Identification of toxic cyclopeptides based on mass spectral library matching

Directory of Open Access Journals (Sweden)

Boris L. Milman

2014-08-01

Full Text Available To gain perspective on the use of tandem mass spectral libraries for identification of toxic cyclic peptides, the new library was built from 263 mass spectra (mainly MS2 spectra of 59 compounds of that group, such as microcystins, amatoxins, and some related compounds. Mass spectra were extracted from the literature or specially acquired on ESI-Q-ToF and MALDI-ToF/ToF tandem instruments. ESI-MS2 product-ion mass spectra appeared to be rather close to MALDI-ToF/ToF fragment spectra which are uncommon for mass spectral libraries. Testing of the library was based on searches where reference spectra were in turn cross-compared. The percentage of 1st rank correct identifications (true positives was 70% in a general case and 88–91% without including knowingly defective (‘one-dimension’ spectra as test ones. The percentage of 88–91% is the principal estimate for the overall performance of this library that can be used in a method of choice for identification of individual cyclopeptides and also for group recognition of individual classes of such peptides. The approach to identification of cyclopeptides based on mass spectral library matching proved to be the most effective for abundant toxins. That was confirmed by analysis of extracts from two cyanobacterial strains.

Towards Spectral Library-free MALDI-TOF MS Bacterial Identification.

Science.gov (United States)

Cheng, Ding; Qiao, Liang; Horvatovich, Péter

2018-05-11

Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, i.e. UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

Science.gov (United States)

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

2011-06-03

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.

Science.gov (United States)

Chen, Gengbo; Walmsley, Scott; Cheung, Gemmy C M; Chen, Liyan; Cheng, Ching-Yu; Beuerman, Roger W; Wong, Tien Yin; Zhou, Lei; Choi, Hyungwon

2017-05-02

Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.

Electron-energy-loss spectral library and its application to materials science

Energy Technology Data Exchange (ETDEWEB)

Zaluzec, N.J.

1983-09-01

An electron energy loss spectral library can be an invaluable tool in materials research from a fundamental as well as a practical standpoint. Although it will not alleviate all the complications associated with quantification, this type of library can help to elucidate details of spectral profiles previously found intractable. This work was supported by the US Department of Energy. The author also wishes to express his gratitude to the organizing committee for partial financial support provided to attend this meeting.

Hyperspectral imaging of polymer banknotes for building and analysis of spectral library

Science.gov (United States)

Lim, Hoong-Ta; Murukeshan, Vadakke Matham

2017-11-01

The use of counterfeit banknotes increases crime rates and cripples the economy. New countermeasures are required to stop counterfeiters who use advancing technologies with criminal intent. Many countries started adopting polymer banknotes to replace paper notes, as polymer notes are more durable and have better quality. The research on authenticating such banknotes is of much interest to the forensic investigators. Hyperspectral imaging can be employed to build a spectral library of polymer notes, which can then be used for classification to authenticate these notes. This is however not widely reported and has become a research interest in forensic identification. This paper focuses on the use of hyperspectral imaging on polymer notes to build spectral libraries, using a pushbroom hyperspectral imager which has been previously reported. As an initial study, a spectral library will be built from three arbitrarily chosen regions of interest of five circulated genuine polymer notes. Principal component analysis is used for dimension reduction and to convert the information in the spectral library to principal components. A 99% confidence ellipse is formed around the cluster of principal component scores of each class and then used as classification criteria. The potential of the adopted methodology is demonstrated by the classification of the imaged regions as training samples.

Library design practices for success in lead generation with small molecule libraries.

Science.gov (United States)

Goodnow, R A; Guba, W; Haap, W

2003-11-01

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.

A Spectral Library of Emissivity Spectra for MERTIS on BepiColombo

Science.gov (United States)

Maturilli, A.; Helbert, J.; Varatharajan, I.; D'Amore, M.; Hiesinger, H.

2018-05-01

At PSL we measured emissivity spectra in vacuum for a suite of Mercury surface analogues for temperatures from 100°C to >400°C. The spectral library is completed by reflectance on samples fresh and post-heating (0.2 to 200 µm spectral range).

THERMLIB, Generator and Edit of Program THERMOS-OTA Library. THERLIB, Library Generated for THERMOS from FACEL Library

International Nuclear Information System (INIS)

Rastas, A.

1985-01-01

1 - Description of problem or function: THERMLIB is a code that generates, revises and expands the input data library to the lattice cell code THERMOS-OTA. It can be used to: - create an entirely new library; - modify the data of library materials, remove materials, add materials; - list the library. 2 - Restrictions on the complexity of the problem: Max. of 30 materials may be modified or removed. Max. of 30 new materials may be created. Max. of 50 velocity groups

Spectral unmixing of urban land cover using a generic library approach

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Degerickx, Jeroen; Lordache, Marian-Daniel; Okujeni, Akpona; Hermy, Martin; van der Linden, Sebastian; Somers, Ben

2016-10-01

Remote sensing based land cover classification in urban areas generally requires the use of subpixel classification algorithms to take into account the high spatial heterogeneity. These spectral unmixing techniques often rely on spectral libraries, i.e. collections of pure material spectra (endmembers, EM), which ideally cover the large EM variability typically present in urban scenes. Despite the advent of several (semi-) automated EM detection algorithms, the collection of such image-specific libraries remains a tedious and time-consuming task. As an alternative, we suggest the use of a generic urban EM library, containing material spectra under varying conditions, acquired from different locations and sensors. This approach requires an efficient EM selection technique, capable of only selecting those spectra relevant for a specific image. In this paper, we evaluate and compare the potential of different existing library pruning algorithms (Iterative Endmember Selection and MUSIC) using simulated hyperspectral (APEX) data of the Brussels metropolitan area. In addition, we develop a new hybrid EM selection method which is shown to be highly efficient in dealing with both imagespecific and generic libraries, subsequently yielding more robust land cover classification results compared to existing methods. Future research will include further optimization of the proposed algorithm and additional tests on both simulated and real hyperspectral data.

The US Geological Survey, digital spectral reflectance library: version 1: 0.2 to 3.0 microns

Science.gov (United States)

Clark, Roger N.; Swayze, Gregg A.; King, Trude V. V.; Gallagher, Andrea J.; Calvin, Wendy M.

1993-01-01

We have developed a digital reflectance spectral library, with management and spectral analysis software. The library includes 500 spectra of 447 samples (some samples include a series of grain sizes) measured from approximately 0.2 to 3.0 microns. The spectral resolution (Full Width Half Maximum) of the reflectance data is less than or equal to 4 nm in the visible (0.2-0.8 microns) and less than or equal 10 nm in the NIR (0.8-2.35 microns). All spectra were corrected to absolute reflectance using an NBS Halon standard. Library management software lets users search on parameters (e.g. chemical formulae, chemical analyses, purity of samples, mineral groups, etc.) as well as spectral features. Minerals from sulfide, oxide, hydroxide, halide, carbonate, nitrate, borate, phosphate, and silicate groups are represented. X-ray and chemical analyses are tabulated for many of the entries, and all samples have been evaluated for spectral purity. The library also contains end and intermediate members for the olivine, garnet, scapolite, montmorillonite, muscovite, jarosite, and alunite solid-solution series. We have included representative spectra of H2O ice, kerogen, ammonium-bearing minerals, rare-earth oxides, desert varnish coatings, kaolinite crystallinity series, kaolinite-smectite series, zeolite series, and an extensive evaporite series. Because of the importance of vegetation to climate-change studies we have include 17 spectra of tree leaves, bushes, and grasses.

Generation of the WIMS code library from the ENDF/B-VI basic library

International Nuclear Information System (INIS)

Aboustta, Mohamed Ali Bashir.

1994-01-01

The WIMS code is being presently used in many research centers and educational institutions in the world. It has proven to be versatile, reliable and diverse as it is used to calculate different reactor systems. Its data library is rich of useful information that can even be condensed to serve other codes, but the copy distributed with the code is not updated. Some of its data has never been changed, others had changed many times to accommodate certain experimental setups and some data is, simply, not included. This work is an attempt to dominate the techniques used in generating a multigroup library as being applied to the WIMS data library. This new library is called UFMGLIB. A new set of consistent data was generated from the basic ENDF/B-VI library, including complete data for the fission product nuclides and more elaborated burnup chains. The performance of the library is comparable to that of the Standard library accompanying the code and a later library, WIMKAL 88, generated by a group of the Korean Research Institute of Atomic Energy. (author). 38 refs., 40 figs., 30 tabs

A quantitative infrared spectral library of vapor phase chemicals: applications to environmental monitoring and homeland defense

Science.gov (United States)

Sharpe, Steven W.; Johnson, Timothy J.; Sams, Robert L.

2004-12-01

The utility of infrared spectroscopy for monitoring and early warning of accidental or deliberate chemical releases to the atmosphere is well documented. Regardless of the monitoring technique (open-path or extractive) or weather the spectrometer is passive or active (Fourier transform or lidar) a high quality, quantitative reference library is essential for meaningful interpretation of the data. Pacific Northwest National Laboratory through the support of the Department of Energy has been building a library of pure, vapor phase chemical species for the last 4 years. This infrared spectral library currently contains over 300 chemicals and is expected to grow to over 400 chemicals before completion. The library spectra are based on a statistical fit to many spectra at different concentrations, allowing for rigorous error analysis. The contents of the library are focused on atmospheric pollutants, naturally occurring chemicals, toxic industrial chemicals and chemicals specifically designed to do damage. Applications, limitations and technical details of the spectral library will be discussed.

Evaluation of the sensitivity of the 'Wiley registry of tandem mass spectral data, MSforID' with MS/MS data of the 'NIST/NIH/EPA mass spectral library'.

Science.gov (United States)

Oberacher, Herbert; Whitley, Graeme; Berger, Bernd

2013-04-01

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.

The Strategies of Academic Library to Serve Net-Generation

Directory of Open Access Journals (Sweden)

candra pratama setiawan

2018-01-01

Full Text Available The fast developments in information and communication technology have rapidly shaped and created enormous changes in the way people live and use libraries. The generation who grow in this era is called net generation. Academic libraries, where the majority of the users are the netgeneration, have started to implement the concept of hybrid library as a response of the technological advances. The trend of digital collections usage is getting increase, on the other hand, the number of library visitor is getting lower significantly. The condition make librarians afraid of being abandoned by its users, whereas libraries still have many physical collections. This paper is written as a result of simple observation in some libraries where the needs of netgeneration has accomodated. The concept of library as place, and library marketing offer the solutions to deal with the problem. Libraries can develop and provide some facilities that suitable with the net-generation characteristics. In addition, libraries can create some events to promote their services even the collections to attract the users to visit library.

Using LUCAS topsoil database to estimate soil organic carbon content in local spectral libraries

Science.gov (United States)

Castaldi, Fabio; van Wesemael, Bas; Chabrillat, Sabine; Chartin, Caroline

2017-04-01

The quantification of the soil organic carbon (SOC) content over large areas is mandatory to obtain accurate soil characterization and classification, which can improve site specific management at local or regional scale exploiting the strong relationship between SOC and crop growth. The estimation of the SOC is not only important for agricultural purposes: in recent years, the increasing attention towards global warming highlighted the crucial role of the soil in the global carbon cycle. In this context, soil spectroscopy is a well consolidated and widespread method to estimate soil variables exploiting the interaction between chromophores and electromagnetic radiation. The importance of spectroscopy in soil science is reflected by the increasing number of large soil spectral libraries collected in the world. These large libraries contain soil samples derived from a consistent number of pedological regions and thus from different parent material and soil types; this heterogeneity entails, in turn, a large variability in terms of mineralogical and organic composition. In the light of the huge variability of the spectral responses to SOC content and composition, a rigorous classification process is necessary to subset large spectral libraries and to avoid the calibration of global models failing to predict local variation in SOC content. In this regard, this study proposes a method to subset the European LUCAS topsoil database into soil classes using a clustering analysis based on a large number of soil properties. The LUCAS database was chosen to apply a standardized multivariate calibration approach valid for large areas without the need for extensive field and laboratory work for calibration of local models. Seven soil classes were detected by the clustering analyses and the samples belonging to each class were used to calibrate specific partial least square regression (PLSR) models to estimate SOC content of three local libraries collected in Belgium (Loam belt

The Strategies of Academic Library to Serve Net-Generation

Directory of Open Access Journals (Sweden)

Chandra Pratama Setiawan

2015-04-01

Full Text Available The  fast  developments  in  information  and  communication  technology  have  rapidly  shaped  and created enormous changes in the way people live and use libraries. The generation who grow in this era is called net generation. Academic libraries, where the majority of the users are the net-generation,  have  started  to  implement  the  concept  of  hybrid  library  as  a  response  of  the technological  advances.  The  trend  of  digital  collections  usage  is  getting  increase,  on  the  other hand,  the  number  of  library  visitor  is  getting  lower  significantly.  The  condition  make  librarians afraid  of  being  abandoned  by  its  users,  whereas  libraries  still  have  many  physical  collections. This paper is written as a result of simple observation in some libraries where the needs of net-generation  has  accommodated.  The  concept  of library  as  place,  and  library  marketing  offer  the solutions to deal with the problem. Libraries can develop and provide some facilities that suitable with  the net-generation  characteristics.  In  addition,  libraries  can  create  some  events  to  promote their services even the collections to attract the users to visit library.

Generation of Matxs-formated nuclear data libraries

International Nuclear Information System (INIS)

Vontobel, P.

1989-01-01

Using the NJOY nuclear data processing system, three multigroup MATXS-formated nuclear data libraries were generated based on the European data files JEF-1 and EFF-1. After processing with TRAMIX, TRANSX, or TRANSX-CTR these libraries can be red into most transport and diffusion codes. For the neutron analysis of gas-cooled or water moderated thermal reactor systems (including high converter PWR's) a 70-group WIMS-BOXER structured library was generated. A general purpose fine group library in 308 groups is provided for thermal as well as for fast reactor systems. A coupled 175 neutron/42 photon-group library in VITAMIN-J structure was created for the analysis of shielding problems and fusion blanket design. A problem found when using CRAY's CFT77 compiler to implement NJOY87 is discussed. The problem of irregular selfshielding factors from UNRESR for some isotopes and (σ 0 , material temperature)-combinations in the unresolved resonance range is addressed

Combining Fragment-Ion and Neutral-Loss Matching during Mass Spectral Library Searching: A New General Purpose Algorithm Applicable to Illicit Drug Identification.

Science.gov (United States)

Moorthy, Arun S; Wallace, William E; Kearsley, Anthony J; Tchekhovskoi, Dmitrii V; Stein, Stephen E

2017-12-19

A mass spectral library search algorithm that identifies compounds that differ from library compounds by a single "inert" structural component is described. This algorithm, the Hybrid Similarity Search, generates a similarity score based on matching both fragment ions and neutral losses. It employs the parameter DeltaMass, defined as the mass difference between query and library compounds, to shift neutral loss peaks in the library spectrum to match corresponding neutral loss peaks in the query spectrum. When the spectra being compared differ by a single structural feature, these matching neutral loss peaks should contain that structural feature. This method extends the scope of the library to include spectra of "nearest-neighbor" compounds that differ from library compounds by a single chemical moiety. Additionally, determination of the structural origin of the shifted peaks can aid in the determination of the chemical structure and fragmentation mechanism of the query compound. A variety of examples are presented, including the identification of designer drugs and chemical derivatives not present in the library.

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

Science.gov (United States)

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

PWR steam generator tubing sample library

International Nuclear Information System (INIS)

Anon.

1987-01-01

In order to compile the tubing sample library, two approaches were employed: (a) tubing sample replication by either chemical or mechanical means, based on field tube data and metallography reports for tubes already destructively examined; and (b) acquisition of field tubes removed from operating or retired steam generators. In addition, a unique mercury modeling concept is in use to guide the selection of replica samples. A compendium was compiled that summarizes field observations and morphologies of steam generator tube degradation types based on available NDE, destructive examinations, and field reports. This compendium was used in selecting candidate degradation types that were manufactured for inclusion in the tube library

Generating and verification of ACE-multigroup library for MCNP

International Nuclear Information System (INIS)

Chen Chaobin; Hu Zehua; Chen Yixue; Wu Jun; Yang Shouhai

2012-01-01

The Monte Carlo code MCNP can handle multigroup calculations and a sample multigroup set based on ENDF/B-V, MGXSNP, is available for MCNP for coupled neutron-photon transport. However, this library is not suit- able for all problems, and there is a need for users to be able to generate multigroup libraries tailored to their specific applications. For these purposes CSPT (cross section processing tool) is created to generate multigroup library for MCNP from deterministic multigroup cross sections (GENDF or ANISN format at present). Several ACE-multigroup libraries based on ENDF/B-VII.0 converted and verified in this work, we drawn the conclusion that the CSPT code works correctly and the libraries produced are credible. (authors)

Software Quality Assurance and Verification for the MPACT Library Generation Process

Energy Technology Data Exchange (ETDEWEB)

Liu, Yuxuan [Univ. of Michigan, Ann Arbor, MI (United States); Williams, Mark L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wiarda, Dorothea [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Clarno, Kevin T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kim, Kang Seog [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Celik, Cihangir [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-05-01

This report fulfills the requirements for the Consortium for the Advanced Simulation of Light-Water Reactors (CASL) milestone L2:RTM.P14.02, “SQA and Verification for MPACT Library Generation,” by documenting the current status of the software quality, verification, and acceptance testing of nuclear data libraries for MPACT. It provides a brief overview of the library generation process, from general-purpose evaluated nuclear data files (ENDF/B) to a problem-dependent cross section library for modeling of light-water reactors (LWRs). The software quality assurance (SQA) programs associated with each of the software used to generate the nuclear data libraries are discussed; specific tests within the SCALE/AMPX and VERA/XSTools repositories are described. The methods and associated tests to verify the quality of the library during the generation process are described in detail. The library generation process has been automated to a degree to (1) ensure that it can be run without user intervention and (2) to ensure that the library can be reproduced. Finally, the acceptance testing process that will be performed by representatives from the Radiation Transport Methods (RTM) Focus Area prior to the production library’s release is described in detail.

