs. While the human operator inherently has the ability to open doors and to climb stairs, the flexible movements introduce irregularities of the trajectory to the system. To compete with other mapping systems, the accuracy of these systems has to be evaluated. In this paper, we present an extensive evaluation of our backpack mobile mapping system in indoor environments. It is shown that the system can deal with the normal human walking motion, but has problems with irregular jittering. Moreover, we demonstrate the applicability of the backpack in a suitable urban scenario.

  16. An experimental evaluation method for the performance of a laser line scanning system with multiple sensors

    Science.gov (United States)

    Tian, Qingguo; Yang, Yujie; Zhang, Xiangyu; Ge, Baozhen

    2014-01-01

    Laser line scanning 3D digitising systems have a wide range of applications. Their working performance is mainly determined by the system calibration procedure and is also affected by the working conditions, CCD camera imperfections, and object surface optical characteristics. Therefore, a comprehensive evaluation of working performance is necessary before and during use. This study proposes an experimental method for the performance evaluation of a laser line scanner (LLS) with 8 scanning sensors developed in our laboratory. This method first obtains the dense point clouds of standard parts composed of disks, cylinders, and squares. Next, the single-layer point clouds located in horizontal planes of different heights are fitted using the least squares method to obtain the enclosed contours S. Three parameters, namely, the standard deviation of the distance distribution between points and S, the mean distance of the distance distribution, and the shape feature sizes, are used to evaluate the performance. The proposed method evaluates both the scanner as a whole and each scanning sensor. Using this method, more comprehensive information can be acquired to evaluate the scanner performance. The experimental results show that the absolute dimension size error and relative error are less than 5 mm and 3%, respectively, and the relative shape error is less than 2%; therefore, the evaluated LLS system can meet the requirements for human anthropometry applications. Although each scanning sensor has different random and systematic error, these errors are the function of measurement depth. These conclusions are helpful for the further use of this scanner system and can be utilised to optimise this LLS system further.

  17. Four-point probe electrical resistivity scanning system for large area conductivity and activation energy mapping.

    Science.gov (United States)

    Shimanovich, Klimentiy; Bouhadana, Yaniv; Keller, David A; Rühle, Sven; Anderson, Assaf Y; Zaban, Arie

    2014-05-01

    The electrical properties of metal oxides play a crucial role in the development of new photovoltaic (PV) systems. Here we demonstrate a general approach for the determination and analysis of these properties in thin films of new metal oxide based PV materials. A high throughput electrical scanning system, which facilitates temperature dependent measurements at different atmospheres for highly resistive samples, was designed and constructed. The instrument is capable of determining conductivity and activation energy values for relatively large sample areas, of about 72 × 72 mm(2), with the implementation of geometrical correction factors. The efficiency of our scanning system was tested using two different samples of CuO and commercially available Fluorine doped tin oxide coated glass substrates. Our high throughput tool was able to identify the electrical properties of both resistive metal oxide thin film samples with high precision and accuracy. The scanning system enabled us to gain insight into transport mechanisms with novel compositions and to use those insights to make smart choices when choosing materials for our multilayer thin film all oxide photovoltaic cells.

  18. Laser cutting of irregular shape object based on stereo vision laser galvanometric scanning system

    Science.gov (United States)

    Qi, Li; Zhang, Yixin; Wang, Shun; Tang, Zhiqiang; Yang, Huan; Zhang, Xuping

    2015-05-01

    Irregular shape objects with different 3-dimensional (3D) appearances are difficult to be shaped into customized uniform pattern by current laser machining approaches. A laser galvanometric scanning system (LGS) could be a potential candidate since it can easily achieve path-adjustable laser shaping. However, without knowing the actual 3D topography of the object, the processing result may still suffer from 3D shape distortion. It is desirable to have a versatile auxiliary tool that is capable of generating 3D-adjusted laser processing path by measuring the 3D geometry of those irregular shape objects. This paper proposed the stereo vision laser galvanometric scanning system (SLGS), which takes the advantages of both the stereo vision solution and conventional LGS system. The 3D geometry of the object obtained by the stereo cameras is used to guide the scanning galvanometers for 3D-shape-adjusted laser processing. In order to achieve precise visual-servoed laser fabrication, these two independent components are integrated through a system calibration method using plastic thin film target. The flexibility of SLGS has been experimentally demonstrated by cutting duck feathers for badminton shuttle manufacture.

  19. Temporal subtraction system on torso FDG-PET scans based on statistical image analysis

    Science.gov (United States)

    Shimizu, Yusuke; Hara, Takeshi; Fukuoka, Daisuke; Zhou, Xiangrong; Muramatsu, Chisako; Ito, Satoshi; Hakozaki, Kenta; Kumita, Shin-ichiro; Ishihara, Kei-ichi; Katafuchi, Tetsuro; Fujita, Hiroshi

    2013-02-01

    Diagnostic imaging on FDG-PET scans was often used to evaluate chemotherapy results of cancer patients. Radiologists compare the changes of lesions' activities between previous and current examinations for the evaluation. The purpose of this study was to develop a new computer-aided detection (CAD) system with temporal subtraction technique for FDGPET scans and to show the fundamental usefulness based on an observer performance study. Z-score mapping based on statistical image analysis was newly applied to the temporal subtraction technique. The subtraction images can be obtained based on the anatomical standardization results because all of the patients' scans were deformed into standard body shape. An observer study was performed without and with computer outputs to evaluate the usefulness of the scheme by ROC (receiver operating characteristics) analysis. Readers responded as confidence levels on a continuous scale from absolutely no change to definitely change between two examinations. The recognition performance of the computer outputs for the 43 pairs was 96% sensitivity with 31.1 false-positive marks per scan. The average of area-under-the-ROC-curve (AUC) from 4 readers in the observer performance study was increased from 0.85 without computer outputs to 0.90 with computer outputs (p=0.0389, DBM-MRMC). The average of interpretation time was slightly decreased from 42.11 to 40.04 seconds per case (p=0.625, Wilcoxon test). We concluded that the CAD system for torso FDG-PET scans with temporal subtraction technique might improve the diagnostic accuracy of radiologist in cancer therapy evaluation.

  20. Study on the parameters of the scanning system for the 300 keV electron accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Leo, K. W.; Chulan, R. M., E-mail: leo@nm.gov.my; Hashim, S. A.; Baijan, A. H.; Sabri, R. M.; Mohtar, M.; Glam, H.; Lojius, L.; Zahidee, M.; Azman, A.; Zaid, M. [Malaysian Nuclear Agency, Bangi, 43000 Kajang. Selangor (Malaysia)

    2016-01-22

    This paper describes the method to identify the magnetic coil parameters of the scanning system. This locally designed low energy electron accelerator with the present energy of 140 keV will be upgraded to 300 keV. In this accelerator, scanning system is required to deflect the energetic electron beam across a titanium foil in vertical and horizontal direction. The excitation current of the magnetic coil is determined by the energy of the electron beam. Therefore, the magnetic coil parameters must be identified to ensure the matching of the beam energy and excitation coil current. As the result, the essential parameters of the effective lengths for X-axis and Y-axis have been found as 0.1198 m and 0.1134 m and the required excitation coil currents which is dependenton the electron beam energies have be identified.

  1. [Hyperspectral acquisition system for tongue inspection based on X-Y scanning galvanometer].

    Science.gov (United States)

    Li, Gang; Zhao, Jing; Lin, Ling; Zhang, Bao-ju

    2011-12-01

    Hyperspectral was used for tongue inspection in the present work to resolve the problem that information of current research for tongue inspection was inadequate. A hyperspectral acquisition system based on X-Y scanning galvanometer was also proposed due to the high cost of the current hyperspectral apparatus. An experiment was made to test the ability of this system. By collecting the hyperspectral information of color pictures with size similar to the tongue, the results of experiment showed that this system can acquire more information of tongue than other methods, and this method can provide a new way for tongue inspection.

  2. Design & Reality of CAD/CAM in Laser Beam Scanning Manufacturing System

    Institute of Scientific and Technical Information of China (English)

    SUN Jianjun; SUN Huilai; ZHAO Fangfang; LIN Shuzhong; QI Xiangyang

    2006-01-01

    In laser beam scanning manufacturing (LSM) system the PLT file was adopted as design file. The data of design file were processed by CAD software programmed. And the control model was adopted DEA control model. The DEA model was concerned with not only the distance of the two swaying mirrors, the distance between the swaying mirror and convex lens, the mirror swaying angle and the lens focal length but also the lens central height, the lens convex radius and the medium refractive index. It improved the precision and reduced the error in LBM system. The application of CAD/CAM system in LSM improved the LSM manufacturing velocity and manufacturing quality.

  3. Accuracy of optical scanning methods of the Cerec®3D system in the process of making ceramic inlays

    Directory of Open Access Journals (Sweden)

    Trifković Branka

    2010-01-01

    Full Text Available Background/Aim. One of the results of many years of Cerec® 3D CAD/CAM system technological development is implementation of one intraoral and two extraoral optical scanning methods which, depending on the current indications, are applied in making fixed restorations. The aim of this study was to determine the degree of precision of optical scanning methods by the use of the Cerec®3D CAD/CAM system in the process of making ceramic inlays. Methods. The study was conducted in three experimental groups of inlays prepared using the procedure of three methods of scanning Cerec ®3D system. Ceramic inlays made by conventional methodology were the control group. The accuracy of optical scanning methods of the Cerec®3D system computer aided designcomputer aided manufacturing (CAD/CAM was indirectly examined by measuring a marginal gap size between inlays and demarcation preparation by scanning electron microscope (SEM. Results. The results of the study showed a difference in the accuracy of the existing methods of scanning dental CAD/CAM systems. The highest level of accuracy was achieved by the extraoral optical superficial scanning technique. The value of marginal gap size inlays made with the technique of extraoral optical superficial scanning was 32.97 ± 13.17 μ. Techniques of intraoral optical superficial and extraoral point laser scanning showed a lower level of accuracy (40.29 ± 21.46 μ for inlays of intraoral optical superficial scanning and 99.67 ± 37.25 μ for inlays of extraoral point laser scanning. Conclusion. Optical scanning methods in dental CAM/CAM technologies are precise methods of digitizing the spatial models; application of extraoral optical scanning methods provides the hightest precision.

  4. Characterization of Anabaena cylindrica Solution System Using Synchronous- Scan Fluorescence Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    LIU Xian-li; DENG Nan-sheng; TAO Shu

    2005-01-01

    The characterization of the algae Anabaena cylindrica solu tion with Fe (Ⅲ) was investigated using fluorescence emission and syn chronous-scan spectroscopy. The ranges of concentrations of algae and Fe (Ⅲ) in aqueous solutions were 5. 0 × 107-2. 5 × 108 cell/L and 10-60μmol/L, respectively. The effective characterization method used was synchronous-scan fluorescence spectroscopy (SFS). The wavelength difference (△λ) of 90 nm was maintained between excitation wavelength (λex) and emission wavelength(λem ). The peak was observed at about λex 236 nm/λem 326 nm for synchronous-scan fluorescence spectroscopy. The fluorescence quenching in system of algae-Fe( Ⅲ)-HA was studied using synchronous-scan spectroscopy for the first time. Fe(Ⅲ) was clearly the effective quencher. The relationship between I0 / I (quenching efficiency)and c (concentration of Fe (Ⅲ) added) was a linear correlation for the al gae solution with Fe(Ⅲ). Also, Aldrich humic acid (HA) was found to be an effective quencher.

  5. Compact Multipurpose Mobile Laser Scanning System — Initial Tests and Results

    Directory of Open Access Journals (Sweden)

    Craig Glennie

    2013-01-01

    Full Text Available We describe a prototype compact mobile laser scanning system that may be operated from a backpack or unmanned aerial vehicle. The system is small, self-contained, relatively inexpensive, and easy to deploy. A description of system components is presented, along with the initial calibration of the multi-sensor platform. The first field tests of the system, both in backpack mode and mounted on a helium balloon for real-world applications are presented. For both field tests, the acquired kinematic LiDAR data are compared with highly accurate static terrestrial laser scanning point clouds. These initial results show that the vertical accuracy of the point cloud for the prototype system is approximately 4 cm (1σ in balloon mode, and 3 cm (1σ in backpack mode while horizontal accuracy was approximately 17 cm (1σ for the balloon tests. Results from selected study areas on the Sacramento River Delta and San Andreas Fault in California demonstrate system performance, deployment agility and flexibility, and potential for operational production of high density and highly accurate point cloud data. Cost and production rate trade-offs place this system in the niche between existing airborne and tripod mounted LiDAR systems.

  6. Design of a MEMS-based retina scanning system for biometric authentication

    Science.gov (United States)

    Woittennek, Franziska; Knobbe, Jens; Pügner, Tino; Schelinski, Uwe; Grüger, Heinrich

    2014-05-01

    There is an increasing need for reliable authentication for a number of applications such as e commerce. Common authentication methods based on ownership (ID card) or knowledge factors (password, PIN) are often prone to manipulations and may therefore be not safe enough. Various inherence factor based methods like fingerprint, retinal pattern or voice identifications are considered more secure. Retina scanning in particular offers both low false rejection rate (FRR) and low false acceptance rate (FAR) with about one in a million. Images of the retina with its characteristic pattern of blood vessels can be made with either a fundus camera or laser scanning methods. The present work describes the optical design of a new compact retina laser scanner which is based on MEMS (Micro Electric Mechanical System) technology. The use of a dual axis micro scanning mirror for laser beam deflection enables a more compact and robust design compared to classical systems. The scanner exhibits a full field of view of 10° which corresponds to an area of 4 mm2 on the retinal surface surrounding the optical disc. The system works in the near infrared and is designed for use under ambient light conditions, which implies a pupil diameter of 1.5 mm. Furthermore it features a long eye relief of 30 mm so that it can be conveniently used by persons wearing glasses. The optical design requirements and the optical performance are discussed in terms of spot diagrams and ray fan plots.

  7. Bore-Sight Calibration of Multiple Laser Range Finders for Kinematic 3D Laser Scanning Systems

    Directory of Open Access Journals (Sweden)

    Jaehoon Jung

    2015-05-01

    Full Text Available The Simultaneous Localization and Mapping (SLAM technique has been used for autonomous navigation of mobile systems; now, its applications have been extended to 3D data acquisition of indoor environments. In order to reconstruct 3D scenes of indoor space, the kinematic 3D laser scanning system, developed herein, carries three laser range finders (LRFs: one is mounted horizontally for system-position correction and the other two are mounted vertically to collect 3D point-cloud data of the surrounding environment along the system’s trajectory. However, the kinematic laser scanning results can be impaired by errors resulting from sensor misalignment. In the present study, the bore-sight calibration of multiple LRF sensors was performed using a specially designed double-deck calibration facility, which is composed of two half-circle-shaped aluminum frames. Moreover, in order to automatically achieve point-to-point correspondences between a scan point and the target center, a V-shaped target was designed as well. The bore-sight calibration parameters were estimated by a constrained least squares method, which iteratively minimizes the weighted sum of squares of residuals while constraining some highly-correlated parameters. The calibration performance was analyzed by means of a correlation matrix. After calibration, the visual inspection of mapped data and residual calculation confirmed the effectiveness of the proposed calibration approach.

  8. A LOW BUDGET MOBILE LASER SCANNING SOLUTION USING ON BOARD SENSORS AND FIELD BUS SYSTEMS OF TODAY'S CONSUMER AUTOMOBILES

    Directory of Open Access Journals (Sweden)

    D. M. M. Vock

    2012-09-01

    Full Text Available Mobile laser scanning systems (MLS offer a great potential for acquiring detailed point cloud data of urban and suburban surroundings with minimum effort. In this paper a new solution for MLSs is presented, requiring solely a combination of a profile laser scanning device and systems that are included in today's serialized end consumer vehicles. While today's mobile laser scan systems require different and expensive additional hardware that needs to be mounted onto the vehicle, the devices included within vehicle electronics offer good alternatives without additional costs.The actual scan consists of a continuous profile scan together with information gathered from on-board sensor modules. In a post- processing step, the sensor data is used to reconstruct the car's trajectory for the period of the scan and, based on this information, the track of the scan device for every measured laser pixel. Synchronization of pixel data and vehicle movement is realized via a timestamp signal which is transmitted to the car's field bus system and the scan device. To generate the final point cloud scenario, the trajectory is interpolated for every single scan point and used to convert its local position within the profile into the global coordinate system (Fig.1, Left.

  9. The CNAO dose delivery system for modulated scanning ion beam radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Giordanengo, S.; Marchetto, F. [Istituto Nazionale di Fisica Nucleare, Section of Torino, Torino 10125 (Italy); Garella, M. A.; Donetti, M. [Istituto Nazionale di Fisica Nucleare, Section of Torino, Torino 10125, Italy and Centro Nazionale Adroterapia Oncologica, Pavia 27100 (Italy); Bourhaleb, F.; Monaco, V.; Hosseini, M. A.; Peroni, C.; Sacchi, R.; Cirio, R. [Istituto Nazionale di Fisica Nucleare, Section of Torino, Torino 10125, Italy and Physics Department, University of Torino, Torino 10125 (Italy); Ciocca, M.; Mirandola, A. [Centro Nazionale Adroterapia Oncologica, Pavia 27100 (Italy)

    2015-01-15

    Purpose: This paper describes the system for the dose delivery currently used at the Centro Nazionale di Adroterapia Oncologica (CNAO) for ion beam modulated scanning radiotherapy. Methods: CNAO Foundation, Istituto Nazionale di Fisica Nucleare and University of Torino have designed, built, and commissioned a dose delivery system (DDS) to monitor and guide ion beams accelerated by a dedicated synchrotron and to distribute the dose with a full 3D scanning technique. Protons and carbon ions are provided for a wide range of energies in order to cover a sizable span of treatment depths. The target volume, segmented in several layers orthogonally to the beam direction, is irradiated by thousands of pencil beams which must be steered and held to the prescribed positions until the prescribed number of particles has been delivered. For the CNAO beam lines, these operations are performed by the DDS. The main components of this system are two independent beam monitoring detectors, called BOX1 and BOX2, interfaced with two control systems performing the tasks of real-time fast and slow control, and connected to the scanning magnets and the beam chopper. As a reaction to any condition leading to a potential hazard, a DDS interlock signal is sent to the patient interlock system which immediately stops the irradiation. The essential tasks and operations performed by the DDS are described following the data flow from the treatment planning system through the end of the treatment delivery. Results: The ability of the DDS to guarantee a safe and accurate treatment was validated during the commissioning phase by means of checks of the charge collection efficiency, gain uniformity of the chambers, and 2D dose distribution homogeneity and stability. A high level of reliability and robustness has been proven by three years of system activity needing rarely more than regular maintenance and working with 100% uptime. Four identical and independent DDS devices have been tested showing

  10. Design and Development of a Scanning Airborne Direct Detection Doppler Lidar System

    Science.gov (United States)

    Gentry, Bruce; McGill, Matthew; Schwemmer, Geary; Hardesty, Michael; Brewer, Alan; Wilkerson, Thomas; Atlas, Robert; Sirota, Marcos; Lindemann, Scott

    2006-01-01

    In the fall of 2005 we began developing an airborne scanning direct detection molecular Doppler lidar. The instrument is being built as part of the Tropospheric Wind Lidar Technology Experiment (TWiLiTE), a three year project selected by the NASA Earth Sun Technology Office under the Instrument Incubator Program. The TWiLiTE project is a collaboration involving scientists and engineers from NASA Goddard Space Flight Center, NOAA ESRL, Utah State University Space Dynamics Lab, Michigan Aerospace Corporation and Sigma Space Corporation. The TWiLiTE instrument will leverage significant research and development investments made by NASA Goddard and it's partners in the past several years in key lidar technologies and sub-systems (lasers, telescopes, scanning systems, detectors and receivers) required to enable spaceborne global wind lidar measurement. These sub-systems will be integrated into a complete molecular direct detection Doppler wind lidar system designed for autonomous operation on a high altitude aircraft, such as the NASA WB57. The WB57 flies at an altitude of 18 km and from this vantage point the nadir viewing Doppler lidar will be able to profile winds through the full troposphere. The TWiLiTE integrated airborne Doppler lidar instrument will be the first demonstration of a airborne scanning direct detection Doppler lidar and will serve as a critical milestone on the path to a future spaceborne tropospheric wind system. In addition to being a technology testbed for space based tropospheric wind lidar, when completed the TWiLiTE high altitude airborne lidar will be used for studying mesoscale dynamics and storm research (e.g. winter storms, hurricanes) and could be used for calibration and validation of satellite based wind systems such as ESA's Aeolus Atmospheric Dynamics Mission. The TWiLiTE Doppler lidar will have the capability to profile winds in clear air from the aircraft altitude of 18 km to the surface with 250 m vertical resolution and < 2mls

  11. Validation of a three-dimensional facial scanning system based on structured light techniques.

    Science.gov (United States)

    Ma, Lili; Xu, Tianmin; Lin, Jiuxiang

    2009-06-01

    The aim of this study was to validate a newly developed three-dimensional (3D) structured light scanning system in recording the facial morphology. The validation was performed in three aspects including accuracy, precision and reliability. The accuracy and precision were investigated using a plaster model with 19 marked landmarks. The accuracy was determined by comparing the coordinates from the 3D images and from the coordinates measure machine (CMM). The precision was quantified through the repeated landmarks location on 3D images. The reliability was investigated in 10 adult volunteers. Each was scanned five times in 3 weeks. The 3D images acquired at different times were compared with each other to measure the reliability. We found that the accuracy was 0.93 mm, the precision was 0.79 mm, the reliability was 0.2mm. These findings suggested that the structured light scanning system was accurate, precise and reliable to record the facial morphology for both clinic and research purposes.

  12. A Flexile and High Precision Calibration Method for Binocular Structured Light Scanning System

    Directory of Open Access Journals (Sweden)

    Jianying Yuan

    2014-01-01

    Full Text Available 3D (three-dimensional structured light scanning system is widely used in the field of reverse engineering, quality inspection, and so forth. Camera calibration is the key for scanning precision. Currently, 2D (two-dimensional or 3D fine processed calibration reference object is usually applied for high calibration precision, which is difficult to operate and the cost is high. In this paper, a novel calibration method is proposed with a scale bar and some artificial coded targets placed randomly in the measuring volume. The principle of the proposed method is based on hierarchical self-calibration and bundle adjustment. We get initial intrinsic parameters from images. Initial extrinsic parameters in projective space are estimated with the method of factorization and then upgraded to Euclidean space with orthogonality of rotation matrix and rank 3 of the absolute quadric as constraint. Last, all camera parameters are refined through bundle adjustment. Real experiments show that the proposed method is robust, and has the same precision level as the result using delicate artificial reference object, but the hardware cost is very low compared with the current calibration method used in 3D structured light scanning system.

  13. A Portable Airborne Scanning Lidar System for Ocean and Coastal Applications

    Science.gov (United States)

    2009-06-26

    2009 R E I N E M A N E T A L . 2633 passenger ferry, as it crossed the San Pedro Channel from Catalina Island to Long Beach, California. Wind speed at...and water vapor fluxes. With the airborne lidar system, we measured the wave field around the island and in the lagoon, with the goal of testing the...wave field of Lady Elliot Island in Australia’s Great Barrier Reef were measured with the air- borne scanning lidar system on eight research flights in

  14. Application of information theory to the design of line-scan imaging systems

    Science.gov (United States)

    Huck, F. O.; Park, S. K.; Halyo, N.; Stallman, S.

    1981-01-01

    Information theory is used to formulate a single figure of merit for assessing the performance of line scan imaging systems as a function of their spatial response (point spread function or modulation transfer function), sensitivity, sampling and quantization intervals, and the statistical properties of a random radiance field. Computational results for the information density and efficiency (i.e., the ratio of information density to data density) are intuitively satisfying and compare well with experimental and theoretical results obtained by earlier investigators concerned with the performance of TV systems.

  15. Foveated scanning: dynamic monodimensional enlargement of resolved field of view in lenses of scanner systems.

    Science.gov (United States)

    Javaherian, Farhang; Rashidian, Bizhan

    2016-09-10

    An inconsistency between the circular symmetric geometry of conventional optical imagers and the geometry of long linear sensors used in today's line-scan cameras results in suboptimal separate design of optics and electronics of scanner systems. Based on the method of foveated optical imaging, a technique named foveated scanning (FS) is proposed in this paper. The FS technique is employed to enlarge the one-dimensional resolved field of view (RFOV) of conventional lenses and permits optimized performance on a line-of-interest in the image plane where the optoelectronic sensor is located. The achieved enlargement of RFOV is verified on a proof-of-concept basic telephoto lens. Both modulation transfer function analysis and the imaging simulation of a standard target have been performed. Results show a twofold increase in RFOV by this technique.

  16. Thermal characterization of starch-water system by photopyroelectric technique and adiabatic scanning calorimetry

    Science.gov (United States)

    Cruz-Orea, A.; Bentefour, E. H.; Jamée, P.; Chirtoc, M.; Glorieux, C.; Pitsi, G.; Thoen, J.

    2003-01-01

    Starch is one of the most important carbohydrate sources in human nutrition. For the thermal analysis of starch, techniques such as differential scanning calorimetry have been extensively used. As an alternative, we have applied a photopyroelectric (PPE) configuration and adiabatic scanning calorimetry (ASC) to study the thermal properties of starch-water systems. For this study we used nixtamalized corn flour and potato starch with different quantities of distilled water, in order to obtain samples with different moisture content. By using PPE and ASC methods we have measured, for each technique separately, the heat capacity by unit volume (ρcp) at room temperature for a corn flour sample at 90% moisture. The obtained values agree within experimental uncertainty. By using these techniques we also studied the thermal behavior of potato starch, at 80% moisture, in the temperature range where phase transitions occur. In this case the PPE signal phase could be used as a sensitive and versatile monitor for phase transitions.

  17. Aberration analysis based on pinhole-z-scan method near the focal point of refractive systems

    Science.gov (United States)

    Castro-Marín, Pablo; Garduño-Mejía, Jesús; Rosete-Aguilar, Martha; Bruce, Neil C.; Reid, Derryck T.; Farrell, C.; Sandoval-Romero, Gabriel E.

    2016-09-01

    In this work we present a method used to study the spherical and chromatic aberrations contribution near the focal point of a refractive optical system. The actual focal position is measured by scanning a pinhole attached on the front of a power detector, which are scanned along the optical axis using a motorized stage with 1 μm resolution. Spherical aberration contribution was analyzed by changing the pupil aperture, by modifying the size of the input iris diaphragm and for each case, measuring the actual laser power vs the detector position. Chromatic aberration was analyzed by performing the same procedure but in this case we used an ultra-broad-band femtosecond laser. The results between ML and CW operation were compare. Experimental results are presented.

  18. Identifying Canadian freshwater fishes through DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Nicolas Hubert

    Full Text Available BACKGROUND: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. METHODOLOGY/PRINCIPAL FINDINGS: We bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%. Most species were represented by multiple individuals (7.6 on average, the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases. The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. CONCLUSIONS/SIGNIFICANCE: The present study evidenced that freshwater fish

  19. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

    Directory of Open Access Journals (Sweden)

    Nuttika Suwannasai

    Full Text Available Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI, we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1 Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2 Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3 Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in

  20. Current advances of DNA barcoding study in plants

    OpenAIRE

    Shuping Ning; Haifei Yan; Gang Hao; Xuejun Ge

    2008-01-01

    DNA barcoding has become one of hotspots of biodiversity research in the last five years. It is a method of rapid and accurate species identification and recognition using a short, standardized DNA region. DNA barcoding is now well established for animals, using a portion of the mitochondrial cytochrome c oxidase subunit 1 (COI or cox1) as the standard universal barcode. However, in plants, progress has been hampered by slow substitution rates in mitochondrial DNA. A number of different chlor...

  1. Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

    Directory of Open Access Journals (Sweden)

    Lobet Guillaume

    2013-01-01

    Full Text Available Abstract This paper presents an original spit-and-combine imaging procedure that enables the complete vectorization of complex root systems grown in rhizotrons. The general principle of the method is to (1 separate the root system into a small number of large pieces to reduce root overlap, (2 scan these pieces one by one, (3 analyze separate images with a root tracing software and (4 combine all tracings into a single vectorized root system. This method generates a rich dataset containing morphological, topological and geometrical information of entire root systems grown in rhizotrons. The utility of the method is illustrated with a detailed architectural analysis of a 20-day old maize root system, coupled with a spatial analysis of water uptake patterns.

  2. The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Indra Neil Sarkar

    Full Text Available With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence-based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form--often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG of the Consortium for the Barcode of Life (CBOL, the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum.

  3. Advance in Researches on DNA Barcoding%植物DNA条形码研究进展

    Institute of Scientific and Technical Information of China (English)

    鲁松

    2012-01-01

    DNA barcoding is a new life identification system which can distinguish species rapidly and accurately by analyzing standard short and easy amplying DNA sequences with enough variation.In order to promote the development of domestic studies in plant DNA barcoding and taxonomy,this paper deals with DNA barcoding screening,application,present studying status in China,challenges and future prospects for plant DNA barcoding development.%DNA条形码技术是利用标准的、具有足够变异的、易扩增且相对较短的DNA片段在物种内的特异性和种间的多样性而创建的一种新的生物身份识别系统,从而实现对物种的快速自动鉴定。本文从植物DNA条形码的开发、应用、国内研究现状、植物DNA条形码面临的挑战以及发展前景等进行了综合分析,以期推动我国植物DNA条形码和分类学研究的发展。

  4. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae

    Directory of Open Access Journals (Sweden)

    Nerea eLarranaga

    2015-07-01

    Full Text Available The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra and A. purpurea and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia and in an interspecific hybrid (A. cherimola x A. squamosa. The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.

  5. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae).

    Science.gov (United States)

    Larranaga, Nerea; Hormaza, José I

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.

  6. Scanning laser optical computed tomography system for large volume 3D dosimetry

    Science.gov (United States)

    Dekker, Kurtis H.; Battista, Jerry J.; Jordan, Kevin J.

    2017-04-01

    Stray light causes artifacts in optical computed tomography (CT) that negatively affect the accuracy of radiation dosimetry in gels or solids. Scatter effects are exacerbated by a large dosimeter volume, which is desirable for direct verification of modern radiotherapy treatment plans such as multiple-isocenter radiosurgery. The goal in this study was to design and characterize an optical CT system that achieves high accuracy primary transmission measurements through effective stray light rejection, while maintaining sufficient scan speed for practical application. We present an optical imaging platform that uses a galvanometer mirror for horizontal scanning, and a translation stage for vertical movement of a laser beam and small area detector for minimal stray light production and acceptance. This is coupled with a custom lens-shaped optical CT aquarium for parallel ray sampling of projections. The scanner images 15 cm diameter, 12 cm height cylindrical volumes at 0.33 mm resolution in approximately 30 min. Attenuation coefficients reconstructed from CT scans agreed with independent cuvette measurements within 2% for both absorbing and scattering solutions as well as small 1.25 cm diameter absorbing phantoms placed within a large, scattering medium that mimics gel. Excellent linearity between the optical CT scanner and the independent measurement was observed for solutions with between 90% and 2% transmission. These results indicate that the scanner should achieve highly accurate dosimetry of large volume dosimeters in a reasonable timeframe for clinical application to radiotherapy dose verification procedures.