Procedure to Generate the MPACT Multigroup Library

Energy Technology Data Exchange (ETDEWEB)

Kim, Kang Seog [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-12-17

The CASL neutronics simulator MPACT is under development for the neutronics and T-H coupled simulation for the light water reactor. The objective of this document is focused on reviewing the current procedure to generate the MPACT multigroup library. Detailed methodologies and procedures are included in this document for further discussion to improve the MPACT multigroup library.

Enzymatically Generated CRISPR Libraries for Genome Labeling and Screening.

Science.gov (United States)

Lane, Andrew B; Strzelecka, Magdalena; Ettinger, Andreas; Grenfell, Andrew W; Wittmann, Torsten; Heald, Rebecca

2015-08-10

CRISPR-based technologies have emerged as powerful tools to alter genomes and mark chromosomal loci, but an inexpensive method for generating large numbers of RNA guides for whole genome screening and labeling is lacking. Using a method that permits library construction from any source of DNA, we generated guide libraries that label repetitive loci or a single chromosomal locus in Xenopus egg extracts and show that a complex library can target the E. coli genome at high frequency. Copyright © 2015 Elsevier Inc. All rights reserved.

Study of old ecological hazards, oil seeps and contaminations using earth observation methods – spectral library for oil seep

Directory of Open Access Journals (Sweden)

Smejkalová Eva

2017-03-01

Full Text Available The possibilities of remote sensing techniques in the field of the Earth surface monitoring and protection specifically for the problems caused by petroleum contaminations, for the mapping of insufficiently plugged and abandoned old oil wells and for the analysis of onshore oil seeps are described. Explained is the methodology for analyzing and detection of potential hydrocarbon contaminations using the Earth observation in the area of interest in Slovakia (Korňa and in Czech Republic (Nesyt, mainly building and calibrating the spectral library for oil seeps. The acquisition of the in-situ field data (ASD, Cropscan spectroradiometers for this purpose, the successful building and verification of hydrocarbon spectral library, the application of hydrocarbon indexes and use of shift in red-edge part of electromagnetic spectra, the spectral analysis of input data are clarified in the paper. Described is approach which could innovate the routine methods for investigating the occurrence of hydrocarbons and can assist during the mapping and locating the potential oil seep sites. Important outcome is the successful establishment of a spectral library (database with calibration data suitable for further application in data classification for identifying the occurrence of hydrocarbons.

Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs.

Science.gov (United States)

Pavlic, Marion; Libiseller, Kathrin; Oberacher, Herbert

2006-09-01

The potential of the combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called "match probability", which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm-an implemented spectral purification option-enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples.

Amplification and Re-Generation of LNA-Modified Libraries

DEFF Research Database (Denmark)

Doessing, Holger; Hansen, Lykke H.; Veedu, Rakesh N.

2012-01-01

Locked nucleic acids (LNA) confer high thermal stability and nuclease resistance to oligonucleotides. The discovery of polymerases that accept LNA triphosphates has led us to propose a scheme for the amplification and re-generation of LNA-containing oligonucleotide libraries. Such libraries could...

Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

Science.gov (United States)

Lyons, Eli; Sheridan, Paul; Tremmel, Georg; Miyano, Satoru; Sugano, Sumio

2017-10-24

High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

Uniqueness: skews bit occurrence frequencies in randomly generated fingerprint libraries.

Science.gov (United States)

Chen, Nelson G

2016-08-01

Requiring that randomly generated chemical fingerprint libraries have unique fingerprints such that no two fingerprints are identical causes a systematic skew in bit occurrence frequencies, the proportion at which specified bits are set. Observed frequencies (O) at which each bit is set within the resulting libraries systematically differ from frequencies at which bits are set at fingerprint generation (E). Observed frequencies systematically skew toward 0.5, with the effect being more pronounced as library size approaches the compound space, which is the total number of unique possible fingerprints given the number of bit positions each fingerprint contains. The effect is quantified for varying library sizes as a fraction of the overall compound space, and for changes in the specified frequency E. The cause and implications for this systematic skew are subsequently discussed. When generating random libraries of chemical fingerprints, the imposition of a uniqueness requirement should either be avoided or taken into account.

Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

Science.gov (United States)

Heredia, Nicholas J

2018-01-01

Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library

Science.gov (United States)

Lee, Hyeyoung; Cuthbertson, Daniel J.; Otter, Don E.; Barile, Daniela

2018-01-01

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

On the construction of a new stellar classification template library for the LAMOST spectral analysis pipeline

Energy Technology Data Exchange (ETDEWEB)

Wei, Peng; Luo, Ali; Li, Yinbi; Tu, Liangping; Wang, Fengfei; Zhang, Jiannan; Chen, Xiaoyan; Hou, Wen; Kong, Xiao; Wu, Yue; Zuo, Fang; Yi, Zhenping; Zhao, Yongheng; Chen, Jianjun; Du, Bing; Guo, Yanxin; Ren, Juanjuan [Key Laboratory of Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Pan, Jingchang; Jiang, Bin; Liu, Jie, E-mail: lal@nao.cas.cn, E-mail: weipeng@nao.cas.cn [School of Mechanical, Electrical, and Information Engineering, Shandong University, Weihai 264209 (China); and others

2014-05-01

The LAMOST spectral analysis pipeline, called the 1D pipeline, aims to classify and measure the spectra observed in the LAMOST survey. Through this pipeline, the observed stellar spectra are classified into different subclasses by matching with template spectra. Consequently, the performance of the stellar classification greatly depends on the quality of the template spectra. In this paper, we construct a new LAMOST stellar spectral classification template library, which is supposed to improve the precision and credibility of the present LAMOST stellar classification. About one million spectra are selected from LAMOST Data Release One to construct the new stellar templates, and they are gathered in 233 groups by two criteria: (1) pseudo g – r colors obtained by convolving the LAMOST spectra with the Sloan Digital Sky Survey ugriz filter response curve, and (2) the stellar subclass given by the LAMOST pipeline. In each group, the template spectra are constructed using three steps. (1) Outliers are excluded using the Local Outlier Probabilities algorithm, and then the principal component analysis method is applied to the remaining spectra of each group. About 5% of the one million spectra are ruled out as outliers. (2) All remaining spectra are reconstructed using the first principal components of each group. (3) The weighted average spectrum is used as the template spectrum in each group. Using the previous 3 steps, we initially obtain 216 stellar template spectra. We visually inspect all template spectra, and 29 spectra are abandoned due to low spectral quality. Furthermore, the MK classification for the remaining 187 template spectra is manually determined by comparing with 3 template libraries. Meanwhile, 10 template spectra whose subclass is difficult to determine are abandoned. Finally, we obtain a new template library containing 183 LAMOST template spectra with 61 different MK classes by combining it with the current library.

Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring.

Science.gov (United States)

Ma, Chun Wai Manson; Lam, Henry

2014-05-02

Discovering novel post-translational modifications (PTMs) to proteins and detecting specific modification sites on proteins is one of the last frontiers of proteomics. At present, hunting for post-translational modifications remains challenging in widely practiced shotgun proteomics workflows due to the typically low abundance of modified peptides and the greatly inflated search space as more potential mass shifts are considered by the search engines. Moreover, most popular search methods require that the user specifies the modification(s) for which to search; therefore, unexpected and novel PTMs will not be detected. Here a new algorithm is proposed to apply spectral library searching to the problem of open modification searches, namely, hunting for PTMs without prior knowledge of what PTMs are in the sample. The proposed tier-wise scoring method intelligently looks for unexpected PTMs by allowing mass-shifted peak matches but only when the number of matches found is deemed statistically significant. This allows the search engine to search for unexpected modifications while maintaining its ability to identify unmodified peptides effectively at the same time. The utility of the method is demonstrated using three different data sets, in which the numbers of spectrum identifications to both unmodified and modified peptides were substantially increased relative to a regular spectral library search as well as to another open modification spectral search method, pMatch.

What Students Want: Generation Y and the Changing Function of the Academic Library

Science.gov (United States)

Gardner, Susan; Eng, Susanna

2005-01-01

This article presents the results of a 2003 undergraduate library user survey as a case study of Generation Y. Survey data support four main traits attributed to Generation Y, which are discussed within the context of library use and satisfaction. Implications for future directions in academic library services based on the new ways Generation Y…

Utilisation of Library Information Resources among Generation Z Students: Facts and Fiction

Directory of Open Access Journals (Sweden)

Oghenere Gabriel Salubi

2018-04-01

Full Text Available Generation Z was the foremost generation to have prevalent access to the Internet from an early age. Technology has strongly influenced this generation in terms of communication, education and consequently their academic information behaviour. With the next generation of scholars already being trained, in a decade, most of the researchers will be mainly digital natives. This study sought to establish the library information resources use pattern in relation to users’ preferred information media in order to render better academic information services to library users. A total of 390 respondents were surveyed at the Nelson Mandela University and the University of Fort Hare using quantitative and qualitative methods. Most of the respondents, 82.3%, were aged between 18 and 23 years; while the average library use time was two hours daily. The most utilised library resource is the Wi-Fi with e-books and e-journals found to be lowly utilised. Records from the E-librarians revealed that undergraduate students account for no more than 6% of total users of electronic databases with 62.3% of the respondents preferring print information resources. Better understanding of library users’ demographics and information media preference is essential in proving the right kind of information services to Generation Z library users.

GC^2: A Generational Conservative Garbage Collector for the ATerm Library

OpenAIRE

Moreau , Pierre-Etienne; Zendra , Olivier

2002-01-01

The ATerm library is a well-designed and well-known library in the term rewriting community. In this paper, we discuss the current garbage collector provided with the library and stress the fact that some peculiarities of this functional library could be taken advantage of by the memory management system. We explain how we designed and implemented GC², a new mark-and-sweep generational garbage collector for the ATerm library that builds upon these peculiarities. Experimental results on variou...

Spectrally modified chirped pulse generation of sustained shock waves

International Nuclear Information System (INIS)

McGrane, S.D.; Moore, D.S.; Funk, D.J.; Rabie, R.L.

2002-01-01

A method is described for generating shock waves with 10-20 ps risetime followed by >200 ps constant pressure, using spectrally modified (clipped) chirped laser pulses. The degree of spectral clipping alters the chirped pulse temporal intensity profile and thereby the time-dependent pressure (tunable via pulse energy) generated in bare and nitrocellulose-coated Al thin films. The method is implementable in common chirped amplified lasers, and allows synchronous probing with a <200 fs pulse

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing.

Science.gov (United States)

Wu, Wells W; Phue, Je-Nie; Lee, Chun-Ting; Lin, Changyi; Xu, Lai; Wang, Rong; Zhang, Yaqin; Shen, Rong-Fong

2018-05-04

Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.

Towards a full reference library of MS(n) spectra. II: A perspective from the library of pesticide spectra extracted from the literature/Internet.

Science.gov (United States)

Milman, Boris L; Zhurkovich, Inna K

2011-12-30

To gain perspective on building full transferable libraries of MS(n) spectra from their diverse/numerous collections, a new library was built from 1723 MS(>1) spectra (mainly MS² spectra) of 490 pesticides and related compounds. Spectra acquired on different types of tandem instruments in various experimental conditions were extracted from 168 literature articles and Internet sites. Testing of the library was based on searches where 'unknown' and reference spectra originated from different sources (mainly from different laboratories) were cross-compared. The NIST 05 MS² library was added to the reference spectra. The library searches were performed with all the test spectra or were divided into different subsamples containing (a) various numbers of replicate spectra of test compounds or (b) spectra acquired from different instrument types. Thus, the dependence of true/false search (identification) result rates on different factors was explored. The percentage of 1st rank correct identifications (true positives) for the only 'unknown' mass spectrum and two and more reference spectra and matching precursor ion m/z values was 89%. For qualified matches, above the cut-off match factor, that rate decreased to 80%. The corresponding rates based on the best match for two and more 'unknown' and reference spectral replicates were 89-94%. For quadrupole instruments, the rates were even higher: 91-95% (one 'unknown' spectrum) and 90-100% (two and more such spectra). This study shows that MS² spectral libraries generated from the numerous literature/Internet sources are not less efficient for the goal of identification of unknown compounds including pesticides than very common EI-MS¹ libraries and are almost as efficient as the most productive from current MS² spectral databases. Such libraries may be used as individual reference databases or supplements to large experimental spectral collections covering many groups of abundant compounds and different types of tandem

Gamma: A C++ Sound Synthesis Library Further Abstracting the Unit Generator

DEFF Research Database (Denmark)

Putnam, Lance Jonathan

2014-01-01

Gamma is a C++ library for sound synthesis that was created to address some of the limitations of existing sound synthesis libraries. The first limitation is that unit generators cannot easily be organized into separate sampling domains. This makes it difficult to use unit generators with different...... sample rates and in other domains, namely the frequency domain. The second limitation is that certain internal unit generator algorithms, such as interpolation, cannot be customized. This tends to lead to closed architectures consisting of multiple unit generators with only slight algorithmic differences...

Development of a dedicated peptide tandem mass spectral library for conservation science.

Science.gov (United States)

Fremout, Wim; Dhaenens, Maarten; Saverwyns, Steven; Sanyova, Jana; Vandenabeele, Peter; Deforce, Dieter; Moens, Luc

2012-05-30

In recent years, the use of liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art. Copyright © 2012 Elsevier B.V. All rights reserved.

Novel search algorithms for a mid-infrared spectral library of cotton contaminants.

Science.gov (United States)

Loudermilk, J Brian; Himmelsbach, David S; Barton, Franklin E; de Haseth, James A

2008-06-01

During harvest, a variety of plant based contaminants are collected along with cotton lint. The USDA previously created a mid-infrared, attenuated total reflection (ATR), Fourier transform infrared (FT-IR) spectral library of cotton contaminants for contaminant identification as the contaminants have negative impacts on yarn quality. This library has shown impressive identification rates for extremely similar cellulose based contaminants in cases where the library was representative of the samples searched. When spectra of contaminant samples from crops grown in different geographic locations, seasons, and conditions and measured with a different spectrometer and accessories were searched, identification rates for standard search algorithms decreased significantly. Six standard algorithms were examined: dot product, correlation, sum of absolute values of differences, sum of the square root of the absolute values of differences, sum of absolute values of differences of derivatives, and sum of squared differences of derivatives. Four categories of contaminants derived from cotton plants were considered: leaf, stem, seed coat, and hull. Experiments revealed that the performance of the standard search algorithms depended upon the category of sample being searched and that different algorithms provided complementary information about sample identity. These results indicated that choosing a single standard algorithm to search the library was not possible. Three voting scheme algorithms based on result frequency, result rank, category frequency, or a combination of these factors for the results returned by the standard algorithms were developed and tested for their capability to overcome the unpredictability of the standard algorithms' performances. The group voting scheme search was based on the number of spectra from each category of samples represented in the library returned in the top ten results of the standard algorithms. This group algorithm was able to identify

Generating Collaborative Systems for Digital Libraries: a Model-Driven Approach

Directory of Open Access Journals (Sweden)

Alessio Malizia

2010-12-01

Full Text Available The design and development of a digital library involves different stakeholders, such as: information architects, librarians, and domain experts, who need to agree on a common language to describe, discuss, and negotiate the services the library has to offer. To this end, high-level, language-neutral models have to be devised. Metamodeling techniques favor the definition of domainspecific visual languages through which stakeholders can share their views and directly manipulate representations of the domain entities. This paper describes CRADLE (Cooperative-Relational Approach to Digital Library Environments, a metamodel-based framework and visual language for the definition of notions and services related to the development of digital libraries. A collection of tools allows the automatic generation of several services, defined with the CRADLE visual language, and of the graphical user interfaces providing access to them for the final user. The effectiveness of the approach is illustrated by presenting digital libraries generated with CRADLE, while the CRADLE environment has been evaluated by using the cognitive dimensions framework.

Production of the next-generation library virtual tour

Science.gov (United States)

Duncan, James M.; Roth, Linda K.

2001-01-01

While many libraries offer overviews of their services through their Websites, only a small number of health sciences libraries provide Web-based virtual tours. These tours typically feature photographs of major service areas along with textual descriptions. This article describes the process for planning, producing, and implementing a next-generation virtual tour in which a variety of media elements are integrated: photographic images, 360-degree “virtual reality” views, textual descriptions, and contextual floor plans. Hardware and software tools used in the project are detailed, along with a production timeline and budget, tips for streamlining the process, and techniques for improving production. This paper is intended as a starting guide for other libraries considering an investment in such a project. PMID:11837254

Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

Science.gov (United States)

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Kim, Kwang-Youl; Kwon, Kyung-Hoon; Yoo, Jong Shin; Omenn, Gilbert S; Baker, Mark S; Hancock, William S; Paik, Young-Ki

2015-12-04

Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ~15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, which contains the simulated spectra of 173 907 human tryptic peptides determined by MassAnalyzer (version 2.3.1). To prove the enhanced analytical performance of the combination of the human iRefSPL and simSPL methods for the identification of missing proteins, we attempted to reanalyze the placental tissue data set (PXD000754). The data from each experiment were analyzed using PeptideProphet, and the results were combined using iProphet. For the quality control, we applied the class-specific false-discovery rate filtering method. All of the results were filtered at a false-discovery rate of libraries, iRefSPL and simSPL, were designed to ensure no overlap of the proteome coverage. They were shown to be complementary to spectral library

Generation of broad-group neutron/photon cross-section libraries for shielding applications

International Nuclear Information System (INIS)

Ingersoll, D.T.; Roussin, R.W.; Fu, C.Y.; White, J.E.

1989-01-01

The generation and use of multigroup cross-section libraries with broad energy group structures is primarily for the economy of computer resources. Also, the establishment of reference broad-group libraries is desirable in order to avoid duplication of effort, both in terms of the data generation and verification, and to assure a common data base for all participants in a specific project. Uncertainties are inevitably introduced into the broad-group cross sections due to approximations in the grouping procedure. The dominant uncertainty is generally with regard to the energy weighting function used to average the pointwise or fine-group data within a single broad group. Intelligent choice of the weighting functions can reduce such uncertainties. Also, judicious selection of the energy group structure can help to reduce the sensitivity of the computed responses to the weighting function, at least for a selected set of problems. Two new multigroup cross section libraries have been recently generated from ENDF/B-V data for two specific shielding applications. The first library was prepared for use in sodium-cooled reactor systems and is available in both broad-group structures. The second library, just recently completed, was prepared for use in air-over-ground environments and is available in a broad-group (46-neutron, 23-photon) energy structure. The selection of the specific group structures and weighting functions was an important part of the generation of both libraries

Generation and tests of the new version 88 library for HAMMER system

International Nuclear Information System (INIS)

Chalhoub, E.S.; Anaf, J.

1988-08-01

A new library, version 88, for the HAMMER system, was generated using the ENDF/B-IV FRENDL evaluated nuclear data libraries. It is composed of epithermal and thermal libraries obtained by processing the new versions of ETOG-3 and FLANGE-II codes, respectively. Test results for two benchmark critical assemblies are presented. (author) [pt

Privacy and Generation Y: Applying Library Values to Social Networking Sites

Science.gov (United States)

Fernandez, Peter

2010-01-01

Librarians face many challenges when dealing with issues of privacy within the mediated space of social networking sites. Conceptually, social networking sites differ from libraries on privacy as a value. Research about Generation Y students, the primary clientele of undergraduate libraries, can inform librarians' relationship to this important…

Generation and validation of the WIMS-D5 library based on JENDL-3.2

International Nuclear Information System (INIS)

Gil, Choong-Sup; Kim, Jung-Do

2002-01-01

A WIMS-D5 library based on JENDL-3.2 has been prepared and is being tested against benchmark problems. Several sensitivity calculations for stability confirmation of the library were carried out, such as fission spectrum dependency and the self-shielding effects of the elastic scattering cross sections and the self-shielding effects 240 Pu and 242 Pu capture cross sections below 4.0 eV. The results of benchmark calculations with the libraries based on JENDL-3.2, ENDF/B-VI.5, JEF-2.2, and the 1986 WIMS-D library were intercompared. The multiplication factors for the thermal lattices are slightly underpredicted by all libraries (up to 1% with ENDF/B-VI.5). The k eff values with the library based on JENDL-3.2 are slightly higher than those of ENDF/B-VI.5 and JEF-2.2. The spectral indices for the lattices with JENDL-3.2 agree with the measured quantities within the uncertainties of the experiments. The calculated amounts of some isotopes such as 149 Sm, 237 Np, 238 Pu, 242 Cm and 243 Cm show large differences from the measured or reference values. (author)

GASPRNG: GPU accelerated scalable parallel random number generator library

Science.gov (United States)

Gao, Shuang; Peterson, Gregory D.

2013-04-01

Graphics processors represent a promising technology for accelerating computational science applications. Many computational science applications require fast and scalable random number generation with good statistical properties, so they use the Scalable Parallel Random Number Generators library (SPRNG). We present the GPU Accelerated SPRNG library (GASPRNG) to accelerate SPRNG in GPU-based high performance computing systems. GASPRNG includes code for a host CPU and CUDA code for execution on NVIDIA graphics processing units (GPUs) along with a programming interface to support various usage models for pseudorandom numbers and computational science applications executing on the CPU, GPU, or both. This paper describes the implementation approach used to produce high performance and also describes how to use the programming interface. The programming interface allows a user to be able to use GASPRNG the same way as SPRNG on traditional serial or parallel computers as well as to develop tightly coupled programs executing primarily on the GPU. We also describe how to install GASPRNG and use it. To help illustrate linking with GASPRNG, various demonstration codes are included for the different usage models. GASPRNG on a single GPU shows up to 280x speedup over SPRNG on a single CPU core and is able to scale for larger systems in the same manner as SPRNG. Because GASPRNG generates identical streams of pseudorandom numbers as SPRNG, users can be confident about the quality of GASPRNG for scalable computational science applications. Catalogue identifier: AEOI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOI_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: UTK license. No. of lines in distributed program, including test data, etc.: 167900 No. of bytes in distributed program, including test data, etc.: 1422058 Distribution format: tar.gz Programming language: C and CUDA. Computer: Any PC or

BUILDING A NEW GENERATION SCIENCE LIBRARY: THE KAUST STORY

KAUST Repository

Al Zahrani, Rashed

2012-06-01

If you had the opportunity to build a science library from scratch for a new generation of researchers and students, what would it look like and how would it operate? We will show you the vision and reality of the new King Abdullah University of Science and Technology (KAUST) Library that won the 2011 ALA/AIA Library Architecture award and that for the last three years has been providing a high level of information services to top level international scientists and graduate students. We will describe the major characteristics in contemporary science research, education, and information management that guided the design of our library facility, technical infrastructure, and services. We will give concrete examples and evaluations of our implementation of new information services and tools. And we will end with the challenges still before us, most notably the effective integration of science knowledge management into the workflow of scientific research and enterprise based information technology organization.

Content Generation and Social Network Interaction within Academic Library Facebook Pages

Science.gov (United States)

Witte, Ginna Gauntner

2014-01-01

The use of Facebook to share resources and engage patrons continues to gain acceptance within academic libraries. While many studies have analyzed the types of content academic libraries share on Facebook, there has not yet been a full examination of how this content is generated. This article examined the posting methods, the user responses, and…

An improved yeast transformation method for the generation of very large human antibody libraries.

Science.gov (United States)

Benatuil, Lorenzo; Perez, Jennifer M; Belk, Jonathan; Hsieh, Chung-Ming

2010-04-01

Antibody library selection by yeast display technology is an efficient and highly sensitive method to identify binders to target antigens. This powerful selection tool, however, is often hampered by the typically modest size of yeast libraries (approximately 10(7)) due to the limited yeast transformation efficiency, and the full potential of the yeast display technology for antibody discovery and engineering can only be realized if it can be coupled with a mean to generate very large yeast libraries. We describe here a yeast transformation method by electroporation that allows for the efficient generation of large antibody libraries up to 10(10) in size. Multiple components and conditions including CaCl(2), MgCl(2), sucrose, sorbitol, lithium acetate, dithiothreitol, electroporation voltage, DNA input and cell volume have been tested to identify the best combination. By applying this developed protocol, we have constructed a 1.4 x 10(10) human spleen antibody library essentially in 1 day with a transformation efficiency of 1-1.5 x 10(8) transformants/microg vector DNA. Taken together, we have developed a highly efficient yeast transformation method that enables the generation of very large and productive human antibody libraries for antibody discovery, and we are now routinely making 10(9) libraries in a day for antibody engineering purposes.

Spatio-spectral analysis of ionization times in high-harmonic generation

Energy Technology Data Exchange (ETDEWEB)

Soifer, Hadas, E-mail: hadas.soifer@weizmann.ac.il [Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100 (Israel); Dagan, Michal; Shafir, Dror; Bruner, Barry D. [Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100 (Israel); Ivanov, Misha Yu. [Department of Physics, Imperial College London, South Kensington Campus, SW7 2AZ London (United Kingdom); Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Strasse 2A, D-12489 Berlin (Germany); Serbinenko, Valeria; Barth, Ingo; Smirnova, Olga [Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Strasse 2A, D-12489 Berlin (Germany); Dudovich, Nirit [Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100 (Israel)

2013-03-12

Graphical abstract: A spatio-spectral analysis of the two-color oscillation phase allows us to accurately separate short and long trajectories and reconstruct their ionization times. Highlights: ► We perform a complete spatio-spectral analysis of the high harmonic generation process. ► We analyze the ionization times across the entire spatio-spectral plane of the harmonics. ► We apply this analysis to reconstruct the ionization times of both short and long trajectories. - Abstract: Recollision experiments have been very successful in resolving attosecond scale dynamics. However, such schemes rely on the single atom response, neglecting the macroscopic properties of the interaction and the effects of using multi-cycle laser fields. In this paper we perform a complete spatio-spectral analysis of the high harmonic generation process and resolve the distribution of the subcycle dynamics of the recolliding electron. Specifically, we focus on the measurement of ionization times. Recently, we have demonstrated that the addition of a weak, crossed polarized second harmonic field allows us to resolve the moment of ionization (Shafir, 2012) [1]. In this paper we extend this measurement and perform a complete spatio-spectral analysis. We apply this analysis to reconstruct the ionization times of both short and long trajectories showing good agreement with the quantum path analysis.

CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

Science.gov (United States)

Duffy, Fergal J; Verniere, Mélanie; Devocelle, Marc; Bernard, Elise; Shields, Denis C; Chubb, Anthony J

2011-04-25

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Generation of a Broad-Group HTGR Library for Use with SCALE

International Nuclear Information System (INIS)

Ellis, Ronald James; Lee, Deokjung; Wiarda, Dorothea; Williams, Mark L.; Mertyurek, Ugur

2012-01-01

With current and ongoing interest in high temperature gas reactors (HTGRs), the U.S. Nuclear Regulatory Commission (NRC) anticipates the need for nuclear data libraries appropriate for use in applications for modeling, assessing, and analyzing HTGR reactor physics and operating behavior. The objective of this work was to develop a broad-group library suitable for production analyses with SCALE for HTGR applications. Several interim libraries were generated from SCALE fine-group 238- and 999-group libraries, and the final broad-group library was created from Evaluated Nuclear Data File/B Version ENDF/B-VII Release 0 cross-section evaluations using new ORNL methodologies with AMPX, SCALE, and other codes. Furthermore, intermediate resonance (IR) methods were applied to the HTGR broadgroup library, and lambda factors and f-factors were incorporated into the library s nuclear data files. A new version of the SCALE BONAMI module named BONAMI-IR was developed to process the IR data in the new library and, thus, eliminate the need for the CENTRM/PMC modules for resonance selfshielding. This report documents the development of the HTGR broad-group nuclear data library and the results of test and benchmark calculations using the new library with SCALE. The 81-group library is shown to model HTGR cases with similar accuracy to the SCALE 238-group library but with significantly faster computational times due to the reduced number of energy groups and the use of BONAMI-IR instead of BONAMI/CENTRM/PMC for resonance self-shielding calculations.

A Fiber-Optic System Generating Pulses of High Spectral Density

Science.gov (United States)

Abramov, A. S.; Zolotovskii, I. O.; Korobko, D. A.; Fotiadi, A. A.

2018-03-01

A cascade fiber-optic system that generates pulses of high spectral density by using the effect of nonlinear spectral compression is proposed. It is demonstrated that the shape of the pulse envelope substantially influences the degree of compression of its spectrum. In so doing, maximum compression is achieved for parabolic pulses. The cascade system includes an optical fiber exhibiting normal dispersion that decreases along the fiber length, thereby ensuring that the pulse envelope evolves toward a parabolic shape, along with diffraction gratings and a fiber spectral compressor. Based on computer simulation, we determined parameters of cascade elements leading to maximum spectral density of radiation originating from a subpicosecond laser pulse of medium energy.

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

Science.gov (United States)

Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

2016-08-31

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Spectral quality requirements for effluent identification

Science.gov (United States)

Czerwinski, R. N.; Seeley, J. A.; Wack, E. C.

2005-11-01

We consider the problem of remotely identifying gaseous materials using passive sensing of long-wave infrared (LWIR) spectral features at hyperspectral resolution. Gaseous materials are distinguishable in the LWIR because of their unique spectral fingerprints. A sensor degraded in capability by noise or limited spectral resolution, however, may be unable to positively identify contaminants, especially if they are present in low concentrations or if the spectral library used for comparisons includes materials with similar spectral signatures. This paper will quantify the relative importance of these parameters and express the relationships between them in a functional form which can be used as a rule of thumb in sensor design or in assessing sensor capability for a specific task. This paper describes the simulation of remote sensing datacontaining a gas cloud.In each simulation, the spectra are degraded in spectral resolution and through the addition of noise to simulate spectra collected by sensors of varying design and capability. We form a trade space by systematically varying the number of sensor spectral channels and signal-to-noise ratio over a range of values. For each scenario, we evaluate the capability of the sensor for gas identification by computing the ratio of the F-statistic for the truth gas tothe same statistic computed over the rest of the library.The effect of the scope of the library is investigated as well, by computing statistics on the variability of the identification capability as the library composition is varied randomly.

An Empirical Template Library of Stellar Spectra for a Wide Range of Spectral Classes, Luminosity Classes, and Metallicities Using SDSS BOSS Spectra

Energy Technology Data Exchange (ETDEWEB)

Kesseli, Aurora Y.; West, Andrew A.; Veyette, Mark; Harrison, Brandon; Feldman, Dan [Boston University Astronomy Department, 725 Commonwealth Ave., Boston, MA 02215 (United States); Bochanski, John J., E-mail: aurorak@bu.edu [Rider University, 2083 Lawrenceville Rd., Lawrence Township, NJ 08648 (United States)

2017-06-01

We present a library of empirical stellar spectra created using spectra from the Sloan Digital Sky Survey’s Baryon Oscillation Spectroscopic Survey. The templates cover spectral types O5 through L3, are binned by metallicity from −2.0 dex through +1.0 dex, and are separated into main-sequence (dwarf) stars and giant stars. With recently developed M dwarf metallicity indicators, we are able to extend the metallicity bins down through the spectral subtype M8, making this the first empirical library with this degree of temperature and metallicity coverage. The wavelength coverage for the templates is from 3650 to 10200 Å at a resolution of better than R  ∼ 2000. Using the templates, we identify trends in color space with metallicity and surface gravity, which will be useful for analyzing large data sets from upcoming missions like the Large Synoptic Survey Telescope. Along with the templates, we are releasing a code for automatically (and/or visually) identifying the spectral type and metallicity of a star.

Quantum mechanical energy-based screening of combinatorially generated library of tautomers. TauTGen: a tautomer generator program.

Science.gov (United States)

Harańczyk, Maciej; Gutowski, Maciej

2007-01-01

We describe a procedure of finding low-energy tautomers of a molecule. The procedure consists of (i) combinatorial generation of a library of tautomers, (ii) screening based on the results of geometry optimization of initial structures performed at the density functional level of theory, and (iii) final refinement of geometry for the top hits at the second-order Möller-Plesset level of theory followed by single-point energy calculations at the coupled cluster level of theory with single, double, and perturbative triple excitations. The library of initial structures of various tautomers is generated with TauTGen, a tautomer generator program. The procedure proved to be successful for these molecular systems for which common chemical knowledge had not been sufficient to predict the most stable structures.

Spectral Properties of Chaotic Signals Generated by the Bernoulli Map

Directory of Open Access Journals (Sweden)

Rafael A. da Costa

2014-11-01

Full Text Available In the last decades, the use of chaotic signals as broadband carriers has been considered in Telecommunications. Despite the relevance of the frequency domain analysis in this field, there are few studies that are concerned with spectral properties of chaotic signals. Bearing this in mind, this paper aims the characterization of the power spectral density (PSD of chaotic orbits generated by Bernoulli maps. We obtain analytic expressions for autocorrelation sequence, PSD and essential bandwidth for chaotic orbits generated by this map as function of the family parameter and Lyapunov exponent. Moreover, we verify that analytical expressions match numerical results. We conclude that the power of the generated orbits is concentrated in low frequencies for all parameters values. Besides, it is possible to obtain chaotic narrowband signals.

Multi-Threaded DNA Tag/Anti-Tag Library Generator for Multi-Core Platforms

Science.gov (United States)

2009-05-01

base pair)  Watson ‐ Crick  strand pairs that bind perfectly within pairs, but poorly across pairs. A variety  of  DNA  strand hybridization metrics...AFRL-RI-RS-TR-2009-131 Final Technical Report May 2009 MULTI-THREADED DNA TAG/ANTI-TAG LIBRARY GENERATOR FOR MULTI-CORE PLATFORMS...TYPE Final 3. DATES COVERED (From - To) Jun 08 – Feb 09 4. TITLE AND SUBTITLE MULTI-THREADED DNA TAG/ANTI-TAG LIBRARY GENERATOR FOR MULTI-CORE

A microfluidic DNA library preparation platform for next-generation sequencing.

Science.gov (United States)

Kim, Hanyoup; Jebrail, Mais J; Sinha, Anupama; Bent, Zachary W; Solberg, Owen D; Williams, Kelly P; Langevin, Stanley A; Renzi, Ronald F; Van De Vreugde, James L; Meagher, Robert J; Schoeniger, Joseph S; Lane, Todd W; Branda, Steven S; Bartsch, Michael S; Patel, Kamlesh D

2013-01-01

Next-generation sequencing (NGS) is emerging as a powerful tool for elucidating genetic information for a wide range of applications. Unfortunately, the surging popularity of NGS has not yet been accompanied by an improvement in automated techniques for preparing formatted sequencing libraries. To address this challenge, we have developed a prototype microfluidic system for preparing sequencer-ready DNA libraries for analysis by Illumina sequencing. Our system combines droplet-based digital microfluidic (DMF) sample handling with peripheral modules to create a fully-integrated, sample-in library-out platform. In this report, we use our automated system to prepare NGS libraries from samples of human and bacterial genomic DNA. E. coli libraries prepared on-device from 5 ng of total DNA yielded excellent sequence coverage over the entire bacterial genome, with >99% alignment to the reference genome, even genome coverage, and good quality scores. Furthermore, we produced a de novo assembly on a previously unsequenced multi-drug resistant Klebsiella pneumoniae strain BAA-2146 (KpnNDM). The new method described here is fast, robust, scalable, and automated. Our device for library preparation will assist in the integration of NGS technology into a wide variety of laboratories, including small research laboratories and clinical laboratories.

A microfluidic DNA library preparation platform for next-generation sequencing.