  7. Scanning laser optical computed tomography system for large volume 3D dosimetry.

    Science.gov (United States)

    Dekker, Kurtis H; Battista, Jerry J; Jordan, Kevin J

    2017-04-07

    Stray light causes artifacts in optical computed tomography (CT) that negatively affect the accuracy of radiation dosimetry in gels or solids. Scatter effects are exacerbated by a large dosimeter volume, which is desirable for direct verification of modern radiotherapy treatment plans such as multiple-isocenter radiosurgery. The goal in this study was to design and characterize an optical CT system that achieves high accuracy primary transmission measurements through effective stray light rejection, while maintaining sufficient scan speed for practical application. We present an optical imaging platform that uses a galvanometer mirror for horizontal scanning, and a translation stage for vertical movement of a laser beam and small area detector for minimal stray light production and acceptance. This is coupled with a custom lens-shaped optical CT aquarium for parallel ray sampling of projections. The scanner images 15 cm diameter, 12 cm height cylindrical volumes at 0.33 mm resolution in approximately 30 min. Attenuation coefficients reconstructed from CT scans agreed with independent cuvette measurements within 2% for both absorbing and scattering solutions as well as small 1.25 cm diameter absorbing phantoms placed within a large, scattering medium that mimics gel. Excellent linearity between the optical CT scanner and the independent measurement was observed for solutions with between 90% and 2% transmission. These results indicate that the scanner should achieve highly accurate dosimetry of large volume dosimeters in a reasonable timeframe for clinical application to radiotherapy dose verification procedures.

  8. A high-resolution pointing system for fast scanning platforms: The EBEX example

    CERN Document Server

    Didier, Joy; Aboobaker, Asad; Araujo, Derek; Grainger, Will; Hanany, Shaul; Helson, Kyle; Hillbrand, Seth; Korotkov, Andrei; Limon, Michele; Miller, Amber; Reichborn-Kjennerud, Britt; Sagiv, Ilan; Tucker, Greg; Vinokurov, Yuri

    2016-01-01

    The E and B experiment (EBEX) is a balloon-borne telescope designed to measure the polarization of the cosmic microwave background with 8' resolution employing a gondola scanning with speeds of order degree per second. In January 2013, EBEX completed 11 days of observations in a flight over Antarctica covering $\\sim$ 6000 square degrees of the sky. The payload is equipped with two redundant star cameras and two sets of three orthogonal gyroscopes to reconstruct the telescope attitude. The EBEX science goals require the pointing to be reconstructed to approximately 10" in the map domain, and in-flight attitude control requires the real time pointing to be accurate to $\\sim$ 0.5$^{\\circ}$ . The high velocity scan strategy of EBEX coupled to its float altitude only permits the star cameras to take images at scan turnarounds, every $\\sim$ 40 seconds, and thus requires the development of a pointing system with low noise gyroscopes and carefully controlled systematic errors. Here we report on the design of the poin...

  9. MEMS scanner mirror based system for retina scanning and in eye projection

    Science.gov (United States)

    Woittennek, Franziska; Knobbe, Jens; Pügner, Tino; Dallmann, Hans-Georg; Schelinski, Uwe; Grüger, Heinrich

    2015-02-01

    Many applications could benefit from miniaturized systems to scan blood vessels behind the retina in the human eye, so called "retina scanning". This reaches from access control to sophisticated security applications and medical devices. High volume systems for consumer applications require low cost and a user friendly operation. For example this includes no need for removal of glasses and self-adjustment, in turn guidance of focus and point of attraction by simultaneous projection for the user. A new system has been designed based on the well-known resonantly driven 2-d scanner mirror of Fraunhofer IPMS. A combined NIR and VIS laser system illuminates the eye through an eye piece designed for an operating distance allowing the use of glasses and granting sufficient field of view. This usability feature was considered to be more important than highest miniaturization. The modulated VIS laser facilitates the projection of an image directly onto the retina. The backscattered light from the continuous NIR laser contains the information of the blood vessels and is detected by a highly sensitive photo diode. A demonstrational setup has been realized including readout and driving electronics. The laser power was adjusted to an eye-secure level. Additional security features were integrated. Test measurements revealed promising results. In a first demonstration application the detection of biometric pattern of the blood vessels was evaluated for issues authentication in.

  10. MIMIC: An Innovative Methodology for Determining Mobile Laser Scanning System Point Density

    Directory of Open Access Journals (Sweden)

    Conor Cahalane

    2014-08-01

    Full Text Available Understanding how various Mobile Mapping System (MMS laser hardware configurations and operating parameters exercise different influence on point density is important for assessing system performance, which in turn facilitates system design and MMS benchmarking. Point density also influences data processing, as objects that can be recognised using automated algorithms generally require a minimum point density. Although obtaining the necessary point density impacts on hardware costs, survey time and data storage requirements, a method for accurately and rapidly assessing MMS performance is lacking for generic MMSs. We have developed a method for quantifying point clouds collected by an MMS with respect to known objects at specified distances using 3D surface normals, 2D geometric formulae and line drawing algorithms. These algorithms were combined in a system called the Mobile Mapping Point Density Calculator (MIMIC and were validated using point clouds captured by both a single scanner and a dual scanner MMS. Results from MIMIC were promising: when considering the number of scan profiles striking the target, the average error equated to less than 1 point per scan profile. These tests highlight that MIMIC is capable of accurately calculating point density for both single and dual scanner MMSs.

  11. Excitation-scanning hyperspectral imaging system for microscopic and endoscopic applications

    Science.gov (United States)

    Mayes, Sam A.; Leavesley, Silas J.; Rich, Thomas C.

    2016-04-01

    Current microscopic and endoscopic technologies for cancer screening utilize white-light illumination sources. Hyper-spectral imaging has been shown to improve sensitivity while retaining specificity when compared to white-light imaging in both microscopy and in vivo imaging. However, hyperspectral imaging methods have historically suffered from slow acquisition times due to the narrow bandwidth of spectral filters. Often minutes are required to gather a full image stack. We have developed a novel approach called excitation-scanning hyperspectral imaging that provides 2-3 orders of magnitude increased signal strength. This reduces acquisition times significantly, allowing for live video acquisition. Here, we describe a preliminary prototype excitation-scanning hyperspectral imaging system that can be coupled with endoscopes or microscopes for hyperspectral imaging of tissues and cells. Our system is comprised of three subsystems: illumination, transmission, and imaging. The illumination subsystem employs light-emitting diode arrays to illuminate at different wavelengths. The transmission subsystem utilizes a unique geometry of optics and a liquid light guide. Software controls allow us to interface with and control the subsystems and components. Digital and analog signals are used to coordinate wavelength intensity, cycling and camera triggering. Testing of the system shows it can cycle 16 wavelengths at as fast as 1 ms per cycle. Additionally, more than 18% of the light transmits through the system. Our setup should allow for hyperspectral imaging of tissue and cells in real time.

  12. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae using nuclear rDNA expansion segments and DNA barcodes

    Directory of Open Access Journals (Sweden)

    Raupach Michael J

    2010-09-01

    Full Text Available Abstract Background The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous. Results We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97% of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95% of the studied Carabidae. Conclusion Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

  13. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    CERN Document Server

    Bos, E G Patrick; Kitaura, Francisco; Cautun, Marius

    2016-01-01

    We describe the Bayesian BARCODE formalism that has been designed towards the reconstruction of the Cosmic Web in a given volume on the basis of the sampled galaxy cluster distribution. Based on the realization that the massive compact clusters are responsible for the major share of the large scale tidal force field shaping the anisotropic and in particular filamentary features in the Cosmic Web. Given the nonlinearity of the constraints imposed by the cluster configurations, we resort to a state-of-the-art constrained reconstruction technique to find a proper statistically sampled realization of the original initial density and velocity field in the same cosmic region. Ultimately, the subsequent gravitational evolution of these initial conditions towards the implied Cosmic Web configuration can be followed on the basis of a proper analytical model or an N-body computer simulation. The BARCODE formalism includes an implicit treatment for redshift space distortions. This enables a direct reconstruction on the ...

  14. Pharmaceutical applications of confocal laser scanning microscopy: the physical characterisation of pharmaceutical systems.

    Science.gov (United States)

    Pygall, Samuel R; Whetstone, Joanne; Timmins, Peter; Melia, Colin D

    2007-12-10

    The application of confocal laser scanning microscopy (CLSM) to the physicochemical characterisation of pharmaceutical systems is not as widespread as its application within the field of cell biology. However, methods have been developed to exploit the imaging capabilities of CLSM to study a wide range of pharmaceutical systems, including phase-separated polymers, colloidal systems, microspheres, pellets, tablets, film coatings, hydrophilic matrices, and chromatographic stationary phases. Additionally, methods to measure diffusion in gels, bioadhesives, and for monitoring microenvironmental pH change within dosage forms have been utilised. CLSM has also been used in the study of the physical interaction of dosage forms with biological barriers such as the eye, skin and intestinal epithelia, and in particular, to determine the effectiveness of a plethora of pharmaceutical systems to deliver drugs through these barriers. In the future, there is continuing scope for wider exploitation of existing techniques, and continuing advancements in instrumentation.

  15. PCR Amplification System of DNA Barcoding Genes ITS, ITS2 and rbcL from Xanthium%DNA条形码基因ITS·ITS2及rbcL在苍耳属可采用相同的PCR条件

    Institute of Scientific and Technical Information of China (English)

    胡伟毅; 汪连军; 盛志超

    2013-01-01

    [目的]为植物 DNA条形码标准基因筛选研究提供参考,减少植物 DNA条形码研究中的工作量。[方法]对7种苍耳属植物 ITS、ITS2及 rbcL基因采用相同的扩增条件(95℃4 min;[35 cycles:94℃30 s;52℃45 s;72℃45 s];72℃10 min;4℃保存)。[结果]3种DNA条形码基因同时成功扩增。[结论]这说明植物 DNA条形码基因中 ITS、ITS2及 rbcL的PCR条件存在合并可能性。%[Objective] This study aimed to provide reference and reduce the workload for screening standard DNA barcoding genes of plants. [Method] Three DNA bar-coding genes ITS, ITS2 and rbcL were amplified from seven Xanthium species un-der the same PCR condition: PCR amplification was started with initial denaturation at 95 ℃ for 4 min, fol owed by 35 cycles of denaturation at 94 ℃ for 30 s, anneal-ing at 52 ℃ for 45 s, and extension at 72 ℃ for 45 s; the amplification was com-pleted by holding the reaction mixture at 72 ℃ for 10 min to al ow complete exten-sion of PCR, and the PCR products were stored at 4 ℃. [Result] Three DNA bar-coding genes ITS, ITS2 and rbcL were al amplified successful y. [Conclusion] This study indicates that PCR amplification conditions for DNA barcoding genes ITS, ITS2 and rbcL in plants may be consistent.

  16. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    Science.gov (United States)

    Bos, E. G. Patrick; van de Weygaert, Rien; Kitaura, Francisco; Cautun, Marius

    2016-10-01

    We describe the Bayesian \\barcode\\ formalism that has been designed towards the reconstruction of the Cosmic Web in a given volume on the basis of the sampled galaxy cluster distribution. Based on the realization that the massive compact clusters are responsible for the major share of the large scale tidal force field shaping the anisotropic and in particular filamentary features in the Cosmic Web. Given the nonlinearity of the constraints imposed by the cluster configurations, we resort to a state-of-the-art constrained reconstruction technique to find a proper statistically sampled realization of the original initial density and velocity field in the same cosmic region. Ultimately, the subsequent gravitational evolution of these initial conditions towards the implied Cosmic Web configuration can be followed on the basis of a proper analytical model or an N-body computer simulation. The BARCODE formalism includes an implicit treatment for redshift space distortions. This enables a direct reconstruction on the basis of observational data, without the need for a correction of redshift space artifacts. In this contribution we provide a general overview of the the Cosmic Web connection with clusters and a description of the Bayesian BARCODE formalism. We conclude with a presentation of its successful workings with respect to test runs based on a simulated large scale matter distribution, in physical space as well as in redshift space.

  17. Highlighting Astyanax Species Diversity through DNA Barcoding

    Science.gov (United States)

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  18. Adsorbate-induced quantum Hall system probed by scanning tunneling spectroscopy combined with transport measurements

    Energy Technology Data Exchange (ETDEWEB)

    Masutomi, Ryuichi, E-mail: masutomi@phys.s.u-tokyo.ac.jp; Okamoto, Tohru [Department of Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2015-06-22

    An adsorbate-induced quantum Hall system at the cleaved InSb surfaces is investigated in magnetic fields up to 14 T using low-temperature scanning tunneling microscopy and spectroscopy combined with transport measurements. We show that an enhanced Zeeman splitting in the Shubnikov-de Haas oscillations is explained by an exchange enhancement of spin splitting and potential disorder, both of which are obtained from the spatially averaged density of states (DOS). Moreover, the Altshuler–Aronov correlation gap is observed in the spatially averaged DOS at 0 T.

  19. A structured light-based system for scanning subcutaneous tumors in laboratory animals.

    Science.gov (United States)

    Girit, Ibrahim Cem; Jure-Kunkel, Maria; McIntyre, Kim W

    2008-06-01

    Tumor size or volume is often the primary endpoint in preclinical efficacy studies of anticancer drugs. Efficient and accurate measurement of such tumors is crucial to rapid evaluation of novel drug candidates. Currently available techniques for acquiring high-throughput data on tumor volume are time-consuming and prone to various inaccuracies and errors. The laser-scanning technology we describe here provides a convenient, high-throughput system for tumor measurement that reduces interoperator variability and bias while providing automated data collection, processing and analysis.

  20. Detection of gait events using an F-Scan in-shoe pressure measurement system.

    Science.gov (United States)

    Catalfamo, Paola; Moser, David; Ghoussayni, Salim; Ewins, David

    2008-10-01

    A portable system capable of accurate detection of initial contact (IC) and foot off (FO) without adding encumbrance to the subject would be extremely useful in many gait analysis applications. Force platforms represent the gold standard method for determining these events and other methods including foot switches and kinematic data have also been proposed. These approaches, however, present limitations in terms of the number of steps that can be analysed per trial, the portability for outdoor measurements or the information needed beforehand. The purpose of this study was to evaluate the F-Scan((R)) Mobile pressure measurement system when detecting IC and FO. Two methods were used, one was the force detection (FD) in-built algorithm used by F-Scan software and a new area detection (AD) method using the loaded area during the gait cycle. Both methods were tested in ten healthy adults and compared with the detection provided by a kinetic detection (KT) algorithm. The absolute mean differences between KT and FD were (mean+/-standard deviation) 42+/-11 ms for IC and 37+/-11 ms for FO. The absolute mean differences between KT and AD were 22+/-9 ms for IC and 10+/-4 ms for FO. The AD method remained closer to KT detection for all subjects providing sufficiently accurate detection of both events and presenting advantages in terms of portability, number of steps analysed per trial and practicality as to make it a system of choice for gait event detection.

  1. Bilateral control-based compensation for rotation in imaging in scan imaging systems

    Science.gov (United States)

    Tian, Dapeng; Wang, Yutang; Wang, Fuchao; Zhang, Yupeng

    2015-12-01

    Scan imaging systems rely on the rotation of a mirror to scan an image. The rotation in the resulting image must be compensated to prevent information loss. Satisfactory performance of an imaging system is difficult to achieve when employing the methods of mechanical transmission and unilateral tracking control, especially when the system suffers from nonlinear factors, disturbances, and dynamic uncertainties. This paper proposes a compensation method based on bilateral control derived from the field of haptic robots. A two-loop disturbance observer was designed to guarantee that the dynamic characteristics of the motor are close to those of the nominal model. The controllers were designed on the basis of the small gain theorem. Experiments were conducted for a comparison with the traditional unilateral control-based compensation. The comparison showed a reduction of 99.83% in the L2 norm of error, which validates the method. The proposed method improves the accuracy of compensation for rotation in imaging, and demonstrates that bilateral control has feasibility for application in various fields, including photogrammetry.

  2. Historical review and future trends of scanning optical systems for laser-beam printers

    Science.gov (United States)

    Minoura, Kazuo

    1993-12-01

    Flying spot scanning technologies providing a constant velocity were presented in 1963 and in 1969, although the concept of `f-0' was not yet explained definitely. After the middle of the 1970s, laser diodes became worthy of notice and a compact-sized laser beam printer was developed. Along with that development, the `f-0 lens' was defined based on the optical design theory in 1979 and also popular-type `f-0 lenses' were developed through the analytical design method. On the other hand, the author and colleagues worked out the best way of enabling metal light deflectors to apply in a popular-type system in 1984; which means the optical system of `deflection error compensation' with the simple composition including a toric lens. The epoch-making optical system raised the productivity of laser beam printers and also has been providing high-definition image printing. As for recent trends, low-priced and compact- sized printers are expanding their share of the market. The author predicts that future laser scanning technologies will be focused in low-priced and process-simplified printers looking closely into high-definition image quality.

  3. Influence of both angle and position error of pentaprism on accuracy of pentaprism scanning system

    Science.gov (United States)

    Xu, Kun; Han, Sen; Zhang, Qiyuan; Wu, Quanying

    2014-11-01

    Pentaprism scanning system has been widely used in the measurement of large flat and wavefront, based on its property that the deviated beam will have no motion in the pitch direction. But the manufacturing and position errors of pentaprisms will bring error to the measurement and so a good error analysis method is indispensable. In this paper, we propose a new method of building mathematic models of pentaprism and through which the size and angle errors of a pentaprism can be put into the model as parameters. 4 size parameters are selected to determine the size and 11 angle parameters are selected to determine the angles of a pentaprism. Yaw, Roll and Pitch are used to describe the position error of a pentaprism and an autocollimator. A pentaprism scanning system of wavefront test is simulated by ray tracing using matlab. We design a method of separating the constant from the measurement results which will improve the measurement accuracy and analyze the system error by Monte Carlo method. This method is simple, rapid, accurate and convenient for computer programming.

  4. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum.

    Directory of Open Access Journals (Sweden)

    Yan-Yan Guo

    Full Text Available Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper, a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%. Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%, whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%. Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.

  5. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum).

    Science.gov (United States)

    Guo, Yan-Yan; Huang, Lai-Qiang; Liu, Zhong-Jian; Wang, Xiao-Quan

    2016-01-01

    Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.

  6. A hand-held 3D laser scanning with global positioning system of subvoxel precision

    Energy Technology Data Exchange (ETDEWEB)

    Arias, Nestor [GOM, Departamento de Fisica y Geologia, Universidad de Pamplona (Colombia); Meneses, Nestor; Meneses, Jaime [GOTS-CENM, Escuela de Fisica, UIS, Bucaramanga (Colombia); Gharbi, Tijani, E-mail: nesariher@unipamplona.edu.co [Departement D' Optique, FEMTO-ST, 16 Route de Gray, 25030 Besancon (France)

    2011-01-01

    In this paper we propose a hand-held 3D laser scanner composed of an optical head device to extract 3D local surface information and a stereo vision system with subvoxel precision to measure the position and orientation of the 3D optical head. The optical head is manually scanned over the surface object by the operator. The orientation and position of the 3D optical head is determined by a phase-sensitive method using a 2D regular intensity pattern. This phase reference pattern is rigidly fixed to the optical head and allows their 3D location with subvoxel precision in the observation field of the stereo vision system. The 3D resolution achieved by the stereo vision system is about 33 microns at 1.8 m with an observation field of 60cm x 60cm.

  7. Analysis of adaptive laser scanning optical system with focus-tunable components

    Science.gov (United States)

    Pokorný, P.; Mikš, A.; Novák, J.; Novák, P.

    2015-05-01

    This work presents a primary analysis of an adaptive laser scanner based on two-mirror beam-steering device and focustunable components (lenses with tunable focal length). It is proposed an optical scheme of an adaptive laser scanner, which can focus the laser beam in a continuous way to a required spatial position using the lens with tunable focal length. This work focuses on a detailed analysis of the active optical or opto-mechanical components (e.g. focus-tunable lenses) mounted in the optical systems of laser scanners. The algebraic formulas are derived for ray tracing through different configurations of the scanning optical system and one can calculate angles of scanner mirrors and required focal length of the tunable-focus component provided that the position of the focused beam in 3D space is given with a required tolerance. Computer simulations of the proposed system are performed using MATLAB.

  8. How many loci does it take to DNA barcode a crocus?

    Directory of Open Access Journals (Sweden)

    Ole Seberg

    Full Text Available BACKGROUND: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. METHODOLOGY AND PRINCIPAL FINDINGS: Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context. CONCLUSIONS/SIGNIFICANCE: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.

  9. Secured Data Encoding Technique in High Capacity Color Barcodes for M-Ticket Application

    Directory of Open Access Journals (Sweden)

    B. Akila

    2013-01-01

    Full Text Available This research aim is to increase the capacity of barcode (i.e. Number of data bits embedded inside barcode will be increased by encoding data through orientation modulation in elliptical dot array. BARCODES that encode digital data on physical media are commonly utilized in commercial applications for tracing/tracking of trade items, in security applications for linking personal documents with a user, or in other applications as an auxiliary channel to encode additional information on a physical medium. which are fundamentally analog, these methods can add security and functionality and features that are associated with digital techniques at the expense of consuming space on the media. For instance, in personal IDs, driving licenses and passports, high capacity can enable the encoding of a sample speech signal, a picture, or other identifying personal information which in turn may be used to establish authenticity of the user. Care must, however, be exercised in designing color barcodes to ensure that they are robust to variations in the color printing and scanning processes, which have a greater impact when considering color rather than black/white reproduction and capture.2D bar codes are being considered for new emerging applications such as M-ticketing, where they carry selected information of a ticket that is received via a mobile phone; reliable and secure personal identification, where they store personal biometric data on the identification document; and visual communications with side information, where they can be used as an auxiliary channel conveying additional data for improving visual communications.

  10. The current state of electronic consultation and electronic referral systems in Canada: an environmental scan.

    Science.gov (United States)

    Liddy, Clare; Hogel, Matthew; Blazkho, Valerie; Keely, Erin

    2015-01-01

    Access to specialist care is a point of concern for patients, primary care providers, and specialists in Canada. Innovative e-health platforms such as electronic consultation (eConsultation) and referral (eReferral) can improve access to specialist care. These systems allow physicians to communicate asynchronously and could reduce the number of unnecessary referrals that clog wait lists, provide a record of the patient's journey through the referral system, and lead to more efficient visits. Little is known about the current state of eConsultation and eReferral in Canada. The purpose of this work was to identify current systems and gain insight into the design and implementation process of existing systems. An environmental scan approach was used, consisting of a systematic and grey literature review, and targeted semi-structured key informant interviews. Only three eConsultation/eReferral systems are currently in operation in Canada. Four themes emerged from the interviews: eReferral is an end goal for those provinces without an active eReferral system, re-organization of the referral process is a necessity prior to automation, engaging the end-user is essential, and technological incompatibilities are major impediments to progress. Despite the acknowledged need to improve the referral system and increase government spending on health information technology, eConsultation and eReferral systems remain scarce as Canada lags behind the rest of the developed world.

  11. The Calibration Model and Simulation Analysis of Circular Scanning Airborne Laser Bathymetry System

    Directory of Open Access Journals (Sweden)

    SHEN Erhua

    2016-08-01

    Full Text Available To improve the positioning accuracy of circular scanning airborne laser bathymetry system, a calibration method is presented in this paper. When the laser points are collected by the bathymetry system on the level area, they should be on the same plane. However, they are not coplanar because of systematic error and random error. So we try to fit the points to a plane, which may help to adjust the errors and then correct the point location.Firstly, the circular scanning airborne laser bathymetry positioning model is derived in the simple mode. The intersection of laser line and sea surface is simulated depending on the mathematical principles of line and plane intersection. Combined with the direction vector of laser line in the water got by the refraction principle, the sea floor plane mathematical equation is used to compute the location of the laser points. Then, the parameter weighted least squares adjustment model is derived with the prior variance introduced, which lays the foundation for the following computing of calibration model. Finally, the calibration adjustment mathematic model and the detailed computing process are derived. The simulation computing and analysis for the calibration process is presented, and some meaningful conclusions for the calibration are achieved.

  12. Sub-pixel processing for super-resolution scanning imaging system with fiber bundle coupling

    Institute of Scientific and Technical Information of China (English)

    Bowen An; Bingbin Xue; Shengda Pan; Guilin Chen

    2011-01-01

    A multilayer fiber bundle is used to couple the image in a remote sensing imaging system. The object image passes through all layers of the fiber bundle in micro-scanning mode. The malposition of adjacent layers arranged in a hexagonal pattern is at sub-pixel scale. Therefore, sub-pixel processing can be applied to improve the spatial resolution. The images coupled by the adjacent layer fibers are separated, and subsequently, the intermediate image is obtained by histogram matching based on one of the separated image called base image. Finally, the intermediate and base images are processed in the frequency domain. The malposition of the adjacent layer fiber is converted to the phase difference in Fourier transform. Considering the limited sensitivity of the experimental instruments and human sight, the image is set as a band-limited signal and the interpolation function of image fusion is found. The results indicate that a super-resolution image with ultra-high spatial resolution is obtained.%@@ A multilayer fiber bundle is used to couple the image in a remote sensing imaging system.The object image passes through all layers of the fiber bundle in micro-scanning mode.The malposition of adjacent layers arranged in a hexagonal pattern is at sub-pixel scale.

  13. Automatic Calibration Method of Voxel Size for Cone-beam 3D-CT Scanning System

    CERN Document Server

    Yang, Min; Liu, Yipeng; Men, Fanyong; Li, Xingdong; Liu, Wenli; Wei, Dongbo

    2013-01-01

    For cone-beam three-dimensional computed tomography (3D-CT) scanning system, voxel size is an important indicator to guarantee the accuracy of data analysis and feature measurement based on 3D-CT images. Meanwhile, the voxel size changes with the movement of the rotary table along X-ray direction. In order to realize the automatic calibration of the voxel size, a new easily-implemented method is proposed. According to this method, several projections of a spherical phantom are captured at different imaging positions and the corresponding voxel size values are calculated by non-linear least square fitting. Through these interpolation values, a linear equation is obtained, which reflects the relationship between the rotary table displacement distance from its nominal zero position and the voxel size. Finally, the linear equation is imported into the calibration module of the 3D-CT scanning system, and when the rotary table is moving along X-ray direction, the accurate value of the voxel size is dynamically expo...

  14. Design and construction of a cost-efficient Arduino-based mirror galvanometer system for scanning optical microscopy

    Science.gov (United States)

    Hsu, Jen-Feng; Dhingra, Shonali; D'Urso, Brian

    2017-01-01

    Mirror galvanometer systems (galvos) are commonly employed in research and commercial applications in areas involving laser imaging, laser machining, laser-light shows, and others. Here, we present a robust, moderate-speed, and cost-efficient home-built galvo system. The mechanical part of this design consists of one mirror, which is tilted around two axes with multiple surface transducers. We demonstrate the ability of this galvo by scanning the mirror using a computer, via a custom driver circuit. The performance of the galvo, including scan range, noise, linearity, and scan speed, is characterized. As an application, we show that this galvo system can be used in a confocal scanning microscopy system.

  15. Multilocus inference of species trees and DNA barcoding

    Science.gov (United States)

    2016-01-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481787

  16. Dissecting host-associated communities with DNA barcodes

    Science.gov (United States)

    Pierce, Naomi E.

    2016-01-01

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481780

  17. Hybrid hydrogel photonic barcodes for multiplex detection of tumor markers.

    Science.gov (United States)

    Xu, Yueshuang; Zhang, Xiaoping; Luan, Chengxin; Wang, Huan; Chen, Baoan; Zhao, Yuanjin

    2017-01-15

    Barcodes-based suspension array have for demonstrated values in multiplex assay of tumor markers. Photonic barcodes which are encoded by their characteristic reflection peaks are the important supports for suspension array due to their stable code, low fluorescent background and high surface-volume ratio. Attempts to develop this technology tend to improve the function of the photonic barcodes. Here, we present a new type of hybrid hydrogel photonic barcodes for efficient multiplex assays. This photonic barcodes are hybrid inverse opal hydrogel composed of poly(ethylene glycol) diacrylate (PEG-DA) and agarose. The polymerized PEG-DA hydrogel could guarantee the stabilities of the inverse opal structure and its resultant code, while the agarose could offer active chemical groups for the probe immobilization and homogeneous water surrounding for the bioassay. In addition, the interconnected pores inverse opal structure could provide channels for biomolecules diffusing and reaction into the voids of barcodes. These features imparted the hybrid hydrogel photonic barcodes with limits of detection (LOD) of 0.78ng/mL for carcinoembryonic antigen (CEA) and 0.21ng/mL for α-fetoprotein (AFP), respectively. It was also demonstrated that the proposed barcodes showed acceptable accuracy and detection reproducibility, and the results were in acceptable agreement with those from common clinic method for the detections of practical clinical samples. Thus, our technique provides a new platform for simultaneous multiplex immunoassay.

  18. Dissecting host-associated communities with DNA barcodes.

    Science.gov (United States)

    Baker, Christopher C M; Bittleston, Leonora S; Sanders, Jon G; Pierce, Naomi E

    2016-09-05

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.This article is part of the themed issue 'From DNA barcodes to biomes'.

  19. Investigation of tomosynthetic perfusion measurements using the scanning-beam digital x-ray (SBDX) system

    Science.gov (United States)

    Nett, Brian E.; Chen, Guang-Hong; Van Lysel, Michael S.; Betts, Timothy; Speidel, Michael; Rowley, Howard A.; Aagaard Kienitz, Beverly D.; Mistretta, Charles A.

    2004-10-01

    The feasibility of making regional perfusion measurements using a tomosynthetic digital subtraction angiography (TDSA) acquisition has been demonstrated. The study of tomosynthetic perfusion measurements was motivated by the clinical desire for perfusion measurements in an interventional angiography suite. These pilot studies were performed using the scanning-beam digital x-ray (SBDX) system which is an inverse-geometry imaging device which utilizes an electromagnetically-scanned x-ray source, and a small CdTe direct conversion photon counting detector. The scanning electron source was used to acquire planar-tomographic images of a 12.5 x 12.5 cm field of view at a frame rate of 15 frames/sec during dynamic contrast injection. A beagle animal model was used to evaluate the tomosynthetic perfusion measurements. A manual bolus injection of iodinated contrast solution was used in order to resolve the parameters of the contrast pass curve. The acquired planar tomosynthetic dataset was reconstructed with a simple back-projection algorithm. Digital subtraction techniques were used to visualize the change in contrast agent intensity in each reconstructed plane. Given the TDSA images, region of interest based analysis was used in the selection of the image pixels corresponding to the artery and tissue bed. The mean transit time (MTT), regional cerebral blood volume (rCBV) and regional cerebral blood flow (rCBF) were extracted from the tomosynthetic data for selected regions in each of the desired reconstructed planes. For the purpose of this study, the arterial contrast enhancement curve was fit with a combination of gamma variate terms, and the MTT was calculated using a deconvolution based on the singular value decomposition (SVD). The results of the contrast pass curves derived with TDSA were consistent with the results from perfusion measurements as implemented with CT acquisition.