Directory of Open Access Journals (Sweden)

Hanyoup Kim

Full Text Available Next-generation sequencing (NGS is emerging as a powerful tool for elucidating genetic information for a wide range of applications. Unfortunately, the surging popularity of NGS has not yet been accompanied by an improvement in automated techniques for preparing formatted sequencing libraries. To address this challenge, we have developed a prototype microfluidic system for preparing sequencer-ready DNA libraries for analysis by Illumina sequencing. Our system combines droplet-based digital microfluidic (DMF sample handling with peripheral modules to create a fully-integrated, sample-in library-out platform. In this report, we use our automated system to prepare NGS libraries from samples of human and bacterial genomic DNA. E. coli libraries prepared on-device from 5 ng of total DNA yielded excellent sequence coverage over the entire bacterial genome, with >99% alignment to the reference genome, even genome coverage, and good quality scores. Furthermore, we produced a de novo assembly on a previously unsequenced multi-drug resistant Klebsiella pneumoniae strain BAA-2146 (KpnNDM. The new method described here is fast, robust, scalable, and automated. Our device for library preparation will assist in the integration of NGS technology into a wide variety of laboratories, including small research laboratories and clinical laboratories.

Library perceptions of using blogs in the idea generation phase of service innovations

DEFF Research Database (Denmark)

Scupola, Ada; Nicolajsen, Hanne Westh

2013-01-01

This article investigates the use of social software such as blogs to communicate with and to involve users in the idea generation process of service innovations. After a theoretical discussion of user involvement and more specifically user involvement using web-tools with specific focus on blogs......, the article reports findings and lessons from a field experiment at a university library. In the experiment, a blog was established to collect service innovation ideas from the library users. The experiment shows that a blog may engage a limited number of users in the idea generation process and generate...

The Python Spectral Analysis Tool (PySAT): A Powerful, Flexible, Preprocessing and Machine Learning Library and Interface

Science.gov (United States)

Anderson, R. B.; Finch, N.; Clegg, S. M.; Graff, T. G.; Morris, R. V.; Laura, J.; Gaddis, L. R.

2017-12-01

Machine learning is a powerful but underutilized approach that can enable planetary scientists to derive meaningful results from the rapidly-growing quantity of available spectral data. For example, regression methods such as Partial Least Squares (PLS) and Least Absolute Shrinkage and Selection Operator (LASSO), can be used to determine chemical concentrations from ChemCam and SuperCam Laser-Induced Breakdown Spectroscopy (LIBS) data [1]. Many scientists are interested in testing different spectral data processing and machine learning methods, but few have the time or expertise to write their own software to do so. We are therefore developing a free open-source library of software called the Python Spectral Analysis Tool (PySAT) along with a flexible, user-friendly graphical interface to enable scientists to process and analyze point spectral data without requiring significant programming or machine-learning expertise. A related but separately-funded effort is working to develop a graphical interface for orbital data [2]. The PySAT point-spectra tool includes common preprocessing steps (e.g. interpolation, normalization, masking, continuum removal, dimensionality reduction), plotting capabilities, and capabilities to prepare data for machine learning such as creating stratified folds for cross validation, defining training and test sets, and applying calibration transfer so that data collected on different instruments or under different conditions can be used together. The tool leverages the scikit-learn library [3] to enable users to train and compare the results from a variety of multivariate regression methods. It also includes the ability to combine multiple "sub-models" into an overall model, a method that has been shown to improve results and is currently used for ChemCam data [4]. Although development of the PySAT point-spectra tool has focused primarily on the analysis of LIBS spectra, the relevant steps and methods are applicable to any spectral data. The

High Affinity, Developability and Functional Size: The Holy Grail of Combinatorial Antibody Library Generation

Directory of Open Access Journals (Sweden)

Kathrin Tissot

2011-05-01

Full Text Available Since the initial description of phage display technology for the generation of human antibodies, a variety of selection methods has been developed. The most critical parameter for all in vitro-based approaches is the quality of the antibody library. Concurrent evolution of the libraries has allowed display and selection technologies to reveal their full potential. They come in different flavors, from naïve to fully synthetic and differ in terms of size, quality, method of preparation, framework and CDR composition. Early on, the focus has mainly been on affinities and thus on library size and diversity. Subsequently, the increased awareness of developability and cost of goods as important success factors has spurred efforts to generate libraries with improved biophysical properties and favorable production characteristics. More recently a major focus on reduction of unwanted side effects through reduced immunogenicity and improved overall biophysical behavior has led to a re-evaluation of library design.

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

Science.gov (United States)

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Spectral fluence of neutrons generated by radiotherapeutic Linacs

International Nuclear Information System (INIS)

Kralik, Miloslav; Solc, Jaroslav; Smoldasova, Jana; Vondracek, Vladimir; Farkasova, Estera; Ticha, Ivana

2015-01-01

Spectral fluences of neutrons generated in the heads of the radiotherapeutic linacs Varian Clinac 2100 C/D and Siemens ARTISTE were measured by means of the Bonner spheres spectrometer whose active detector of thermal neutrons was replaced by an activation detector, i.e. a tablet made of pure manganese. Measurements with different collimator settings reveal an interesting dependence of neutron fluence on the area defined by the collimator jaws. The determined neutron spectral fluences were used to derive ambient dose equivalent rate along the treatment coach. To clarify at which components of the linac neutrons are mainly created, the measurements were complemented with MCNPX calculations based on a realistic model of the Varian Clinac. (authors)

Phase spectral composition of wind generated ocean surface waves

Digital Repository Service at National Institute of Oceanography (India)

Varkey, M.J.

A study of the composition of the phase spectra of wind generated ocean surface waves is carried out using wave records collected employing a ship borne wave recorder. It is found that the raw phase spectral estimates could be fitted by the Uniform...

ARP: A PC-compatible scheme for generating ORIGEN-S cross section library

International Nuclear Information System (INIS)

Leal, L.C.; Hermann, O.W.; Parks, C.V.

1995-01-01

The SAS2H sequence of the SCALE code system has been widely used for treating problems related to the characterization of nuclear systems for disposal, storage, and shipment. The calculations, in general, consist of determining the isotope compositions of the different materials present in the problem as a function of time, which subsequently enable determination of the heat generation and radiation source terms. In the SAS2H scheme, time-dependent material concentrations are obtained using the ORIGEN-S code based on a point-depletion calculation that utilizes problem-dependent cross-section libraries generated by distinct codes of the SAS2H sequence. In this paper we will be concerned with the methodology utilized in the SAS2H control module to create cross-section libraries for point-depletion calculations with the ORIGEN-S code. A brief description of the SAS2H scheme will be given, and a new capability, the automatic rapid processing (ARP), for generating problem-dependent ORIGEN-S cross-section libraries will be presented. Use of ARP can enable execution of ORIGEN-S on a personal computer with identical accuracy to that obtained with SAS2H

Description of the ENDF-NJOY system for the generation of cross sections libraries

International Nuclear Information System (INIS)

Alonso V, G.

1991-01-01

The physics of nuclear reactors requires of a great number of data to be able to evaluate the different phenomena that happen in a nuclear reactor; these data are mainly the microscopic neutron cross sections, but it is also required of data of radioactive decay and of nuclear structure for a great number of materials as well as of the cross sections of the photons and the production of these for the neutron interaction. These data group in nuclear databases, being the main ones: ENDF Nuclear Evaluated File, ENDL Dates Nuclear Evaluated Library it Dates (of the Laboratory Lawrence Livermore). JENDL Japanese Nuclear Evaluated Library Dates. Soviet SOKRATOR Nuclear Evaluated KEDAF Nuclear Karlsruhe File Dates. JEF Join Evaluated File (coordinated by NEA Data Bank). The existent codes that execute neutron and photon calculations require libraries of data that are very different some of other and of the databases. Of here that it is required of a series of processing codes that use the database like enter and its generate a secondary library of cross sections, which is read as enter for a code of spectra generation. Generally average cross sections by group are obtained; this library is that it is used in the codes that execute neutron calculations. (Author)

Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching.

Science.gov (United States)

Nessen, Merel A; van der Zwaan, Dennis J; Grevers, Sander; Dalebout, Hans; Staats, Martijn; Kok, Esther; Palmblad, Magnus

2016-05-11

Proteomics methodology has seen increased application in food authentication, including tandem mass spectrometry of targeted species-specific peptides in raw, processed, or mixed food products. We have previously described an alternative principle that uses untargeted data acquisition and spectral library matching, essentially spectral counting, to compare and identify samples without the need for genomic sequence information in food species populations. Here, we present an interlaboratory comparison demonstrating how a method based on this principle performs in a realistic context. We also increasingly challenge the method by using data from different types of mass spectrometers, by trying to distinguish closely related and commercially important flatfish, and by analyzing heavily contaminated samples. The method was found to be robust in different laboratories, and 94-97% of the analyzed samples were correctly identified, including all processed and contaminated samples.

Development of the tool for generating ORIGEN2 library based on JENDL-3.2 for FBR

International Nuclear Information System (INIS)

Ohkawachi, Yasushi; Fukushima, Manabu

1999-05-01

ORIGEN2 is one of the most widely-used burnup analysis code in the world. This code has one-grouped cross section libraries compiled for various types of reactors. However, these libraries have some problems. One is that these libraries were developed from old nuclear data libraries (ENDF/B-IV,V) and the other is that core and fuel designs from which these libraries are generated do not match the current analysis. In order to solve the problems, analysis tool is developed for generating ORIGEN2 library from JENDL-3.2 considering multi-energy neutron spectrum. And eight new libraries are prepared using this tool for analysis of sodium-cooled FBR. These new libraries are prepared for eight kinds of cores in total. Seven of them are made by changing core size (small core - large core), fuel type (oxide, nitride, metal) and Pu vector as a parameter. The eighth one is a Pu burner core. Burnup calculation using both new and original libraries, shows large difference in buildup or depletion numbers of nuclides among the libraries. It is estimated that the analysis result is greatly influenced by the neutron spectrum which is used in collapse of cross section. By using this tool or new libraries, it seems to improve evaluation accuracy of buildup or depletion numbers of nuclides in transmutation research on FBR fuel cycle. (author)

Multi-Group Library Generation with Explicit Resonance Interference Using Continuous Energy Monte Carlo Calculation

Energy Technology Data Exchange (ETDEWEB)

Park, Ho Jin; Cho, Jin Young [KAERI, Daejeon (Korea, Republic of); Kim, Kang Seog [Oak Ridge National Laboratory, Oak Ridge (United States); Hong, Ser Gi [Kyung Hee University, Yongin (Korea, Republic of)

2016-05-15

In this study, multi-group cross section libraries for the DeCART code were generated using a new procedure. The new procedure includes generating the RI tables based on the MC calculations, correcting the effective fission product yield calculations, and considering most of the fission products as resonant nuclides. KAERI (Korea Atomic Energy Research Institute) has developed the transport lattice code KARMA (Kernel Analyzer by Ray-tracing Method for fuel Assembly) and DeCART (Deterministic Core Analysis based on Ray Tracing) for a multi-group neutron transport analysis of light water reactors (LWRs). These codes adopt the method of characteristics (MOC) to solve the multi-group transport equation and resonance fixed source problem, the subgroup and the direct iteration method with resonance integral tables for resonance treatment. With the development of the DeCART and KARMA code, KAERI has established its own library generation system for a multi-group transport calculation. In the KAERI library generation system, the multi-group average cross section and resonance integral (RI) table are generated and edited using PENDF (point-wise ENDF) and GENDF (group-wise ENDF) produced by the NJOY code. The new method does not need additional processing because the MC method can handle any geometry information and material composition. In this study, the new method is applied to the dominant resonance nuclide such as U{sup 235} and U{sup 238} and the conventional method is applied to the minor resonance nuclides. To examine the newly generated multi-group cross section libraries, various benchmark calculations such as pin-cell, FA, and core depletion problem are performed and the results are compared with the reference solutions. Overall, the results by the new method agree well with the reference solution. The new procedure based on the MC method were verified and provided the multi-group library that can be used in the SMR nuclear design analysis.

Identification of meat products by shotgun spectral matching

DEFF Research Database (Denmark)

Ohana, D.; Dalebout, H.; Marissen, R. J.

2016-01-01

A new method, based on shotgun spectral matching of peptide tandem mass spectra, was successfully applied to the identification of different food species. The method was demonstrated to work on raw as well as processed samples from 16 mammalian and 10 bird species by counting spectral matches...... to spectral libraries in a reference database with one spectral library per species. A phylogenetic tree could also be constructed directly from the spectra. Nearly all samples could be correctly identified at the species level, and 100% at the genus level. The method does not use any genomic information...

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening.

Science.gov (United States)

Köferle, Anna; Worf, Karolina; Breunig, Christopher; Baumann, Valentin; Herrero, Javier; Wiesbeck, Maximilian; Hutter, Lukas H; Götz, Magdalena; Fuchs, Christiane; Beck, Stephan; Stricker, Stefan H

2016-11-14

The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cost-effective methods enabling large-scale screening approaches. Here we describe CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a method for the generation of comprehensive gRNA libraries for CRISPR-based screens. CORALINA gRNA libraries can be derived from any source of DNA without the need of complex oligonucleotide synthesis. We show the utility of CORALINA for human and mouse genomic DNA, its reproducibility in covering the most relevant genomic features including regulatory, coding and non-coding sequences and confirm the functionality of CORALINA generated gRNAs. The simplicity and cost-effectiveness make CORALINA suitable for any experimental system. The unprecedented sequence complexities obtainable with CORALINA libraries are a necessary pre-requisite for less biased large scale genomic and epigenomic screens.

Advanced Spectral Library (ASTRAL): Atomic Fluorescence in Cool, Evolved Stars

Science.gov (United States)

Carpenter, Ken G.; Nielsen, Krister E.; Kober, Gladys V.; Rau, Gioia

2018-01-01

The "Advanced Spectral Library (ASTRAL) Project: Cool Stars" (PI = T. Ayres) collected a definitive set of representative, high-resolution (R~46,000 in the FUV up to ~1700 Å, R~30,000 for 1700-2150 Å, and R~114,000 >2150 Å) and high signal/noise (S/N>100) UV spectra of eight F-M evolved cool stars. These extremely high-quality STIS UV echelle spectra are available from the HST archive and from the Univ. of Colorado (http://casa.colorado.edu/~ayres/ASTRAL/) and will enable investigations of a broad range of problems -- stellar, interstellar, and beyond -- for many years. In this paper, we extend our study of the very rich emission-line spectra of the four evolved K-M stars in the sample, Beta Gem (K0 IIIb), Gamma Dra (K5 III), Gamma Cru (M3.4 III), and Alpha Ori (M2 Iab), to study the atomic fluorescence processes operating in their outer atmospheres. We summarize the pumping transitions and fluorescent line products known on the basis of previous work (e.g. Carpenter 1988, etc.) and newly identified in our current, on-going analysis of these extraordinary ASTRAL STIS spectra.

The Crossover Generation: Baby Boomers and the Role of the Public Library

Science.gov (United States)

Williamson, Kirsty; Bannister, Marion; Sullivan, Jen

2010-01-01

The article explores the concept of baby boomers as a "crossover" generation, one that embodies characteristics of previous and later generations. The context is the retirement of the baby boomers and its potential impact on the public library. Ethnographic method within a constructivist framework was used, employing the techniques of…

Validation of Fully Automated VMAT Plan Generation for Library-Based Plan-of-the-Day Cervical Cancer Radiotherapy

OpenAIRE

Sharfo, Abdul Wahab M.; Breedveld, Sebastiaan; Voet, Peter W. J.; Heijkoop, Sabrina T.; Mens, Jan-Willem M.; Hoogeman, Mischa S.; Heijmen, Ben J. M.

2016-01-01

textabstractPurpose: To develop and validate fully automated generation of VMAT plan-libraries for plan-of-the-day adaptive radiotherapy in locally-advanced cervical cancer. Material and Methods: Our framework for fully automated treatment plan generation (Erasmus-iCycle) was adapted to create dual-arc VMAT treatment plan libraries for cervical cancer patients. For each of 34 patients, automatically generated VMAT plans (autoVMAT) were compared to manually generated, clinically delivered 9-be...

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2).

Science.gov (United States)

de Oliveira, Gilberto Santos; Kawahara, Rebeca; Rosa-Fernandes, Livia; Mule, Simon Ngao; Avila, Carla Cristi; Teixeira, Marta M G; Larsen, Martin R; Palmisano, Giuseppe

2018-04-01

Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2. The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms. This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method

Ligation bias in Illumina next-generation DNA libraries

DEFF Research Database (Denmark)

Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel

2013-01-01

Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...... for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.......Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by......-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate...

Digital generation of stochastic signals of arbitrary spectral shape

International Nuclear Information System (INIS)

Behringer, K.; Nishihara, H.; Spiekerman, G.

1986-01-01

For computer-simulation experiments in the development of noise monitoring systems three methods of generating ergodic Gaussian random noise with specified spectral properties have been investigated: digital filtering of white noise with optimum symmetric FIR filters, a modified Rice formulation and an approximation of the Kac representation of noise. The proposed modified Rice formulation is a new noise generation method which is most efficient with regard to the computation time. By windowing subsequent Rice sequences a smooth noise record of any desired length can be produced. (author)

Digital generation of stochastic signals of arbitrary spectral shape

International Nuclear Information System (INIS)

Behringer, K.; Nishihara, H.; Spiekerman, G.

1986-10-01

For computer-simulation experiments in the development of noise monitoring systems three methods of generating ergodic Gaussian random noise with specified spectral properties have been investigated: digital filtering of white noise optimum symmetric FIR filters, a modified Rice formulation and an approximation of the Kac representation of noise. The proposed modified Rice formulation is a new noise generation method which is most efficient with regard to the computation time. By windowing subsequent Rice sequences a smooth noise record of any desired length can be produced. (author)

Generation of spectral clusters in a mixture of noble and Raman-active gases.