  20. An Automated and Intelligent Medical Decision Support System for Brain MRI Scans Classification.

    Directory of Open Access Journals (Sweden)

    Muhammad Faisal Siddiqui

    Full Text Available A wide interest has been observed in the medical health care applications that interpret neuroimaging scans by machine learning systems. This research proposes an intelligent, automatic, accurate, and robust classification technique to classify the human brain magnetic resonance image (MRI as normal or abnormal, to cater down the human error during identifying the diseases in brain MRIs. In this study, fast discrete wavelet transform (DWT, principal component analysis (PCA, and least squares support vector machine (LS-SVM are used as basic components. Firstly, fast DWT is employed to extract the salient features of brain MRI, followed by PCA, which reduces the dimensions of the features. These reduced feature vectors also shrink the memory storage consumption by 99.5%. At last, an advanced classification technique based on LS-SVM is applied to brain MR image classification using reduced features. For improving the efficiency, LS-SVM is used with non-linear radial basis function (RBF kernel. The proposed algorithm intelligently determines the optimized values of the hyper-parameters of the RBF kernel and also applied k-fold stratified cross validation to enhance the generalization of the system. The method was tested by 340 patients' benchmark datasets of T1-weighted and T2-weighted scans. From the analysis of experimental results and performance comparisons, it is observed that the proposed medical decision support system outperformed all other modern classifiers and achieves 100% accuracy rate (specificity/sensitivity 100%/100%. Furthermore, in terms of computation time, the proposed technique is significantly faster than the recent well-known methods, and it improves the efficiency by 71%, 3%, and 4% on feature extraction stage, feature reduction stage, and classification stage, respectively. These results indicate that the proposed well-trained machine learning system has the potential to make accurate predictions about brain abnormalities

  1. An Automated and Intelligent Medical Decision Support System for Brain MRI Scans Classification.

    Science.gov (United States)

    Siddiqui, Muhammad Faisal; Reza, Ahmed Wasif; Kanesan, Jeevan

    2015-01-01

    A wide interest has been observed in the medical health care applications that interpret neuroimaging scans by machine learning systems. This research proposes an intelligent, automatic, accurate, and robust classification technique to classify the human brain magnetic resonance image (MRI) as normal or abnormal, to cater down the human error during identifying the diseases in brain MRIs. In this study, fast discrete wavelet transform (DWT), principal component analysis (PCA), and least squares support vector machine (LS-SVM) are used as basic components. Firstly, fast DWT is employed to extract the salient features of brain MRI, followed by PCA, which reduces the dimensions of the features. These reduced feature vectors also shrink the memory storage consumption by 99.5%. At last, an advanced classification technique based on LS-SVM is applied to brain MR image classification using reduced features. For improving the efficiency, LS-SVM is used with non-linear radial basis function (RBF) kernel. The proposed algorithm intelligently determines the optimized values of the hyper-parameters of the RBF kernel and also applied k-fold stratified cross validation to enhance the generalization of the system. The method was tested by 340 patients' benchmark datasets of T1-weighted and T2-weighted scans. From the analysis of experimental results and performance comparisons, it is observed that the proposed medical decision support system outperformed all other modern classifiers and achieves 100% accuracy rate (specificity/sensitivity 100%/100%). Furthermore, in terms of computation time, the proposed technique is significantly faster than the recent well-known methods, and it improves the efficiency by 71%, 3%, and 4% on feature extraction stage, feature reduction stage, and classification stage, respectively. These results indicate that the proposed well-trained machine learning system has the potential to make accurate predictions about brain abnormalities from the

  2. DNA Barcoding for Identification of "Candidatus Phytoplasmas" Using a Fragment of the Elongation Factor Tu Gene

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta;

    2012-01-01

    barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. Conclusions/Significance This study demonstrates that DNA barcoding principles can be applied...

  3. Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

    Institute of Scientific and Technical Information of China (English)

    Zhong-e HOU; Zhu LI; Shu-qiang LI

    2009-01-01

    Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection[Current Zoology 55(2):158-164,2009].

  4. [Hydrophidae identification through analysis on Cyt b gene barcode].

    Science.gov (United States)

    Liao, Li-xi; Zeng, Ke-wu; Tu, Peng-fei

    2015-08-01

    Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification.

  5. Identification of herbal medicinal materials using DNA barcodes

    Institute of Scientific and Technical Information of China (English)

    Ming LI; Hui CAO; Paul Pui-Hay BUT; pang-Chui SHAW

    2011-01-01

    Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety and efficacy. Identification of herbal medicinal materials by DNA technology has been widely applied,started from the mid-1990s. In recent years, DNA barcoding of global plant species using four standard barcodes (rbcL, matK, trnH-psbA and ITS) has been a major focus in the fields of biodiversity and conservation. These DNA barcodes can also be used as reliable tools to facilitate the identification of herbal medicinal materials for the safe use of herbs, quality control, and forensic investigation. Many studies have applied these DNA barcodes for the identification of herbal medicinal species and their adulterants. The present article reviews efforts in the identification of herbal medicinal materials using the standard DNA barcodes and other DNA sequence-based markers.

  6. The application status of two-dimensional barcode technology and feasibility analysis of its application to traceability system for food additives%二维码技术的应用现状及用于食品添加剂系统管理的可行性

    Institute of Scientific and Technical Information of China (English)

    刘飞; 冷小京

    2013-01-01

    Two-dimensional barcode identification is a high-tech approach for data carrying and transmit-ting which can efficiently encode Chinese characters and store large amounts of data with an easy and conve-nient way to process. In this paper, a supplemental project of traceability system for food additives was de-signed based on two-dimensional barcode. The project can not only provide consumers with detailed informa-tion of food additives, but also provide a good platform for manufacturers and supervision departments.%二维码识别技术是一种具有汉字编码特性,可以储存大量产品信息,使用方式简单便捷的数据携带、传递的高科技手段。基于该技术,本文探讨了食品添加剂可追溯系统的补充方案。该方案不仅可以为消费者提供详细的食品添加剂信息,而且为生产企业和监管部门提供了良好的管理和监督平台。

  7. Tree Root System Characterization and Volume Estimation by Terrestrial Laser Scanning and Quantitative Structure Modeling

    Directory of Open Access Journals (Sweden)

    Aaron Smith

    2014-12-01

    Full Text Available The accurate characterization of three-dimensional (3D root architecture, volume, and biomass is important for a wide variety of applications in forest ecology and to better understand tree and soil stability. Technological advancements have led to increasingly more digitized and automated procedures, which have been used to more accurately and quickly describe the 3D structure of root systems. Terrestrial laser scanners (TLS have successfully been used to describe aboveground structures of individual trees and stand structure, but have only recently been applied to the 3D characterization of whole root systems. In this study, 13 recently harvested Norway spruce root systems were mechanically pulled from the soil, cleaned, and their volumes were measured by displacement. The root systems were suspended, scanned with TLS from three different angles, and the root surfaces from the co-registered point clouds were modeled with the 3D Quantitative Structure Model to determine root architecture and volume. The modeling procedure facilitated the rapid derivation of root volume, diameters, break point diameters, linear root length, cumulative percentages, and root fraction counts. The modeled root systems underestimated root system volume by 4.4%. The modeling procedure is widely applicable and easily adapted to derive other important topological and volumetric root variables.

  8. DNA Barcoding and the International Barcode of Life Project in China

    Institute of Scientific and Technical Information of China (English)

    CHE Jing; HUANG Dawei; LI Dezhu; MA Juncai; ZHANG Yaping

    2010-01-01

    @@ 1.Scientific and Social Benefits of DNA Barcoding Along with the accelerated global trade and climate change,the needs for sustainable development and for understanding biodiversity are increasing.Rapid and accurate species identification and sustainable utility of biodiversity resources have become a great need for the world.

  9. Permanent 3D laser scanning system for an active landslide in Gresten (Austria)

    Science.gov (United States)

    Canli, Ekrem; Höfle, Bernhard; Hämmerle, Martin; Benni, Thiebes; Glade, Thomas

    2015-04-01

    Terrestrial laser scanners (TLS) have widely been used for high spatial resolution data acquisition of topographic features and geomorphic analyses. Existing applications encompass different landslides including rockfall, translational or rotational landslides, debris flow, but also coastal cliff erosion, braided river evolution or river bank erosion. The main advantages of TLS are (a) the high spatial sampling density of XYZ-measurements (e.g. 1 point every 2-3 mm at 10 m distance), particularly in comparison with the low data density monitoring techniques such as GNSS or total stations, (b) the millimeter accuracy and precision of the range measurement to centimeter accuracy of the final DEM, and (c) the highly dense area-wide scanning that enables to look through vegetation and to measure bare ground. One of its main constraints is the temporal resolution of acquired data due to labor costs and time requirements for field campaigns. Thus, repetition measurements are generally performed only episodically. However, for an increased scientific understanding of the processes as well as for early warning purposes, we present a novel permanent 3D monitoring setup to increase the temporal resolution of TLS measurements. This accounts for different potential monitoring deliverables such as volumetric calculations, spatio-temporal movement patterns, predictions and even alerting. This system was installed at the active Salcher landslide in Gresten (Austria) that is situated in the transition zone of the Gresten Klippenbelt (Helvetic) and the Flyschzone (Penninic). The characteristic lithofacies are the Gresten Beds of Early Jurassic age that are covered by a sequence of marly and silty beds with intercalated sandy limestones. Permanent data acquisition can be implemented into our workflow with any long-range TLS system offering fully automated capturing. We utilize an Optech ILRIS-3D scanner. The time interval between two scans is currently set to 24 hours, but can be

  10. An In silico approach for the evaluation of DNA barcodes

    Directory of Open Access Journals (Sweden)

    Shehzad Wasim

    2010-07-01

    Full Text Available Abstract Background DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Results Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality: barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. Conclusions In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.

  11. Automatic barcode recognition method based on adaptive edge detection and a mapping model

    Science.gov (United States)

    Yang, Hua; Chen, Lianzheng; Chen, Yifan; Lee, Yong; Yin, Zhouping

    2016-09-01

    An adaptive edge detection and mapping (AEDM) algorithm to address the challenging one-dimensional barcode recognition task with the existence of both image degradation and barcode shape deformation is presented. AEDM is an edge detection-based method that has three consecutive phases. The first phase extracts the scan lines from a cropped image. The second phase involves detecting the edge points in a scan line. The edge positions are assumed to be the intersecting points between a scan line and a corresponding well-designed reference line. The third phase involves adjusting the preliminary edge positions to more reasonable positions by employing prior information of the coding rules. Thus, a universal edge mapping model is established to obtain the coding positions of each edge in this phase, followed by a decoding procedure. The Levenberg-Marquardt method is utilized to solve this nonlinear model. The computational complexity and convergence analysis of AEDM are also provided. Several experiments were implemented to evaluate the performance of AEDM algorithm. The results indicate that the efficient AEDM algorithm outperforms state-of-the-art methods and adequately addresses multiple issues, such as out-of-focus blur, nonlinear distortion, noise, nonlinear optical illumination, and situations that involve the combinations of these issues.

  12. On-line Scanned Probe Microscopy Transparently Integrated with DualBeam SEM/FIB Systems

    Science.gov (United States)

    Ignatov, Andrey; Komissar, Anatoly; Lewis, Aaron

    2013-03-01

    A multifunctional scanning probe microscope (SPM) will be described that transparently integrates with a DualBeam SEM/FIB System. This is done without perturbing any of the capabilities of the Dual Beam in terms of detectors, gas injectors, analyzers etc while allowing for a completely exposed probe tip to be imaged online even with immersion objectives at working distances as short as 4 mm. In addition, the completely free motion of the rotation axis of the stage is maintained with the probe tip at the eucentric point, this makes it possible to orient the sample in any direction on any structure The X and Y scan range of the atomic force microscopic (AFM) imaging achieves 35 microns with rough motion over 10 millimeters. This permits the SPM to tilt into position perpendicular to the SEM or FIB or under an angle for rapid and accurate placement of the probe tip at or on structures such as biopolymeric materials that are nanometric in X, Y and Z extent. Thus, not only can a structure's nanometric height be accurately profiled but this can be accomplished with the on-line excellence of SEM for X, Y metrology. Furthermore, electron and ion beam sensitive samples can be imaged and characterized by AFM at high resolution.

  13. Secretory glands and microvascular systems imaged in aqueous solution by atmospheric scanning electron microscopy (ASEM).

    Science.gov (United States)

    Yamazawa, Toshiko; Nakamura, Naotoshi; Sato, Mari; Sato, Chikara

    2016-12-01

    Exocrine glands, e.g., salivary and pancreatic glands, play an important role in digestive enzyme secretion, while endocrine glands, e.g., pancreatic islets, secrete hormones that regulate blood glucose levels. The dysfunction of these secretory organs immediately leads to various diseases, such as diabetes or Sjögren's syndrome, by poorly understood mechanisms. Gland-related diseases have been studied by optical microscopy (OM), and at higher resolution by transmission electron microscopy (TEM) of Epon embedded samples, which necessitates hydrophobic sample pretreatment. Here, we report the direct observation of tissue in aqueous solution by atmospheric scanning electron microscopy (ASEM). Salivary glands, lacrimal glands, and pancreas were fixed, sectioned into slabs, stained with phosphotungstic acid (PTA), and inspected in radical scavenger d-glucose solution from below by an inverted scanning electron microscopy (SEM), guided by optical microscopy from above to target the tissue substructures. A 2- to 3-µm specimen thickness was visualized by the SEM. In secretory cells, cytoplasmic vesicles and other organelles were clearly imaged at high resolution, and the former could be classified according to the degree of PTA staining. In islets of Langerhans, the microvascular system used as an outlet by the secretory cells was also clearly observed. Microvascular system is also critically involved in the onset of diabetic complications and was clearly visible in subcutaneous tissue imaged by ASEM. The results suggest the use of in-solution ASEM for histology and to study vesicle secretion systems. Further, the high-throughput of ASEM makes it a potential tool for the diagnosis of exocrine and endocrine-related diseases.

  14. Three-dimensional microscope vision system based on micro laser line scanning and adaptive genetic algorithms

    Science.gov (United States)

    Apolinar, J.; Rodríguez, Muñoz

    2017-02-01

    A microscope vision system to retrieve small metallic surface via micro laser line scanning and genetic algorithms is presented. In this technique, a 36 μm laser line is projected on the metallic surface through a laser diode head, which is placed to a small distance away from the target. The micro laser line is captured by a CCD camera, which is attached to the microscope. The surface topography is computed by triangulation by means of the line position and microscope vision parameters. The calibration of the microscope vision system is carried out by an adaptive genetic algorithm based on the line position. In this algorithm, an objective function is constructed from the microscope geometry to determine the microscope vision parameters. Also, the genetic algorithm provides the search space to calculate the microscope vision parameters with high accuracy in fast form. This procedure avoids errors produced by the missing of references and physical measurements, which are employed by the traditional microscope vision systems. The contribution of the proposed system is corroborated by an evaluation via accuracy and speed of the traditional microscope vision systems, which retrieve micro-scale surface topography.

  15. Possibilities of a Personal Laser Scanning System for Forest Mapping and Ecosystem Services

    Directory of Open Access Journals (Sweden)

    Xinlian Liang

    2014-01-01

    Full Text Available A professional-quality, personal laser scanning (PLS system for collecting tree attributes was demonstrated in this paper. The applied system, which is wearable by human operators, consists of a multi-constellation navigation system and an ultra-high-speed phase-shift laser scanner mounted on a rigid baseplate and consisting of a single sensor block. A multipass-corridor-mapping method was developed to process PLS data and a 2,000 m2 forest plot was utilized in the test. The tree stem detection accuracy was 82.6%; the root mean square error (RMSE of the estimates of tree diameter at breast height (DBH was 5.06 cm; the RMSE of the estimates of tree location was 0.38 m. The relative RMSE of the DBH estimates was 14.63%. The results showed, for the first time, the potential of the PLS system in mapping large forest plots. Further research on mapping accuracy in various forest conditions, data correction methods and multi-sensoral positioning techniques is needed. The utilization of this system in different applications, such as harvester operations, should also be explored. In addition to collecting tree-level and plot-level data for forest inventory, other possible applications of PLS for forest ecosystem services include mapping of canopy gaps, measuring leaf area index of large areas, documenting and visualizing forest routes feasible for recreation, hiking and berry and mushroom picking.

  16. Possibilities of a personal laser scanning system for forest mapping and ecosystem services.

    Science.gov (United States)

    Liang, Xinlian; Kukko, Antero; Kaartinen, Harri; Hyyppä, Juha; Yu, Xiaowei; Jaakkola, Anttoni; Wang, Yunsheng

    2014-01-10

    A professional-quality, personal laser scanning (PLS) system for collecting tree attributes was demonstrated in this paper. The applied system, which is wearable by human operators, consists of a multi-constellation navigation system and an ultra-high-speed phase-shift laser scanner mounted on a rigid baseplate and consisting of a single sensor block. A multipass-corridor-mapping method was developed to process PLS data and a 2,000 m2 forest plot was utilized in the test. The tree stem detection accuracy was 82.6%; the root mean square error (RMSE) of the estimates of tree diameter at breast height (DBH) was 5.06 cm; the RMSE of the estimates of tree location was 0.38 m. The relative RMSE of the DBH estimates was 14.63%. The results showed, for the first time, the potential of the PLS system in mapping large forest plots. Further research on mapping accuracy in various forest conditions, data correction methods and multi-sensoral positioning techniques is needed. The utilization of this system in different applications, such as harvester operations, should also be explored. In addition to collecting tree-level and plot-level data for forest inventory, other possible applications of PLS for forest ecosystem services include mapping of canopy gaps, measuring leaf area index of large areas, documenting and visualizing forest routes feasible for recreation, hiking and berry and mushroom picking.

  17. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

    Directory of Open Access Journals (Sweden)

    Aron J Fazekas

    Full Text Available A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s. We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples. The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA to 59% (trnH-psbA of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci, with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs. Several loci (matK, psbK-psbI, trnH-psbA were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations. This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the

  18. A Combination of Stop-and-Go and Electro-Tricycle Laser Scanning Systems for Rural Cadastral Surveys

    Directory of Open Access Journals (Sweden)

    Liang Zhong

    2016-09-01

    Full Text Available Over the past decade, land-based laser scanning technologies have been actively studied and implemented, in response to the need for detailed three-dimensional (3D data about our rural and urban environment for topographic mapping, cadastral mapping, and other street-level features, which are difficult and time consuming to measure by other instruments. For rural areas in China, the complex terrain and poor planning limit the applicability of this advanced technology. To improve the efficiency of rural surveys, we present two SSW (Shoushi and SiWei laser scanning systems for rapid topographic mapping: stop-and-go and electro-tricycle laser scanning systems. The objective of this paper is to evaluate whether laser scanning data collected by the developed SSW systems meet the accuracy requirements for rural homestead mapping. We investigated the performance of the two laser scanning systems on Ma’anshan Village, a small, typical village in Hubei Province, China. To obtain full coverage of the village, we fused the stop-and-go and electro-tricycle laser scanning data. The performance of the developed SSW systems is described by the results of building contours extracted from the fused data against the established building vector map.

  19. Identification of Amazonian trees with DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Mailyn Adriana Gonzalez

    Full Text Available BACKGROUND: Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. METHODOLOGY/PRINCIPAL FINDINGS: Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS, matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone to 96% (morphology and molecular of the individuals assigned to a known tree taxon. CONCLUSION/SIGNIFICANCE: We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.

  20. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens.

    Science.gov (United States)

    Shokralla, Shadi; Gibson, Joel F; Nikbakht, Hamid; Janzen, Daniel H; Hallwachs, Winnie; Hajibabaei, Mehrdad

    2014-09-01

    DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.

  1. Resolution enhancement of scanning four-point-probe measurements on two-dimensional systems

    DEFF Research Database (Denmark)

    Hansen, Torben Mikael; Stokbro, Kurt; Hansen, Ole;

    2003-01-01

    A method to improve the resolution of four-point-probe measurements of two-dimensional (2D) and quasi-2D systems is presented. By mapping the conductance on a dense grid around a target area and postprocessing the data, the resolution can be improved by a factor of approximately 50 to better than 1....../15 of the four-point-probe electrode spacing. The real conductance sheet is simulated by a grid of discrete resistances, which is optimized by means of a standard optimization algorithm, until the simulated voltage-to-current ratios converges with the measurement. The method has been tested against simulated...... data as well as real measurements and is found to successfully deconvolute the four-point-probe measurements. In conjunction with a newly developed scanning four-point probe with electrode spacing of 1.1 µm, the method can resolve the conductivity with submicron resolution. ©2003 American Institute...

  2. Ultrasonic Guided-Wave Scan System Used to Characterize Microstructure and Defects in Ceramic Composites

    Science.gov (United States)

    Roth, Don J.; Cosgriff, Laura M.; Martin, Richard E.; Verrilli, Michael J.; Bhatt, Ramakrishna T.

    2004-01-01

    Ceramic matrix composites (CMCs) are being developed for advanced aerospace propulsion applications to save weight, improve reuse capability, and increase performance. However, mechanical and environmental loads applied to CMCs can cause discrete flaws and distributed microdamage, significantly reducing desirable physical properties. Such microdamage includes fiber/matrix debonding (interface failure), matrix microcracking, fiber fracture and buckling, oxidation, and second phase formation. A recent study (ref. 1) of the durability of a C/SiC CMC discussed the requirement for improved nondestructive evaluation (NDE) methods for monitoring degradation in these materials. Distributed microdamage in CMCs has proven difficult to characterize nondestructively because of the complex microstructure and macrostructure of these materials. This year, an ultrasonic guided-wave scan system developed at the NASA Glenn Research Center was used to characterize various microstructural and flaw conditions in SiC/SiC (silicon carbide fiber in silicon carbide matrix) and C/SiC (carbon fiber in silicon carbide matrix) CMC samples.

  3. Development of a Mechanical Scanning-type Intravascular Ultrasound System Using a Miniature Ultrasound Motor

    Science.gov (United States)

    Tanabe, Masayuki; Xie, Shangping; Tagawa, Norio; Moriya, Tadashi; Furukawa, Yuji

    2007-07-01

    Intravascular ultrasound (IVUS) plays an important role for the detection of arteriosclerosis, which causes the ischemic heart disease. In mechanical scanning-type IVUS, it is necessary to rotate a transducer or a reflecting mirror. A method that involves rotating the transducer using a torque wire causes image distortion (NURD: non uniform rotation distortion). For a method that involves placing an electromagnetic motor on the tip of an IVUS probe is difficult to miniaturize the probe. Our objectives are to miniaturize the probe (1 mm in diameter, 5 mm in length) and to remove NURD. Therefore, we conducted a study to assess the feasibility of attaining these objectives by constructing a prototype IVUS system, in which an ultrasound motor using a stator in the form of a helical coil (abbreviated as CS-USM: coiled stator-ultrasonic motor) is incorporated, and to clarify problems that need to be solved in constructing the probe.

  4. CT scan findings and EEG in systemic lupus erythematodes patients with neuro-psychiatric disorders

    Energy Technology Data Exchange (ETDEWEB)

    Kan, Rumiko; Hagiwara, Mariko; Katayose, Keiko; Yashima, Yuko; Kumashiro, Hisashi

    1988-06-01

    In 14 patients with systemic lupus erythematodes presenting with neuro-psychiatric disorders, CT scans were compared with encephalographic (EEG) findings. CT findings were markedly abnormal in 6, slight with a sulcal enlargement in 3, and normal in 5. In the group of markedly abnormal CT findings, focal abnormal low density areas were detected in 2, severe generalized cerebral atrophy in one, and severe atrophy of the right hemisphere in one. EEG findings included focal paroxysmal abnormality of high voltage slow burst at the left frontal dominance and positive spike on the right hemisphere. Epileptic seizure and depressed sensorium seemed to be related to CT abnormality. In 3 patients with epileptic seizures, their symptoms were closely related to CT abnormality. Parkinsonisms and depressed sensorium were also related to CT abnormality. (Namekawa, K).

  5. Tip alignment system in a sextupole-corrected scanning transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, S. (The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States)); Kapp, O.H. (The Department of Radiology and The Enrico Fermi Institute, The University of Chicago, Chicago, Illinois 60637 (United States))

    1993-03-01

    Tip alignment and replacement in ultrahigh vacuum field-emission electron microscopes is traditionally a time-consuming endeavor. A convenient autodrive system for the 200 kV scanning transmission electron microscope was developed to facilitate the alignment of field-emission tips, thus saving a great deal of experimenter time. Under computer control, a series of automatic electrical and mechanical processes are initiated to systematically adjust various parameters to effect passage of the electron beam through the various apertures of the microscope column. The task of finding the beam'' is thus performed automatically. In this process the tip holder is moved in a raster parallel to the first anode. Feedback from various detectors placed throughout the column direct the positioning of the tip for optimal alignment. This process is routinely performed in about 45 min.

  6. Calculation of scanning tunnelling microscopy images for Kr/graphite system

    Institute of Scientific and Technical Information of China (English)

    周晓林; 陈向荣; 杨向东; 芶清泉

    2003-01-01

    The scanning-tunnelling-microscopy(STM)images of Kr atoms adsorbed on a monolayer graphite sheet(Kr/graphite system)are calculated using the first-principle total-energy electronic structure calculations within the density functional theory in the local density approximation.The results obtained agree well with the observations.It is found that the optimal site of the adsorbed Kr atom is at the top of the centre of the carbon hexagon,and its equilibrium distance from monolayer graphite surface is about 0.335nm.It is shown that the hybridization of C 2p electronic states(π-electronic states)and Kr 4p and 5s electronic states is the main origin of the Fermi-level local density of state.

  7. Friedel oscillations in graphene-based systems probed by Scanning Tunneling Microscopy

    Science.gov (United States)

    Mallet, Pierre; Brihuega, Iván; Cherkez, Vladimir; Gómez-Rodríguez, Jose Marìa; Veuillen, Jean-Yves

    2016-03-01

    For the last 25 years, scientists have demonstrated the capabilities of Scanning Tunneling Microscopy (STM) to visualize in real space the response of a two-dimensional electron gas to atomic-scale impurities. The analysis of the Friedel oscillations surrounding the impurities yields valuable information regarding the elastic scattering properties, the band structure, the doping level and the symmetry of the electronic states in the two-dimensional host system. We will address in this article the use of this technique for probing the electronic properties of graphene, the star two-dimensional compound of the last decade. In particular, we will emphasize how this technique can be pushed up to unravel the electronic pseudospin, a distinctive degree of freedom of graphene's Dirac fermions.

  8. Comparative assessment of 3D surface scanning systems in breast plastic and reconstructive surgery.

    Science.gov (United States)

    Patete, Paolo; Eder, Maximilian; Raith, Stefan; Volf, Alexander; Kovacs, Laszlo; Baroni, Guido

    2013-10-01

    In this work, we compared accuracy, repeatability, and usability in breast surface imaging of 2 commercial surface scanning systems and a hand-held laser surface scanner prototype coupled with a patient's motion acquisition and compensation methodology. The accuracy of the scanners was assessed on an anthropomorphic phantom, and to evaluate the usability of the scanners on humans, thorax surface images of 3 volunteers were acquired. Both the intrascanner repeatability and the interscanner comparative accuracy were assessed. The results showed surface-to-surface distance errors inferior to 1 mm and to 2 mm, respectively, for the 2 commercial scanners and for the prototypical one. Moreover, comparable performances of the 3 scanners were found when used for acquiring the breast surface. On the whole, this study demonstrated that handheld laser surface scanners coupled with subject motion compensation methods lend themselves as competitive technologies for human body surface modeling.

  9. Geometric validation of a mobile laser scanning system for urban applications

    Science.gov (United States)

    Guan, Haiyan; Li, Jonathan; Yu, Yongtao; Liu, Yan

    2016-03-01

    Mobile laser scanning (MLS) technologies have been actively studied and implemented over the past decade, as their application fields are rapidly expanding and extending beyond conventional topographic mapping. Trimble's MX-8, as one of the MLS systems in the current market, generates rich survey-grade laser and image data for urban surveying. The objective of this study is to evaluate whether Trimble MX-8 MLS data satisfies the accuracy requirements of urban surveying. According to the formula of geo-referencing, accuracies of navigation solution and laser scanner determines the accuracy of the collected LiDAR point clouds. Two test sites were selected to test the performance of Trimble MX-8. Those extensive tests confirm that Trimble MX-8 offers a very promising tool to survey complex urban areas.

  10. CHARACTERISING THE EOS SLOT-SCANNING SYSTEM WITH THE EFFECTIVE DETECTIVE QUANTUM EFFICIENCY.

    Science.gov (United States)

    Clavel, A H; Monnin, P; Létang, J M; Verdun, F R; Darbon, A

    2016-06-01

    As opposed to the standard detective quantum efficiency (DQE), effective DQE (eDQE) is a figure of merit that allows comparing the performances of imaging systems in the presence of scatter rejection devices. The geometry of the EOS™ slot-scanning system is such that the detector is self-collimated and rejects scattered radiation. In this study, the EOS system was characterised using the eDQE in imaging conditions similar to those used in clinical practice: with phantoms of different widths placed in the X-ray beam, for various incident air kerma and tube voltages corresponding to the phantom thickness. Scatter fractions in EOS images were extremely low, around 2 % for all configurations. Maximum eDQE values spanned 9-14.8 % for a large range of air kerma at the detector plane from 0.01 to 1.34 µGy. These figures were obtained with non-optimised EOS setting but still over-performed most of the maximum eDQEs recently assessed for various computed radiology and digital radiology systems with antiscatter grids.

  11. LiDAR Scan Matching Aided Inertial Navigation System in GNSS-Denied Environments.

    Science.gov (United States)

    Tang, Jian; Chen, Yuwei; Niu, Xiaoji; Wang, Li; Chen, Liang; Liu, Jingbin; Shi, Chuang; Hyyppä, Juha

    2015-07-10

    A new scan that matches an aided Inertial Navigation System (INS) with a low-cost LiDAR is proposed as an alternative to GNSS-based navigation systems in GNSS-degraded or -denied environments such as indoor areas, dense forests, or urban canyons. In these areas, INS-based Dead Reckoning (DR) and Simultaneous Localization and Mapping (SLAM) technologies are normally used to estimate positions as separate tools. However, there are critical implementation problems with each standalone system. The drift errors of velocity, position, and heading angles in an INS will accumulate over time, and on-line calibration is a must for sustaining positioning accuracy. SLAM performance is poor in featureless environments where the matching errors can significantly increase. Each standalone positioning method cannot offer a sustainable navigation solution with acceptable accuracy. This paper integrates two complementary technologies-INS and LiDAR SLAM-into one navigation frame with a loosely coupled Extended Kalman Filter (EKF) to use the advantages and overcome the drawbacks of each system to establish a stable long-term navigation process. Static and dynamic field tests were carried out with a self-developed Unmanned Ground Vehicle (UGV) platform-NAVIS. The results prove that the proposed approach can provide positioning accuracy at the centimetre level for long-term operations, even in a featureless indoor environment.

  12. 3-D ultrasonic strain imaging based on a linear scanning system.

    Science.gov (United States)

    Huang, Qinghua; Xie, Bo; Ye, Pengfei; Chen, Zhaohong

    2015-02-01

    This paper introduces a 3-D strain imaging method based on a freehand linear scanning mode. We designed a linear sliding track with a position sensor and a height-adjustable holder to constrain the movement of an ultrasound probe in a freehand manner. When moving the probe along the sliding track, the corresponding positional measures for the probe are transmitted via a wireless communication module based on Bluetooth in real time. In a single examination, the probe is scanned in two sweeps in which the height of the probe is adjusted by the holder to collect the pre- and postcompression radio-frequency echoes, respectively. To generate a 3-D strain image, a volume cubic in which the voxels denote relative strains for tissues is defined according to the range of the two sweeps. With respect to the post-compression frames, several slices in the volume are determined and the pre-compression frames are re-sampled to precisely correspond to the post-compression frames. Thereby, a strain estimation method based on minimizing a cost function using dynamic programming is used to obtain the 2-D strain image for each pair of frames from the re-sampled pre-compression sweep and the post-compression sweep, respectively. A software system is developed for volume reconstruction, visualization, and measurement of the 3-D strain images. The experimental results show that high-quality 3-D strain images of phantom and human tissues can be generated by the proposed method, indicating that the proposed system can be applied for real clinical applications (e.g., musculoskeletal assessments).

  13. Measuring contact area, force, and pressure for bioengineering applications: using Fuji Film and TekScan systems.

    Science.gov (United States)

    Bachus, Kent N; DeMarco, Alyssa L; Judd, Kyle T; Horwitz, Daniel S; Brodke, Darrel S

    2006-06-01

    The goal of this study was to compare the TekScan I-Scan Pressure Measurement System with two methods of analysis involving the Fuji Film Prescale Pressure Measuring System in estimating area, force and pressure. Fuji Film and TekScan sensors were alternately placed between a cylindrical peg and a finely ground steel base plate, and compressed with known forces. All Fuji stains were digitally scanned and analyzed. The Erase method of Fuji Film analysis consisted of manually removing portions of the image judged by the user to be outside the perimeter of the stain. The second method of Fuji Film analysis, termed the Threshold method, used the threshold tool to analyze only those pixels that were stained from loading. The TekScan system utilized special matrix-based sensors interfaced with a Windows compatible desktop computer that was equipped with specialized data acquisition hardware and analysis software. The data from this study did not support the hypothesis that all three methods would have accuracies within +/-5% of a known value, when estimating area, force and pressure. Specifically, the TekScan system was found to be more accurate than either of the Fuji Film methods when estimating area and pressure.