Science.gov (United States)

Hosseini, Pooria; Abdolvand, Amir; St J Russell, Philip

2016-12-01

We report a novel scheme for the generation of dense clusters of Raman sidebands. The scheme uses a broadband-guiding hollow-core photonic crystal fiber (HC-PCF) filled with a mixture of H2, D2, and Xe for efficient interaction between the gas mixture and a green laser pump pulse (532 nm, 1 ns) of only 5 μJ of energy. This results in the generation from noise of more than 135 rovibrational Raman sidebands covering the visible spectral region with an average spacing of only 2.2 THz. Such a spectrally dense and compact fiber-based source is ideal for applications where closely spaced narrow-band laser lines with high spectral power density are required, such as in spectroscopy and sensing. When the HC-PCF is filled with a H2-D2 mixture, the Raman comb spans the spectral region from the deep UV (280 nm) to the near infrared (1000 nm).

The Baby Boomer Generation--Impact on Public Libraries: Theoretical and Practical Evidence.

Science.gov (United States)

Kahlert, Maureen V.

This paper discusses the impact of the Baby Boomer generation on public libraries. The paper has five main objectives: (1) to provide a statistical and demographic profile of the Baby Boomers at the local, state, and national levels within Australia; (2) to provide characteristics of the Baby Boomer generation; (3) to present comparative results…

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

Science.gov (United States)

Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2016-07-01

Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. chengji@missouri.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ProDaMa: an open source Python library to generate protein structure datasets.

Science.gov (United States)

Armano, Giuliano; Manconi, Andrea

2009-10-02

The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://iasc.diee.unica.it/prodama.

Development of ANJOYMC Program for Automatic Generation of Monte Carlo Cross Section Libraries

International Nuclear Information System (INIS)

Kim, Kang Seog; Lee, Chung Chan

2007-03-01

The NJOY code developed at Los Alamos National Laboratory is to generate the cross section libraries in ACE format for the Monte Carlo codes such as MCNP and McCARD by processing the evaluated nuclear data in ENDF/B format. It takes long time to prepare all the NJOY input files for hundreds of nuclides with various temperatures, and there can be some errors in the input files. In order to solve these problems, ANJOYMC program has been developed. By using a simple user input deck, this program is not only to generate all the NJOY input files automatically, but also to generate a batch file to perform all the NJOY calculations. The ANJOYMC program is written in Fortran90 and can be executed under the WINDOWS and LINUX operating systems in Personal Computer. Cross section libraries in ACE format can be generated in a short time and without an error by using a simple user input deck

Generation and Verification of ENDF/B-VII.0 Cross section Libraries for Monte Carlo Calculations

International Nuclear Information System (INIS)

Park, Ho Jin; Kwak, Min Su; Joo, Han Gyu; Kim, Chang Hyo

2007-01-01

For Monte Carlo neutronics calculations, a continuous energy nuclear data library is needed. It can be generated from various evaluated nuclear data files such as ENDF/B using the ACER routine of the NJOY.code after a series of prior processing involving various other NJOY routines. Recently, a utility code, which generates the NJOY input decks in an automated mode, named ANJOYMC became available. The use of this code greatly reduces the user's effort and the possibility of input errors. In December 2006, the initial version of the ENDF/BVII nuclear data library was released. It was reported that the new data files have much better data which reduces the errors noted in the previous versions. Thus it is worthwhile to examine the performance of the new data files particularly using an independent Monte Carlo code, MCCARD and the ANJOYMC utility code. The verification of the newly generated library can be readily performed by analyzing numerous standard criticality benchmark problems

Evaluation of spectral libraries and sample preparation for DIA-LC-MS analysis of host cell proteins

DEFF Research Database (Denmark)

Heissel, Søren; Bunkenborg, Jakob; Kristiansen, Max Per

2018-01-01

in the field of tuberculosis and has not previously been studied by LC-MS. The developed method and acquired experiences served to develop a generalized strategy for HCP-characterization in our laboratory. We evaluated the use of different spectral libraries, recorded in data-dependent mode for obtaining...... the highest HCP coverage, combined with SWATH-based absolute quantification. The accuracy of two label-free absolute quantification strategies was evaluated using stable isotope peptides. Two different sample preparation workflows were evaluated for optimal HCP yield. . The label-free strategy produced...... accurate quantification across several orders of magnitude, and the calculated purity was found to be in agreement with previously obtained ELISA data....

Spectral Phase Modulation and chirped pulse amplification in High Gain Harmonic Generation

CERN Document Server

Wu, Zilu; Krinsky, Sam; Loos, Henrik; Murphy, James; Shaftan, Timur; Sheehy, Brian; Shen, Yuzhen; Wang, Xijie; Yu Li Hua

2004-01-01

High Gain Harmonic Generation (HGHG), because it produces longitudinally coherent pulses derived from a coherent seed, presents remarkable possibilities for manipulating FEL pulses. If spectral phase modulation imposed on the seed modulates the spectral phase of the HGHG in a deterministic fashion, then chirped pulse amplification, pulse shaping, and coherent control experiments at short wavelengths become possible. In addition, the details of the transfer function will likely depend on electron beam and radiator dynamics and so prove to be a useful tool for studying these. Using the DUVFEL at the National Synchrotron Light Source at Brookhaven National Laboratory, we present spectral phase analyses of both coherent HGHG and incoherent SASE ultraviolet FEL radiation, applying Spectral Interferometry for Direct Electric Field Reconstruction (SPIDER), and assess the potential for employing compression and shaping techniques.

Efficient concept for generation of diffraction-limited green light by sum-frequency generation of spectrally combined tapered diode lasers

DEFF Research Database (Denmark)

Müller, André; Jensen, Ole Bjarlin; Hasler, Karl-Heinz

2012-01-01

In order to increase the power of visible diode laser systems in an efficient manner, we propose spectral beam combining with subsequent sum-frequency generation. We show that this approach, in comparison with second harmonic generation of single emitters, can enhance the available power signific......In order to increase the power of visible diode laser systems in an efficient manner, we propose spectral beam combining with subsequent sum-frequency generation. We show that this approach, in comparison with second harmonic generation of single emitters, can enhance the available power...... significantly. By combining two distributed Bragg reflector tapered diode lasers we achieve a 2.5–3.2 fold increase in power and a maximum of 3.9 W of diffraction-limited green light. At this power level, green diode laser systems have a high application potential, e.g., within the biomedical field. Our concept...

Design and Development of a Spectral Library for Different Vegetation and Landcover Types for Arctic, Antarctic and Chihuahua Desert Ecosystem

Science.gov (United States)

Matharasi, K.; Goswami, S.; Gamon, J.; Vargas, S.; Marin, R.; Lin, D.; Tweedie, C. E.

2008-12-01

All objects on the Earth's surface absorb and reflect portions of the electromagnetic spectrum. Depending on the composition of the material, every material has its characteristic spectral profile. The characteristic spectral profile for vegetation is often used to study how vegetation patterns at large spatial scales affect ecosystem structure and function. Analysis of spectroscopic data from the laboratory, and from various other platforms like aircraft or spacecraft, requires a knowledge base that consists of different characteristic spectral profiles for known different materials. This study reports on establishment of an online and searchable spectral library for a range of plant species and landcover types in the Arctic, Anatarctic and Chihuahuan desert ecosystems. Field data were collected from Arctic Alaska, the Antarctic Peninsula and the Chihuahuan desert in the visible to near infrared (IR) range using a handheld portable spectrometer. The data have been archived in a database created using postgre sql with have been made publicly available on a plone web-interface. This poster describes the data collected in more detail and offers instruction to users who wish to make use of this free online resource.

Locally Generated Information and Referral Services in Indian Libraries. Guide 8: Generating Information in Indian Libraries.

Science.gov (United States)

Townley, Charles T.

Libraries and information centers are rapidly becoming an integral part of American Indian live. A primary concern of Indian people is the availability of dependable information on those issues and programs which directly affect their day to day lives. As the community information agency, the library plays a key role in improving access to local…

ProDaMa: an open source Python library to generate protein structure datasets

Directory of Open Access Journals (Sweden)

Manconi Andrea

2009-10-01

Full Text Available Abstract Background The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. Findings To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. Conclusion ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://iasc.diee.unica.it/prodama.

Codon-Precise, Synthetic, Antibody Fragment Libraries Built Using Automated Hexamer Codon Additions and Validated through Next Generation Sequencing

Directory of Open Access Journals (Sweden)

Laura Frigotto

2015-05-01

Full Text Available We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR in antibody fragment libraries and next generation sequencing (NGS analysis of their quality and diversity.

The Next Generation Library Catalog: A Comparative Study of the OPACs of Koha, Evergreen, and Voyager

Directory of Open Access Journals (Sweden)

Sharon Q. Yang

2010-09-01

Full Text Available Open source has been the center of attention in the library world for the past several years. Koha and Evergreen are the two major open-source integrated library systems (ILSs, and they continue to grow in maturity and popularity. The question remains as to how much we have achieved in open-source development toward the next-generation catalog compared to commercial systems. Little has been written in the library literature to answer this question. This paper intends to answer this question by comparing  the next-generation features of the OPACs of two open-source ILSs (Koha and Evergreen and one proprietary ILS (Voyager’s WebVoyage.

Computer generated multi-color graphics in whole body gamma spectral analysis

International Nuclear Information System (INIS)

Phillips, W.G.; Curtis, S.P.; Environmental Protection Agency, Las Vegas, NV)

1984-01-01

A medium resolution color graphics terminal (512 x 512 pixels) was appended to a computerized gamma spectrometer for the display of whole body counting data. The color display enhances the ability of a spectroscopist to identify at a glance multicolored spectral regions of interest immediate qualitative interpretation. Spectral data from subjects containing low concentrations of gamma emitters obtained by both NaI(T1) and phoswich detectors are viewed by the method. In addition, software generates a multispectral display by which the gross, background, and net spectra are displayed in color simultaneously on a single screen

Global Learning Spectral Archive- A new Way to deal with Unknown Urban Spectra -

Science.gov (United States)

Jilge, M.; Heiden, U.; Habermeyer, M.; Jürgens, C.

2015-12-01

Rapid urbanization processes and the need of identifying urban materials demand urban planners and the remote sensing community since years. Urban planners cannot overcome the issue of up-to-date information of urban materials due to time-intensive fieldwork. Hyperspectral remote sensing can facilitate this issue by interpreting spectral signals to provide information of occurring materials. However, the complexity of urban areas and the occurrence of diverse urban materials vary due to regional and cultural aspects as well as the size of a city, which makes identification of surface materials a challenging analysis task. For the various surface material identification approaches, spectral libraries containing pure material spectra are commonly used, which are derived from field, laboratory or the hyperspectral image itself. One of the requirements for successful image analysis is that all spectrally different surface materials are represented by the library. Currently, a universal library, applicable in every urban area worldwide and taking each spectral variability into account, is and will not be existent. In this study, the issue of unknown surface material spectra and the demand of an urban site-specific spectral library is tackled by the development of a learning spectral archive tool. Starting with an incomplete library of labelled image spectra from several German cities, surface materials of pure image pixels will be identified in a hyperspectral image based on a similarity measure (e.g. SID-SAM). Additionally, unknown image spectra of urban objects are identified based on an object- and spectral-based-rule set. The detected unknown surface material spectra are entered with additional metadata, such as regional occurrence into the existing spectral library and thus, are reusable for further studies. Our approach is suitable for pure surface material detection of urban hyperspectral images that is globally applicable by taking incompleteness into account

LIBVERSIONINGCOMPILER: An easy-to-use library for dynamic generation and invocation of multiple code versions

Science.gov (United States)

Cherubin, S.; Agosta, G.

2018-01-01

We present LIBVERSIONINGCOMPILER, a C++ library designed to support the dynamic generation of multiple versions of the same compute kernel in a HPC scenario. It can be used to provide continuous optimization, code specialization based on the input data or on workload changes, or otherwise to dynamically adjust the application, without the burden of a full dynamic compiler. The library supports multiple underlying compilers but specifically targets the LLVM framework. We also provide examples of use, showing the overhead of the library, and providing guidelines for its efficient use.

AMZ, multigroup constant library for EXPANDA code, generated by NJOY code from ENDF/B-IV

International Nuclear Information System (INIS)

Chalhoub, E.S.; Moraes, Marisa de

1985-01-01

It is described a library of multigroup constants with 70 energy groups and 37 isotopes to fast reactor calculation. The cross sections, scattering matrices and self-shielding factors were generated by NJOY code and RGENDF interface program, from ENDF/B-IV'S evaluated data. The library is edited in adequated format to be used by EXPANDA code. (M.C.K.) [pt

Library 3.0 intelligent libraries and apomediation

CERN Document Server

Kwanya, Tom; Underwood, Peter

2015-01-01

The emerging generation of research and academic library users expect the delivery of user-centered information services. 'Apomediation' refers to the supporting role librarians can give users by stepping in when users need help. Library 3.0 explores the ongoing debates on the "point oh” phenomenon and its impact on service delivery in libraries. This title analyses Library 3.0 and its potential in creating intelligent libraries capable of meeting contemporary needs, and the growing role of librarians as apomediators. Library 3.0 is divided into four chapters. The first chapter introduces and places the topic in context. The second chapter considers "point oh” libraries. The third chapter covers library 3.0 librarianship, while the final chapter explores ways libraries can move towards '3.0'.

Spectral broadening of acoustic tones generated by unmanned aerial vehicles in a turbulent atmosphere

DEFF Research Database (Denmark)

Ostashev, Vladimir E.; Wilson, D. K.; Finn, Anthony

2016-01-01

The acoustic spectrum emitted by unmanned aerial vehicles (UAVs) and other aircraft can be distorted by propagation through atmospheric turbulence. Since most UAVs are propeller-based, they generate a series of acoustic tones and harmonics. In this paper, spectral broadening of these tones due......, spectral broadening is calculated and analyzed for typical meteorological regimes of the atmospheric boundary layer and different flight trajectories of UAVs. Experimental results are presented and compared with theoretical predictions. Spectral broadening might also provide a means for remotely sensing...

Generation of a library of two-group diffusion parameters for SPPS-1,6 by HELIOS

International Nuclear Information System (INIS)

Petkov, P.T.; Haralampieva, C.V.; Simeonov, T.; Stojanova, I.; Kamenov, K.

2000-01-01

The two-group three-dimensional nodal diffusion code SPPS-1.6 has been used for many years for steady-state neutronics calculations of the WWER-440 reactors at Kozloduy NPP. The old library of two-group diffusion parameters for SPPS-1.6 has been generated by WIMSD4 with a nuclear data library compiled from three different libraries. The current paper presents our experience in generating a new library for SPPS-1.6 by the HELIOS lattice code. The accuracy of the current-coupling collision probability (CCCP) method in calculating a single WWER-440 assembly has been studied first. Among all possible angular discretization of the interface partial currents, called coupling orders, only coupling order 3 is suitable for hexagonal cells. Dividing each cell side into 3 segments an accuracy of 100 pcm has been achieved. The accuracy in calculating the absorber problem was estimated at 1%, which means about 10% error in the control assemblies efficiency. The accuracy for small core-reflector problems is 1% as well. The general conclusion is that HELIOS is accurate enough for assembly calculations, but inadequate for absorber and core-reflector problems. (Authors)

SPAM- SPECTRAL ANALYSIS MANAGER (UNIX VERSION)

Science.gov (United States)

Solomon, J. E.

1994-01-01

The Spectral Analysis Manager (SPAM) was developed to allow easy qualitative analysis of multi-dimensional imaging spectrometer data. Imaging spectrometers provide sufficient spectral sampling to define unique spectral signatures on a per pixel basis. Thus direct material identification becomes possible for geologic studies. SPAM provides a variety of capabilities for carrying out interactive analysis of the massive and complex datasets associated with multispectral remote sensing observations. In addition to normal image processing functions, SPAM provides multiple levels of on-line help, a flexible command interpretation, graceful error recovery, and a program structure which can be implemented in a variety of environments. SPAM was designed to be visually oriented and user friendly with the liberal employment of graphics for rapid and efficient exploratory analysis of imaging spectrometry data. SPAM provides functions to enable arithmetic manipulations of the data, such as normalization, linear mixing, band ratio discrimination, and low-pass filtering. SPAM can be used to examine the spectra of an individual pixel or the average spectra over a number of pixels. SPAM also supports image segmentation, fast spectral signature matching, spectral library usage, mixture analysis, and feature extraction. High speed spectral signature matching is performed by using a binary spectral encoding algorithm to separate and identify mineral components present in the scene. The same binary encoding allows automatic spectral clustering. Spectral data may be entered from a digitizing tablet, stored in a user library, compared to the master library containing mineral standards, and then displayed as a timesequence spectral movie. The output plots, histograms, and stretched histograms produced by SPAM can be sent to a lineprinter, stored as separate RGB disk files, or sent to a Quick Color Recorder. SPAM is written in C for interactive execution and is available for two different

Generation and selection of naïve Fab library for parasitic antigen: Anti-BmSXP antibodies for lymphatic filariasis.