  14. STUDY ON THE LINE SCAN CCD CAMERA CALIBRATION OF VEHICLE-BORNE 3D DATA ACQUISITION SYSTEM

    OpenAIRE

    Han, Y; Yang, B.; F. Zhang

    2012-01-01

    Based on the characters of the line scan CCD camera and the Vehicle-borne 3D data acquisition system, it presented a novel method to calibrate the line Scan Camera (LSC) based on the laser scanner. Using the angle information in the original laser scanner data, combing the principle of the line scan camera, it built a calibration model for LSC and designed some experiment methods to implement that. Using the new model and the special experiment methods it computed out high precision ...

  15. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India.

    Directory of Open Access Journals (Sweden)

    Stalin Nithaniyal

    Full Text Available BACKGROUND: India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK correctly identified 136 out of 143 species (95%. This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS: We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.

  16. A transcontinental challenge--a test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera).

    Science.gov (United States)

    Zahiri, Reza; Lafontaine, J Donald; Schmidt, B Christian; Dewaard, Jeremy R; Zakharov, Evgeny V; Hebert, Paul D N

    2014-01-01

    This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or "owlet" moths (Lepidoptera: Noctuoidea) based on vouchered records for 1,541 species (99.1% species coverage), and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN) distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN) system with 1,082 species (70%) assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.

  17. Current Progress of DNA Barcoding%DNA条形码研究进展

    Institute of Scientific and Technical Information of China (English)

    程希婷; 王爱民; 顾志峰; 王嫣; 战欣; 石耀华

    2011-01-01

    DNA barcoding is a new life identification system which can distinguish species rapidly and accurately by analyzing standard short DNA sequences with enough variation. In 2003, the concept of DNA barcoding was formally proposed by Hebert and his colleagues, Canada biologists from University of Guelph. In 2004, Consortium for the Barcode of Life (CBOL) was subsequently constructed. There are more than 200 group members from 50 different countries in CBOL. The first DNA barcode identifying center came into existence in the University of Guelph in May, 2007. In January, 2009, International Barcode of Life (iBOL) was started up. Chinese Academy of Sciences, deputy of China, was one of four subcenter of iBOL, the same as others in Canda, USA and European Union. Mitochondrion cytochrome c oxidase subunit I (CO I ) was ideal DNA barcoding sequence for animal because of its various advantages, such as high primer universality and evolutionary rate. However, CO I was not so good DNA barcoding in plant as in animal. Thus, ribosome Internal Transcribed Spacer (ITS) and plastid rbcL, matK, trnH-psbA sequences were used as DNA barcoding in plant studying. Although it is on the initial phase for DNA barcoding, facing great challenge, more and more studies showed that DNA barcoding can be widely used in life taxonomy and identification. DNA barcoding, a simple effective accurate species identification method, is now one of the fastest development discipline hot in biological study. Here, in order to promote develonment of Chinese study in DNA barcoding and taxonomy, we introduced DNA barcoding screening, application,present studying status in China, challenges and future prospects for DNA barcoding development.%DNA条形码是应用有足够变异的标准化短基因片段对物种进行快速、准确鉴定的新的生物身份识别系统。2003年,加拿大Guelph大学Hebert等首次正式提出了DNA条形码概念,2004年成立了生物条形

  18. Current Progress of DNA Barcoding%DNA条形码研究进展

    Institute of Scientific and Technical Information of China (English)

    程希婷; 王爱民; 顾志峰; 王嫣; 战欣; 石耀华

    2011-01-01

    DNA barcoding is a new life identification system which can distinguish species rapidly and accurately by analyzing standard short DNA sequences with enough variation. In 2003, the concept of DNA barcoding was formally proposed by Hebert and his colleagues, Canada biologists from University of Guelph. In 2004, Consortium for the Barcode of Life (CBOL) was subsequently constructed. There are more than 200 group members from 50 different countries in CBOL. The first DNA barcode identifying center came into existence in the University of Guelph in May, 2007. In January, 2009, International Barcode of Life (iBOL) was started up. Chinese Academy of Sciences, deputy of China, was one of four subcenter of iBOL, the same as others in Canda, USA and European Union. Mitochondrion cytochrome c oxidase subunit I (CO I ) was ideal DNA barcoding sequence for animal because of its various advantages, such as high primer universality and evolutionary rate. However, CO I was not so good DNA barcoding in plant as in animal. Thus, ribosome Internal Transcribed Spacer (ITS) and plastid rb-cL, matK, trnH-psbA sequences were used as DNA barcoding in plant studying. Although it is on the initial phase for DNA barcoding, facing great challenge, more and more studies showed that DNA barcoding can be widely used in life taxonomy and identification. DNA barcoding, a simple effective accurate species identification method, is now one of the fastest development discipline hot in biological study. Here, in order to promote development of Chinese study in DNA barcoding and taxonomy, we introduced DNA barcoding screening, application,present studying status in China, challenges and future prospects for DNA barcoding development.%DNA条形码是应用有足够变异的标准化短基因片段对物种进行快速、准确鉴定的新的生物身份识别系统.2003年,加拿大Guelph大学Hebert等首次正式提出了DNA条形码概念,2004年成立了生物条形码联盟,目前有来自50个

  19. Imaging of aphakic intraocular lens with a slit-scanning tomography system

    Science.gov (United States)

    Oliveira, Cristina M.; Almeida, J. B.; Franco, S.

    2011-05-01

    Nowadays, cataract extraction with IOL implantation aims not only to restore the crystalline lens' transparency, but also to improve patients' retinal image quality. The refractive outcome and visual quality in pseudophakic eyes is mainly determined by the combination of corneal and internal optics resulting from the implanted IOLs. The optical function of the IOLs depends on its position in the eye. The IOL distance to the corneal apex determines the optical power needed for optical correction. In this paper it is described the usage of a slit-scanning imaging system to determine IOL positioning. Through the projection of the light from a slit onto the eye, this tomography system allows to acquire multiple sections of the anterior eye segment, at different meridians. The developed system's software corrects geometric and optical distortion of the images and provides 3-dimentional models of the eye's structures from the 2-dimensional sections. With this noninvasive technique, cross-sectional images of an eye with an aphakic IOL were obtained in order to reconstruct its 3- dimensional model of the lens and assess its position in the anterior segment camera.

  20. Characterization of a new generation of computed radiography system based on line scanning and phosphor needles

    Science.gov (United States)

    Dragusin, Octavian; Rogge, Frank; Pauwels, Herman; Marchal, Guy; Bosmans, Hilde

    2006-03-01

    A new generation CR system that is based on phosphor needles and that uses a digitizer with line scan technology was compared to a clinically used CR system. Purely technical and more clinically related tests were run on both systems. This included the calculation of the DQE, signal-to-noise and contrast to noise ratios from Aluminum inserts, contrast detail analysis with the CDRAD phantom and the use of anthropomorphic phantoms (wrist, chest and skull) with scoring by a radiologist. X-ray exposures with various dose levels and 50kV, 70kV and 125kV were acquired. For detector doses above 0.8 μGy, all noise related measurements showed the superiority of the new technology. The MTF confirmed the improvement in sharpness: between 1 and 3 lp/mm increases ranged from 20 to 50%. Further work should be devoted to the determination of the required dose levels in the plate for the different radiological applications.

  1. Environmental barcoding reveals massive dinoflagellate diversity in marine environments.

    Directory of Open Access Journals (Sweden)

    Rowena F Stern

    Full Text Available BACKGROUND: Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we assembled a large cytochrome c oxidase 1 (COI barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean, including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. CONCLUSIONS/SIGNIFICANCE: COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a

  2. Ag nanoparticle/polymer composite barcode nanorods

    Institute of Scientific and Technical Information of China (English)

    Hongxu Chen[1; Tieqiang Wang[2; Huaizhong Shen[1; Wendong Liu[1; Shuli Wang[1; Kun Liu[1; Junhu Zhang[1; Bai Yang[1

    2015-01-01

    We demonstrate a facile method combining colloidal lithography, selective ion-exchange, and the in situ reduction of Ag ions (Ag+) for the fabrication of multi-segmented barcode nanorods. First, polymer multilayer films were prepared by spin-coating alternating thin films of polystyrene and polyacrylic acid (PAA), and then multi-segmented polymer nanorods were fabricated via reactive ion etching with colloidal masks. Second, Ag nanoparticles (Ag NPs) were incorporated into the PAA segments by an ion exchange and the in situ reduction of the Ag~. The selective incorporation of the Ag NPs permitted the modification of the specific bars of the nanorods. Lastly, the Ag NP/polymer composite nanorods were released from the substrate to form suspensions for further coding applications. By increasing the number of segments and changing the length of each segment in the nanorods, the coding capacity of nanorods was improved. More importantly, this method can easily realize the density tuning of Ag NPs in different segments of a single nanorod by varying the composition of the PAA segments. We believe that numerous other coded materials can also be obtained, which introduces new approaches for fabricating barcoded nanomaterials.

  3. Exploring Canadian Echinoderm Diversity through DNA Barcodes

    Science.gov (United States)

    2016-01-01

    DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs. PMID:27870868

  4. A simple and accurate grading system for orthoiodohippurate renal scans in the assessment of post-transplant renal function

    Energy Technology Data Exchange (ETDEWEB)

    Zaki, S.K.; Bretan, P.N.; Go, R.T.; Rehm, P.K.; Streem, S.B.; Novick, A.C. (Cleveland Clinic Foundation, OH (USA))

    1990-06-01

    Orthoiodohippurate renal scanning has proved to be a reliable, noninvasive method for the evaluation and followup of renal allograft function. However, a standardized system for grading renal function with this test is not available. We propose a simple grading system to distinguish the different functional phases of hippurate scanning in renal transplant recipients. This grading system was studied in 138 patients who were evaluated 1 week after renal transplantation. There was a significant correlation between the isotope renographic functional grade and clinical correlates of allograft function such as the serum creatinine level (p = 0.0001), blood urea nitrogen level (p = 0.0001), urine output (p = 0.005) and need for hemodialysis (p = 0.007). We recommend this grading system as a simple and accurate method to interpret orthoiodohippurate renal scans in the evaluation and followup of renal allograft recipients.

  5. Atmospheric scanning electron microscope system with an open sample chamber: Configuration and applications

    Energy Technology Data Exchange (ETDEWEB)

    Nishiyama, Hidetoshi, E-mail: hinishiy@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Koizumi, Mitsuru, E-mail: koizumi@jeol.co.jp [JEOL Technics Ltd., 2-6-38 Musashino, Akishima, Tokyo 196-0021 (Japan); Ogawa, Koji, E-mail: kogawa@jeol.co.jp [JEOL Technics Ltd., 2-6-38 Musashino, Akishima, Tokyo 196-0021 (Japan); Kitamura, Shinich, E-mail: kitamura@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Konyuba, Yuji, E-mail: ykonyuub@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Watanabe, Yoshiyuki, E-mail: watanabeyoshiy@pref.yamagata.jp [Yamagata Research Institute of Technology, 2-2-1, Matsuei, Yamagata 990-2473 (Japan); Ohbayashi, Norihiko, E-mail: n.ohbayashi@m.tohoku.ac.jp [Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Fukuda, Mitsunori, E-mail: nori@m.tohoku.ac.jp [Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Suga, Mitsuo, E-mail: msuga@jeol.co.jp [JEOL Ltd., 3-1-2, Musashino, Akishima, Tokyo 196-8558 (Japan); Sato, Chikara, E-mail: ti-sato@aist.go.jp [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-4, Umezono, Tsukuba 305-8568 (Japan)

    2014-12-15

    An atmospheric scanning electron microscope (ASEM) with an open sample chamber and optical microscope (OM) is described and recent developments are reported. In this ClairScope system, the base of the open sample dish is sealed to the top of the inverted SEM column, allowing the liquid-immersed sample to be observed by OM from above and by SEM from below. The optical axes of the two microscopes are aligned, ensuring that the same sample areas are imaged to realize quasi-simultaneous correlative microscopy in solution. For example, the cathodoluminescence of ZnO particles was directly demonstrated. The improved system has (i) a fully motorized sample stage, (ii) a column protection system in the case of accidental window breakage, and (iii) an OM/SEM operation system controlled by a graphical user interface. The open sample chamber allows the external administration of reagents during sample observation. We monitored the influence of added NaCl on the random motion of silica particles in liquid. Further, using fluorescence as a transfection marker, the effect of small interfering RNA-mediated knockdown of endogenous Varp on Tyrp1 trafficking in melanocytes was examined. A temperature-regulated titanium ASEM dish allowed the dynamic observation of colloidal silver nanoparticles as they were heated to 240 °C and sintered. - Highlights: • Atmospheric SEM (ASEM) allows observation of samples in liquid or gas. • Open sample chamber allows in situ monitoring of evaporation and sintering processes. • in situ monitoring of processes during reagent administration is also accomplished. • Protection system for film breakage is developed for ASEM. • Usability of ASEM has been improved significantly including GUI control.

  6. DNA barcodes for marine fungal identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Velmurugan, S.; Prasannakumar, C.; Manokaran, S.; AjithKumar, T.; Samkamaleson, A.; Palavesam, A.

    history: Received 1 May 2012 Revision received 24 February 2013 Accepted 7 May 2013 Available online 5 July 2013 Corresponding editor: Felix B€arlocher Keywords: Barcoding gap DNA barcode Internal transcribed spacer Species boundary 5.8S rRNA 18S rRNA 28S... rRNA a b s t r a c t We employed DNA barcodes for identification of fungal species in marine sediments. Sediments were collected seasonally along the Southeast coast of India from which a cul- turable fungal library was constructed. All cultured...

  7. A Quantitative Nanodiffraction System for Ultrahigh Vacuum Scanning Transmission Electron Microscopy

    Science.gov (United States)

    Hembree, Gary G.; Koch, Christoph; Spence, John C. H.

    2003-10-01

    Of all the long-lived particles available as probes of condensed matter, and of all the signals available on a modern electron microscope, electron nanodiffraction patterns provide the strongest signal from the smallest volume. The technique is therefore perfectly suited to nanostructural investigations in inorganic chemistry and materials science. The Vacuum Generators HB501S, an ultrahigh vacuum (UHV) variant of the HB501 scanning transmission electron microscope (STEM), with side-entry double-tilt stage, specimen preparation and analysis chamber, three postspecimen lenses, and cold field-emission tip with integral magnetic gun lens, has therefore been modified to optimize nanodiffraction and quantitative convergent beam electron diffraction (QCBED) performance. A one-micrometer grain-size phosphor screen lying on a fiber-optic faceplate atop the instrument is fiber-optically coupled to a 2048 × 2048 charge-coupled device (CCD), 16-bit camera. This arrangement promises to provide much greater sensitivity, larger dynamic range, and a better modulation transfer function (MTF) than conventional single crystal scintillator (YAG) CCD systems, with noticeable absence of cross talk between pixels. The design of the nanodiffraction detector system is discussed, the gain of the detector is measured, the spherical aberration constant of the objective lens is measured by the Ronchigram method, and preliminary results from the modified instrument are shown.

  8. Surface scanning inspection system particle detection dependence on aluminum film morphology

    Science.gov (United States)

    Prater, Walter; Tran, Natalie; McGarvey, Steve

    2012-03-01

    Physical vapor deposition (PVD) aluminum films present unique challenges when detecting particulate defects with a Surface Scanning Inspection System (SSIS). Aluminum (Al) films 4500Å thick were deposited on 300mm particle grade bare Si wafers at two temperatures using a Novellus Systems INOVA® NExT,.. Film surface roughness and morphology measurements were performed using a Veeco Vx310® atomic force microscope (AFM). AFM characterization found the high deposition temperature (TD) Al roughness (Root Mean Square 16.5 nm) to be five-times rougher than the low-TD Al roughness (rms 3.7 nm). High-TD Al had grooves at the grain boundaries that were measured to be 20 to 80 nm deep. Scanning electron microscopy (SEM) examination, with a Hitachi RS6000 defect review SEM, confirmed the presence of pronounced grain grooves. SEM images established that the low-TD filmed wafers have fine grains (0.1 to 0.3 um diameter) and the high-TD film wafers have fifty-times larger equiaxed plateletshape grains (5 to 15 um diameter). Calibrated Poly-Styrene Latex (PSL) spheres ranging in size from 90 nm to 1 μm were deposited in circular patterns on the wafers using an aerosol deposition chamber. PSL sphere depositions at each spot were controlled to yield 2000 to 5000 counts. A Hitachi LS9100® dark field full wafer SSIS was used to experimentally determine the relationship of the PSL sphere scattered light intensity with S-polarized light, a measure of scattering cross-section, with respect to the calibrated PSL sphere diameter. Comparison of the SSIS scattered light versus PSL spot size calibration curves shows two distinct differences. Scattering cross-section (intensity) of the PSL spheres increased on the low-TD Al film with smooth surface roughness and the low-TD Al film defect detection sensitivity was 126 nm compared to 200 nm for the rougher high- TD Al film. This can be explained by the higher signal to noise attributed to the smooth low-TD Al. Dark field defect detection on

  9. Nuclear Scans

    Science.gov (United States)

    Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

  10. Issues of Security and Informational Privacy in relation to an Environmental Scanning System for Fighting Organized Crime

    DEFF Research Database (Denmark)

    2013-01-01

    This paper clarifies privacy challenges related to the EU project, ePOOLICE, which aims at developing an environmental scanning system for fighting organized crime by improving law enforcement agencies opportunities for strategic proactive planning in response to emerging organized crime threats....... The environmental scanning is carried out on public online data streams, focusing on modus operandi and crime trends, not on individuals. Hence, ethical and technical issues - related to societal security and potential privacy infringements in public online contexts - are being discussed in order to safeguard...... privacy all through the system design process....

  11. Application of a hybrid 3D-2D laser scanning system to the characterization of slate slabs.

    Science.gov (United States)

    López, Marcos; Martínez, Javier; Matías, José María; Vilán, José Antonio; Taboada, Javier

    2010-01-01

    Dimensional control based on 3D laser scanning techniques is widely used in practice. We describe the application of a hybrid 3D-2D laser scanning system to the characterization of slate slabs with structural defects that are difficult for the human eye to characterize objectively. Our study is based on automating the process using a 3D laser scanner and a 2D camera. Our results demonstrate that the application of this hybrid system optimally characterizes slate slabs in terms of the defects described by the Spanish UNE-EN 12326-1 standard.

  12. Technical Development of Gamma Scanning for Irradiated Fuel Rod after Upgrade of System in Hot-cell

    Energy Technology Data Exchange (ETDEWEB)

    Ryu, Woo Seog; Kim, Hee Moon; Baik, Seung Je; Yoo, Byung Ok; Choo, Yong Sun

    2007-06-15

    Non-destructive test system was installed at hot-cell(M1) in IMEF(Irradiated Materials Examination Facility) more than 10 years ago for the diametric measurement and gamma scanning of fuel rod. But this system must be needed to be remodeled for the effective operations. In 2006, the system was upgraded for 3 months. The collimator bench can be movable with horizontal direction(x-direction) by motorized system for sectional gamma scanning and 3-dimensional tomography of fuel rod. So, gamma scanning for fuel rod can be detectable by x, y and rotation directions. It may be possible to obtain the radioactivities with radial and axial directions of pellet. This system is good for the series experiments with several positions. Operation of fuel bench and gamma detection program were linked each other by new program tools. It can control detection and bench moving automatically when gamma inspection of fuel rod is carried out with axial or radial positions. Some of electronic parts were added in PLC panel, and operating panel was re-designed for the remote control. To operate the fuel bench by computer, AD converter and some I/O cards were installed in computer. All of software were developed in Windows-XP system instead of DOS system. Control programs were made by visual-C language. After upgrade of system, DUPIC fuel which was irradiated in HANARO research reactor was detected by gamma scanning. The results were good and operation of gamma scanning showed reduced inspection time and easy control of data on series of detection with axial positions. With consideration of ECT(Eddy Current Test) installation, the computer program and hardware were set up as well. But ECT is not installed yet, so we have to check abnormal situation of program and hardware system. It is planned to install ECT in 2007.

  13. DNA barcoding Satyrine butterflies (Lepidoptera: Nymphalidae) in China.

    Science.gov (United States)

    Yang, Mingsheng; Zhai, Qing; Yang, Zhaofu; Zhang, Yalin

    2016-07-01

    We investigated the effectiveness of the standard 648 bp mitochondrial COI barcode region in discriminating among Satyrine species from China. A total of 214 COI sequences were obtained from 90 species, including 34 species that have never been barcoded. Analyses of genetic divergence show that the mean interspecific genetic divergence is about 16-fold higher than within species, and little overlap occurs between them. Neighbour-joining (NJ) analyses showed that 48 of the 50 species with two or more individuals, including two cases with deep intraspecific divergence (>3%), are monophyletic. Furthermore, when our sequences are combined with the conspecific sequences sampled from distantly geographic regions, the "barcoding gap" still exists, and all related species are recovered to be monophyletic in NJ analysis. Our study demonstrates that COI barcoding is effective in discriminating among the satyrine species of China, and provides a reference library for their future molecular identification.

  14. 75 FR 56922 - Implementation of the Intelligent Mail Package Barcode

    Science.gov (United States)

    2010-09-17

    ... integration of multiple extra services. IMpb and Electronic Documentation The IMpb will provide piece-level..., reducing the number of barcodes on a package. Permit the use of a 6-digit or 9-digit numeric Mailer ID...

  15. Testing evolutionary hypotheses for DNA barcoding failure in willows.

    Science.gov (United States)

    Twyford, Alex D

    2014-10-01

    The goal of DNA barcoding is to enable the rapid identification of taxa from short diagnostic DNA sequence profiles. But how feasible is this objective when many evolutionary processes, such as hybridization and selective sweeps, cause alleles to be shared among related taxa? In this issue of Molecular Ecology, Percy et al. (2014) test the full suite of seven candidate plant barcoding loci in a broad geographic sample of willow species. They show exceptional plastid haplotype sharing between species across continents, with most taxa not possessing a unique barcode sequence. Using population genetic and molecular dating analyses, they implicate hybridization and selective sweeps, but not incomplete lineage sorting, as the historical processes causing widespread haplotype sharing among willow taxa. This study represents an exceptional case of how poorly barcoding can perform, and highlights methodological issues using universal organellar regions for species identification.

  16. DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines.

    Science.gov (United States)

    Casas, Princess Angelie S; Sing, Kong-Wah; Lee, Ping-Shin; Nuñeza, Olga M; Villanueva, Reagan Joseph T; Wilson, John-James

    2017-02-03

    Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.

  17. Topological mapping and navigation in indoor environment with invisible barcode

    Energy Technology Data Exchange (ETDEWEB)

    Huh, Jin Wook [Agency for Defense Development, Daejeon (Korea, Republic of); Chung, Woong Sik [Microrobot, Seoul (Korea, Republic of); Chung, Wan Kyun [Pohang University of Science and Technology, Pohang (Korea, Republic of)

    2006-09-15

    This paper addresses the localization and navigation problem using invisible two dimensional barcodes on the floor. Compared with other methods using natural/artificial landmark, the proposed localization method has great advantages in cost and appearance, since the location of the robot is perfectly known using the barcode information after the mapping is finished. We also propose a navigation algorithm which uses the topological structure. For the topological information, we define nodes and edges which are suitable for indoor navigation, especially for large area having multiple rooms, many walls and many static obstacles. The proposed algorithm also has an advantage that errors occurred in each node are mutually independent and can be compensated exactly after some navigation using barcode. Simulation and experimental results were performed to verify the algorithm in the barcode environment, and the result showed an excellent performance. After mapping, it is also possible to solve the kidnapped case and generate paths using topological information.

  18. INS/GPS/LiDAR Integrated Navigation System for Urban and Indoor Environments Using Hybrid Scan Matching Algorithm

    Directory of Open Access Journals (Sweden)

    Yanbin Gao

    2015-09-01

    Full Text Available This paper takes advantage of the complementary characteristics of Global Positioning System (GPS and Light Detection and Ranging (LiDAR to provide periodic corrections to Inertial Navigation System (INS alternatively in different environmental conditions. In open sky, where GPS signals are available and LiDAR measurements are sparse, GPS is integrated with INS. Meanwhile, in confined outdoor environments and indoors, where GPS is unreliable or unavailable and LiDAR measurements are rich, LiDAR replaces GPS to integrate with INS. This paper also proposes an innovative hybrid scan matching algorithm that combines the feature-based scan matching method and Iterative Closest Point (ICP based scan matching method. The algorithm can work and transit between two modes depending on the number of matched line features over two scans, thus achieving efficiency and robustness concurrently. Two integration schemes of INS and LiDAR with hybrid scan matching algorithm are implemented and compared. Real experiments are performed on an Unmanned Ground Vehicle (UGV for both outdoor and indoor environments. Experimental results show that the multi-sensor integrated system can remain sub-meter navigation accuracy during the whole trajectory.

  19. OCCLUSION AND ARTICULATION IN BRUXISM AND BRUXOMANIA INVESTIGATED WITH THE SYSTEM T-SCAN III.

    Directory of Open Access Journals (Sweden)

    Mariana Dimova

    2014-11-01

    Full Text Available Aim: To be analyzed common features of occlusal relationships in patients with bruxism and bruxomania at maximum intercuspation (MIP and eccentric jaw movements. Materials and Methods: 30 patients (22 women and 8 men, mean aged of 42,8 ± 13,3 with bruxism and/or bruxomania are examined with the system T-Scan III. Sequence of records is - at maximum intercuspation (MIP; in manual leading to central relation and in eccentric jaw movements. In the same sequence is investigated control group - 30 people (15 women and 15 men aged between 21 and 45 who didn’t have bruxism and/or bruxomania and dentition is preserved. Results: In the control group 85% of cases there is a balance of forces in both halves of the dental arch. In patients with bruxism is established uneven distribution of forces in MIP and articulation blockages (95%. There are three major reasons that impede spontaneous bilateral closing - force outliers (93% of cases; low force outliers (82% and presence of interceptive contacts and sliding occurring in the beginning of occlusion time until MIP (in all patients. Conclusions: In order to achieve a balanced occlusion in patients with bruxism and/or bruxomania required are correct diagnosis, registration and removal of preliminary contacts, articulation blockages and infraocclusion. Occlusal analysis is objective and an indicator of subsequent treatment only when it is a combination of clinical, instrumental and computerized occlusal analysis.

  20. Feasibility of fiber optic displacement sensor scanning system for imaging of dental cavity

    Science.gov (United States)

    Rahman, Husna Abdul; Che Ani, Adi Izhar; Harun, Sulaiman Wadi; Yasin, Moh.; Apsari, Retna; Ahmad, Harith

    2012-07-01

    The purpose of this study is to investigate the potential of intensity modulated fiber optic displacement sensor scanning system for the imaging of dental cavity. Here, we discuss our preliminary results in the imaging of cavities on various teeth surfaces, as well as measurement of the diameter of the cavities which are represented by drilled holes on the teeth surfaces. Based on the analysis of displacement measurement, the sensitivities and linear range for the molar, canine, hybrid composite resin, and acrylic surfaces are obtained at 0.09667 mV/mm and 0.45 mm 0.775 mV/mm and 0.4 mm 0.5109 mV/mm and 0.5 mm and 0.25 mV/mm and 0.5 mm, respectively, with a good linearity of more than 99%. The results also show a clear distinction between the cavity and surrounding tooth region. The stability, simplicity of design, and low cost of fabrication make it suitable for restorative dentistry.

  1. Optical detection of metastatic cancer cells using a scanned laser pico-projection system

    Science.gov (United States)

    Huang, Chih-Ling; Chiu, Wen-Tai; Lo, Yu-Lung; Chuang, Chin-Ho; Chen, Yu-Bin; Chang, Shu-Jing; Ke, Tung-Ting; Cheng, Hung-Chi; Wu, Hua-Lin

    2015-03-01

    Metastasis is responsible for 90% of all cancer-related deaths in humans. As a result, reliable techniques for detecting metastatic cells are urgently required. Although various techniques have been proposed for metastasis detection, they are generally capable of detecting metastatic cells only once migration has already occurred. Accordingly, the present study proposes an optical method for physical characterization of metastatic cancer cells using a scanned laser pico-projection system (SLPP). The validity of the proposed method is demonstrated using five pairs of cancer cell lines and two pairs of non-cancer cell lines treated by IPTG induction in order to mimic normal cells with an overexpression of oncogene. The results show that for all of the considered cell lines, the SLPP speckle contrast of the high-metastatic cells is significantly higher than that of the low-metastatic cells. As a result, the speckle contrast measurement provides a reliable means of distinguishing quantitatively between low- and high-metastatic cells of the same origin. Compared to existing metastasis detection methods, the proposed SLPP approach has many advantages, including a higher throughput, a lower cost, a larger sample size and a more reliable diagnostic performance. As a result, it provides a highly promising solution for physical characterization of metastatic cancer cells in vitro.

  2. Application of chemometric methods to differential scanning calorimeter (DSC) to estimate nimodipine polymorphs from cosolvent system.

    Science.gov (United States)

    Siddiqui, Akhtar; Rahman, Ziyaur; Khan, Mansoor A

    2015-06-01

    The focus of this study was to evaluate the applicability of chemometrics to differential scanning calorimetry data (DSC) to evaluate nimodipine polymorphs. Multivariate calibration models were built using DSC data from known mixtures of the nimodipine modification. The linear baseline correction treatment of data was used to reduce dispersion in thermograms. Principal component analysis of the treated and untreated data explained 96% and 89% of the data variability, respectively. Score and loading plots correlated variability between samples with change in proportion of nimodipine modifications. The R(2) for principal component regression (PCR) and partial lease square regression (PLS) were found to be 0.91 and 0.92. The root mean square of standard error of the treated samples for calibration and validation in PCR and PLS was found to be lower than the untreated sample. These models were applied to samples recrystallized from a cosolvent system, which indicated different proportion of modifications in the mixtures than those obtained by placing samples under different storage conditions. The model was able to predict the nimodipine modifications with known margin of error. Therefore, these models can be used as a quality control tool to expediently determine the nimodipine modification in an unknown mixture.

  3. A FEASIBILITY STUDY ON USE OF GENERIC MOBILE LASER SCANNING SYSTEM FOR DETECTING ASPHALT PAVEMENT CRACKS

    Directory of Open Access Journals (Sweden)

    X. Chen

    2016-06-01

    Full Text Available This study aims to automatically detect pavement cracks on urban roads by employing the 3D point clouds acquired by a mobile laser scanning (MLS system. Our method consists of four steps: ground point filtering, high-pass convolution, matched filtering, and noise removal. First, a voxel-based upward growing method is applied to construct Digital Terrain Model (DTM of the road surface. Then, a high-pass filter convolutes the DTM to detect local elevation changes that may embed cracking information. Next, a two-step matched filter is applied to extract crack features. Lastly, a noise removal process is conducted to refine the results. Instead of using MLS intensity, this study takes advantages of the MLS elevation information to perform automated crack detection from large-volume, mixed-density, unstructured MLS point clouds. Four types of cracks including longitudinal, transvers, random, and alligator cracks are detected. Our results demonstrated that the proposed method works well with the RIEGL VMX-450 point clouds and can detect cracks in moderate-to-severe severity (13 - 25 mm within a 200 m by 30 m urban road segment located in Kingston, Ontario, at one time. Due to the resolution capability, small cracks with slight severity remain unclear in the MLS point cloud.