Science.gov (United States)

Omar, Noorsharmimi; Hamidon, Nurul Hamizah; Yunus, Muhammad Hafiznur; Noordin, Rahmah; Choong, Yee Siew; Lim, Theam Soon

2018-05-01

Phage display has been applied successfully as a tool for the generation of monoclonal antibodies (mAbs). Naive antibody libraries are unique as they are able to overcome several limitations associated with conventional mAb generation methods like the hybridoma technology. Here, we performed an in vitro selection and generation of Fab antibodies against Brugia malayi SXP protein (BmSXP), a recombinant antigen for the detection of lymphatic filariasis. We developed a naïve multi ethnic Fab antibody library with an estimated diversity of 2.99 × 10 9 . The antibody library was used to screen for mAbs against BmSXP recombinant antigen. Soluble monoclonal Fab antibodies against BmSXP were successfully isolated from the naïve library. The Fab antibodies obtained were expressed and analyzed to show its binding capability. The diversity obtained from a pool of donors from various ethnic groups allowed for a diverse antibody library to be generated. The mAbs obtained were also functional in soluble form, which makes it useful for further downstream applications. We believe that the Fab mAbs are valuable for further studies and could also contribute to improvements in the diagnosis of filariasis. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

Organization of GC/MS and LC/MS metabolomics data into chemical libraries

Directory of Open Access Journals (Sweden)

DeHaven Corey D

2010-10-01

Full Text Available Abstract Background Metabolomics experiments involve generating and comparing small molecule (metabolite profiles from complex mixture samples to identify those metabolites that are modulated in altered states (e.g., disease, drug treatment, toxin exposure. One non-targeted metabolomics approach attempts to identify and interrogate all small molecules in a sample using GC or LC separation followed by MS or MSn detection. Analysis of the resulting large, multifaceted data sets to rapidly and accurately identify the metabolites is a challenging task that relies on the availability of chemical libraries of metabolite spectral signatures. A method for analyzing spectrometry data to identify and Quantify Individual Components in a Sample, (QUICS, enables generation of chemical library entries from known standards and, importantly, from unknown metabolites present in experimental samples but without a corresponding library entry. This method accounts for all ions in a sample spectrum, performs library matches, and allows review of the data to quality check library entries. The QUICS method identifies ions related to any given metabolite by correlating ion data across the complete set of experimental samples, thus revealing subtle spectral trends that may not be evident when viewing individual samples and are likely to be indicative of the presence of one or more otherwise obscured metabolites. Results LC-MS/MS or GC-MS data from 33 liver samples were analyzed simultaneously which exploited the inherent biological diversity of the samples and the largely non-covariant chemical nature of the metabolites when viewed over multiple samples. Ions were partitioned by both retention time (RT and covariance which grouped ions from a single common underlying metabolite. This approach benefitted from using mass, time and intensity data in aggregate over the entire sample set to reject outliers and noise thereby producing higher quality chemical identities. The

Generation of multigroup cross sections from ENDF/B-IV nuclear data library

International Nuclear Information System (INIS)

Chapot, J.L.C.; Thome Filho, Z.D.

1980-04-01

The generation of nuclear data compacted in energy groups is made. The nuclear data library ENDF/B-IV, Evaluated Nuclear Data File, and the new version of the codes ETOG-3 and ETOT-3 are utilized. The data obtained are compared with data from other sources. (L.F.) [pt

Generation of neutron cross sections library for the Thermos code of the Fuel management System (FMS)

International Nuclear Information System (INIS)

Alonso V, G.; Viais J, J.

1990-10-01

There is developed a method to generate the library of neutron cross sections for the Thermos code by means of the database ENDF-B/IV and the NJOY code. The obtained results are compared with the version previous of the library of neutron cross sections which was processed using the version ENDF-B/III. (Author)

Generation and analyses of human synthetic antibody libraries and their application for protein microarrays.

Science.gov (United States)

Säll, Anna; Walle, Maria; Wingren, Christer; Müller, Susanne; Nyman, Tomas; Vala, Andrea; Ohlin, Mats; Borrebaeck, Carl A K; Persson, Helena

2016-10-01

Antibody-based proteomics offers distinct advantages in the analysis of complex samples for discovery and validation of biomarkers associated with disease. However, its large-scale implementation requires tools and technologies that allow development of suitable antibody or antibody fragments in a high-throughput manner. To address this we designed and constructed two human synthetic antibody fragment (scFv) libraries denoted HelL-11 and HelL-13. By the use of phage display technology, in total 466 unique scFv antibodies specific for 114 different antigens were generated. The specificities of these antibodies were analyzed in a variety of immunochemical assays and a subset was further evaluated for functionality in protein microarray applications. This high-throughput approach demonstrates the ability to rapidly generate a wealth of reagents not only for proteome research, but potentially also for diagnostics and therapeutics. In addition, this work provides a great example on how a synthetic approach can be used to optimize library designs. By having precise control of the diversity introduced into the antigen-binding sites, synthetic libraries offer increased understanding of how different diversity contributes to antibody binding reactivity and stability, thereby providing the key to future library optimization. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Generation of seven group cross section library for TRIGA LEU fuel in CITATION format and benchmarking some experimental and operational data

International Nuclear Information System (INIS)

Sarker, M.M.; Bhuiyan, S.I.; Akramuzzaman, M.

2007-01-01

The principal objective of this study is to validate the seven group cross section library in CITATION format for TRIGA LEU Fuel. This presentation deals with the 'generation of a cross section library for the CITATION and its validation. We used WIMSD-5B version for the generation of all group constants. The overall strategy is: (1) use WIMS package to generate few group neutron macroscopic cross section (cell constants) for all of the materials in the core and its immediate neighborhood (2) use 3-D code CITATION to perform the global analysis of the core to study: multiplication factor, neutron flux distribution and power peaking factors. Various options available in WIMS program were studied in depth to finalize the models to generate the most appropriate group constants. For the global analysis the code CITATION and a post processing program FCAP were chosen. Thus a seven group cross section library for the calculations of TRIGA Research Reactor was generated. To investigate the validity of the generated library a critical experiment of the TRIGA research reactor was benchmarked. (author)

Temporal and spectral studies of high-order harmonics generated by polarization-modulated infrared fields

International Nuclear Information System (INIS)

Sola, I. J.; Zaier, A.; Cormier, E.; Mevel, E.; Constant, E.; Lopez-Martens, R.; Johnsson, P.; Varju, K.; Mauritsson, J.; L'Huillier, A.; Strelkov, V.

2006-01-01

The temporal confinement of high harmonic generation (HHG) via modulation of the polarization of the fundamental pulse is studied in both temporal and spectral domains. In the temporal domain, a collinear cross-correlation setup using a 40 fs IR pump for the HHG and a 9 fs IR pulse to probe the generated emission is used to measure the XUV pulse duration. The observed temporal confinement is found to be consistent with theoretical predictions. An increased confinement is observed when a 9 fs pulse is used to generate the harmonics. An important spectral broadening, including a continuum background, is also measured. Theoretical calculations show that with 10 fs driving pulses, either one or two main attosecond pulses are created depending on the value of the carrier envelope phase

Development of the CPXSD Methodology for Generation of Fine-Group Libraries for Shielding Applications

International Nuclear Information System (INIS)

Alpan, F. Arzu; Haghighat, Alireza

2005-01-01

Multigroup cross sections are one of the major factors that cause uncertainties in the results of deterministic transport calculations. Thus, it is important to prepare effective cross-section libraries that include an appropriate group structure and are based on an appropriate spectrum. There are several multigroup cross-section libraries available for particular applications. For example, the 47-neutron, 20-gamma group BUGLE library that is derived from the 199-neutron, 42-gamma group VITAMIN-B6 library is widely used for light water reactor (LWR) shielding and pressure vessel dosimetry applications. However, there is no publicly available methodology that can construct problem-dependent libraries. Thus, the authors have developed the Contributon and Point-wise Cross Section Driven (CPXSD) methodology for constructing effective fine- and broad-group structures. In this paper, new fine-group structures were constructed using the CPXSD, and new fine-group cross-section libraries were generated. The 450-group LIB450 and 589-group LIB589 libraries were developed for neutrons sensitive to the fast and thermal energy ranges, respectively, for LWR shielding problems. As compared to a VITAMIN-B6-like library, the new fine-group library developed for fast neutron dosimetry calculations resulted in closer agreement to the continuous-energy predictions. For example, for the fast neutron cavity dosimetry, ∼4% improvement was observed for the 237 Np(n,f) reaction rate. For the thermal neutron 1 H(n, γ) reaction, a maximum improvement of ∼14% was observed in the reaction rate at the middowncomer position

Generation and testing of the shielding data library EURLIB for fission and fusion technology

International Nuclear Information System (INIS)

Caglioti, E.; Hehn, G.; Herrnberger, V.; Mattes, M.; Nicks, R.; Penkuhn, H.

1977-01-01

For the common field of core physics and shielding, the CSEWG group structure of 239 fast neutron groups had been proposed, of which the 100 neutron groups of the EURLIB Library is a sub-set for shielding. This standard group Library EURLIB had been initiated by the NEA-specialist group on shielding benchmarks in 1974. The wide acceptance of the Library for interpretation of benchmarks in the NEA program represents an important step forward in the standardization of group data which is the basic requirement for a useful collaboration. On the other side the interpretation of a series of different benchmark experiments with the EURLIB Library provides the best check of the cross section data for neutron and gamma-rays showing the needs for further improvements. The paper describes the joint work of IKE, Stuttgart and EURATOM, Ispra in generating multigroup libraries for neutron and gamma-rays. Special effort has been devoted to improve the flux weighting for both types of radiation and proper treatment of thermal neutrons. The coupled multigroup Library of 100 neutron and 20 gamma groups is collapsed into few group structures for typical designs of LWR, LMFBR, gas cooled and thermonuclear reactors. The work for optimal few group representation is done in cooperation with EIR, Wurenlingen. The testing of the EURLIB Library is a common effort of several institutions participating in the NEA shielding benchmark program

The Research Process and the Library: First-Generation College Seniors vs. Freshmen

Science.gov (United States)

Pickard, Elizabeth; Logan, Firouzeh

2013-01-01

In a follow-up study to the ERIAL (Ethnographic Research in Illinois Academic Libraries) Project, librarians at UIC compared the responses of first-generation college freshmen from the original study to those of seniors. The study's aim was to determine whether student information literacy increases as a result of undergraduate education and to…

Use of CPXSD for generation of effective fast multigroup libraries for pressure vessel fluence calculations

International Nuclear Information System (INIS)

Alpan, F. Arzu; Haghighat, Alireza

2008-01-01

Multigroup (i.e., broad-group) libraries play a significant role in the accuracy of transport calculations. There are several broad-group libraries available for particular applications. For example the 47-neutron (26 fast groups), 20-gamma-group BUGLE libraries are commonly used for light water reactor shielding and pressure vessel dosimetry problems. However, there is no publicly available methodology to construct group structures for a problem and objective of interest. Therefore, we have developed the Contribution and Point-wise Cross-Section Driven (CPXSD) methodology, which constructs effective fine-and broad-group structures. In this paper, we use the CPXSD methodology to construct broad-group structures for fast neutron dosimetry problems. It is demonstrated that the broad-group libraries generated from CPXSD constructed group structures, while only 14 groups (rather than 26 groups) in the fast energy range are in good agreement (similar to 1 %-2 %) with the fine-group library from which they were derived, in reaction rate calculations.

Organic Contaminants Library for the Sample Analysis at Mars

Science.gov (United States)

Misra, P.; Garcia-Sanchez, R.; Canham, J.; Mahaffy, P. R.

2012-12-01

A library containing mass spectra for Sample Analysis at Mars (SAM) materials has been developed with the purpose of contamination identification and control. Based on analysis of the Gas Chromatography-Mass Spectrometric (GCMS) data through thermal desorption, organic compounds were successfully identified from material samples, such as polymers, paints and adhesives. The library contains the spectra for all the compounds found in each of these analyzed files and is supplemented by a file information spreadsheet, a spreadsheet-formatted library for easy searching, and a Perfluorotributylamine (PFTBA) based normalization protocol to make corrections to SAM data in order to meet the standard set by commercial libraries. An example of the library in use can be seen in Figure 1, where the abundances match closely, the spectral shape is retained, and the library picks up on it with an 88% identification probability. Of course, there are also compounds that have not been identified and are retained as unknowns. The library we have developed, along with its supplemental materials, is useful from both organizational and practical viewpoints. Through them we are able to organize large volumes of GCMS data, while at the same time breaking down the components that each material sample is made of. This approach in turn allows us straightforward and fast access to information that will be critical while performing analysis on the data recorded by the SAM instrumentation. In addition, the normalization protocol dramatically increased the identification probability. In SAM GCMS, PFTBA signals were obfuscated, resulting in library matches far away from PFTBA; by using the normalization protocol we were able to transform it into a 92% probable spectral match for PFTBA. The project has demonstrated conclusively that the library is successful in identifying unknown compounds utilizing both the Automated Mass Spectral Deconvolution & Identification System (AMDIS) and the Ion

Morphological Interpretation of Reflectance Spectrum (MIRS using libraries looking towards soil classification

Directory of Open Access Journals (Sweden)

José Alexandre Melo Demattê

2014-12-01

Full Text Available The search for tools to perform soil surveying faster and cheaper has led to the development of technological innovations such as remote sensing (RS and the so-called spectral libraries in recent years. However, there are no studies which collate all the RS background to demonstrate how to use this technology for soil classification. The present study aims to describe a simple method of how to classify soils by the morphology of spectra associated with a quantitative view (400-2,500 nm. For this, we constructed three spectral libraries: (i one for quantitative model performance; (ii a second to function as the spectral patterns; and (iii a third to serve as a validation stage. All samples had their chemical and granulometric attributes determined by laboratory analysis and prediction models were created based on soil spectra. The system is based on seven steps summarized as follows: i interpretation of the spectral curve intensity; ii observation of the general shape of curves; iii evaluation of absorption features; iv comparison of spectral curves between the same profile horizons; v quantification of soil attributes by spectral library models; vi comparison of a pre-existent spectral library with unknown profile spectra; vii most probable soil classification. A soil cannot be classified from one spectral curve alone. The behavior between the horizons of a profile, however, was correlated with its classification. In fact, the validation showed 85 % accuracy between the Morphological Interpretation of Reflectance Spectrum (MIRS method and the traditional classification, showing the importance and potential of a combination of descriptive and quantitative evaluations.

Status of the Monte Carlo library least-squares (MCLLS) approach for non-linear radiation analyzer problems

Science.gov (United States)

Gardner, Robin P.; Xu, Libai

2009-10-01

The Center for Engineering Applications of Radioisotopes (CEAR) has been working for over a decade on the Monte Carlo library least-squares (MCLLS) approach for treating non-linear radiation analyzer problems including: (1) prompt gamma-ray neutron activation analysis (PGNAA) for bulk analysis, (2) energy-dispersive X-ray fluorescence (EDXRF) analyzers, and (3) carbon/oxygen tool analysis in oil well logging. This approach essentially consists of using Monte Carlo simulation to generate the libraries of all the elements to be analyzed plus any other required background libraries. These libraries are then used in the linear library least-squares (LLS) approach with unknown sample spectra to analyze for all elements in the sample. Iterations of this are used until the LLS values agree with the composition used to generate the libraries. The current status of the methods (and topics) necessary to implement the MCLLS approach is reported. This includes: (1) the Monte Carlo codes such as CEARXRF, CEARCPG, and CEARCO for forward generation of the necessary elemental library spectra for the LLS calculation for X-ray fluorescence, neutron capture prompt gamma-ray analyzers, and carbon/oxygen tools; (2) the correction of spectral pulse pile-up (PPU) distortion by Monte Carlo simulation with the code CEARIPPU; (3) generation of detector response functions (DRF) for detectors with linear and non-linear responses for Monte Carlo simulation of pulse-height spectra; and (4) the use of the differential operator (DO) technique to make the necessary iterations for non-linear responses practical. In addition to commonly analyzed single spectra, coincidence spectra or even two-dimensional (2-D) coincidence spectra can also be used in the MCLLS approach and may provide more accurate results.

Spectral and spatial characteristics of third-harmonic generation in conical light beams

International Nuclear Information System (INIS)

Peet, V.E.; Shchemeljov, S.V.

2003-01-01

Generation of resonance-enhanced third harmonic in Bessel and other conical beams is analyzed from a simple picture, where the fundamental light field is decomposed into elementary configurations of crossed plain-wave sub-beams. We show that the overall harmonic output can be derived as a superposition of all partial harmonic components driven by elementary configurations of the fundamental field. Good agreement with experimental observations has been obtained in simulation of spectral and spatial characteristics of the generated third harmonic. Some peculiarities of harmonic generation in conical light fields are discussed

Generation of the problem-dependent data libraries for IFIN-HH WWR-S spent fuel storage criticality and dose calculation

International Nuclear Information System (INIS)

Ene, Daniela; Tigau, F.

1998-01-01

The methods used for the radioactivity inventory calculation and dose evaluation of the fuel elements irradiated in the WWR-S IFIN-HH reactor are discussed in this work. A particular attention is paid to the processed problem-dependent nuclear libraries. SAS2H, a complex sequence of the SCALE-4.3 code system containing the modules BONAMI - NITAWL - XSDRNPM - COUPLE - ORIGEN-S - XSDOSE, has been assimilated on the IFIN-HH computer and applied to update the ORIGEN-S libraries by producing problem-dependent processed data libraries needed to perform the depletion and shielding analysis. This sequence uses one of the eight associated data libraries of the SCALE-4.3 system according to the choice of the user. The method consists in the following analysis processes: i) lattice cell neutron analysis to produce the flux weighting spectrum for activation library updating; ii) update of the nuclear data constants of the ORIGEN-S libraries; iii) depletion and decay analysis for a specified fuel assembly and irradiation history in order to generate gamma and neutron source strength and spectra. iv) one-dimensional radial shielding calculation for the evaluation of the angular neutron and gamma flux at the surface of a spent fuel shipping cask and further calculation of the dose rates at various points outside the cask. An efficient alternative of the calculation sequence mentioned above is the ARP (Automatic Rapid Processing) method conceived in order to generate independently ORIGEN-S libraries and to reduce substantially the running time. The substance of this method is the generation of the problem-dependent libraries from basis libraries a priori created by SAS2H for specific fuel assembly type and further interpolation of two independent variables, enrichment and burnup. Specific applications concerning WWR-S spent fuel were performed: i) generation of three problem-dependent libraries for the S-36 fuel assembly taking into account the maximum value of the burnup of this

Rapid and Easy Protocol for Quantification of Next-Generation Sequencing Libraries.

Science.gov (United States)

Hawkins, Steve F C; Guest, Paul C

2018-01-01

The emergence of next-generation sequencing (NGS) over the last 10 years has increased the efficiency of DNA sequencing in terms of speed, ease, and price. However, the exact quantification of a NGS library is crucial in order to obtain good data on sequencing platforms developed by the current market leader Illumina. Different approaches for DNA quantification are available currently and the most commonly used are based on analysis of the physical properties of the DNA through spectrophotometric or fluorometric methods. Although these methods are technically simple, they do not allow exact quantification as can be achieved using a real-time quantitative PCR (qPCR) approach. A qPCR protocol for DNA quantification with applications in NGS library preparation studies is presented here. This can be applied in various fields of study such as medical disorders resulting from nutritional programming disturbances.