  4. a Feasibility Study on Use of Generic Mobile Laser Scanning System for Detecting Asphalt Pavement Cracks

    Science.gov (United States)

    Chen, Xinqu; Li, Jonathan

    2016-06-01

    This study aims to automatically detect pavement cracks on urban roads by employing the 3D point clouds acquired by a mobile laser scanning (MLS) system. Our method consists of four steps: ground point filtering, high-pass convolution, matched filtering, and noise removal. First, a voxel-based upward growing method is applied to construct Digital Terrain Model (DTM) of the road surface. Then, a high-pass filter convolutes the DTM to detect local elevation changes that may embed cracking information. Next, a two-step matched filter is applied to extract crack features. Lastly, a noise removal process is conducted to refine the results. Instead of using MLS intensity, this study takes advantages of the MLS elevation information to perform automated crack detection from large-volume, mixed-density, unstructured MLS point clouds. Four types of cracks including longitudinal, transvers, random, and alligator cracks are detected. Our results demonstrated that the proposed method works well with the RIEGL VMX-450 point clouds and can detect cracks in moderate-to-severe severity (13 - 25 mm) within a 200 m by 30 m urban road segment located in Kingston, Ontario, at one time. Due to the resolution capability, small cracks with slight severity remain unclear in the MLS point cloud.

  5. Inter-laboratory performance between two nanoparticle air filtration systems using scanning mobility particle analyzers

    Science.gov (United States)

    Lore, Michael B.; Sambol, Anthony R.; Japuntich, Daniel A.; Franklin, Luke M.; Hinrichs, Steven H.

    2011-04-01

    The performance of two aerosol testing systems, at two different laboratories (University of Nebraska Medical Center—UNMC and 3M Company), was compared to evaluate which calibration procedures minimized variability in filter testing of nanoparticles. Both charged electret and uncharged flat-web fibrous filters were used with Scanning Mobility Particle Sizers to give upstream and downstream size distributions and calculate filter penetration. Challenge aerosols were polydisperse nanoparticles of sodium chloride (NaCl) ranging from approximately 10-300 nm and monodisperse polystyrene latex (PSL) spheres of preselected sizes, including 40, 60, 100, and 200 nm. The implementation of optimized procedures resulted in comparable filtration performance at the two testing sites with challenges of NaCl particles and PSL spheres. The penetration results for the uncharged filter were nearly identical for both challenges, while lower penetration through the charged filter was observed with NaCl aerosol, probably due to differences in NaCl and PSL dielectric constants. Results showed that reproducible, comparable nanoparticle filtration data could be achieved between two separate laboratories when sources of error and proper calibration procedures were addressed.

  6. A-scan ultrasound system for real-time puncture safety assessment during percutaneous nephrolithotomy

    Science.gov (United States)

    Rodrigues, Pedro L.; Rodrigues, Nuno F.; Fonseca, Jaime C.; von Krüger, M. A.; Pereira, W. C. A.; Vilaça, João. L.

    2015-03-01

    Background: Kidney stone is a major universal health problem, affecting 10% of the population worldwide. Percutaneous nephrolithotomy is a first-line and established procedure for disintegration and removal of renal stones. Its surgical success depends on the precise needle puncture of renal calyces, which remains the most challenging task for surgeons. This work describes and tests a new ultrasound based system to alert the surgeon when undesirable anatomical structures are in between the puncture path defined through a tracked needle. Methods: Two circular ultrasound transducers were built with a single 3.3-MHz piezoelectric ceramic PZT SN8, 25.4 mm of radius and resin-epoxy matching and backing layers. One matching layer was designed with a concave curvature to work as an acoustic lens with long focusing. The A-scan signals were filtered and processed to automatically detect reflected echoes. Results: The transducers were mapped in water tank and tested in a study involving 45 phantoms. Each phantom mimics different needle insertion trajectories with a percutaneous path length between 80 and 150 mm. Results showed that the beam cross-sectional area oscillates around the ceramics radius and it was possible to automatically detect echo signals in phantoms with length higher than 80 mm. Conclusions: This new solution may alert the surgeon about anatomical tissues changes during needle insertion, which may decrease the need of X-Ray radiation exposure and ultrasound image evaluation during percutaneous puncture.

  7. Robust dead reckoning system for mobile robots based on particle filter and raw range scan.

    Science.gov (United States)

    Duan, Zhuohua; Cai, Zixing; Min, Huaqing

    2014-09-04

    Robust dead reckoning is a complicated problem for wheeled mobile robots (WMRs), where the robots are faulty, such as the sticking of sensors or the slippage of wheels, for the discrete fault models and the continuous states have to be estimated simultaneously to reach a reliable fault diagnosis and accurate dead reckoning. Particle filters are one of the most promising approaches to handle hybrid system estimation problems, and they have also been widely used in many WMRs applications, such as pose tracking, SLAM, video tracking, fault identification, etc. In this paper, the readings of a laser range finder, which may be also interfered with by noises, are used to reach accurate dead reckoning. The main contribution is that a systematic method to implement fault diagnosis and dead reckoning in a particle filter framework concurrently is proposed. Firstly, the perception model of a laser range finder is given, where the raw scan may be faulty. Secondly, the kinematics of the normal model and different fault models for WMRs are given. Thirdly, the particle filter for fault diagnosis and dead reckoning is discussed. At last, experiments and analyses are reported to show the accuracy and efficiency of the presented method.

  8. Cosmetic and aesthetic skin photosurgery using a computer-assisted CO2 laser-scanning system

    Science.gov (United States)

    Dutu, Doru C. A.; Dumitras, Dan C.; Nedelcu, Ioan; Ghetie, Sergiu D.

    1997-12-01

    Since the first application of CO2 laser in skin photosurgery, various techniques such as laser pulsing, beam scanning and computer-assisted laser pulse generator have been introduced for the purpose of reducing tissue carbonization and thermal necrosis. Using a quite simple XY optical scanner equipped with two galvanometric driven mirrors and an appropriate software to process the scanning data and control the interaction time and energy density in the scanned area, we have obtained a device which can improve CO2 laser application in cosmetic and aesthetic surgery. The opto-mechanical CO2 laser scanner based on two total reflecting flat mirrors placed at 90 degree(s) in respect to the XY scanning directions and independently driven through a magnetic field provides a linear movement of the incident laser beam in the operating field. A DA converter supplied with scanning data by the software enables a scanning with linearity better than 1% for a maximum angular deviation of 20 degree(s). Because the scanning quality of the laser beam in the operating field is given not only by the displacement function of the two mirrors, but also by the beam characteristics in the focal plane and the cross distribution in the laser beam, the surgeon can control through software either the scanning field dimensions or the distance between two consecutive points of the vertically and/or horizontally sweep line. The development of computer-assisted surgical scanning techniques will help control the surgical laser, to create either a reproducible incision with a controlled depth or a controlled incision pattern with minimal incision width, a long desired facility for plastic surgery, neurosurgery, ENT and dentistry.

  9. DNA Barcoding of the Mexican Sedative and Anxiolytic Plant Galphimia glauca

    Science.gov (United States)

    Sharma, Ashutosh; Folch, Jorge Luis; Cardoso-Taketa, Alexandre; Lorence, Argelia; Villarreal, María Luisa

    2015-01-01

    Ethnopharmacology relevance Galphimiaglauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study The aim of this investigation is to find out if populations of Galphimiaglauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations. Materials and methods We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by 1H-NMR and multivariate data analysis. Results and conclusions This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines, as well as for any breeding programs for this species. PMID:23010364

  10. Improved COI barcoding primers for Southeast Asian perching birds (Aves: Passeriformes).

    Science.gov (United States)

    Lohman, David J; Prawiradilaga, Dewi M; Meier, Rudolf

    2009-01-01

    The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes.

  11. DNA barcoding the native flowering plants and conifers of Wales.

    Science.gov (United States)

    de Vere, Natasha; Rich, Tim C G; Ford, Col R; Trinder, Sarah A; Long, Charlotte; Moore, Chris W; Satterthwaite, Danielle; Davies, Helena; Allainguillaume, Joel; Ronca, Sandra; Tatarinova, Tatiana; Garbett, Hannah; Walker, Kevin; Wilkinson, Mike J

    2012-01-01

    We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

  12. DNA barcoding the native flowering plants and conifers of Wales.

    Directory of Open Access Journals (Sweden)

    Natasha de Vere

    Full Text Available We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species. Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85% are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments, formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

  13. Graded core/shell semiconductor nanorods and nanorod barcodes

    Science.gov (United States)

    Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

    2010-12-14

    Graded core/shell semiconductor nanorods and shaped nanorods are disclosed comprising Group II-VI, Group III-V and Group IV semiconductors and methods of making the same. Also disclosed are nanorod barcodes using core/shell nanorods where the core is a semiconductor or metal material, and with or without a shell. Methods of labeling analytes using the nanorod barcodes are also disclosed.

  14. Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.

    Science.gov (United States)

    Mark, Kristiina; Cornejo, Carolina; Keller, Christine; Flück, Daniela; Scheidegger, Christoph

    2016-09-01

    Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

  15. The neuromuscular system of Pycnophyes kielensis (Kinorhyncha: Allomalorhagida investigated by confocal laser scanning microscopy

    Directory of Open Access Journals (Sweden)

    Andreas Altenburger

    2016-11-01

    Full Text Available Abstract Background Kinorhynchs are ecdysozoan animals with a phylogenetic position close to priapulids and loriciferans. To understand the nature of segmentation within Kinorhyncha and to infer a probable ancestry of segmentation within the last common ancestor of Ecdysozoa, the musculature and the nervous system of the allomalorhagid kinorhynch Pycnophyes kielensis were investigated by use of immunohistochemistry, confocal laser scanning microscopy, and 3D reconstruction software. Results The kinorhynch body plan comprises 11 trunk segments. Trunk musculature consists of paired ventral and dorsal longitudinal muscles in segments 1–10 as well as dorsoventral muscles in segments 1–11. Dorsal and ventral longitudinal muscles insert on apodemes of the cuticle inside the animal within each segment. Strands of longitudinal musculature extend over segment borders in segments 1–6. In segments 7–10, the trunk musculature is confined to the segments. Musculature of the digestive system comprises a strong pharyngeal bulb with attached mouth cone muscles as well as pharyngeal bulb protractors and retractors. The musculature of the digestive system shows no sign of segmentation. Judged by the size of the pharyngeal bulb protractors and retractors, the pharyngeal bulb, as well as the introvert, is moved passively by internal pressure caused by concerted action of the dorsoventral muscles. The nervous system comprises a neuropil ring anterior to the pharyngeal bulb. Associated with the neuropil ring are flask-shaped serotonergic somata extending anteriorly and posteriorly. A ventral nerve cord is connected to the neuropil ring and runs toward the anterior until an attachment point in segment 1, and from there toward the posterior with one ganglion in segment 6. Conclusions Segmentation within Kinorhyncha likely evolved from an unsegmented ancestor. This conclusion is supported by continuous trunk musculature in the anterior segments 1–6, continuous

  16. Design and operation of gamma scan and fission gas sampling systems for characterization of irradiated commercial nuclear fuel

    Energy Technology Data Exchange (ETDEWEB)

    Knox, C.A.; Thornhill, R.E.; Mellinger, G.B.

    1989-09-01

    One of the primary objectives of the Materials Characterization Center (MCC) is to acquire and characterize spent fuels used in waste form testing related to nuclear waste disposal. The initial steps in the characterization of a fuel rod consist of gamma scanning the rod and sampling the gas contained in the fuel rod (referred to as fission gas sampling). The gamma scan and fission gas sampling systems used by the MCC are adaptable to a wide range of fuel types and have been successfully used to characterize both boiling water reactor (BWR) and pressurized water reactor (PWR) fuel rods. This report describes the design and operation of systems used to gamma scan and fission gas sample full-length PWR and BWR fuel rods. 1 ref., 10 figs., 1 tab.

  17. Equivalente esférico e valores da espessura da camada de fibras nervosas obtidas com o GDX TM Scanning Laser System® Spherical equivalent and nerve fiber layer thickness assessed with GDX TM Scanning Laser System®

    Directory of Open Access Journals (Sweden)

    Lênio Souza Alvarenga

    1999-12-01

    Full Text Available Objetivo: Estudar a influência do equivalente esférico nos valores obtidos pelo GDX TM Scanning Laser System®. Métodos: Foram avaliados 41 olhos de 41 voluntários sem doenças oculares e com campo visual sem alterações. Foi realizada a polarimetria de varredura a laser com o GDX TM Scanning Laser System® de acordo com as instruções contidas no manual do aparelho. Foram comparados os valores obtidos nesse exame em um grupo de pacientes com equivalente esférico positivo e em um outro com este valor nulo ou negativo, pelo teste de Mann-Whitney. Resultados: Não se verificou diferença estatística entre os valores obtidos nos olhos de pacientes do grupo I e os do grupo II. Não foi encontrada correlação entre o equivalente esférico e os valores obtidos com o GDX TM Scanning Laser System®. Conclusões: Na amostra estudada não houve diferença estatística entre os valores obtidos em um grupo de olhos com equivalente esférico positivo e outro com este valor negativo ou nulo, usando-se o GDX TM Scanning Laser System®.Purpose: To evaluate the effect of spherical equivalent on the acquisition of nerve fiber layer (NFL thickness with GDX TM Scanning Laser System®. Methods: Forty-one eyes of 41 volunteers were enrolled in this study. All of them presented with no ocular disease and no visual field defect. The NFL thickness was measured with GDX TM Scanning Laser System® as described in its manual. The values obtained in a group of volunteers with negative spherical equivalent (group I were compared to those from a group with a positive spherical equivalent (group II by the Mann-Whitney test. Results: There was no statistical difference between mea-surements in eyes of group I and those in group II. The NFL thickness measurements were not correlated with the sphe-rical equivalent. Conclusions: In the studied group there was no statistical difference in the GDX TM Scanning Laser System® parameters related to spherical equivalent.

  18. Image-based tracking system for vibration measurement of a rotating object using a laser scanning vibrometer

    Science.gov (United States)

    Kim, Dongkyu; Khalil, Hossam; Jo, Youngjoon; Park, Kyihwan

    2016-06-01

    An image-based tracking system using laser scanning vibrometer is developed for vibration measurement of a rotating object. The proposed system unlike a conventional one can be used where the position or velocity sensor such as an encoder cannot be attached to an object. An image processing algorithm is introduced to detect a landmark and laser beam based on their colors. Then, through using feedback control system, the laser beam can track a rotating object.

  19. Assessment of candidate plant DNA barcodes using the Rutaceae family.

    Science.gov (United States)

    Luo, Kun; Chen, ShiLin; Chen, KeLi; Song, JingYuan; Yao, Hui; Ma, XinYe; Zhu, YingJie; Pang, XiaoHui; Yu, Hua; Li, XiWen; Liu, Zhen

    2010-06-01

    DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (psbA-trnH, matK, ycf5, rpoC1, rbcL, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode's utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.

  20. DNA barcoding of Gaultheria L.in China (Ericaceae: Vaccinioideae)

    Institute of Scientific and Technical Information of China (English)

    He REN; Lu LU; Hong WANG; De-Zhu LI

    2011-01-01

    Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer (ITS),were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance,Wilcoxon signed rank test,and tree-based analyses.This study included 186 individuals from 89 populations representing 30 species.For all individuals,single locus markers showed high levels of sequencing universality but were ineffective for species resolvability.Polymerase chain reaction amplification and sequencing were successful for all four loci.Both ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA.A combination ofmatK and ITS was the most efficient DNA barcode among all studied regions,however,they do not represent an appropriate candidate barcode for Chinese Gaultheria,by which only 11 out of 30 species can be separated.Loci rbcL,matK,and trnH-psbA,which were recently proposed as universal plant barcodes,have a very poor capacity for species separation for Chinese Gaultheria.DNA barcodes may be reliable tools to identify the evolutionary units of this group,so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories.

  1. DNA barcoding: error rates based on comprehensive sampling.

    Directory of Open Access Journals (Sweden)

    Christopher P Meyer

    2005-12-01

    Full Text Available DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries. We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1 identifying samples against a well-characterized phylogeny, and (2 assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a "barcoding gap" between the two, we find substantial overlap, leading to minimal error rates of approximately 17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations.

  2. A High-Precision Registration Technology Based on Bundle Adjustment in Structured Light Scanning System

    Directory of Open Access Journals (Sweden)

    Jianying Yuan

    2014-01-01

    Full Text Available The multiview 3D data registration precision will decrease with the increasing number of registrations when measuring a large scale object using structured light scanning. In this paper, we propose a high-precision registration method based on multiple view geometry theory in order to solve this problem. First, a multiview network is constructed during the scanning process. The bundle adjustment method from digital close range photogrammetry is used to optimize the multiview network to obtain high-precision global control points. After that, the 3D data under each local coordinate of each scan are registered with the global control points. The method overcomes the error accumulation in the traditional registration process and reduces the time consumption of the following 3D data global optimization. The multiview 3D scan registration precision and efficiency are increased. Experiments verify the effectiveness of the proposed algorithm.

  3. An automatic scanning method for high throughput microscopic system to facilitate medical genetic diagnosis: an initial study

    Science.gov (United States)

    Qiu, Yuchen; Chen, Xiaodong; Li, Zheng; Li, Yuhua; Chen, Wei R.; Zheng, Bin; Li, Shibo; Liu, Hong

    2012-03-01

    The purpose of this paper is to report a new automatic scanning scheme for high throughput microscopic systems aiming to facilitate disease diagnosis in genetic laboratories. To minimize the impact of the random vibration and mechanical drifting of the scanning stage in microscopic image acquisition, auto-focusing operations are usually applied repeatedly during the scanning process. Such methods ensure the acquisition of well focused images for clinical diagnosis, but are time consuming. The technique investigated in this preliminary study applies the auto-focusing operations at a limited number of locations on the slide. For the rest of the imaging field, the focusing position is quickly adjusted through linear interpolation. In this initial validation study, blood pathological slides containing both metaphase and interphase cells are scanned. For a selected area of 6.9mm×6.9mm, a number of 2×2, 3×2, 3×3, and 4×4 positions are evenly sampled for auto-focusing operations. Respectively, 25, 29, 40, and 41 clinically meaningful cells are identified for each sampling scheme. For the specific case investigated, the results demonstrate that the 4 position auto-focusing scheme could obtain the adequate number of clinically meaningful cells for the diagnosis. The schemes with more auto-focusing operations provide an option for high reliability diagnosis when clinically necessary. More comprehensive research is planned, and that may lead to optimal design of trade-off for developing the scanning scheme of the high throughput microscopic systems.

  4. A new centering method of the measuring probe for spiral scanning-based surface profile measurement systems

    Science.gov (United States)

    Du, Hui-Lin; Zeng, Pei-Yang; Ju, Bing-Feng; Zhou, Zhao-Zhong; Xu, Shaoning; Sun, Anyu

    2017-02-01

    Spiral scanning is a high-efficiency scanning mode for surface profile measurement systems. The most important priority to realize the spiral scanning mode is to accurately align the measuring probe with the rotational centre of the spindle. This paper proposes a novel centre alignment method of the measuring probe, which is considered to be suitable for any type of spiral scanning surface measurement systems. The proposed method, which only needs a tilted flat mirror as the artefact, makes the time-consuming centre alignment process of the measuring probe become much easier and faster. The operational steps of the proposed method are presented. Experiments have also been carried out based on a self-developed optical profiler with spiral scanning operation to verity the feasibility of the proposed method. The experimental results show that the proposed method is capable of conducting a fast alignment (only takes 3 min) while maintaining a high alignment accuracy. Evaluation of the alignment accuracy shows that the centering error is less than 10 µm on the mechanical guide rail stage and about 1.7 µm on the air-bearing stage.

  5. Computer-assisted evaluation of pulmonary emphysema in CT scans: comparison between a locally developed system and a freeware system

    Energy Technology Data Exchange (ETDEWEB)

    Felix, John Hebert da Silva; Cortez, Paulo Cesar; Costa, Rodrigo Carvalho Sousa [Federal University of Ceara (UFC), Fortaleza, CE (Brazil). Dept. of Computer Engineering. Computing Systems Engineering Lab.], e-mail: jhsfelix@gmail.com; Fortaleza, Simone Castelo Branco; Pereira, Eanes Delgado Barros; Holanda, Marcelo Alcantara [Federal University of Ceara (UFC), Fortaleza, CE (Brazil). Walter Cantidio University Hospital

    2009-09-15

    Objective: to present a locally developed system of computer vision for use with HRCT images, designated SIStema para a Deteccao e a quantificacao de Enfisema Pulmonar (SISDEP, System to Detect and Quantify Pulmonary Emphysema), and to compare this system with a free ware system tool. Methods: thirty-three HRCT images scanned at the apex, hilum and base of the lungs of 11 patients with COPD were analyzed. The SISDEP was compared with the Osiris Medical Imaging Software Program regarding lung parenchyma segmentation, precision of the measurement of the cross-sectional area of the lungs in mm{sup 2}, mean lung density (MLD), relative area (RA) of the lung occupied by voxels with attenuation values < -950 Hounsfield units (RA -950), 15th percentile point (Perc15) and visualization of hyper inflated areas using a color mask. Results: although both computational systems were efficient in segmenting the lungs, the SISDEP performed this task automatically and more rapidly. There were significant correlations between the two systems in terms of the results obtained for lung cross-sectional area, MLD, RA -950 and Perc15 (r{sup 2} = 0.99, 0.99, 0.99 and 1.00, respectively). The color mask tool of the SISDEP allowed excellent visualization of hyper inflated areas, discriminating them from normal areas. Conclusions: the SISDEP was efficient in segmenting the lungs and quantifying lung hyper inflation, presenting an excellent correlation with the Osiris system. The SISDEP constitutes a promising computational tool for diagnosing and assessing the progression of emphysema in HRCT images of COPD patients. (author)

  6. DNA barcoding of Pedicularis L.(Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus

    Institute of Scientific and Technical Information of China (English)

    Wen-Bin YU; pan-Hui HUANG; Richard H. REE; Min-Lu LIU; De-Zhu LI; Hong WANG

    2011-01-01

    One application ofDNA barcoding is species identification based on sequences of a short and standardized DNA region.In plants,various DNA regions,alone or in combination,have been proposed and investigated,but consensus on a universal plant barcode remains elusive.In this study,we tested the utility of four candidate barcoding regions (rbcL,matK,trnH-psbA,and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae).Amplification and sequencing was successful using single primer pairs for rbcL,trnH-psbA,and ITS,whereas two primer pairs were required for matK.Patterns of sequence divergence commonly showed a “barcoding gap”,that is,a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species,respectively Considering primer universality,ease of amplification and sequencing,and performance in discriminating species,we found the most effective single-region barcode for Pedicularis to be ITS,and the most effective two-region barcode to be rbcL +ITS.Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample,and were effective in placing unidentified samples in known species groups.Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis,a species-rich cosmopolitan clade much in need of revision,as well as ecological studies in its center of diversity,the Hengduan Mountains region of China.

  7. DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China

    Science.gov (United States)

    Li, Yuling; Tong, Yi; Xing, Fuwu

    2016-01-01

    The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history. PMID:27994608

  8. DNA Barcoding: Amplification and sequence analysis of rbcl and matK genome regions in three divergent plant species

    Directory of Open Access Journals (Sweden)

    Javed Iqbal Wattoo

    2016-11-01

    Full Text Available Background: DNA barcoding is a novel method of species identification based on nucleotide diversity of conserved sequences. The establishment and refining of plant DNA barcoding systems is more challenging due to high genetic diversity among different species. Therefore, targeting the conserved nuclear transcribed regions would be more reliable for plant scientists to reveal genetic diversity, species discrimination and phylogeny. Methods: In this study, we amplified and sequenced the chloroplast DNA regions (matk+rbcl of Solanum nigrum, Euphorbia helioscopia and Dalbergia sissoo to study the functional annotation, homology modeling and sequence analysis to allow a more efficient utilization of these sequences among different plant species. These three species represent three families; Solanaceae, Euphorbiaceae and Fabaceae respectively. Biological sequence homology and divergence of amplified sequences was studied using Basic Local Alignment Tool (BLAST. Results: Both primers (matk+rbcl showed good amplification in three species. The sequenced regions reveled conserved genome information for future identification of different medicinal plants belonging to these species. The amplified conserved barcodes revealed different levels of biological homology after sequence analysis. The results clearly showed that the use of these conserved DNA sequences as barcode primers would be an accurate way for species identification and discrimination. Conclusion: The amplification and sequencing of conserved genome regions identified a novel sequence of matK in native species of Solanum nigrum. The findings of the study would be applicable in medicinal industry to establish DNA based identification of different medicinal plant species to monitor adulteration.

  9. Reliability of the TekScan MatScan® system for the measurement of plantar forces and pressures during barefoot level walking in healthy adults

    OpenAIRE

    Munteanu Shannon E; Menz Hylton B; Zammit Gerard V

    2010-01-01

    Abstract Background Plantar pressure systems are increasingly being used to evaluate foot function in both research settings and in clinical practice. The purpose of this study was to investigate the reliability of the TekScan MatScan® system in assessing plantar forces and pressures during barefoot level walking. Methods Thirty participants were assessed for the reliability of measurements taken one week apart for the variables maximum force, peak pressure and average pressure. The following...

  10. A new scanning system for alpha decay events as calibration sources for range-energy relation in nuclear emulsion

    Science.gov (United States)

    Yoshida, J.; Kinbara, S.; Mishina, A.; Nakazawa, K.; Soe, M. K.; Theint, A. M. M.; Tint, K. T.

    2017-03-01

    A new scanning system named "Vertex picker" has been developed to rapid collect alpha decay events, which are calibration sources for the range-energy relation in nuclear emulsion. A computer-controlled optical microscope scans emulsion layers exhaustively, and a high-speed and high-resolution camera takes their micrographs. A dedicated image processing picks out vertex-like shapes. Practical operations of alpha decay search were demonstrated by emulsion sheets of the KEK-PS E373 experiment. Alpha decays of nearly 28 events were detected in eye-check work on a PC monitor per hour. This yield is nearly 20 times more effective than that by the conventional eye-scan method. The speed and quality is acceptable for the coming new experiment, J-PARC E07.

  11. DNA barcoding in the media: does coverage of cool science reflect its social context?

    Science.gov (United States)

    Geary, Janis; Camicioli, Emma; Bubela, Tania

    2016-09-01

    Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.

  12. JPEG color barcode images analysis: A camera phone capture channel model with auto-focus

    Directory of Open Access Journals (Sweden)

    Keng T. Tan

    2009-12-01

    Full Text Available As camera phones have permeated into our everyday lives, two dimensional (2D barcode has attracted researchers and developers as a cost-effective ubiquitous computing tool. A variety of 2D barcodes and their applications have been developed. Often, only monochrome2D barcodes are used due to their robustness in an uncontrolled operating environment of camera phones. However, we are seeing an emerging use of color 2D barcodes for camera phones. Nonetheless, using a greater multitude of colors introduces errors that can negatively affect the robustness of barcode reading. This is especially true when developing a 2D barcode for camera phones which capture and store these barcode images in the baselineJPEG format. This paper presents one aspect of the errors introduced by such camera phones by modeling the camera phone capture channel for JPEG color barcode images wherein there is camera auto-focus.

  13. Multi-Range Conditional Random Field for Classifying Railway Electrification System Objects Using Mobile Laser Scanning Data

    OpenAIRE

    Jaewook Jung; Leihan Chen; Gunho Sohn; Chao Luo; Jong-Un Won

    2016-01-01

    Railways have been used as one of the most crucial means of transportation in public mobility and economic development. For safe railway operation, the electrification system in the railway infrastructure, which supplies electric power to trains, is an essential facility for stable train operation. Due to its important role, the electrification system needs to be rigorously and regularly inspected and managed. This paper presents a supervised learning method to classify Mobile Laser Scanning ...

  14. International Barcode of Life: Evolution of a global research community.

    Science.gov (United States)

    Adamowicz, Sarah J

    2015-05-01

    The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses-and for studies of food webs spanning three or more trophic levels-as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. "What is this specimen on an agricultural shipment?", "Who eats whom in this whole food web?", and even "How many species are there?" are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources.

  15. Patterns of DNA barcode variation in Canadian marine molluscs.

    Directory of Open Access Journals (Sweden)

    Kara K S Layton

    Full Text Available BACKGROUND: Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. METHODOLOGY/PRINCIPAL FINDINGS: This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2% intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%, and showed a significant positive correlation with nearest neighbour distances. CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation

  16. Streamlining DNA barcoding protocols: automated DNA extraction and a new cox1 primer in arachnid systematics.

    Directory of Open Access Journals (Sweden)

    Nina Vidergar

    Full Text Available BACKGROUND: DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences--mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1--are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1 improving an automated DNA extraction protocol, (2 testing the performance of commonly used primer combinations, and (3 developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses. METHODOLOGY: We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor-an automated high throughput DNA extraction system-and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs. RESULTS: The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198 that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93% matched that of C1-J-2183. CONCLUSIONS: The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.

  17. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

    KAUST Repository

    Coll, Francesc

    2014-09-01

    Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.

  18. Scanning Electron Microscopy (SEM) Procedure for HE Powders on a LEO 438VP System

    Energy Technology Data Exchange (ETDEWEB)

    Zaka, Fowzia [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Energetic Materials Center

    2016-03-21

    This method describes the characterization of HE powders by Scanning Electron Microscopy (SEM). HE particles are dispersed onto an aluminum standard SEM specimen mount. Electron micrographs are collected at various magnifications (150 to 10,000 X) depending on HE particle size.

  19. Scanning Electron Microscopy (SEM) Procedure for HE Powders on a LEO 438VP System

    Energy Technology Data Exchange (ETDEWEB)

    Zaka, Fowzia [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Energetic Materials Center

    2016-03-08

    This method describes the characterization of HE powders by Scanning Electron Microscopy (SEM). HE particles are dispersed onto an aluminum standard SEM specimen mount. Electron micrographs are collected at various magnifications (150 to 10,000 X) depending on HE particle size.

  20. Use of Slow-Scan Television Systems in Telemedicine, Distance Education, Government, and Industrial Applications.

    Science.gov (United States)

    Southworth, Glen

    Reducing the costs of teaching by television through slow-scan methods is discussed. Conventional television is costly to use, largely because the wide-band communications circuits required are in limited supply. One technical answer is bandwidth compression to fit an image into less spectrum space. A simpler and far less costly answer is to…

  1. Compensation for Target Motion in Magnetic Raster Scanning System at GSI

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Conformal radiation therapy methods including the magnetic raster scanning used at GSI yield a very high dose inside tumor volume while drastically reducing the dose contribution to surrounding healthy tissue.This is achieved by delivering a previously calculated dose to every single volume element(voxel)of the tumor and

  2. Field Demonstration of Electro-Scan Defect Location Technology for Condition Assessment of Wastewater Collection Systems

    Science.gov (United States)

    The purpose of the field demonstration program is to gather technically reliable cost and performance information on selected condition assessment technologies under defined field conditions. The selected technologies include zoom camera, electro-scan (FELL-41), and a multi-sens...

  3. Surface and subsurface inspection of food safety and quality using a line-scan Raman system

    Science.gov (United States)

    This paper presents a line-scan Raman platform for food safety and quality research, which can be configured for Raman chemical imaging (RCI) mode for surface inspection and spatially offset Raman spectroscopy (SORS) mode for subsurface inspection. In the RCI mode, macro-scale imaging was achieved u...

  4. Analysis of the Possibilities of Using Low-Cost Scanning System in 3d Modeling

    Science.gov (United States)

    Kedzierski, M.; Wierzbickia, D.; Fryskowska, A.; Chlebowska, B.

    2016-06-01

    The laser scanning technique is still a very popular and fast growing method of obtaining information on modeling 3D objects. The use of low-cost miniature scanners creates new opportunities for small objects of 3D modeling based on point clouds acquired from the scan. The same, the development of accuracy and methods of automatic processing of this data type is noticeable. The article presents methods of collecting raw datasets in the form of a point-cloud using a low-cost ground-based laser scanner FabScan. As part of the research work 3D scanner from an open source FabLab project was constructed. In addition, the results for the analysis of the geometry of the point clouds obtained by using a low-cost laser scanner were presented. Also, some analysis of collecting data of different structures (made of various materials such as: glass, wood, paper, gum, plastic, plaster, ceramics, stoneware clay etc. and of different shapes: oval and similar to oval and prism shaped) have been done. The article presents two methods used for analysis: the first one - visual (general comparison between the 3D model and the real object) and the second one - comparative method (comparison between measurements on models and scanned objects using the mean error of a single sample of observations). The analysis showed, that the low-budget ground-based laser scanner FabScan has difficulties with collecting data of non-oval objects. Items built of glass painted black also caused problems for the scanner. In addition, the more details scanned object contains, the lower the accuracy of the collected point-cloud is. Nevertheless, the accuracy of collected data (using oval-straight shaped objects) is satisfactory. The accuracy, in this case, fluctuates between ± 0,4 mm and ± 1,0 mm whereas when using more detailed objects or a rectangular shaped prism the accuracy is much more lower, between 2,9 mm and ± 9,0 mm. Finally, the publication presents the possibility (for the future expansion of

  5. Range 7 Scanner Integration with PaR Robot Scanning System

    Science.gov (United States)

    Schuler, Jason; Burns, Bradley; Carlson, Jeffrey; Minich, Mark

    2011-01-01

    An interface bracket and coordinate transformation matrices were designed to allow the Range 7 scanner to be mounted on the PaR Robot detector arm for scanning the heat shield or other object placed in the test cell. A process was designed for using Rapid Form XOR to stitch data from multiple scans together to provide an accurate 3D model of the object scanned. An accurate model was required for the design and verification of an existing heat shield. The large physical size and complex shape of the heat shield does not allow for direct measurement of certain features in relation to other features. Any imaging devices capable of imaging the entire heat shield in its entirety suffers a reduced resolution and cannot image sections that are blocked from view. Prior methods involved tools such as commercial measurement arms, taking images with cameras, then performing manual measurements. These prior methods were tedious and could not provide a 3D model of the object being scanned, and were typically limited to a few tens of measurement points at prominent locations. Integration of the scanner with the robot allows for large complex objects to be scanned at high resolution, and for 3D Computer Aided Design (CAD) models to be generated for verification of items to the original design, and to generate models of previously undocumented items. The main components are the mounting bracket for the scanner to the robot and the coordinate transformation matrices used for stitching the scanner data into a 3D model. The steps involve mounting the interface bracket to the robot's detector arm, mounting the scanner to the bracket, and then scanning sections of the object and recording the location of the tool tip (in this case the center of the scanner's focal point). A novel feature is the ability to stitch images together by coordinates instead of requiring each scan data set to have overlapping identifiable features. This setup allows models of complex objects to be developed

  6. ANALYSIS OF THE POSSIBILITIES OF USING LOW-COST SCANNING SYSTEM IN 3D MODELING

    Directory of Open Access Journals (Sweden)

    M. Kedzierski

    2016-06-01

    Full Text Available The laser scanning technique is still a very popular and fast growing method of obtaining information on modeling 3D objects. The use of low-cost miniature scanners creates new opportunities for small objects of 3D modeling based on point clouds acquired from the scan. The same, the development of accuracy and methods of automatic processing of this data type is noticeable. The article presents methods of collecting raw datasets in the form of a point-cloud using a low-cost ground-based laser scanner FabScan. As part of the research work 3D scanner from an open source FabLab project was constructed. In addition, the results for the analysis of the geometry of the point clouds obtained by using a low-cost laser scanner were presented. Also, some analysis of collecting data of different structures (made of various materials such as: glass, wood, paper, gum, plastic, plaster, ceramics, stoneware clay etc. and of different shapes: oval and similar to oval and prism shaped have been done. The article presents two methods used for analysis: the first one - visual (general comparison between the 3D model and the real object and the second one - comparative method (comparison between measurements on models and scanned objects using the mean error of a single sample of observations. The analysis showed, that the low-budget ground-based laser scanner FabScan has difficulties with collecting data of non-oval objects. Items built of glass painted black also caused problems for the scanner. In addition, the more details scanned object contains, the lower the accuracy of the collected point-cloud is. Nevertheless, the accuracy of collected data (using oval-straight shaped objects is satisfactory. The accuracy, in this case, fluctuates between ± 0,4 mm and ± 1,0 mm whereas when using more detailed objects or a rectangular shaped prism the accuracy is much more lower, between 2,9 mm and ± 9,0 mm. Finally, the publication presents the possibility (for the

  7. Q-Bank Phytoplasma: A DNA Barcoding Tool for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Contaldo, Nicoletta; Paltrinieri, Samanta; Makarova, Olga;

    2015-01-01

    DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. This phytoplasma DNA barcoding protocol based on the tuf gene has been shown to identify phytoplasmas...

  8. SCANS (Shipping Cask ANalysis System) a microcomputer-based analysis system for shipping cask design review: User`s manual to Version 3a. Volume 1, Revision 2

    Energy Technology Data Exchange (ETDEWEB)

    Mok, G.C.; Thomas, G.R.; Gerhard, M.A.; Trummer, D.J.; Johnson, G.L. [Lawrence Livermore National Lab., CA (United States)

    1998-03-01

    SCANS (Shipping Cask ANalysis System) is a microcomputer-based system of computer programs and databases developed at the Lawrence Livermore National Laboratory (LLNL) for evaluating safety analysis reports on spent fuel shipping casks. SCANS is an easy-to-use system that calculates the global response to impact loads, pressure loads and thermal conditions, providing reviewers with an independent check on analyses submitted by licensees. SCANS is based on microcomputers compatible with the IBM-PC family of computers. The system is composed of a series of menus, input programs, cask analysis programs, and output display programs. All data is entered through fill-in-the-blank input screens that contain descriptive data requests. Analysis options are based on regulatory cases described in the Code of Federal Regulations 10 CFR 71 and Regulatory Guides published by the US Nuclear Regulatory Commission in 1977 and 1978.

  9. Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae).

    Science.gov (United States)

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-04-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using "best match" and "best close match" methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  10. Assessment of candidate plant DNA barcodes using the Rutaceae family

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.

  11. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Giovanna Câmara Giudicelli

    2015-04-01

    Full Text Available DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1 region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  12. Plant DNA barcoding and framework for biodiversity data sharing platform

    Directory of Open Access Journals (Sweden)

    Chunxia Zeng

    2014-05-01

    Full Text Available DNA barcoding technology provides an opportunity for rapid, accurate, and standardized species-level identification using short DNA sequences. This method speeds up species identification and classification, and presents a new tool for the management, conservation and sustainable development of biodiversity at a global level. Due to improvements in plant barcode database availability and functionality, it is becoming feasible to meet increasing demands for biodiversity information. A framework is needed for a barcoding server platform that utilizes, integrates, and shares among different data types. Such a platform would be an important step towards enabling the public to rapidly identify species and acquire species-related digital information. In this paper, we review current progress on plant DNA barcoding. Secondly, we summarize the current status of, and identify bottlenecks for, plant DNA barcode reference libraries specifically. Thirdly, in the Big Data era, it is indispensable to manage and make good use of massive amounts of plant information. We provide the following suggestions for the framework of server platform: (1 metadata should be substantial, accurate and correlative; (2 data should be normalized; (3 query entrance is convenient, efficient, easy to manage, and available for large-scale data sharing and global communication.

  13. A comparative analysis of DNA barcode microarray feature size

    Directory of Open Access Journals (Sweden)

    Smith Andrew M

    2009-10-01

    Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

  14. DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).

    Science.gov (United States)

    Oba, Yuichi; Ôhira, Hitoo; Murase, Yukio; Moriyama, Akihiko; Kumazawa, Yoshinori

    2015-01-01

    Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.

  15. Laser Scanning in Forests

    OpenAIRE

    Håkan Olsson; Juha Hyyppä; Markus Holopainen

    2012-01-01

    The introduction of Airborne Laser Scanning (ALS) to forests has been revolutionary during the last decade. This development was facilitated by combining earlier ranging lidar discoveries [1–5], with experience obtained from full-waveform ranging radar [6,7] to new airborne laser scanning systems which had components such as a GNSS receiver (Global Navigation Satellite System), IMU (Inertial Measurement Unit) and a scanning mechanism. Since the first commercial ALS in 1994, new ALS-based fore...

  16. HIGH RESOLUTION AND FAST SCANNING SQUID BASED NON-DESTRUCTIVE INSPECTION SYSTEM OF NIOBIUM SHEETS FOR SRF CAVITIES

    Energy Technology Data Exchange (ETDEWEB)

    SHU, QUAN-SHENG

    2008-06-08

    Applications in high energy physics accelerators and other fields require the use of thousands of superconducting RF (SRF) cavities that are made of high purity Nb material and the purity of niobium is critical for these cavities to reach the highest accelerating fields. Tantalum is the most prolific of metal inclusions, which can cause thermal breakdown and prevent the cavities from reaching their theoretical performance limits of 45-50 MV/m, and DOE Labs are searching for a technology that could detect small impurities in superconducting Nb sheets reaching the highest possible accelerating fields. The proposed innovative SQUID-based Nondestructive system can scan Niobium sheets used in the manufacturing of SRF cavities with both high speed and high resolution. A highly sensitive SQUID system with a gradiometer probe, non-magnetic dewar, data acquisition system, and a scanning system will be developed for fast detection of impurities in planar Nb sheets. In phase I, we will modify our existing SQUID-based eddy current system to detect 100 micron size Ta defects and a great effort will focus on achieving fast scanning of a large number of niobium sheets in a shorter time and with reasonable resolution. An older system operated by moving the sample 1 mm, stopping and waiting for 1-2 seconds, then activating a measurement by the SQUID after the short settle time is modified. A preliminary designed and implemented a SQUID scanning system that is fast and is capable of scanning a 30 cm x 30 cm Nb sheet in 15 minutes by continuously moving the table at speeds up to 10 mm/s while activating the SQUID at 1mm interval is modified and reached the Phase I goal of 100mm resolution. We have successfully demonstrated the feasibility that a fast speed SQUID scanner without sacrificing the resolution of detection can be done, and a data acquisition and analysis system is also preliminary developed. The SQUID based scanner will help reach the highest accelerating field in SRF

  17. Development of Kinematic 3D Laser Scanning System for Indoor Mapping and As-Built BIM Using Constrained SLAM

    Directory of Open Access Journals (Sweden)

    Jaehoon Jung

    2015-10-01

    Full Text Available The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM. The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m according to the guidelines of the General Services Administration for BIM accuracy.

  18. Development of kinematic 3D laser scanning system for indoor mapping and as-built BIM using constrained SLAM.

    Science.gov (United States)

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-10-16

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy.

  19. Development of Kinematic 3D Laser Scanning System for Indoor Mapping and As-Built BIM Using Constrained SLAM

    Science.gov (United States)

    Jung, Jaehoon; Yoon, Sanghyun; Ju, Sungha; Heo, Joon

    2015-01-01

    The growing interest and use of indoor mapping is driving a demand for improved data-acquisition facility, efficiency and productivity in the era of the Building Information Model (BIM). The conventional static laser scanning method suffers from some limitations on its operability in complex indoor environments, due to the presence of occlusions. Full scanning of indoor spaces without loss of information requires that surveyors change the scanner position many times, which incurs extra work for registration of each scanned point cloud. Alternatively, a kinematic 3D laser scanning system, proposed herein, uses line-feature-based Simultaneous Localization and Mapping (SLAM) technique for continuous mapping. Moreover, to reduce the uncertainty of line-feature extraction, we incorporated constrained adjustment based on an assumption made with respect to typical indoor environments: that the main structures are formed of parallel or orthogonal line features. The superiority of the proposed constrained adjustment is its reduction for uncertainties of the adjusted lines, leading to successful data association process. In the present study, kinematic scanning with and without constrained adjustment were comparatively evaluated in two test sites, and the results confirmed the effectiveness of the proposed system. The accuracy of the 3D mapping result was additionally evaluated by comparison with the reference points acquired by a total station: the Euclidean average distance error was 0.034 m for the seminar room and 0.043 m for the corridor, which satisfied the error tolerance for point cloud acquisition (0.051 m) according to the guidelines of the General Services Administration for BIM accuracy. PMID:26501292

  20. Research and Development of High-speed Laser Scanning Galvanometer System

    Directory of Open Access Journals (Sweden)

    Chao-Ching Ho

    2013-12-01

    Full Text Available This study developed and controlled laser scanning mechanism and circuit design, in order to reduce the vibratory magnitude resulted from high-speed operation. The principle of mechanism design is that the output end mirror can swing within ± 3° when the laser scanning mechanism is in operation, the accuracy value is ± 0.2°. The static simulation and dynamic measurement were carried out for mutual validation. The vibration generated in the operation of machine causes dynamic unbalance, influencing the stability of machine. In order to overcome and improve the dynamic unbalance generated when the mechanism is in motion, different solutions were proposed, such as changing the output end mass, to add elastic material in or to change constant speed control of input end motor to variable speed control.

  1. A pipette-based calibration system for fast-scan cyclic voltammetry with fast response times.

    Science.gov (United States)

    Ramsson, Eric S

    2016-01-01

    Fast-scan cyclic voltammetry (FSCV) is an electrochemical technique that utilizes the oxidation and/or reduction of an analyte of interest to infer rapid changes in concentrations. In order to calibrate the resulting oxidative or reductive current, known concentrations of an analyte must be introduced under controlled settings. Here, I describe a simple and cost-effective method, using a Petri dish and pipettes, for the calibration of carbon fiber microelectrodes (CFMs) using FSCV.

  2. Wide area scanning system and carbon microbeams at the external microbeam facility of the INFN LABEC laboratory in Florence

    Energy Technology Data Exchange (ETDEWEB)

    Giuntini, L. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Dipartimento di Fisica e Astronomia, Università di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Massi, M. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Calusi, S. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Dipartimento di Fisica e Astronomia, Università di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Castelli, L. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Carraresi, L. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Dipartimento di Fisica e Astronomia, Università di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Fedi, M.E.; Gelli, N. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Liccioli, L.; Mandò, P.A.; Mazzinghi, A. [Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Dipartimento di Fisica e Astronomia, Università di Firenze, Via Sansone 1, I-50019 Sesto Fiorentino, Firenze (Italy); Palla, L. [INFN, Sezione di Pisa and Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Romano, F.P. [Consiglio Nazionale delle Ricerche (CNR), Istituto per i Beni Archeologici e Monumentali (IBAM), Via Biblioteca, 4, 95124 Catania (Italy); Istituto Nazionale di Fisica Nucleare (INFN), LNS, Via S.Sofia 62, 95125 Catania (Italy); and others

    2015-04-01

    Recently, developments have been made to the external scanning microbeam of INFN-LABEC laboratory in Florence. A new system for mechanical sample scanning was implemented. This system allows us to acquire large maps (up to 20 × 20 cm{sup 2}), of great interest in the Cultural Heritage field. In parallel, the possibility of using carbon microbeams for experiments, such as, for example, ion beam modification of materials and MeV Secondary Ion Mass Spectrometry, has been investigated. As a test application, Particle Induced X-ray Emission with carbon microbeams has been performed on a lapis lazuli stone. First results for both wide area imaging and external carbon microbeams are briefly reported.

  3. Wide area scanning system and carbon microbeams at the external microbeam facility of the INFN LABEC laboratory in Florence

    Science.gov (United States)

    Giuntini, L.; Massi, M.; Calusi, S.; Castelli, L.; Carraresi, L.; Fedi, M. E.; Gelli, N.; Liccioli, L.; Mandò, P. A.; Mazzinghi, A.; Palla, L.; Romano, F. P.; Ruberto, C.; Taccetti, F.

    2015-04-01

    Recently, developments have been made to the external scanning microbeam of INFN-LABEC laboratory in Florence. A new system for mechanical sample scanning was implemented. This system allows us to acquire large maps (up to 20 × 20 cm2), of great interest in the Cultural Heritage field. In parallel, the possibility of using carbon microbeams for experiments, such as, for example, ion beam modification of materials and MeV Secondary Ion Mass Spectrometry, has been investigated. As a test application, Particle Induced X-ray Emission with carbon microbeams has been performed on a lapis lazuli stone. First results for both wide area imaging and external carbon microbeams are briefly reported.

  4. Feasibility of Concurrent Treatment with the Scanning Ultrasound Reflector Linear Array System (SURLAS) and the Helical Tomotherapy System

    Science.gov (United States)

    Peñagarícano, José A.; Moros, Eduardo; Novák, Petr; Yan, Yulong; Corry, Peter

    2010-01-01

    Purpose To evaluate the feasibility of concurrent treatment with the Scanning Ultrasound Reflector Linear Array System (SURLAS) and helical tomotherapy (HT) intensity modulated radiation therapy (IMRT). Methods The SURLAS was placed on a RANDO phantom simulating a patient with superficial or deep recurrent breast cancer. A Megavoltage CT (MVCT) of the phantom with and without the SURLAS was obtained in the HT system. MVCT images with the SURLAS were obtained for two configurations: i) with the SURLAS' long axis parallel and ii) perpendicular to the longitudinal axis of the phantom. The MVCT simulation data set was then transferred to a radiation therapy planning station. Organs at risk (OAR) were contoured including the lungs, heart, abdomen and spinal cord. The metallic parts of the SURLAS were contoured as well and constraints were assigned to completely or directionally block radiation through them. The MVCT-simulation data set and regions of interest (ROI) files were subsequently transferred to the HT planning station. Several HT plans were obtained with optimization parameters that are usually used in the clinic. For comparison purposes, planning was also performed without the SURLAS on the phantom. Results All plans with the SURLAS on the phantom showed adequate dose covering 95% of the planning target volume (PTV D95%), average dose and coefficient of variation of the planning target volume (PTV) dose distribution regardless of the SURLAS' orientation with respect to the RANDO phantom. Likewise, all OAR showed clinically acceptable dose values. Spatial dose distributions and dose-volume histogram (DVH) evaluation showed negligible plan degradation due to the presence of the SURLAS. Beam-on time varied depending on the selected optimization parameters. Conclusion From the perspective of the radiation dosage, concurrent treatment with the SURLAS and HT IMRT is feasible as demonstrated by the obtained clinically acceptable treatment plans. In addition, proper

  5. Inductively coupled plasma-atomic emission spectroscopy: a computer controlled, scanning monochromator system for the rapid determination of the elements

    Energy Technology Data Exchange (ETDEWEB)

    Floyd, M.A.

    1980-03-01

    A computer controlled, scanning monochromator system specifically designed for the rapid, sequential determination of the elements is described. The monochromator is combined with an inductively coupled plasma excitation source so that elements at major, minor, trace, and ultratrace levels may be determined, in sequence, without changing experimental parameters other than the spectral line observed. A number of distinctive features not found in previously described versions are incorporated into the system here described. Performance characteristics of the entire system and several analytical applications are discussed.

  6. A versatile dual spot laser scanning confocal microscopy system for advanced fluorescence correlation spectroscopy analysis in living cell

    CERN Document Server

    Ferrand, P; Kress, A; Aillaud, A; Rigneault, H; Marguet, D

    2009-01-01

    A fluorescence correlation spectroscopy (FCS) system based on two independent measurement volumes is presented. The optical setup and data acquisition hardware are detailed, as well as a complete protocol to control the location, size and shape of the measurement volumes. A method that allows to monitor independently the excitation and collection efficiency distribution is proposed. Finally, a few examples of measurements that exploit the two spots in static and/or scanning schemes, are reported.

  7. DNA barcoding of fungi causing infections in humans and animals.

    Science.gov (United States)

    Irinyi, Laszlo; Lackner, Michaela; de Hoog, G Sybren; Meyer, Wieland

    2016-02-01

    Correct species identification is becoming increasingly important in clinical diagnostics. Till now, many mycological laboratories rely on conventional phenotypic identification. But this is slow and strongly operator-dependent. Therefore, to improve the quality of pathogen identification, rapid, reliable, and objective identification methods are essential. One of the most encouraging approaches is molecular barcoding using the internal transcribed spacer (ITS) of the rDNA, which is rapid, easily achievable, accurate, and applicable directly from clinical specimens. It relies on the comparison of a single ITS sequence with a curated reference database. The International Society for Human and Animal Mycology (ISHAM) working group for DNA barcoding has recently established such a database, focusing on the majority of human and animal pathogenic fungi (ISHAM-ITS, freely accessible at http://www.isham.org/ or directly from http://its.mycologylab.org). For some fungi the use of secondary barcodes may be necessary.

  8. Pollen DNA barcoding: current applications and future prospects.

    Science.gov (United States)

    Bell, Karen L; de Vere, Natasha; Keller, Alexander; Richardson, Rodney T; Gous, Annemarie; Burgess, Kevin S; Brosi, Berry J

    2016-09-01

    Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

  9. Counting animal species with DNA barcodes: Canadian insects.

    Science.gov (United States)

    Hebert, Paul D N; Ratnasingham, Sujeevan; Zakharov, Evgeny V; Telfer, Angela C; Levesque-Beaudin, Valerie; Milton, Megan A; Pedersen, Stephanie; Jannetta, Paul; deWaard, Jeremy R

    2016-09-05

    Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.This article is part of the

  10. DNA barcoding of commercially important catfishes in the Philippines.

    Science.gov (United States)

    Quilang, Jonas P; Yu, Shiny Cathlynne S

    2015-06-01

    Many species of catfish are important resources for human consumption, for sport fishing and for use in aquarium industry. In the Philippines, some species are cultivated and some are caught in the wild for food and a few introduced species have become invasive. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was done on commercially and economically important Philippine catfishes. A total of 75 specimens belonging to 11 species and 5 families were DNA barcoded. The genetic distances were computed and Neighbor-Joining (NJ) trees were constructed based on the Kimura 2-Parameter (K2P) method. The average K2P distances within species, genus, family and order were 0.2, 8.2, 12.7 and 21.9%, respectively. COI sequences clustered according to their species designation for 7 of the 11 catfishes. DNA barcoding was not able to discriminate between Arius dispar and A. manillensis and between Pterygoplichthys disjunctivus and P. pardalis. The morphological characters that are used to distinguish between these species do not complement molecular identification through DNA barcoding. DNA barcoding also showed that Clarias batrachus from the Philippines is different from the species found in India and Thailand, which supports earlier suggestions based on morphology that those found in India should be designated as C. magur and those in mainland Southeast Asia as C. aff. batrachus "Indochina". This study has shown that DNA barcoding can be used for species delineation and for tagging some species for further taxonomic investigation, which has implications on proper management and conservation strategies.

  11. Counting animal species with DNA barcodes: Canadian insects

    Science.gov (United States)

    Ratnasingham, Sujeevan; Zakharov, Evgeny V.; Telfer, Angela C.; Levesque-Beaudin, Valerie; Milton, Megan A.; Pedersen, Stephanie; Jannetta, Paul; deWaard, Jeremy R.

    2016-01-01

    Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the

  12. DNA barcoding works in practice but not in (neutral theory.

    Directory of Open Access Journals (Sweden)

    Mark Y Stoeckle

    Full Text Available BACKGROUND: DNA barcode differences within animal species are usually much less than differences among species, making it generally straightforward to match unknowns to a reference library. Here we aim to better understand the evolutionary mechanisms underlying this usual "barcode gap" pattern. We employ avian barcode libraries to test a central prediction of neutral theory, namely, intraspecific variation equals 2 Nµ, where N is population size and µ is mutations per site per generation. Birds are uniquely suited for this task: they have the best-known species limits, are well represented in barcode libraries, and, most critically, are the only large group with documented census population sizes. In addition, we ask if mitochondrial molecular clock measurements conform to neutral theory prediction of clock rate equals µ. RESULTS: Intraspecific COI barcode variation was uniformly low regardless of census population size (n = 142 species in 15 families. Apparent outliers reflected lumping of reproductively isolated populations or hybrid lineages. Re-analysis of a published survey of cytochrome b variation in diverse birds (n = 93 species in 39 families further confirmed uniformly low intraspecific variation. Hybridization/gene flow among species/populations was the main limitation to DNA barcode identification. CONCLUSIONS/SIGNIFICANCE: To our knowledge, this is the first large study of animal mitochondrial diversity using actual census population sizes and the first to test outliers for population structure. Our finding of universally low intraspecific variation contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. We argue that the weight of evidence-low intraspecific variation and the molecular clock-indicates neutral evolution plays a minor role in mitochondrial sequence evolution. As an alternate paradigm consistent with empirical data, we propose extreme

  13. Towards a deep characterization of a 64-fold-pixelated position sensitive detector for a new {gamma}-scanning system of HPGe segmented detectors

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Prieto, A.; Quintana, B. [Laboratorio de Radiaciones Ionizantes, Univ. of Salamanca, 37007 (Spain)

    2011-07-01

    Characterization of the electrical response of the HPGe segmented detectors is one of the current goals for the Nuclear Physics community in order to perform {gamma}-ray tracking or even imaging with these detectors. For this purpose, scanning devices have to be developed to achieve the signal-position association with the highest precision. In this laboratory, a new scanning system, SALSA (Salamanca Lyso-based Scanning Array), consisting on a high spatial resolution {gamma} camera, is a under development. In this work the whole scanning system is presented and first results for the characterization of the {gamma} camera are shown. (authors)

  14. DNA Barcodes for Marine Biodiversity: Moving Fast Forward?

    Directory of Open Access Journals (Sweden)

    Adriana E. Radulovici

    2010-03-01

    Full Text Available ‘Biodiversity’ means the variety of life and it can be studied at different levels (genetic, species, ecosystem and scales (spatial and temporal. Last decades showed that marine biodiversity has been severely underestimated at all levels. In order to investigate diversity patterns and underlying processes, there is a need to know what species live in the marine environment. An emerging tool for species identification, DNA barcoding can reliably assign unknown specimens to known species, also flagging potential cryptic species and genetically distant populations. This paper will review the role of DNA barcoding for the study of marine biodiversity at the species level.

  15. Study of the KNO3-Al2O3 system by differential scanning calorimetry

    Science.gov (United States)

    Amirov, A. M.; Gafurov, M. M.; Rabadanov, K. Sh.

    2016-09-01

    The structural and the thermodynamic properties of potassium nitrate KNO3 and its composites with nanosized aluminum oxide Al2O3 have been studied by differential scanning calorimetry. It has been found that an amorphous phase forms in composites (1- x)KNO3- x Al2O3. The thermal effect corresponding to this phase has been observed at 316°C. It has been found that the phase transition heats of potassium nitrate decreased as the aluminum oxide fraction increased.

  16. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.

    Science.gov (United States)

    Hawlitschek, Oliver; Nagy, Zoltán T; Berger, Johannes; Glaw, Frank

    2013-01-01

    In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.

  17. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.

    Directory of Open Access Journals (Sweden)

    Oliver Hawlitschek

    Full Text Available In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.

  18. A Visualization Method for Corrosion Damage on Aluminum Plates Using an Nd:YAG Pulsed Laser Scanning System

    Directory of Open Access Journals (Sweden)

    Inbok Lee

    2016-12-01

    Full Text Available This paper proposes a non-contact nondestructive evaluation (NDE technique that uses laser-induced ultrasonic waves to visualize corrosion damage in aluminum alloy plate structures. The non-contact, pulsed-laser ultrasonic measurement system generates ultrasonic waves using a galvanometer-based Q-switched Nd:YAG laser and measures the ultrasonic waves using a piezoelectric (PZT sensor. During scanning, a wavefield can be acquired by changing the excitation location of the laser point and measuring waves using the PZT sensor. The corrosion damage can be detected in the wavefield snapshots using the scattering characteristics of the waves that encounter corrosion. The structural damage is visualized by calculating the logarithmic values of the root mean square (RMS, with a weighting parameter to compensate for the attenuation caused by geometrical spreading and dispersion of the waves. An intact specimen is used to conduct a comparison with corrosion at different depths and sizes in other specimens. Both sides of the plate are scanned with the same scanning area to observe the effect of the location where corrosion has formed. The results show that the damage can be successfully visualized for almost all cases using the RMS-based functions, whether it formed on the front or back side. Also, the system is confirmed to have distinguished corroded areas at different depths.

  19. A Visualization Method for Corrosion Damage on Aluminum Plates Using an Nd:YAG Pulsed Laser Scanning System.

    Science.gov (United States)

    Lee, Inbok; Zhang, Aoqi; Lee, Changgil; Park, Seunghee

    2016-12-16

    This paper proposes a non-contact nondestructive evaluation (NDE) technique that uses laser-induced ultrasonic waves to visualize corrosion damage in aluminum alloy plate structures. The non-contact, pulsed-laser ultrasonic measurement system generates ultrasonic waves using a galvanometer-based Q-switched Nd:YAG laser and measures the ultrasonic waves using a piezoelectric (PZT) sensor. During scanning, a wavefield can be acquired by changing the excitation location of the laser point and measuring waves using the PZT sensor. The corrosion damage can be detected in the wavefield snapshots using the scattering characteristics of the waves that encounter corrosion. The structural damage is visualized by calculating the logarithmic values of the root mean square (RMS), with a weighting parameter to compensate for the attenuation caused by geometrical spreading and dispersion of the waves. An intact specimen is used to conduct a comparison with corrosion at different depths and sizes in other specimens. Both sides of the plate are scanned with the same scanning area to observe the effect of the location where corrosion has formed. The results show that the damage can be successfully visualized for almost all cases using the RMS-based functions, whether it formed on the front or back side. Also, the system is confirmed to have distinguished corroded areas at different depths.

  20. High-field flux mapping of (RE)BCO bulk superconductors-Development of an in situ scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Withnell, T.D. [Superconductivity Group, Cambridge University Engineering Department, Trumpington Street, Cambridge CB2 1PZ (United Kingdom)], E-mail: tdw25@cantab.net; Hari-Babu, N.; Ganney, I.; Dennis, A.; Cardwell, D.A. [Superconductivity Group, Cambridge University Engineering Department, Trumpington Street, Cambridge CB2 1PZ (United Kingdom)

    2008-06-15

    Flux mapping of Y-Ba-Cu-O (YBCO) melt-processed, bulk high-temperature superconductors (HTS) is used to visualise the profile of trapped magnetic field on a magnetised sample and to measure the extent of current flow, and hence field penetration, within the bulk microstructure. Grain structure and defects below the sample surface are observed non-destructively by this technique. This paper outlines the design, development and construction of a novel, in situ Hall scanning system using an 8 T magnet and variable temperature insert (VTI). This system is then used to characterise the field trapping properties of bulk samples for different applied field history.

  1. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Science.gov (United States)

    Sass, Chodon; Little, Damon P; Stevenson, Dennis Wm; Specht, Chelsea D

    2007-11-07

    Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  2. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Directory of Open Access Journals (Sweden)

    Chodon Sass

    Full Text Available Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL, and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS, were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  3. Novel digital laser dental scanning system%新型数字化牙模激光扫描系统

    Institute of Scientific and Technical Information of China (English)

    陈新禹; 胡英; 马孜; 聂建辉

    2012-01-01

    为了快速获取牙齿模型的数字型面信息,提出一种基于三轴联动平台的数字化牙模激光扫描系统.该系统基于光机电一体化技术和三维数据处理技术实现了牙齿模型三维型面信息提取和牙齿模型的造型设计.系统由线结构光视觉传感器、三轴联动平台、电气控制系统、主控计算机及上位机软件组成.通过线结构光视觉传感器和三轴联动平台的协调控制实现牙齿模型的无缝数据获取.实验结果表明,该数字化牙模激光扫描系统的测量精度可达0.182mm,速度为8000点/s.该系统扫描速度快、测量精度较高、操作灵活方便,可以满足牙模三维型面数据采集的要求.%In order to quickly obtain the 3D digital surface of the dental wax, an original design and achievement of a novel digital laser dental scanning system is introduced based on three - axis platform. 3 D surface and design of Dental model are implemented by the presented system which integrates optical, mechanical, electronic technologies, data processing technology and so on. The system consists of laser probe, three - axis platform, electronic control system, master computer and system software. 3D point cloud of Dental wax without any blind point can be scanned through controlling line structured light vision sensor and three - axis platform in phase. Experiment demonstrates that the scanning precision of the system is 0. 182mm, scanning speed is 8 000 pts/s. Therefore, the system works fast with high accuracy, its operation is simple and flexi- ble, so it can meet requirements of collecting 3D surface of the dental wax.