Library and Education

Directory of Open Access Journals (Sweden)

Gheorghe Buluţă

2011-01-01

Full Text Available The psycho-social phenomena generated by mass-media and the new information and communication technologies at the level of the young generations have led to new communication practices that bypass libraries and revolutionized the intellectual labor practices, with texts being rather used than read. In this context, our article examines the need to increase the library's role in developing the quality of education and research and brings to attention a few possible solutions which include a partnership between various types of libraries and between librarians' associations and NGOs to facilitate education through library and safeguard reading.

Medium-resolution Isaac Newton Telescope library of empirical spectra - II. The stellar atmospheric parameters

NARCIS (Netherlands)

Cenarro, A. J.; Peletier, R. F.; Sanchez-Blazquez, P.; Selam, S. O.; Toloba, E.; Cardiel, N.; Falcon-Barroso, J.; Gorgas, J.; Jimenez-Vicente, J.; Vazdekis, A.

2007-01-01

We present a homogeneous set of stellar atmospheric parameters (T-eff, log g, [Fe/H]) for MILES, a new spectral stellar library covering the range lambda lambda 3525-7500 angstrom at 2.3 angstrom (FWHM) spectral resolution. The library consists of 985 stars spanning a large range in atmospheric

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

Science.gov (United States)

2012-01-01

Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches. PMID:22554201

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

Directory of Open Access Journals (Sweden)

Chen Bo-Ruei

2012-05-01

Full Text Available Abstract Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning

Library 2.0: Service for the Next-Generation Library

Science.gov (United States)

Casey, Michael E.; Savastinuk, Laura C.

2006-01-01

Libraries are changing. Funding limits and customer demands are transforming staffing levels, service models, access to resources, and services to the public. Administrators and taxpayers are seeking more efficient ways of delivering services to achieve greater returns on financial investments. In this article, the author discusses the benefits of…

Generation and analyses of human synthetic antibody libraries and their application for protein microarrays

DEFF Research Database (Denmark)

Säll, Anna; Walle, Maria; Wingren, Christer

2016-01-01

in a high-throughput manner. To address this we designed and constructed two human synthetic antibody fragment (scFv) libraries denoted HelL-11 and HelL-13. By the use of phage display technology, in total 466 unique scFv antibodies specific for 114 different antigens were generated. The specificities......Antibody-based proteomics offers distinct advantages in the analysis of complex samples for discovery and validation of biomarkers associated with disease. However, its large-scale implementation requires tools and technologies that allow development of suitable antibody or antibody fragments...... for diagnostics and therapeutics. In addition, this work provides a great example on how a synthetic approach can be used to optimize library designs. By having precise control of the diversity introduced into the antigen-binding sites, synthetic libraries offer increased understanding of how different diversity...

Normalized cDNA libraries

Science.gov (United States)

Soares, Marcelo B.; Efstratiadis, Argiris

1997-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

The Planetary Terrestrial Analogues Library (PTAL)

Science.gov (United States)

Werner, S. C.; Dypvik, H.; Poulet, F.; Rull Perez, F.; Bibring, J.-P.; Bultel, B.; Casanova Roque, C.; Carter, J.; Cousin, A.; Guzman, A.; Hamm, V.; Hellevang, H.; Lantz, C.; Lopez-Reyes, G.; Manrique, J. A.; Maurice, S.; Medina Garcia, J.; Navarro, R.; Negro, J. I.; Neumann, E. R.; Pilorget, C.; Riu, L.; Sætre, C.; Sansano Caramazana, A.; Sanz Arranz, A.; Sobron Grañón, F.; Veneranda, M.; Viennet, J.-C.; PTAL Team

2018-04-01

The Planetary Terrestrial Analogues Library project aims to build and exploit a spectral data base for the characterisation of the mineralogical and geological evolution of terrestrial planets and small solar system bodies.

SPAM- SPECTRAL ANALYSIS MANAGER (DEC VAX/VMS VERSION)

Science.gov (United States)

Solomon, J. E.

1994-01-01

The Spectral Analysis Manager (SPAM) was developed to allow easy qualitative analysis of multi-dimensional imaging spectrometer data. Imaging spectrometers provide sufficient spectral sampling to define unique spectral signatures on a per pixel basis. Thus direct material identification becomes possible for geologic studies. SPAM provides a variety of capabilities for carrying out interactive analysis of the massive and complex datasets associated with multispectral remote sensing observations. In addition to normal image processing functions, SPAM provides multiple levels of on-line help, a flexible command interpretation, graceful error recovery, and a program structure which can be implemented in a variety of environments. SPAM was designed to be visually oriented and user friendly with the liberal employment of graphics for rapid and efficient exploratory analysis of imaging spectrometry data. SPAM provides functions to enable arithmetic manipulations of the data, such as normalization, linear mixing, band ratio discrimination, and low-pass filtering. SPAM can be used to examine the spectra of an individual pixel or the average spectra over a number of pixels. SPAM also supports image segmentation, fast spectral signature matching, spectral library usage, mixture analysis, and feature extraction. High speed spectral signature matching is performed by using a binary spectral encoding algorithm to separate and identify mineral components present in the scene. The same binary encoding allows automatic spectral clustering. Spectral data may be entered from a digitizing tablet, stored in a user library, compared to the master library containing mineral standards, and then displayed as a timesequence spectral movie. The output plots, histograms, and stretched histograms produced by SPAM can be sent to a lineprinter, stored as separate RGB disk files, or sent to a Quick Color Recorder. SPAM is written in C for interactive execution and is available for two different

T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones.

Science.gov (United States)

Theaker, Sarah M; Rius, Cristina; Greenshields-Watson, Alexander; Lloyd, Angharad; Trimby, Andrew; Fuller, Anna; Miles, John J; Cole, David K; Peakman, Mark; Sewell, Andrew K; Dolton, Garry

2016-03-01

Isolation of peptide-specific T-cell clones is highly desirable for determining the role of T-cells in human disease, as well as for the development of therapies and diagnostics. However, generation of monoclonal T-cells with the required specificity is challenging and time-consuming. Here we describe a library-based strategy for the simple parallel detection and isolation of multiple peptide-specific human T-cell clones from CD8(+) or CD4(+) polyclonal T-cell populations. T-cells were first amplified by CD3/CD28 microbeads in a 96U-well library format, prior to screening for desired peptide recognition. T-cells from peptide-reactive wells were then subjected to cytokine-mediated enrichment followed by single-cell cloning, with the entire process from sample to validated clone taking as little as 6 weeks. Overall, T-cell libraries represent an efficient and relatively rapid tool for the generation of peptide-specific T-cell clones, with applications shown here in infectious disease (Epstein-Barr virus, influenza A, and Ebola virus), autoimmunity (type 1 diabetes) and cancer. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Quality control of next-generation sequencing library through an integrative digital microfluidic platform.

Science.gov (United States)

Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F; Bartsch, Michael S; Meagher, Robert J; Patel, Kamlesh D

2012-12-01

We have developed an automated quality control (QC) platform for next-generation sequencing (NGS) library characterization by integrating a droplet-based digital microfluidic (DMF) system with a capillary-based reagent delivery unit and a quantitative CE module. Using an in-plane capillary-DMF interface, a prepared sample droplet was actuated into position between the ground electrode and the inlet of the separation capillary to complete the circuit for an electrokinetic injection. Using a DNA ladder as an internal standard, the CE module with a compact LIF detector was capable of detecting dsDNA in the range of 5-100 pg/μL, suitable for the amount of DNA required by the Illumina Genome Analyzer sequencing platform. This DMF-CE platform consumes tenfold less sample volume than the current Agilent BioAnalyzer QC technique, preserving precious sample while providing necessary sensitivity and accuracy for optimal sequencing performance. The ability of this microfluidic system to validate NGS library preparation was demonstrated by examining the effects of limited-cycle PCR amplification on the size distribution and the yield of Illumina-compatible libraries, demonstrating that as few as ten cycles of PCR bias the size distribution of the library toward undesirable larger fragments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generation of the library of neutron cross sections for the Record code of the Fuel Management System (FMS)

International Nuclear Information System (INIS)

Alonso V, G.; Hernandez L, H.

1991-11-01

On the basis of the library structure of the RECORD code a method to generate the neutron cross sections by means of the ENDF-B/IV database and the NJOY code has been developed. The obtained cross sections are compared with those of the current library which was processed using the ENDF-B/III version. (Author)

AutoWIG: automatic generation of python bindings for C++ libraries

Directory of Open Access Journals (Sweden)

Pierre Fernique

2018-04-01

Full Text Available Most of Python and R scientific packages incorporate compiled scientific libraries to speed up the code and reuse legacy libraries. While several semi-automatic solutions exist to wrap these compiled libraries, the process of wrapping a large library is cumbersome and time consuming. In this paper, we introduce AutoWIG, a Python package that wraps automatically compiled libraries into high-level languages using LLVM/Clang technologies and the Mako templating engine. Our approach is automatic, extensible, and applies to complex C++ libraries, composed of thousands of classes or incorporating modern meta-programming constructs.

Efficient Multiple Exciton Generation Observed in Colloidal PbSe Quantum Dots with Temporally and Spectrally Resolved Intraband Excitation

KAUST Repository

Ji, Minbiao

2009-03-11

We have spectrally resolved the intraband transient absorption of photogenerated excitons to quantify the exciton population dynamics in colloidal PbSe quantum dots (QDs). These measurements demonstrate that the spectral distribution, as well as the amplitude, of the transient spectrum depends on the number of excitons excited in a QD. To accurately quantify the average number of excitons per QD, the transient spectrum must be spectrally integrated. With spectral integration, we observe efficient multiple exciton generation In colloidal PbSe QDs. © 2009 American Chemical Society.

Efficient Multiple Exciton Generation Observed in Colloidal PbSe Quantum Dots with Temporally and Spectrally Resolved Intraband Excitation

KAUST Repository

Ji, Minbiao; Park, Sungnam; Connor, Stephen T.; Mokari, Taleb; Cui, Yi; Gaffney, Kelly J.

2009-01-01

We have spectrally resolved the intraband transient absorption of photogenerated excitons to quantify the exciton population dynamics in colloidal PbSe quantum dots (QDs). These measurements demonstrate that the spectral distribution, as well as the amplitude, of the transient spectrum depends on the number of excitons excited in a QD. To accurately quantify the average number of excitons per QD, the transient spectrum must be spectrally integrated. With spectral integration, we observe efficient multiple exciton generation In colloidal PbSe QDs. © 2009 American Chemical Society.

Inspiring the generations: the Knitting Reference Library

OpenAIRE

Newington, Linda

2013-01-01

The Knitting Reference Library (KRL) is part of the University of Southampton Library, and is located at Winchester School of Art, a campus of the University. The KRL was launched at the first In the loop conference in 2008 and is founded on the bibliographic collections of Richard Rutt, Montse Stanley and Jane Waller. Each collector possessed a serious passion for knitting, their individual approaches are illustrated through the resources they collected and established as an essential part o...

The WIMSLIB library - neutron data library for WIMS-D

International Nuclear Information System (INIS)

Liu Ping

1998-05-01

During a visit to the IAEA Nuclear Data Section from 13 June to 12 December 1997, the author processed the Chinese Evaluated Nuclear Data Library (CENDL), Version 2.1, using the NJOY Nuclear Data Processing System, Version 94.105, to generate the working library WIMSLIB for input to WIMS-D/4 and WIMS-D/5A. The WIMSLIB library was then used to perform benchmark testing of CENDL-2.1. (author)

Diagnostic spectral characteristics of damouritization in granite type uranium deposit

International Nuclear Information System (INIS)

He Jianguo; Mao Yuxian; Li Jianzhong; Wang Changliang; Feng Mingyue; Rong Jiashu; Zhu Minqiang; Rao Minghui

2008-01-01

Spectral characteristics of different alteration type in uranium deposit are the prerequisite of selecting remote sensing spectral bands for uranium reconnaissance and exploration. It is also a basis for mapping alteration zone using imaging spectral data. Taking the No. 201 uranium deposit as example, the paper is focused on the spectral characteristics researching of damouritization in granite type uranium deposite. Through extracting diagnostic spectral feature of damourite and analyzing the reason causing absorption valley, it was found that spectral characteristics of damouritization in Chinese uranium deposit is different from that of illite in the spectral library published abroad. (authors)

Diagnostic spectral characteristics of damouritization in granite type uranium deposit

Energy Technology Data Exchange (ETDEWEB)

Jianguo, He; Yuxian, Mao; Jianzhong, Li; Changliang, Wang; Mingyue, Feng; Jiashu, Rong [Beijing Research Inst. of Uranium Geology, Beijing (China); Minqiang, Zhu; Minghui, Rao [East China Univ. of Technology, Fuzhou (China)

2008-07-15

Spectral characteristics of different alteration type in uranium deposit are the prerequisite of selecting remote sensing spectral bands for uranium reconnaissance and exploration. It is also a basis for mapping alteration zone using imaging spectral data. Taking the No. 201 uranium deposit as example, the paper is focused on the spectral characteristics researching of damouritization in granite type uranium deposite. Through extracting diagnostic spectral feature of damourite and analyzing the reason causing absorption valley, it was found that spectral characteristics of damouritization in Chinese uranium deposit is different from that of illite in the spectral library published abroad. (authors)

WIMSTAR-4: a computer program for generating WIMS library data from ENDF/B

International Nuclear Information System (INIS)

Wilkin, G.B.

1981-08-01

WIMSTAR (Version 4) is a FORTRAN-IV computer program developed to generate data files for the WIMS lattice code library from the ENDF/B data base. The program must be used in conjunction with the AMPX-II system and has been designed for implementation as a module of that system. This report describes the structure, implementation and use of the AMPX/WIMSTAR system

FENDL multigroup libraries

International Nuclear Information System (INIS)

Ganesan, S.; Muir, D.W.

1992-01-01

Selected neutron reaction nuclear data libraries and photon-atomic interaction cross section libraries for elements of interest to the IAEA's program on Fusion Evaluated Nuclear Data Library (FENDL) have been processed into MATXSR format using the NJOY system on the VAX4000 computer of the IAEA. This document lists the resulting multigroup data libraries. All the multigroup data generated are available cost-free upon request from the IAEA Nuclear Data Section. (author). 9 refs

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

Science.gov (United States)

Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

2018-05-09

Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

Spectral distribution of the efficiency of terahertz difference frequency generation upon collinear propagation of interacting waves in semiconductor crystals

International Nuclear Information System (INIS)

Orlov, Sergei N; Polivanov, Yurii N

2007-01-01

Dispersion phase matching curves and spectral distributions of the efficiency of difference frequency generation in the terahertz range are calculated for collinear propagation of interacting waves in zinc blende semiconductor crystals (ZnTe, CdTe, GaP, GaAs). The effect of the pump wavelength, the nonlinear crystal length and absorption in the terahertz range on the spectral distribution of the efficiency of difference frequency generation is analysed. (nonlinear optical phenomena)

Method for construction of normalized cDNA libraries

Science.gov (United States)

Soares, Marcelo B.; Efstratiadis, Argiris

1998-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

Localized Spectral Analysis of Fluctuating Power Generation from Solar Energy Systems

Directory of Open Access Journals (Sweden)

Johan Nijs

2007-01-01

Full Text Available Fluctuations in solar irradiance are a serious obstacle for the future large-scale application of photovoltaics. Occurring regularly with the passage of clouds, they can cause unexpected power variations and introduce voltage dips to the power distribution system. This paper proposes the treatment of such fluctuating time series as realizations of a stochastic, locally stationary, wavelet process. Its local spectral density can be estimated from empirical data by means of wavelet periodograms. The wavelet approach allows the analysis of the amplitude of fluctuations per characteristic scale, hence, persistence of the fluctuation. Furthermore, conclusions can be drawn on the frequency of occurrence of fluctuations of different scale. This localized spectral analysis was applied to empirical data of two successive years. The approach is especially useful for network planning and load management of power distribution systems containing a high density of photovoltaic generation units.

Efficient generation of 3.9 W of diffraction-limited green light with spectrally combined tapered diode lasers

DEFF Research Database (Denmark)

Müller, André; Jensen, Ole Bjarlin; Andersen, Peter E.

We propose an efficient concept increasing the power of diode laser systems in the visible spectral range. In comparison with second harmonic generation of single emitters, spectral beam combining with subsequent sum-frequency generation enhances the available power significantly. Combining two...... 1060 nm tapered diode lasers, we achieve a 2.5-3.2 fold increase of green light with a maximum power of 3.9 Watts in a diffraction-limited beam. At this level, diode lasers have a high application potential, for example, within the biomedical field. In order to enhance the power even further, our...

Function generation and regulation libraries and their application to the control of the new main power converter (POPS) at the CERN CPS

International Nuclear Information System (INIS)

King, Q.; Page, S.T.; Thiesen, H.; Veenstra, M.

2012-01-01

Power converter control for the LHC is based on an embedded control computer called a Function Generator/Controller (FGC). Every converter includes an FGC with responsibility for the generation of the reference current as a function of time and the regulation of the circuit current, as well as control of the converter state. With many new converter controls software classes in development it was decided to generalize several key components of the FGC software in the form of C libraries: function generation in libfg, regulation, limits and simulation in libreg and DCCT, ADC and DAC calibration in libcal. These libraries were first used in the software class dedicated to controlling the new 60 MW main power converter (POPS) at the CERN Proton Synchrotron (CPS) where regulation of both magnetic field and circuit current is supported. This paper reports on the functionality provided by each library and in particular libfg and libreg. The libraries are already being used by software classes in development for the next generation FGC for Linac4 converters, as well as the CERN SPS converter controls (MUGEF) and MedAustron converter regulation board. (authors)

Comparison of the Spectral Properties of Pansharpened Images Generated from AVNIR-2 and Prism Onboard Alos

Science.gov (United States)

Matsuoka, M.