  4. 77 FR 59941 - Prospective Grant of Exclusive License: Terahertz Scanning Systems for Cancer Pathology

    Science.gov (United States)

    2012-10-01

    ... Systems for Cancer Pathology AGENCY: National Institutes of Health, Public Health Service, HHS. ACTION... systems for cancer pathology. Upon the expiration or termination of the exclusive evaluation...

  5. Assessment of DNA replication in central nervous system by Laser Scanning Cytometry

    Science.gov (United States)

    Lenz, Dominik; Mosch, Birgit; Bocsi, Jozsef; Arendt, Thomas; Tárnok, Attila

    2004-07-01

    μIn neurons of patients with Alzheimers's disease (AD) signs of cell cycle re-entry as well as polyploidy have been reported1, 2, indicating that the entire or a part of the genome of the neurons is duplicated before its death but mitosis is not initiated so that the cellular DNA content remains tetraploid. It was concluded, that this imbalance is the direct cause of the neuronal loss in AD3. Manual counting of polyploidal cells is possible but time consuming and possibly statistically insufficient. The aim of this study was to develop an automated method that detects the neuronal DNA content abnormalities with Laser Scanning Cytometry (LSC).Frozen sections of formalin-fixed brain tissue of AD patients and control subjects were labelled with anti-cyclin B and anti-NeuN antibodies. Immunolabelling was performed using Cy5- and Cy2-conjugated secondary antibodies and biotin streptavidin or tyramid signal amplification. In the end sections of 20m thickness were incubated with propidium iodide (PI) (50μg/ml) and covered on slides. For analysis by the LSC PI was used as trigger. Cells identified as neurons by NeuN expression were analyzed for cyclin B expression. Per specimen data of at least 10,000 neurons were acquired. In the frozen brain sections an automated quantification of the amount of nuclear DNA is possible with LSC. The DNA ploidy as well as the cell cycle distribution can be analyzed. A high number of neurons can be scanned and the duration of measuring is shorter than a manual examination. The amount of DNA is sufficiently represented by the PI fluorescence to be able to distinguish between eu- and polyploid neurons.

  6. Machining accuracy of crowns by CAD/CAM system using TCP/IP: influence of restorative material and scanning condition.

    Science.gov (United States)

    Tomita, Sachiko; Shin-ya, Akiyoshi; Gomi, Harunori; Shin-ya, Akikazu; Yokoyama, Daiichiro

    2007-07-01

    The purpose of this study was to determine the optimal condition for fabricating accurate crowns efficiently using an internet-based CAD/CAM system. The influences of three different CAD/CAM restorative materials (titanium, porcelain, and composite resin) and three different step-over scanning distances (0.01 mm, 0.11 mm, and 0.21 mm) were evaluated, and their interactive effects were carefully examined. Several points on the inner and outer surfaces of machined crowns - as well as height - were measured. These measurements were then compared with the original models, from which machining accuracy was obtained. At all measuring points, the inner surface of all crowns was machined larger than the die model, whereas the cervical area of porcelain crown was machined smaller than the crown model. Results of this study revealed that a step-over distance of 0.11 mm was an optimal scanning condition, taking into consideration the interactive effects of scanning time required, data volume, and machining accuracy.

  7. The research on calibration methods of dual-CCD laser three-dimensional human face scanning system

    Science.gov (United States)

    Wang, Jinjiang; Chang, Tianyu; Ge, Baozhen; Tian, Qingguo; Yang, Fengting; Shi, Shendong

    2013-09-01

    In this paper, on the basis of considering the performance advantages of two-step method, we combines the stereo matching of binocular stereo vision with active laser scanning to calibrate the system. Above all, we select a reference camera coordinate system as the world coordinate system and unity the coordinates of two CCD cameras. And then obtain the new perspective projection matrix (PPM) of each camera after the epipolar rectification. By those, the corresponding epipolar equation of two cameras can be defined. So by utilizing the trigonometric parallax method, we can measure the space point position after distortion correction and achieve stereo matching calibration between two image points. Experiments verify that this method can improve accuracy and system stability is guaranteed. The stereo matching calibration has a simple process with low-cost, and simplifies regular maintenance work. It can acquire 3D coordinates only by planar checkerboard calibration without the need of designing specific standard target or using electronic theodolite. It is found that during the experiment two-step calibration error and lens distortion lead to the stratification of point cloud data. The proposed calibration method which combining active line laser scanning and binocular stereo vision has the both advantages of them. It has more flexible applicability. Theory analysis and experiment shows the method is reasonable.

  8. Speed and accuracy of a beam tracking system for treatment of moving targets with scanned ion beams

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Nami; Bert, Christoph; Chaudhri, Naved; Gemmel, Alexander; Schardt, Dieter; Durante, Marco; Rietzel, Eike [GSI Helmholtz Centre for Heavy Ion Research GmbH, Planckstrasse 1, 64291 Darmstadt (Germany)], E-mail: n.saito@gsi.de

    2009-08-21

    The technical performance of an integrated three-dimensional carbon ion pencil beam tracking system that was developed at GSI was investigated in phantom studies. Aim of the beam tracking system is to accurately treat tumours that are subject to respiratory motion with scanned ion beams. The current system provides real-time control of ion pencil beams to track a moving target laterally using the scanning magnets and longitudinally with a dedicated range shifter. The system response time was deduced to be approximately 1 ms for lateral beam tracking. The range shifter response time has been measured for various range shift amounts. A value of 16 {+-} 2 ms was achieved for a water equivalent shift of 5 mm. An additional communication delay of 11 {+-} 2 ms was taken into account in the beam tracking process via motion prediction. Accuracy of the lateral beam tracking was measured with a multi-wire position detector to {<=}0.16 mm standard deviation. Longitudinal beam tracking accuracy was parameterized based on measured responses of the range shifter and required time durations to maintain a specific particle range. For example, 5 mm water equivalence (WE) longitudinal beam tracking results in accuracy of 1.08 and 0.48 mm WE in root mean square for time windows of 10 and 50 ms, respectively.

  9. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

    Science.gov (United States)

    Wong, Alan S L; Choi, Gigi C G; Cui, Cheryl H; Pregernig, Gabriela; Milani, Pamela; Adam, Miriam; Perli, Samuel D; Kazer, Samuel W; Gaillard, Aleth; Hermann, Mario; Shalek, Alex K; Fraenkel, Ernest; Lu, Timothy K

    2016-03-01

    The orchestrated action of genes controls complex biological phenotypes, yet the systematic discovery of gene and drug combinations that modulate these phenotypes in human cells is labor intensive and challenging to scale. Here, we created a platform for the massively parallel screening of barcoded combinatorial gene perturbations in human cells and translated these hits into effective drug combinations. This technology leverages the simplicity of the CRISPR-Cas9 system for multiplexed targeting of specific genomic loci and the versatility of combinatorial genetics en masse (CombiGEM) to rapidly assemble barcoded combinatorial genetic libraries that can be tracked with high-throughput sequencing. We applied CombiGEM-CRISPR to create a library of 23,409 barcoded dual guide-RNA (gRNA) combinations and then perform a high-throughput pooled screen to identify gene pairs that inhibited ovarian cancer cell growth when they were targeted. We validated the growth-inhibiting effects of specific gene sets, including epigenetic regulators KDM4C/BRD4 and KDM6B/BRD4, via individual assays with CRISPR-Cas-based knockouts and RNA-interference-based knockdowns. We also tested small-molecule drug pairs directed against our pairwise hits and showed that they exerted synergistic antiproliferative effects against ovarian cancer cells. We envision that the CombiGEM-CRISPR platform will be applicable to a broad range of biological settings and will accelerate the systematic identification of genetic combinations and their translation into novel drug combinations that modulate complex human disease phenotypes.

  10. Micrometric precision of prosthetic dental crowns obtained by optical scanning and computer-aided designing/computer-aided manufacturing system

    Science.gov (United States)

    das Neves, Flávio Domingues; de Almeida Prado Naves Carneiro, Thiago; do Prado, Célio Jesus; Prudente, Marcel Santana; Zancopé, Karla; Davi, Letícia Resende; Mendonça, Gustavo; Soares, Carlos José

    2014-08-01

    The current study evaluated prosthetic dental crowns obtained by optical scanning and a computer-aided designing/computer-aided manufacturing system using micro-computed tomography to compare the marginal fit. The virtual models were obtained with four different scanning surfaces: typodont (T), regular impressions (RI), master casts (MC), and powdered master casts (PMC). Five virtual models were obtained for each group. For each model, a crown was designed on the software and milled from feldspathic ceramic blocks. Micro-CT images were obtained for marginal gap measurements and the data were statistically analyzed by one-way analysis of variance followed by Tukey's test. The mean vertical misfit was T=62.6±65.2 μm; MC=60.4±38.4 μm; PMC=58.1±38.0 μm, and RI=89.8±62.8 μm. Considering a percentage of vertical marginal gap of up to 75 μm, the results were T=71.5%, RI=49.2%, MC=69.6%, and PMC=71.2%. The percentages of horizontal overextension were T=8.5%, RI=0%, MC=0.8%, and PMC=3.8%. Based on the results, virtual model acquisition by scanning the typodont (simulated mouth) or MC, with or without powder, showed acceptable values for the marginal gap. The higher result of marginal gap of the RI group suggests that it is preferable to scan this directly from the mouth or from MC.

  11. Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

    OpenAIRE

    2012-01-01

    Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  12. Prospects for discriminating Zingiberaceae species in India using DNA barcodes

    Institute of Scientific and Technical Information of China (English)

    Meenakshi Ramaswamy Vinitha; Unnikrishnan Suresh Kumar; Kizhakkethil Aishwarya; Mamiyil Sabu; George Thomas

    2014-01-01

    We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in al the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two para-phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.

  13. High universality of matK primers for barcoding gymnosperms

    Institute of Scientific and Technical Information of China (English)

    Yan LI; Lian-Ming GAO; RAM C.POUDEL; De-Zhu Li; Alan FORREST

    2011-01-01

    DNA barcoding is a tool to provide rapid and accurate taxonomic identification using a standard DNA region. A two-marker combination of rnatK+rbcL was formally proposed as the core barcode for land plants by the Consortium for the Barcode of Life Plant Working Group. However, there are currently no barcoding primers for matK showing high universality in gymnosperms. We used 57 gymnosperm species representing 40 genera, 11families and four subclasses to evaluate the universality of nine candidate matK primers and one rbcL primer in this study. Primer (1F/724R) of rbcL is proposed here as a universal primer for gymnosperms due to high universality. One of the nine candidate matK primers (Gym_F1A/Gym_R1A) is proposed as the best "universal" matK primer for gynnosperms because of high polymerase chain reaction success and routine generation of high quality bidirectional sequences. A specific matK primer for Ephedra was newly designed in this study, which performed well on the sampled species. The primers proposed here for rbcL and matK can be easily and successfully amplified for most gymnosperms.

  14. Testing four barcoding markers for species identification of Potamogetonaceae

    Institute of Scientific and Technical Information of China (English)

    Zhi-Yuan DU; Alitong QIMIKE; Chun-Feng YANG; Jin-Ming CHEN; Qing-Feng WANG

    2011-01-01

    The pondweeds (Potamogetonaceae) are among the most important plant groups in the aquatic environment. Owing to their high morphological and ecological diversity, species identification of this aquatic family remains problematic. DNA barcoding involves sequencing a standard DNA region and has been shown to be a powerful tool for species identification. In the present study, we tested four barcoding markers (rbcL, matK, internal transcribed spacer (ITS), and trnH-psbA) in 15 Potamogeton species and two Stuckenia species, representing most species of the Potamogetonaceae in China. The results show that all four regions can distinguish and support the newly proposed genera of Stuckenia from Potamogeton. Using ITS and trnH-psbA, significant interspecific genetic variability was shown. However, intraspecific genetic variability of trnH-psbA is high and so it is not suitable for barcoding in Potamogetonaceae. The ITS and matK regions showed good discrimination. However, matK was not easy to sequence using universal primers. The best performing single locus was ITS, making it a potentially useful DNA barcode in Potamogetonaceae.

  15. A retrospective approach to testing the DNA barcoding method.

    Directory of Open Access Journals (Sweden)

    David G Chapple

    Full Text Available A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters, and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%, and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%. But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%. For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.

  16. Telling plant species apart with DNA: from barcodes to genomes

    Science.gov (United States)

    Li, De-Zhu; van der Bank, Michelle

    2016-01-01

    Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481790

  17. Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.

    Science.gov (United States)

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Beduschi, Giovanni

    2009-09-01

    Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

  18. Identification of echinoderms (Echinodermata) from an anchialine cave in Cozumel Island, Mexico, using DNA barcodes.

    Science.gov (United States)

    Bribiesca-Contreras, Guadalupe; Solís-Marín, Francisco A; Laguarda-Figueras, Alfredo; Zaldívar-Riverón, Alejandro

    2013-11-01

    The echinoderm species richness of the Aerolito de Paraiso anchialine cave, on Cozumel Island, in the Mexican Caribbean, is assessed on the basis of morphological and DNA barcoding data. We included specimens from this cave system and from different open sea areas, and employed two different approaches for species delineation based on DNA barcoding data: a 2% cox1 divergence and the general mixed Yule-coalescent (GMYC) approaches. We subsequently compared the results derived from these approaches with our morphospecies discrimination. A total of 188 cox1 sequences belonging to specimens of four echinoderm classes were examined. The 2% cox1 divergence and GMYC approaches recovered 78 and 70 putative species, respectively, 24 and 22 of which corresponded to specimens from the anchialine system. Of 26 echinoderm species identified in the cave system, seven appear to be endemic to it. Among these are Copidaster carvenicola Solís-Marín & Laguarda-Figueras, 2010, two morphologically distinctive, undescribed species belonging to Asterinides and Ophionereis and four probably cryptic undescribed species originally assigned to Amphipholis squamata (Delle Chiaje, 1839), Astropecten duplicatus Gray, 1840, Copidaster lymani (AH Clark, 1948) and Ophiothrix angulata (Say, 1825). Further research and protection of this particularly fragile ecosystem becomes urgent because construction of tourism developments is planned nearby.

  19. Using the T-scan III system to analyze occlusal function in mandibular reconstruction patients: A pilot study

    Directory of Open Access Journals (Sweden)

    Chao-Wei Liu

    2015-02-01

    Full Text Available Background: This study was designed to analyze the post-rehabilitation occlusal function of subjects treated with complex mandibular resection and subsequently rehabilitated with fibula osteoseptocutaneous flaps, dental implants, and fixed prostheses utilizing the T-scan system. Methods: Ten mandibular complex resection cases that adopted fibula osteoseptocutaneous flaps, dental implants, and fixed prostheses to reconstruct occlusal function were analyzed. The mandibular reconstructions were divided into three groups based on size: full mandibular reconstructions, mandibular reconstructions larger than half of the arch, and mandibular reconstructions smaller than half of the arch. The T-scan III system was used to measure maximum occlusal force, occlusal time, anterior-posterior as well as left-right occlusal force asymmetries, and anterior-posterior as well as left-right asymmetrical locations of occlusal centers. Results: Subjects with larger mandibular reconstructions and dental implants with fixed partial dentures demonstrated decreased average occlusal force; however, the difference did not reach the statistically significant level (p > 0.05. The most significant asymmetry of occlusal center location occurred among subjects with mandibular reconstructed areas larger than half of the mandibular arch. Conclusions: Comparison of the parameters of T-scan system used to analyze the occlusal function showed that the occlusal force was not an objective reference. Measurements of the location of the occlusal center appeared more repeatable, and were less affected by additional factors. The research results of this study showed that the size of a reconstruction did not affect the occlusal force after reconstruction and larger reconstructed areas did not decrease the average occlusal force. The most significant parameter was left and right asymmetry of the occlusion center (LROC and was measured in subjects with reconstruction areas larger than half

  20. Electro interstitial scan system: assessment of 10 years of research and development

    Directory of Open Access Journals (Sweden)

    Maarek A

    2012-03-01

    Full Text Available Albert MaarekResearch and Development, LD Technology, Miami, FL, USABackground: Ten years of research and development have allowed an understanding of how the electro interstitial scan (EIS works and what its clinical applications may be.Materials and methods: The EIS is a galvanic skin response device. The measurements are performed by electrical stimulation of the post sympathetic cholinergic fiber with weak DC current and voltage 1.28V applied during 2 minutes and in bipolar mode.Current scientific knowledge: EIS electrical measurements are related to: (1 the concentration of free chloride ions in the interstitial fluid, which affects the transfer of electrical current and the ratio intensity/voltage; (2 the morphology of the interstitial fluid, which is related to the electrical dispersion calculated from the Cole equation (α parameter; (3 electrical stimulation, which causes a change in sweat rate at the passive electrodes – post sympathetic cholinergic fiber electrical stimulation appears to be responsible for activating M2 receptors, which regulate nitric oxide (NO production in the endothelial cell and cause vasodilation and a released sweat response; and (4 the electrochemical redox reactions (electrolysis of the released sweat on electrodes, which are different on the bulk of the metal electrodes (O2 + [4H+] + [4e-] and on the Ag/AgCl disposable electrodes (AgCl precipitation.Results: For each of the EIS clinical results, various explanations were posited, such as: (1 electrical stimulation of the postsympathetic cholinergic fiber-activating NO production in the endothelial cell, which causes vasodilation and a released sweat response (diabetes detection; (2 estimation of interstitial fluid's acid–base balance, which is reflected in an electrochemical reaction on the bulk of the electrodes through the released sweat (prostate cancer detection; (3 estimation of cerebral interstitial fluid chloride ions (detection of ADHD in

  1. Evaluation of enthalpy change due to hydrogen desorption for lithium amide/imide system by differential scanning calorimetry

    OpenAIRE

    2008-01-01

    Enthalpy change (ΔH) due to hydrogen desorption (H-desorption) for the lithium amide/imide system was evaluated by differential scanning calorimetry (DSC) measurement. In order to obtain the accurate and precise value of ΔH, we have paid special attention to following two points for correcting raw experimental data. One is to determine a cell constant of DSC equipment, which was evaluated by using the TiO2-doped MgH2 compound as a reference because of its quite similar hydrogen desorption pro...

  2. A Scanning Multi-Axis Differential Optical Absorption Spectroscopy System for Measurement of Tropospheric NO2 in Beijing

    Institute of Scientific and Technical Information of China (English)

    LI Ang; XIE Pin-Hua; LIU Cheng; LIU Jian-Guo; LIU Wen-Qing

    2007-01-01

    A scanning multi-axis differential optical absorption spectroscopy (DOAS) system is developed for monitoring tropospheric NO2 abundance. Measurements at different viewing angles near the horizon can be performed sequentially with one telescope collecting scattered sunlight reflected by a moving mirror. Tropospheric NO2 diurnal variations can be derived from slant column densities (SCDs) of different elevation angles. The result from a field campaign in Beijing in summer of 2005 reveals potential possibility for the monitoring of tropospheric NO2 by multi-axis DOAS technique.

  3. DNA barcoding: a genomic-based tool for authentication of phytomedicinals and its products

    Directory of Open Access Journals (Sweden)

    Balachandran KRS

    2015-12-01

    Full Text Available Karpaga Raja Sundari Balachandran, Saravanan Mohanasundaram, Sathishkumar Ramalingam Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India Abstract: DNA barcoding helps to identify the plant materials based on short, standardized gene sequences in a rapid, accurate, and cost-effective manner. Recent reports reveal that DNA barcoding can be used for the assignment of unknown specimens to a taxonomic group, authentic identification of phytomedicinals, and in plant biodiversity conservation. Research indicates that there is no single universal barcode candidate for identification of all plant groups. Hence, comparative analysis of plant barcode loci is essential for choosing a best candidate for authenticating particular medicinal plant genus/families. Currently, both chloroplast/nuclear regions are used as universal barcodes for the authentication of phytomedicinals. A recent advance in genomics has further enhanced the progress in DNA barcoding of plants by the introduction of high-throughput techniques like next generation sequencing, which has paved the way for complete plastome sequencing that is now termed as super-barcodes. These approaches could improve the traditional ethno-botanical and scientific knowledge of phytomedicinals and their safe use. Hence, current focus is on the investigation of phytomedicinals and herbal product integrity and authenticity through DNA barcoding with the goal of protecting consumers from potential health risks associated with product substitution and contamination. Keywords: phytomedicinals, DNA barcoding, NGS, super-barcodes, authentication, ethno-genetics

  4. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    Full Text Available Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.

  5. DNA barcoding in plants: evolution and applications of in silico approaches and resources.

    Science.gov (United States)

    Bhargava, Mili; Sharma, Ashok

    2013-06-01

    Bioinformatics has played an important role in the analysis of DNA barcoding data. The process of DNA barcoding initially involves the available data collection from the existing databases. Many databases have been developed in recent years, e.g. MMDBD [Medicinal Materials DNA Barcode Database], BioBarcode, etc. In case of non-availability of sequences, sequencing has to be done in vitro for which a recently developed software ecoPrimers can be helpful. This is followed by multiple sequence alignment. Further, basic sequence statistics computation and phylogenetic analysis can be performed by MEGA and PHYLIP/PAUP tools respectively. Some of the recent tools for in silico and statistical analysis specifically designed for barcoding viz. CAOS (Character Based DNA Barcoding), BRONX (DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability), Spider (Analysis of species identity and evolution, particularly DNA barcoding), jMOTU and Taxonerator (Turning DNA Barcode Sequences into Annotated OTUs), OTUbase (Analysis of OTU data and taxonomic data), SAP (Statistical Assignment Package), etc. have been discussed and analysed in this review. The paper presents a comprehensive overview of the various in silico methods, tools, softwares and databases used for DNA barcoding of plants.

  6. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

    Science.gov (United States)

    Xiang, Xiao-Guo; Huang, Lu-Qi; Jin, Xiao-Hua

    2017-01-01

    DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera. PMID:28182623

  7. A Test of Seven Candidate Barcode Regions from the Plastome in Picea (Pinaceae)

    Institute of Scientific and Technical Information of China (English)

    Jin-Hua Ran; Pei-Pei Wang; Hui-Juan Zhao; Xiao-Quan Wang

    2010-01-01

    DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbl) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.

  8. MRI Scans

    Science.gov (United States)

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...

  9. Identification of aphid (Hemiptera: Aphididae) species of economic importance in Kenya using DNA barcodes and PCR-RFLP-based approach.

    Science.gov (United States)

    Kinyanjui, G; Khamis, F M; Mohamed, S; Ombura, L O; Warigia, M; Ekesi, S

    2016-02-01

    Aphids are among pests of economic importance throughout the world. Together with transmitting plant viruses, aphids are capable of inflicting severe crop production losses. They also excrete honeydew that favours the growth of sooty mold which reduces the quality of vegetables and fruits and hence their market values. Rapid and accurate identification of aphids to the species level is a critical component in effective pest management and plant quarantine systems. Even though morphological taxonomy has made a tremendous impact on species-level identifications, polymorphism, morphological plasticity and immature stages are among the many challenges to accurate identification. In addition, their small size, presence of cryptic species and damaged specimens dictate the need for a strategy that will ensure timely and accurate identification. In this study, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based on mitochondrial cytochrome c oxidase subunit I gene and DNA barcoding were applied to identify different aphid species collected from different agro-ecological zones of Kenya. Three restriction enzymes RsaI, AluI and Hinf1 produced patterns that allowed unambiguous identification of the species except Aphis craccivora and Aphis fabae. Analyses of the barcode region indicated intraspecific and interspecific sequence divergences of 0.08 and 6.63%, respectively. DNA barcoding identified all species, including the morphologically indistinguishable A. craccivora and A. fabae and separated two subspecies of A. fabae. Based on these results, both PCR-RFLPs and DNA barcoding could provide quick and accurate tools for identification of aphid species within Aphididae subsequently aiding in effective pest management programmes and enhance plant quarantine systems.

  10. Analyzing mosquito (Diptera: culicidae diversity in Pakistan by DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Muhammad Ashfaq

    Full Text Available BACKGROUND: Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. METHODOLOGY/PRINCIPAL FINDINGS: Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection. The genus Aedes (Stegomyia comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. CONCLUSIONS: As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

  11. DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses.

    Science.gov (United States)

    Müller, Lívia; Gonçalves, Gislene L; Cordeiro-Estrela, Pedro; Marinho, Jorge R; Althoff, Sérgio L; Testoni, André F; González, Enrique M; Freitas, Thales R O

    2013-01-01

    Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.

  12. DNA Barcoding of Sigmodontine Rodents: Identifying Wildlife Reservoirs of Zoonoses

    Science.gov (United States)

    Müller, Lívia; Gonçalves, Gislene L.; Cordeiro-Estrela, Pedro; Marinho, Jorge R.; Althoff, Sérgio L.; Testoni, André. F.; González, Enrique M.; Freitas, Thales R. O.

    2013-01-01

    Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments. PMID:24244670

  13. The changing epitome of species identification – DNA barcoding

    Science.gov (United States)

    Ajmal Ali, M.; Gyulai, Gábor; Hidvégi, Norbert; Kerti, Balázs; Al Hemaid, Fahad M.A.; Pandey, Arun K.; Lee, Joongku

    2014-01-01

    The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The ‘DNA barcodes’ show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more. PMID:24955007

  14. DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses.

    Directory of Open Access Journals (Sweden)

    Lívia Müller

    Full Text Available Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera, mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera. Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.

  15. CO-REGISTRATION OF DSMs GENERATED BY UAV AND TERRESTRIAL LASER SCANNING SYSTEMS

    Directory of Open Access Journals (Sweden)

    R. A. Persad

    2016-06-01

    Full Text Available An approach for the co-registration of Digital Surface Models (DSMs derived from Unmanned Aerial Vehicles (UAVs and Terrestrial Laser Scanners (TLS is proposed. Specifically, a wavelet-based feature descriptor for matching surface keypoints on the 2.5D DSMs is developed. DSMs are useful in wide-scope of various applications such as 3D building modelling and reconstruction, cultural heritage, urban and environmental planning, aircraft navigation/path routing, accident and crime scene reconstruction, mining as well as, topographic map revision and change detection. For these listed applications, it is not uncommon that there will be a need for automatically aligning multi-temporal DSMs which may have been acquired from multiple sensors, with different specifications over a period of time, and may have various overlaps. Terrestrial laser scanners usually capture urban facades in an accurate manner; however this is not the case for building roof structures. On the other hand, vertical photography from UAVs can capture the roofs. Therefore, the automatic fusion of UAV and laser-scanning based DSMs is addressed here as it serves various geospatial applications.

  16. Co-Registration of DSMs Generated by Uav and Terrestrial Laser Scanning Systems

    Science.gov (United States)

    Ancil Persad, Ravi; Armenakis, Costas

    2016-06-01

    An approach for the co-registration of Digital Surface Models (DSMs) derived from Unmanned Aerial Vehicles (UAVs) and Terrestrial Laser Scanners (TLS) is proposed. Specifically, a wavelet-based feature descriptor for matching surface keypoints on the 2.5D DSMs is developed. DSMs are useful in wide-scope of various applications such as 3D building modelling and reconstruction, cultural heritage, urban and environmental planning, aircraft navigation/path routing, accident and crime scene reconstruction, mining as well as, topographic map revision and change detection. For these listed applications, it is not uncommon that there will be a need for automatically aligning multi-temporal DSMs which may have been acquired from multiple sensors, with different specifications over a period of time, and may have various overlaps. Terrestrial laser scanners usually capture urban facades in an accurate manner; however this is not the case for building roof structures. On the other hand, vertical photography from UAVs can capture the roofs. Therefore, the automatic fusion of UAV and laser-scanning based DSMs is addressed here as it serves various geospatial applications.

  17. The evaluation of unmanned aerial system-based photogrammetry and terrestrial laser scanning to generate DEMs of agricultural watersheds

    Science.gov (United States)

    Ouédraogo, Mohamar Moussa; Degré, Aurore; Debouche, Charles; Lisein, Jonathan

    2014-06-01

    Agricultural watersheds tend to be places of intensive farming activities that permanently modify their microtopography. The surface characteristics of the soil vary depending on the crops that are cultivated in these areas. Agricultural soil microtopography plays an important role in the quantification of runoff and sediment transport because the presence of crops, crop residues, furrows and ridges may impact the direction of water flow. To better assess such phenomena, 3-D reconstructions of high-resolution agricultural watershed topography are essential. Fine-resolution topographic data collection technologies can be used to discern highly detailed elevation variability in these areas. Knowledge of the strengths and weaknesses of existing technologies used for data collection on agricultural watersheds may be helpful in choosing an appropriate technology. This study assesses the suitability of terrestrial laser scanning (TLS) and unmanned aerial system (UAS) photogrammetry for collecting the fine-resolution topographic data required to generate accurate, high-resolution digital elevation models (DEMs) in a small watershed area (12 ha). Because of farming activity, 14 TLS scans (≈ 25 points m- 2) were collected without using high-definition surveying (HDS) targets, which are generally used to mesh adjacent scans. To evaluate the accuracy of the DEMs created from the TLS scan data, 1098 ground control points (GCPs) were surveyed using a real time kinematic global positioning system (RTK-GPS). Linear regressions were then applied to each DEM to remove vertical errors from the TLS point elevations, errors caused by the non-perpendicularity of the scanner's vertical axis to the local horizontal plane, and errors correlated with the distance to the scanner's position. The scans were then meshed to generate a DEMTLS with a 1 × 1 m spatial resolution. The Agisoft PhotoScan and MicMac software packages were used to process the aerial photographs and generate a DEMPSC

  18. NAVIS-An UGV Indoor Positioning System Using Laser Scan Matching for Large-Area Real-Time Applications

    Directory of Open Access Journals (Sweden)

    Jian Tang

    2014-07-01

    Full Text Available Laser scan matching with grid-based maps is a promising tool for real-time indoor positioning of mobile Unmanned Ground Vehicles (UGVs. While there are critical implementation problems, such as the ability to estimate the position by sensing the unknown indoor environment with sufficient accuracy and low enough latency for stable vehicle control, further development work is necessary. Unfortunately, most of the existing methods employ heuristics for quick positioning in which numerous accumulated errors easily lead to loss of positioning accuracy. This severely restricts its applications in large areas and over lengthy periods of time. This paper introduces an efficient real-time mobile UGV indoor positioning system for large-area applications using laser scan matching with an improved probabilistically-motivated Maximum Likelihood Estimation (IMLE algorithm, which is based on a multi-resolution patch-divided grid likelihood map. Compared with traditional methods, the improvements embodied in IMLE include: (a Iterative Closed Point (ICP preprocessing, which adaptively decreases the search scope; (b a totally brute search matching method on multi-resolution map layers, based on the likelihood value between current laser scan and the grid map within refined search scope, adopted to obtain the global optimum position at each scan matching; and (c a patch-divided likelihood map supporting a large indoor area. A UGV platform called NAVIS was designed, manufactured, and tested based on a low-cost robot integrating a LiDAR and an odometer sensor to verify the IMLE algorithm. A series of experiments based on simulated data and field tests with NAVIS proved that the proposed IMEL algorithm is a better way to perform local scan matching that can offer a quick and stable positioning solution with high accuracy so it can be part of a large area localization/mapping, application. The NAVIS platform can reach an updating rate of 12 Hz in a feature

  19. Real-time B-scan ultrasonic imaging using a digital phased array system for NDE

    Science.gov (United States)

    Dunki-Jacobs, Robert; Thomas, Lewis

    A demonstration is presented of the ability to produce real-time images of metals on the basis of a phased-array ultrasound system. Attention is given to the critical role played by a beam-former. It is established that the present imaging system's resolution approaches the theoretical capabilities of the given aperture size and wavelength.

  20. Comparison of pain scores between patients undergoing panretinal photocoagulation using navigated or pattern scan laser systems

    Directory of Open Access Journals (Sweden)

    Umit Ubeyt Inan

    2016-02-01

    Full Text Available ABSTRACT Purpose: To compare the pain responses of patients with proliferative diabetic retinopathy (PDR undergoing panretinal photocoagulation (PRP using either pattern scan laser (PASCAL or navigated laser photocoagulation (NAVILAS. Methods: Patients diagnosed with PDR were randomly assigned to undergo either PASCAL or NAVILAS photocoagulation treatment. PRP was performed using the multi-shot mode with a spot size of 200-400 µm and a pulse duration of 30 ms to obtain a white-grayish spot on the retina. Parameters were identical in both procedures. After 30 min of PRP application, patients were asked to verbally describe their pain perception as either "none," "mild," "moderate," "severe," or "very severe" using a verbal rating scale (VRS and visual analog scale (VAS by indicating a score from "0" to "10," representing the severity of pain from "no pain" to "severe pain." Results: A total of 60 eyes of 60 patients (20 females and 40 males diagnosed with PDR were treated. The mean age of patients was 62.22 ± 9.19 years, and the mean diabetes duration was 195.47 ± 94.54 months. The mean number of laser spots delivered during PRP was 389.47 ± 71.52 in the NAVILAS group and 392.70 ± 54.33 in the PASCAL group (p=0.57. The difference in pain responses between patients in the NAVILAS and PASCAL groups was significant with regard to the mean VRS (1.10 ± 0.67 and 1.47 ± 0.69, respectively; p=0.042 and mean VAS (2.13 ± 1.17 and 2.97 ± 1.35, respectively; p=0.034 scores. Conclusions: Pain responses in patients undergoing PRP with a 30-ms pulse duration were significantly milder in the NAVILAS group than in the PASCAL group.

  1. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Wenpan Dong

    Full Text Available BACKGROUND: At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species. METHODOLOGY/PRINCIPAL FINDINGS: We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnS(UGA-trnG(UCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA-trnG(UCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species. SIGNIFICANCE/CONCLUSIONS: Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve

  2. Total Measurement Uncertainty for the Plutonium Finishing Plant (PFP) Segmented Gamma Scan Assay System

    CERN Document Server

    Fazzari, D M

    2001-01-01

    This report presents the results of an evaluation of the Total Measurement Uncertainty (TMU) for the Canberra manufactured Segmented Gamma Scanner Assay System (SGSAS) as employed at the Hanford Plutonium Finishing Plant (PFP). In this document, TMU embodies the combined uncertainties due to all of the individual random and systematic sources of measurement uncertainty. It includes uncertainties arising from corrections and factors applied to the analysis of transuranic waste to compensate for inhomogeneities and interferences from the waste matrix and radioactive components. These include uncertainty components for any assumptions contained in the calibration of the system or computation of the data. Uncertainties are propagated at 1 sigma. The final total measurement uncertainty value is reported at the 95% confidence level. The SGSAS is a gamma assay system that is used to assay plutonium and uranium waste. The SGSAS system can be used in a stand-alone mode to perform the NDA characterization of a containe...

  3. Laser-ranging scanning system to observe topographical deformations of volcanoes.

    Science.gov (United States)

    Aoki, T; Takabe, M; Mizutani, K; Itabe, T

    1997-02-20

    We have developed a laser-ranging system to observe the topographical structure of volcanoes. This system can be used to measure the distance to a target by a laser and shows the three-dimensional topographical structure of a volcano with an accuracy of 30 cm. This accuracy is greater than that of a typical laser-ranging system that uses a corner-cube reflector as a target because the reflected light jitters as a result of inclination and unevenness of the target ground surface. However, this laser-ranging system is useful for detecting deformations of topographical features in which placement of a reflector is difficult, such as in volcanic regions.

  4. A high sensitivity optically stimulated luminescence scanning system for measurement of single sand-sized grains

    DEFF Research Database (Denmark)

    Duller, G.A.T.; Bøtter-Jensen, L.; Kohsiek, P.;

    1999-01-01

    An instrument has been designed for the routine analysis of the optically stimulated luminescence signal from single grains of sand. The system is capable of analysing over 3000 individual grains in a single measurement sequence, and the OSL signal from each grain can be read in less than 3 s....... The design principles are described, along with preliminary measurements that illustrate the operation of the system and its capabilities....

  5. DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Mofolusho O. Falade

    2016-06-01

    Full Text Available DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S and cytochrome oxidase subunit I (COI for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ and maximum likelihood (ML methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average, which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.

  6. Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead.

    Science.gov (United States)

    Joly, Simon; Davies, T Jonathan; Archambault, Annie; Bruneau, Anne; Derry, Alison; Kembel, Steven W; Peres-Neto, Pedro; Vamosi, Jana; Wheeler, Terry A

    2014-03-01

    Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.

  7. X-ray imaging system for PaxScan2520 fiat-panel detector%PaxScan2520平板探测器X射线成像系统设计

    Institute of Scientific and Technical Information of China (English)

    王宇

    2012-01-01

    PaxScan2520 flat-panel detector as a research object, this paper used multithreading programming techniques of VC ++ , combined with the characteristics of flat-panel detector, developed x-ray real-time imaging system based on PaxScan1313 flat-panel detector. Through experimental demonstration, the system achieves very good imaging effect, meets performance, stability and accuracy of x-real-time radiographic testing.%以PaxScan2520平板探测器作为研究对象,利用VC++多线程的编程技术,结合平板探测器的特点,开发了基于PaxScan1313平板探测器的X射线实时成像系统.通过实验论证该系统可以达到很好的成像效果,可以满足X射线检测的实时性、稳定性与精确性.

  8. A Case Study Correlating Innovative Gamma Ray Scanning Detection Systems Data to Surface Soil Gamma Spectrometry Results - 13580

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Shannon; Rodriguez, Rene; Billock, Paul [HydroGeoLogic, Inc., 11107 Sunset Hills Road, Suite 400, Reston, VA 20190 (United States); Lit, Peter [Nomad Science Group, 7738 Nautilus Shell Street, Las Vegas, NV 89139 (United States)

    2013-07-01

    HydroGeoLogic (HGL), Inc. completed a United States Environmental Protection Agency (USEPA) study to characterize radiological contamination at a site near Canoga Park, California. The characterized area contained 470 acres including the site of a prototype commercial nuclear reactor and other nuclear design, testing, and support operations from the 1950's until 1988 [1]. The site history included radiological releases during operation followed by D and D activities. The characterization was conducted under an accelerated schedule and the results will support the project remediation. The project has a rigorous cleanup to background agenda and does not allow for comparison to risk-based guidelines. To target soil sample locations, multiple lines of evidence were evaluated including a gamma radiation survey, geophysical surveys, historical site assessment, aerial photographs, and former worker interviews. Due to the time since production and decay, the primary gamma emitting radionuclide remaining is cesium-137 (Cs-137). The gamma ray survey covered diverse, rugged terrain using custom designed sodium iodide thallium-activated (NaI(Tl)) scintillation detection systems. The survey goals included attaining 100% ground surface coverage and detecting gamma radiation as sensitively as possible. The effectiveness of innovative gamma ray detection systems was tested by correlating field Cs-137 static count ratios to Cs-137 laboratory gamma spectrometry results. As a case study, the area encompassing the former location of the first nuclear power station in the U. S. was scanned, and second by second global positioning system (GPS)-linked gamma spectral data were evaluated by examining total count rate and nuclide-specific regions of interest. To compensate for Compton scattering from higher energy naturally occurring radionuclides (U-238, Th-232 and their progeny, and K-40), count rate ratios of anthropogenic nuclide-specific regions of interest to the total count rate

  9. Forensic species identification of large macaws using DNA barcodes and microsatellite profiles.

    Science.gov (United States)

    Abe, Hideaki; Hayano, Azusa; Inoue-Murayama, Miho

    2012-01-01

    Using mitochondrial and nuclear markers species identification was conducted in the case of seized feathers. Earlier, we had sequenced cytochrome c oxidase subunit I (COI) both from 10 seized specimens and 43 validation specimens from captive macaws belonging to 4 Ara species (A. macao, A. chloropterus, A. ararauna, and A. ambiguus) and identified 19 haplotypes based on COI sequences. Species-level identification using Barcode of Life Data Systems showed that seized feathers shared the highest similarity with scarlet macaws (A. macao), and this result was supported by the tree-base identification with high bootstrap values. Moreover, microsatellite profiles in AgGT17 locus showed that patterns of allelic distribution in the seized feathers were apparently distinct from those of red-and-green macaw (A. chloropterus), but were overlapped with those of A. macao, suggesting that all of seized feathers were derived from several individuals of A. macao. We also determined the parentage of hybrid macaws by the combination of COI barcodes and microsatellite profiles. The technique presented here will contribute to forensic identification and future conservation of large macaws that have been lost due to deforestation.

  10. Application of DNA barcoding for controlling of the species from Octopus genus

    Directory of Open Access Journals (Sweden)

    Francesco Debenedetti

    2014-12-01

    Full Text Available The DNA barcoding proposes the use of a particular sequence from a single genomic region as the base for an identifying system capable to determine all animal species. This methodology comprises the analysis of a 655 base-pair region from the mithocondrial cytochrome C oxidase gene (COI. Its application in the species identification of fishery products has been very promising. However, in the last years some doubts about its usage have emerged. In this work, we make use of the DNA barcoding for the identification of some of the octopus species with higher commercial interest (Octopus membranaceus, Octopus vulgaris, Octopus aegina, Octopus cyanea focusing the attention on the reliability and completeness of the available information on the databases. The study looked over 51 individuals apparently belonging to the Octopus genus. For the identification of O.aegina, O.cyanea, O.vulgaris species no particular problems were found. On the other hand, most of the samples of O.membranaceus, though they clearly presented the morphological characteristics of the species, were not identified with the biomolecular analyses.

  11. An integrative approach to species discovery in odonates: from character-based DNA barcoding to ecology.

    Science.gov (United States)

    Damm, Sandra; Schierwater, Bernd; Hadrys, Heike

    2010-09-01

    Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision-making. Such an approach can enhance both species identification and species discovery. The character-based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA-barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.

  12. A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy.

    Science.gov (United States)

    Chen, Robert; Rishi, Harneet S; Potapov, Vladimir; Yamada, Masaki R; Yeh, Vincent J; Chow, Thomas; Cheung, Celia L; Jones, Austin T; Johnson, Terry D; Keating, Amy E; DeLoache, William C; Dueber, John E

    2015-11-20

    Dramatic progress has been made in the design and build phases of the design-build-test cycle for engineering cells. However, the test phase usually limits throughput, as many outputs of interest are not amenable to rapid analytical measurements. For example, phenotypes such as motility, morphology, and subcellular localization can be readily measured by microscopy, but analysis of these phenotypes is notoriously slow. To increase throughput, we developed microscopy-readable barcodes (MiCodes) composed of fluorescent proteins targeted to discernible organelles. In this system, a unique barcode can be genetically linked to each library member, making possible the parallel analysis of phenotypes of interest via microscopy. As a first demonstration, we MiCoded a set of synthetic coiled-coil leucine zipper proteins to allow an 8 × 8 matrix to be tested for specific interactions in micrographs consisting of mixed populations of cells. A novel microscopy-readable two-hybrid fluorescence localization assay for probing candidate interactions in the cytosol was also developed using a bait protein targeted to the peroxisome and a prey protein tagged with a fluorescent protein. This work introduces a generalizable, scalable platform for making microscopy amenable to higher-throughput library screening experiments, thereby coupling the power of imaging with the utility of combinatorial search paradigms.

  13. Application of DNA Barcoding for Controlling of the Species from Octopus Genus

    Science.gov (United States)

    Debenedetti, Francesco; Dalmasso, Alessandra; Bottero, Maria Teresa; Gilli, Maurizio; Gili, Stefano; Tepedino, Valentina

    2014-01-01

    The DNA barcoding proposes the use of a particular sequence from a single genomic region as the base for an identifying system capable to determine all animal species. This methodology comprises the analysis of a 655 base-pair region from the mithocondrial cytochrome C oxidase gene (COI). Its application in the species identification of fishery products has been very promising. However, in the last years some doubts about its usage have emerged. In this work, we make use of the DNA barcoding for the identification of some of the octopus species with higher commercial interest (Octopus membranaceus, Octopus vulgaris, Octopus aegina, Octopus cyanea) focusing the attention on the reliability and completeness of the available information on the databases. The study looked over 51 individuals apparently belonging to the Octopus genus. For the identification of O.aegina, O.cyanea, O.vulgaris species no particular problems were found. On the other hand, most of the samples of O.membranaceus, though they clearly presented the morphological characteristics of the species, were not identified with the biomolecular analyses. PMID:27800370

  14. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

    Directory of Open Access Journals (Sweden)

    Matthias Dodt

    2012-12-01

    Full Text Available Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a specific to the sequencing platform and library construction method (e.g., adapter sequences; (b have been introduced by experimental design (e.g., sample barcodes; or (c constitute some biological signal (e.g., splice leader sequences in nematodes. Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/.

  15. PreScan, madymo and vehil design and evaluation tools for integrated safety systems

    NARCIS (Netherlands)

    Lupker, H.; Lemmen, P.; Ploeg, J.

    2006-01-01

    Pre-Crash Systems (PCS) use environment sensors and electronic control functions to improve the effectiveness of passive safety devices by activating them before a collision occurs. In view of the autonomous character and high demands on reliability, dedicated design tools and methodologies are requ

  16. Exploration of two-enzyme coupled catalysis system using scanning electrochemical microscopy.

    Science.gov (United States)

    Wu, Zeng-Qiang; Jia, Wen-Zhi; Wang, Kang; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua

    2012-12-18

    In biological metabolism, a given metabolic process usually occurs via a group of enzymes working together in sequential pathways. To explore the metabolism mechanism requires the understanding of the multienzyme coupled catalysis systems. In this paper, an approach has been proposed to study the kinetics of a two-enzyme coupled reaction using SECM combining numerical simulations. Acetylcholine esterase and choline oxidase are immobilized on cysteamine self-assembled monolayers on tip and substrate gold electrodes of SECM via electrostatic interactions, respectively. The reaction kinetics of this two-enzyme coupled system upon various separation distance precisely regulated by SECM are measured. An overall apparent Michaelis-Menten constant of this enzyme cascade is thus measured as 2.97 mM at an optimal tip-substrate gap distance of 18 μm. Then, a kinetic model of this enzyme cascade is established for evaluating the kinetic parameters of individual enzyme by using the finite element method. The simulated results demonstrate the choline oxidase catalytic reaction is the rate determining step of this enzyme cascade. The Michaelis-Menten constant of acetylcholine esterase is evaluated as 1.8 mM. This study offers a promising approach to exploring mechanism of other two-enzyme coupled reactions in biological system and would promote the development of biosensors and enzyme-based logic systems.

  17. QRCode二维条码在火车票中的实现%Application of 2D QR Code Barcode in Train Tickets

    Institute of Scientific and Technical Information of China (English)

    向隅

    2011-01-01

    2D QR Code barcode, having the super high speed, over-all decoding, powerful capacity of correcting mistakes and the effective way of demonstrating Chinese characters, will be of bright future. With the 2D QR Code barcode as the carrier, the system uses the third-party control and accomplishes the applicatiOn of coding 2D QR Code barcodes in train tickets. The experiment shows that the system can use the camera to decode the information without the professional CCD 2D barcode equipment. It can meet the demand for time and accuracy, which provides an effective way for the application of 2D barcode in the ticketing system.%QRCode二维条码具有超高速全方位识读、纠错能力强、能有效表示汉字等特点,具有良好的应用前景。该系统以QRCode二维条码为载体,利用第三方控件,使QRCode二维条码在火车票中得以实现。实验表明,该系统不使用专用的CCD二维条码设备就能够通过摄像头拍照识别信息,在时间和准确度上能满足要求,为二维条码在票务系统中的使用提供了一条有效的途径。

  18. Reducing Inherent Deviations in Galvanometer Scanning Systems for Large Area Processing

    OpenAIRE

    Ortega Delgado, Moisés Alberto

    2017-01-01

    Galvanometer laser machining is a well-established laser machining technique in which the laser beam is positioned on a working field by means of mirrors mounted in galvanometers. Nonetheless, new applications make necessary the development of innovative techniques for increasing the performance of such systems. Aside all the advantages of this technique like given resolution, repeatability and velocity, a limited working area is an important drawback. In this thesis work, the limitation...

  19. A Prototype Two-Axis Laser Scanning System used in Stereolithography Apparatus with New Algorithms for Computerized Model Slicing

    Directory of Open Access Journals (Sweden)

    M. Habibi

    2009-01-01

    Full Text Available Problem statement: A successful operation of rapid prototyping process depends on software and hardware which are used in RP machines. About software, an efficient technique is required to slice the CAD model. Several slicing methods are used for slicing from Standard Triangulation Language (STL files, such as direct slicing and adaptive slicing. Using these methods reduce accuracy of physical part or increase process time. About hardware, in Stereolithography (SLA apparatus, two mirrors have been used to reflect laser beam. Approach: In this study new algorithms were developed for part slicing from STL file and modifying the laser beam path such as: Derivation of contours in each layer, generate contour family tree, detective arcs and modifying laser beam path. A modified mechanism was designed and developed based on only one mirror to reflect laser beam. Results: These algorithms were used in a visual basic interface and the developed mechanism was implemented in a prototype apparatus. Conclusion: Developed algorithms decreased CAD model slicing time and generated more accurate laser beam path than usual methods and fabricated apparatus decreased scanning mechanism complexity and volume of the scanning system.

  20. High Precision Magnetic Field Scanning System for the New Muon g-2 Experiment

    Science.gov (United States)

    Hong, Ran; Muon g-2 collaboration Collaboration

    2017-01-01

    The New Muon g-2 Experiment (E989) at Fermilab will measure the anomalous magnetic moment of muon aμ aiming at a precision of 140 ppb. This new experiment will shed light on the long-standing 3.5 standard deviation between the previous muon g-2 measurement (E821) at Brookhaven National Laboratory and the Standard Model calculation, and potentially discover new physics. The New Muon g-2 Experiment measures the precession frequency of muon in a uniform magnetic field, and the magnetic field experienced by the muons needs to be measured with a precision better than 70 ppb. For the measurement of the magnetic field in the muon storage region, the former trolley system from E821 with 17 NMR probes was refurbished and upgraded with new electronics, probes and a modern motion control system. A test solenoid magnet was set up at Argonne National Laboratory for calibrating the NMR probes and the precision studies of systematic uncertainties. In this presentation, we will describe the trolley motion control scheme, the trolley position measurement methods, the electronic system for activating and reading the NMR probes and the test solenoid facility.

  1. DNA barcode goes two-dimensions: DNA QR code web server.

    Science.gov (United States)

    Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  2. DNA barcode goes two-dimensions: DNA QR code web server.

    Directory of Open Access Journals (Sweden)

    Chang Liu

    Full Text Available The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  3. Evaluation of the DNA barcodes in Dendrobium (Orchidaceae from mainland Asia.

    Directory of Open Access Journals (Sweden)

    Songzhi Xu

    Full Text Available DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.

  4. Pyrosequencing for mini-barcoding of fresh and old museum specimens.

    Directory of Open Access Journals (Sweden)

    Shadi Shokralla

    Full Text Available DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53-97 year-old. The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.

  5. Applications of Barcode Images by Enhancing the Two-Dimensional Recognition Rate

    Directory of Open Access Journals (Sweden)

    Kun-Hsien Lin

    2012-07-01

    Full Text Available The paper not only proposed the latest Two-Dimensional Barcodes Image-processing Module, but also captured the smallest camera screens (320 240 with different focal distances and tried to find out “Finder Pattern” for positioning images. Further, use CROBU (Conversion Ratio of Basic Unit the thesis proposed to convert 2-D barcodes into 1-pixel ratio to match images before judging recognition rate of 2-D barcodes through matching. Normally speaking, 2-D barcodes are deciphered and recognized by software while the thesis recognizes 2-D barcodes and enhances implementation speed up to 10-cm accurate max. using image matching. The 2-D barcodes image-processing module the thesis proposed does capture and standardize image with complicated background or raw edge, which enhances 2-D barcodes recognition rate. The main point of this study is to construct a platform to manage or suggest nutrients human body needs. The Quick Response Code image of 2-D barcodes represents vitamin and calories information. 2-D barcodes taken instantly by MATLAB and CCD camera can be used to list nutrients from foods you eat recently and suggest what else you should eat for the purpose of health management.

  6. Pyrosequencing for mini-barcoding of fresh and old museum specimens.

    Science.gov (United States)

    Shokralla, Shadi; Zhou, Xin; Janzen, Daniel H; Hallwachs, Winnie; Landry, Jean-François; Jacobus, Luke M; Hajibabaei, Mehrdad

    2011-01-01

    DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53-97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.

  7. Scan Statistics

    CERN Document Server

    Glaz, Joseph

    2009-01-01

    Suitable for graduate students and researchers in applied probability and statistics, as well as for scientists in biology, computer science, pharmaceutical science and medicine, this title brings together a collection of chapters illustrating the depth and diversity of theory, methods and applications in the area of scan statistics.

  8. Bone scanning in otolaryngology.

    Science.gov (United States)

    Noyek, A M

    1979-09-01

    Modern radionuclide bone scanning has introduced a new concept in physiologic and anatomic diagnostic imaging to general medicine. As otolaryngologists must diagnose and treat disease in relation to the bony and/or cartilaginous supporting structures of the neurocranium and upper airway, this modality should be included in the otolaryngologist's diagnostic armamentarium. It is the purpose of this manuscript to study the specific applications of bone scanning to our specialty at this time, based on clinical experience over the past three years. This thesis describes the development of bone scanning in general (history of nuclear medicine and nuclear physics; history of bone scanning in particular). General concepts in nuclear medicine are then presented; these include a discussion of nuclear semantics, principles of radioactive emmissions, the properties 99mTc as a radionuclide, and the tracer principle. On the basis of these general concepts, specific concepts in bone scanning are then brought forth. The physiology of bone and the action of the bone scan agents is presented. Further discussion considers the availability and production of the bone scan agent, patient factors, the gamma camera, the triphasic bone scan and the ultimate diagnostic principle of the bone scan. Clinical applications of bone scanning in otolaryngology are then presented in three sections. Proven areas of application include the evaluation of malignant tumors of the head and neck, the diagnosis of temporomandibular joint disorders, the diagnosis of facial fractures, the evaluation of osteomyelitis, nuclear medicine imaging of the larynx, and the assessment of systemic disease. Areas of adjunctive or supplementary value are also noted, such as diagnostic imaging of meningioma. Finally, areas of marginal value in the application of bone scanning are described.

  9. LIDAR COMBINED SCANNING UNIT

    Directory of Open Access Journals (Sweden)

    V. V. Elizarov

    2016-11-01

    Full Text Available Subject of Research. The results of lidar combined scanning unit development for locating leaks of hydrocarbons are presented The unit enables to perform high-speed scanning of the investigated space in wide and narrow angle fields. Method. Scanning in a wide angular field is produced by one-line scanning path by means of the movable aluminum mirror with a frequency of 20Hz and amplitude of 20 degrees of swing. Narrowband scanning is performed along a spiral path by the deflector. The deflection of the beam is done by rotation of the optical wedges forming part of the deflector at an angle of ±50. The control function of the scanning node is performed by a specialized software product written in C# programming language. Main Results. This scanning unit allows scanning the investigated area at a distance of 50-100 m with spatial resolution at the level of 3 cm. The positioning accuracy of the laser beam in space is 15'. The developed scanning unit gives the possibility to browse the entire investigated area for the time not more than 1 ms at a rotation frequency of each wedge from 50 to 200 Hz. The problem of unambiguous definition of the beam geographical coordinates in space is solved at the software level according to the rotation angles of the mirrors and optical wedges. Lidar system coordinates are determined by means of GPS. Practical Relevance. Development results open the possibility for increasing the spatial resolution of scanning systems of a wide range of lidars and can provide high positioning accuracy of the laser beam in space.

  10. Resolution enhancement of scanning four-point-probe measurements on two-dimensional systems.

    OpenAIRE

    Hansen, Torben Mikael; Stokbro, Kurt; Hansen, Ole; Hassenkam, T.; Shiraki, I.; Hasegawa, S.; Bøggild, Peter

    2003-01-01

    A method to improve the resolution of four-point-probe measurements of two-dimensional (2D) and quasi-2D systems is presented. By mapping the conductance on a dense grid around a target area and postprocessing the data, the resolution can be improved by a factor of approximately 50 to better than 1/15 of the four-point-probe electrode spacing. The real conductance sheet is simulated by a grid of discrete resistances, which is optimized by means of a standard optimization algorithm, until the ...

  11. Acquisition of a Scanning Laser Vibrometer System for Experimental Studies on Nonparametric Nonlinear System Identification and Aeroelastic Instability Suppression

    Science.gov (United States)

    2011-03-06

    The PIs current research and development, funded by AFOSR, aims to develop novel means of vibration control for aerospace systems, system ... identification procedures for strongly nonlinear dynamical systems, and a fully passive limit cycle oscillation (LCO) suppression system for a model generic

  12. A versatile variable field module for Asylum Cypher scanning probe system

    Science.gov (United States)

    Liu, Hongxue; Comes, Ryan; Lu, Jiwei; Wolf, Stuart; Hodgson, Jim; Rutgers, Maarten

    2013-03-01

    Atomic force microscopy (AFM) has become one of the most widely used techniques for measuring and manipulating various characteristics of materials at the nanoscale. However, there are very limited option for the characterization of field dependence properties. In this work, we demonstrate a versatile variable field module (VFM) with magnetic field up to 1800 Oe for the Asylum Research Cypher system. The magnetic field is changed by adjusting the distance between a rare earth magnet and the AFM probe. A built-in Hall sensor makes it possible to perform in-situ measurements of the field. Rotating the magnet makes it possible to do angular field dependent measurements. The capability of the VFM system is demonstrated by degaussing a floppy disk media with increasing magnetic field. The written bits are erased at about 800 Oe. Angular dependence measurements clearly show the evolution of magnetic domain structures. A completely reversible magnetic force microscopy (MFM) phase contrast is observed when the magnetic field is rotated by 180°. Further demonstration of successful magnetic switching of CoFe2O4 pillars in CoFe2O4-BiFeO3 nanocomposites will be presented and field dependent MFM and piezoresponse force microscopy (PFM) will be discussed. The work at University of Virginia was supported by DARPA under contract no. HR-0011-10-1-0072.

  13. Data processing and quality evaluation of a boat-based mobile laser scanning system.

    Science.gov (United States)

    Vaaja, Matti; Kukko, Antero; Kaartinen, Harri; Kurkela, Matti; Kasvi, Elina; Flener, Claude; Hyyppä, Hannu; Hyyppä, Juha; Järvelä, Juha; Alho, Petteri

    2013-09-17

    Mobile mapping systems (MMSs) are used for mapping topographic and urban features which are difficult and time consuming to measure with other instruments. The benefits of MMSs include efficient data collection and versatile usability. This paper investigates the data processing steps and quality of a boat-based mobile mapping system (BoMMS) data for generating terrain and vegetation points in a river environment. Our aim in data processing was to filter noise points, detect shorelines as well as points below water surface and conduct ground point classification. Previous studies of BoMMS have investigated elevation accuracies and usability in detection of fluvial erosion and deposition areas. The new findings concerning BoMMS data are that the improved data processing approach allows for identification of multipath reflections and shoreline delineation. We demonstrate the possibility to measure bathymetry data in shallow (0-1 m) and clear water. Furthermore, we evaluate for the first time the accuracy of the BoMMS ground points classification compared to manually classified data. We also demonstrate the spatial variations of the ground point density and assess elevation and vertical accuracies of the BoMMS data.

  14. DNA barcoding as a screening tool for cryptic diversity

    DEFF Research Database (Denmark)

    Huemer, Peter; Karsholt, Ole; Mutanen, Marko

    2014-01-01

    of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum...... crypticum sp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely......We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c...

  15. Ultrasonic sensor properties characterized by a PC-controlled scanning measuring system

    Science.gov (United States)

    Henning; Prange; Dierks; Daur

    2000-03-01

    The use of ultrasonic sensors for process control is currently widespread for flow, level or distance measurements. Recently, interest has increased, too in the application of ultrasonic sensors to concentration measurements in complex liquids. In this application there are high demands for a defined and stable quality of the properties of both the sensor transfer function and the sound field characteristic. For a detailed investigation and characterization of ultrasonic sensor propertiess, an efficient PC-controlled measuring system was developed by the Institut fur Automation und Kommunikation (IFAK). In this contribution, this high performance approach is presented to make visible the vibrating ultrasonic sensor surface as well as the sound field in front of acoustic sensors in liquids.

  16. VPI - VIBRATION PATTERN IMAGER: A CONTROL AND DATA ACQUISITION SYSTEM FOR SCANNING LASER VIBROMETERS

    Science.gov (United States)

    Rizzi, S. A.

    1994-01-01

    The Vibration Pattern Imager (VPI) system was designed to control and acquire data from laser vibrometer sensors. The PC computer based system uses a digital signal processing (DSP) board and an analog I/O board to control the sensor and to process the data. The VPI system was originally developed for use with the Ometron VPI Sensor (Ometron Limited, Kelvin House, Worsley Bridge Road, London, SE26 5BX, England), but can be readily adapted to any commercially available sensor which provides an analog output signal and requires analog inputs for control of mirror positioning. VPI's graphical user interface allows the operation of the program to be controlled interactively through keyboard and mouse-selected menu options. The main menu controls all functions for setup, data acquisition, display, file operations, and exiting the program. Two types of data may be acquired with the VPI system: single point or "full field". In the single point mode, time series data is sampled by the A/D converter on the I/O board at a user-defined rate for the selected number of samples. The position of the measuring point, adjusted by mirrors in the sensor, is controlled via a mouse input. In the "full field" mode, the measurement point is moved over a user-selected rectangular area with up to 256 positions in both x and y directions. The time series data is sampled by the A/D converter on the I/O board and converted to a root-mean-square (rms) value by the DSP board. The rms "full field" velocity distribution is then uploaded for display and storage. VPI is written in C language and Texas Instruments' TMS320C30 assembly language for IBM PC series and compatible computers running MS-DOS. The program requires 640K of RAM for execution, and a hard disk with 10Mb or more of disk space is recommended. The program also requires a mouse, a VGA graphics display, a Four Channel analog I/O board (Spectrum Signal Processing, Inc.; Westborough, MA), a break-out box and a Spirit-30 board (Sonitech

  17. High Pressure Scanning Tunneling Microscopy Studies of AdsorbateStructure and Mobility during Catalytic Reactions: Novel Design of anUltra High Pressure, High Temperature Scanning Tunneling MicroscopeSystem for Probing Catalytic Conversions

    Energy Technology Data Exchange (ETDEWEB)

    Tang, David Chi-Wai [Univ. of California, Berkeley, CA (United States)

    2005-05-16

    The aim of the work presented therein is to take advantage of scanning tunneling microscope’s (STM) capability for operation under a variety of environments under real time and at atomic resolution to monitor adsorbate structures and mobility under high pressures, as well as to design a new generation of STM systems that allow imaging in situ at both higher pressures (35 atm) and temperatures (350 °C).

  18. Volumetric rendering and metrology of spherical gradient refractive index lens imaged by angular scan optical coherence tomography system.

    Science.gov (United States)

    Yao, Jianing; Thompson, Kevin P; Ma, Bin; Ponting, Michael; Rolland, Jannick P

    2016-08-22

    In this paper, we develop the methodology, including the refraction correction, geometrical thickness correction, coordinate transformation, and layer segmentation algorithms, for 3D rendering and metrology of a layered spherical gradient refractive index (S-GRIN) lens based on the imaging data collected by an angular scan optical coherence tomography (OCT) system. The 3D mapping and rendering enables direct 3D visualization and internal defect inspection of the lens. The metrology provides assessment of the surface geometry, the lens thickness, the radii of curvature of the internal layer interfaces, and the misalignment of the internal S-GRIN distribution with respect to the lens surface. The OCT metrology results identify the manufacturing defects, and enable targeted process development for optimizing the manufacturing parameters. The newly fabricated S-GRIN lenses show up to a 7x spherical aberration reduction that allows a significantly increased utilizable effective aperture.

  19. Solitary pulmonary amyloidoma mimicking lung cancer on 18F-FDG PET-CT scan in systemic lupus erythematosus patient.

    Science.gov (United States)

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