2012-07-01

A considerable number of methods for pansharpening remote-sensing images have been developed to generate higher spatial resolution multispectral images by the fusion of lower resolution multispectral images and higher resolution panchromatic images. Because pansharpening alters the spectral properties of multispectral images, method selection is one of the key factors influencing the accuracy of subsequent analyses such as land-cover classification or change detection. In this study, seven pixel-based pansharpening methods (additive wavelet intensity, additive wavelet principal component, generalized Laplacian pyramid with spectral distortion minimization, generalized intensity-hue-saturation (GIHS) transform, GIHS adaptive, Gram-Schmidt spectral sharpening, and block-based synthetic variable ratio) were compared using AVNIR-2 and PRISM onboard ALOS from the viewpoint of the preservation of spectral properties of AVNIR-2. A visual comparison was made between pansharpened images generated from spatially degraded AVNIR-2 and original images over urban, agricultural, and forest areas. The similarity of the images was evaluated in terms of the image contrast, the color distinction, and the brightness of the ground objects. In the quantitative assessment, three kinds of statistical indices, correlation coefficient, ERGAS, and Q index, were calculated by band and land-cover type. These scores were relatively superior in bands 2 and 3 compared with the other two bands, especially over urban and agricultural areas. Band 4 showed a strong dependency on the land-cover type. This was attributable to the differences in the observing spectral wavelengths of the sensors and local scene variances.

MCBooster: a library for fast Monte Carlo generation of phase-space decays on massively parallel platforms.

Science.gov (United States)

Alves Júnior, A. A.; Sokoloff, M. D.

2017-10-01

MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. This contribution summarizes the main features of MCBooster. A basic description of the user interface and some examples of applications are provided, along with measurements of performance in a variety of environments

Use of multispectral satellite imagery and hyperspectral endmember libraries for urban land cover mapping at the metropolitan scale

Science.gov (United States)

Priem, Frederik; Okujeni, Akpona; van der Linden, Sebastian; Canters, Frank

2016-10-01

The value of characteristic reflectance features for mapping urban materials has been demonstrated in many experiments with airborne imaging spectrometry. Analysis of larger areas requires satellite-based multispectral imagery, which typically lacks the spatial and spectral detail of airborne data. Consequently the need arises to develop mapping methods that exploit the complementary strengths of both data sources. In this paper a workflow for sub-pixel quantification of Vegetation-Impervious-Soil urban land cover is presented, using medium resolution multispectral satellite imagery, hyperspectral endmember libraries and Support Vector Regression. A Landsat 8 Operational Land Imager surface reflectance image covering the greater metropolitan area of Brussels is selected for mapping. Two spectral libraries developed for the cities of Brussels and Berlin based on airborne hyperspectral APEX and HyMap data are used. First the combined endmember library is resampled to match the spectral response of the Landsat sensor. The library is then optimized to avoid spectral redundancy and confusion. Subsequently the spectra of the endmember library are synthetically mixed to produce training data for unmixing. Mapping is carried out using Support Vector Regression models trained with spectra selected through stratified sampling of the mixed library. Validation on building block level (mean size = 46.8 Landsat pixels) yields an overall good fit between reference data and estimation with Mean Absolute Errors of 0.06, 0.06 and 0.08 for vegetation, impervious and soil respectively. Findings of this work may contribute to the use of universal spectral libraries for regional scale land cover fraction mapping using regression approaches.

UFMGLIB: a multigroup library for the WIMS code

International Nuclear Information System (INIS)

Aboustta, Mohamed A.; Mello, Jair Carlos

1995-01-01

The British code WIMS is distributed by the NEA in its D4 version. It has a proper data library (Standard Library) in 69 energy groups covering, in its 1981 version, more than 100 materials with sufficient details. The Standard library was generated, basically, from the UKNDL data files and has been submitted to many alterations since the 1960's. Completely new versions such as the WIMKAL 88, generated from the basic library ENDF/B-V, were introduced and are available from the IAEA. The library UFMGLIB was generated from the ENDF/B-VI basic data library with some of the Standard data being maintained. The library contains evaluations for 131 different materials including the most common in thermal reactors. Results obtained from running the WIMS-D4 code with this library compare very well with results from the other libraries when running benchmark cases. This paper shows a general description of the library and some of the steps taken to generate it. (author). 12 refs, 2 tabs

Generation of Stationary Non-Gaussian Time Histories with a Specified Cross-spectral Density

Directory of Open Access Journals (Sweden)

David O. Smallwood

1997-01-01

Full Text Available The paper reviews several methods for the generation of stationary realizations of sampled time histories with non-Gaussian distributions and introduces a new method which can be used to control the cross-spectral density matrix and the probability density functions (pdfs of the multiple input problem. Discussed first are two methods for the specialized case of matching the auto (power spectrum, the skewness, and kurtosis using generalized shot noise and using polynomial functions. It is then shown that the skewness and kurtosis can also be controlled by the phase of a complex frequency domain description of the random process. The general case of matching a target probability density function using a zero memory nonlinear (ZMNL function is then covered. Next methods for generating vectors of random variables with a specified covariance matrix for a class of spherically invariant random vectors (SIRV are discussed. Finally the general case of matching the cross-spectral density matrix of a vector of inputs with non-Gaussian marginal distributions is presented.

Spectral Properties, Generation Order Parameters, and Luminosities for Spin-powered X-Ray Pulsars

Science.gov (United States)

Wang, Wei; Zhao, Yongheng

2004-02-01

We show the spectral properties of 15 spin-powered X-ray pulsars, and the correlation between the average power-law photon index and spin-down rate. Generation order parameters (GOPs) based on polar cap models are introduced to characterize the X-ray pulsars. We calculate three definitions of generation order parameters arising from the different effects of magnetic and electric fields on photon absorption during cascade processes, and study the relations between the GOPs and spectral properties of X-ray pulsars. There exists a possible correlation between the photon index and GOP in our pulsar sample. Furthermore, we present a method stemming from the concept of GOPs to estimate the nonthermal X-ray luminosity for spin-powered pulsars. Then X-ray luminosity is calculated in the context of our polar cap accelerator model, which is consistent with most observed X-ray pulsar data. The ratio between the X-ray luminosity estimated by our method and the pulsar's spin-down power is consistent with the LX~10-3Lsd feature.

MCNP4c JEFF-3.1 Based Libraries. Eccolib-Jeff-3.1 libraries

International Nuclear Information System (INIS)

Sublet, J.Ch.

2006-01-01

Continuous-energy and multi-temperatures MCNP Ace types libraries, derived from the Joint European Fusion-Fission JEFF-3.1 evaluations, have been generated using the NJOY-99.111 processing code system. They include the continuous-energy neutron JEFF-3.1/General Purpose, JEFF-3.1/Activation-Dosimetry and thermal S(α,β) JEFF-3.1/Thermal libraries and data tables. The processing steps and features are explained together with the Quality Assurance processes and records linked to the generation of such multipurpose libraries. (author)

MARS-ORNL, Processing Program Collection for AMPX, CCCC, ANISN, DOT, MORSE Format Library. LINX, MINX Library Utility, Data Merge. BINX, MINX Utility and SPHINX Utility, BCD to BIN Library Conversion. CINX, MINX Utility and SPHINX Utility, Library Data Collapsing

International Nuclear Information System (INIS)

2001-01-01

Description of problem or function: MARS-ORNL is a selection of computer codes for the generation of problem-dependent multigroup cross section libraries. They are selected modules from the AMPX-2 system for AMPX interface format libraries, LASL codes for CCCC interfaces, and processing codes for libraries to be used by ANISN, DOT, or MORSE codes. The codes in the collection are used in connection with the following DLC data libraries: ZZ-LIB-IV (DLC-0040), ZZ-VITAMIN-C (DLC-0041), VITAMIN-4C (DLC-0053), ZZ-CLEAR/42B (DLC-0042), ZZ-CSRL/43B (DLC-0043), and EPRMASTER (DLC-0052). The functions of these processing codes are briefly described: A. AMPX Modules: AIM: Converts AMPX Master Interface Files from EBCDIC to binary form and back. AJAX: Merges, collects, assembles, re-orders, joins, and copies selected nuclides from AMPX Master Interfaces. BONAMI: Accesses Bondarenko factors from an AMPX Master Library and performs resonance self-shielding calculations. CHOX: Produces a coupled interface library in AMPX format by combining neutron libraries (generated by module XLACS), gamma libraries (generated by module SMUG), and photon production libraries (generated by module LAPHNGAS). CHOXM: Combines self-shielding factors as generated by the code SPHINX (PSR-0129) and an infinite dilution neutron master interface (generated by XLACS) to generate a self-shielded neutron AMPX Interface File. The interface produced by CHOXM is an input to the NITAWL module of AMPX. CHOXM is a modified version of CHOX. COMAND: Collapses ANISN cross section libraries. DIAL: Produces edits from AMPX Master Interfaces. ICE-II: Accepts cross sections from an AMPX working library and produces mixed cross sections in four formats: (1) AMPX working library format; (2) ANISN format; (3) group-independent ANISN format; (4) Monte Carlo processed cross section library format. NITAWL: Produces self-shielded and working cross section libraries in the formats required by the ANISN, DOT, or MORSE codes

A rural virtual health sciences library project: research findings with implications for next generation library services.

Science.gov (United States)

Richwine, M P; McGowan, J J

2001-01-01

The Shared Hospital Electronic Library of Southern Indiana (SHELSI) research project was designed to determine whether access to a virtual health sciences library and training in its use would support medical decision making in rural southern Indiana and achieve the same level of impact seen by targeted information services provided by health sciences librarians in urban hospitals. Based on the results of a needs assessment, a virtual medical library was created; various levels of training were provided. Virtual library users were asked to complete a Likert-type survey, which included questions on intent of use and impact of use. At the conclusion of the project period, structured interviews were conducted. Impact of the virtual health sciences library showed a strong correlation with the impact of information provided by health sciences librarians. Both interventions resulted in avoidance of adverse health events. Data collected from the structured interviews confirmed the perceived value of the virtual library. While librarians continue to hold a strong position in supporting information access for health care providers, their roles in the information age must begin to move away from providing information toward selecting and organizing knowledge resources and instruction in their use.

PROF-DD, Generator of Multigroup Cross-Sections Library DDX for MORSE-DD, ANISN-DD, DOT-DD

International Nuclear Information System (INIS)

Mori, Takamasa; Nakagawa, Masayuki; Ishiguro, Yukio

2002-01-01

1 - Description of program or function: The code system PROF-DD generates a multi-group double-differential cross section library DDX from evaluated data in ENDF/B-IV or ENDF/B-V format. The system consists of the following five modules: PROF-DDX is the main module of the system. It calculates the multigroup DDX and stores them on a master PDS file. MCFILEF generates a control file for PROF-DDX, which contains energy group and angle bin structures. SPINPTF prepares an input data file for PROF-DDX by combining the control file with other input data. DDXLIBMK edits a DDX library from the master PDS file for transport calculations. RESENDD performs resonance cross section and Doppler broadening calculations. 2 - Restrictions on the complexity of the problem: The numbers of energy groups and angle bins are less than 150 and 40, respectively

Database and Library Development of Organic Species using Gas Chromatography and Mass Spectral Measurements in Support of the Mars Science Laboratory

Science.gov (United States)

Garcia, Raul; Mahaffy, Paul; Misra, Prabhakar

2010-02-01

Our work involves the development of an organic contaminants database that will allow us to determine which compounds are found here on Earth and would be inadvertently detected in the Mars soil and gaseous samples as impurities. It will be used for the Sample Analysis at Mars (SAM) instrumentation analysis in the Mars Science Laboratory (MSL) rover scheduled for launch in 2011. In order to develop a comprehensive target database, we utilize the NIST Mass Spectral Library, Automated Mass Spectral Deconvolution and Identification System (AMDIS) and Ion Fingerprint Deconvolution (IFD) software to analyze the GC-MS data. We have analyzed data from commercial samples, such as paint and polymers, which have not been implemented into the rover and are now analyzing actual data from pyrolyzation on the rover. We have successfully developed an initial target compound database that will aid SAM in determining whether the components being analyzed come from Mars or are contaminants from either the rover itself or the Earth environment and are continuing to make improvements and adding data to the target contaminants database. )

School Libraries and Innovation

Science.gov (United States)

McGrath, Kevin G.

2015-01-01

School library programs have measured success by improved test scores. But how do next-generation school libraries demonstrate success as they strive to be centers of innovation and creativity? These libraries offer solutions for school leaders who struggle to restructure existing systems built around traditional silos of learning (subjects and…

A rural virtual health sciences library project: research findings with implications for next generation library services*

Science.gov (United States)

Richwine, Margaret (Peggy); McGowan, Julie J.

2001-01-01

Purpose: The Shared Hospital Electronic Library of Southern Indiana (SHELSI) research project was designed to determine whether access to a virtual health sciences library and training in its use would support medical decision making in rural southern Indiana and achieve the same level of impact seen by targeted information services provided by health sciences librarians in urban hospitals. Methods: Based on the results of a needs assessment, a virtual medical library was created; various levels of training were provided. Virtual library users were asked to complete a Likert-type survey, which included questions on intent of use and impact of use. At the conclusion of the project period, structured interviews were conducted. Results: Impact of the virtual health sciences library showed a strong correlation with the impact of information provided by health sciences librarians. Both interventions resulted in avoidance of adverse health events. Data collected from the structured interviews confirmed the perceived value of the virtual library. Conclusion: While librarians continue to hold a strong position in supporting information access for health care providers, their roles in the information age must begin to move away from providing information toward selecting and organizing knowledge resources and instruction in their use. PMID:11209799

AMPX: a modular code system for generating coupled multigroup neutron-gamma libraries from ENDF/B

Energy Technology Data Exchange (ETDEWEB)

Greene, N.M.; Lucius, J.L.; Petrie, L.M.; Ford, W.E. III; White, J.E.; Wright, R.Q.

1976-03-01

AMPX is a modular system for producing coupled multigroup neutron-gamma cross section sets. Basic neutron and gamma cross-section data for AMPX are obtained from ENDF/B libraries. Most commonly used operations required to generate and collapse multigroup cross-section sets are provided in the system. AMPX is flexibly dimensioned; neutron group structures, and gamma group structures, and expansion orders to represent anisotropic processes are all arbitrary and limited only by available computer core and budget. The basic processes provided will (1) generate multigroup neutron cross sections; (2) generate multigroup gamma cross sections; (3) generate gamma yields for gamma-producing neutron interactions; (4) combine neutron cross sections, gamma cross sections, and gamma yields into final ''coupled sets''; (5) perform one-dimensional discrete ordinates transport or diffusion theory calculations for neutrons and gammas and, on option, collapse the cross sections to a broad-group structure, using the one-dimensional results as weighting functions; (6) plot cross sections, on option, to facilitate the ''evaluation'' of a particular multigroup set of data; (7) update and maintain multigroup cross section libraries in such a manner as to make it not only easy to combine new data with previously processed data but also to do it in a single pass on the computer; and (8) output multigroup cross sections in convenient formats for other codes. (auth)

Theoretical Analysis of Spectral Correlations Between Photon Pairs Generated in Nanoscale Silicon Waveguides

International Nuclear Information System (INIS)

Lu Liang-Liang; Xu Ping; Xu Jian-Ning; Zhu Shi-Ning; He Guang-Qiang

2015-01-01

Spontaneous four wave mixing in nonlinear waveguide is one of the excellent technique for generating photon pairs in well-defined guided modes. Here we present a comprehensive study of the frequency characteristic of correlated photon pairs generated in telecom C-band from a dispersion-engineered silicon wire waveguide. We have demonstrated that the waveguide configuration, shape of pump pulse, two-photon absorption as well as linear losses have significant influences on the biphoton spectral characteristics and the amount of frequency entanglement generated. The superior performance as well as the structural compactness and CMOS compatibility makes the silicon wire waveguide an ideal integrated platform for the implementation of on-chip quantum technologies. (paper)

AMZ, library of multigroup constants for EXPANDA computer codes, generated by NJOY computer code from ENDF/B-IV

International Nuclear Information System (INIS)

Chalhoub, E.S.; Moraes, M. de.

1984-01-01

A 70-group, 37-isotope library of multigroup constants for fast reactor nuclear design calculations is described. Nuclear cross sections, transfer matrices, and self-shielding factors were generated with NJOY code and an auxiliary program RGENDF using evaluated data from ENDF/B-IV. The output is being issued in a format suitable for EXPANDA code. Comparisons with JFS-2 library, as well as, test resuls for 14 CSEWG benchmark critical assemblies are presented. (Author) [pt

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

Energy Technology Data Exchange (ETDEWEB)

Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

2016-03-31

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

International Nuclear Information System (INIS)

Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

2016-01-01

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Our Stories Transforming Our Libraries: The York County Library System

Directory of Open Access Journals (Sweden)

Mina Edmondson

2016-11-01

Full Text Available These narratives chronicle the authors’ journeys to collaborate and discover the transformative impact that stories have on library culture and library staff. This study describes a research collaboration between York County Libraries and Penn State York. In Phase I, we collected stories from library staff as the library system was being challenged to reimage public libraries for the future. The major themes and types of organizational stories identified in the initial narrative project were presented during a county-wide all-staff in-service training. The library District Consultant (first author and the Penn State professor (second author then facilitated a workshop designed to lead staff in their exploration of these topics and generate a written record of their storytelling/discussions. This data became the basis for Phase II of the project and allowed the system to strategically assess its evolving culture and identity.

VO-compliant libraries of high resolution spectra of cool stars

Science.gov (United States)

Montes, D.

2008-10-01

In this contribution we describe a Virtual Observatory (VO) compliant version of the libraries of high resolution spectra of cool stars described by Montes et al. (1997; 1998; and 1999). Since their publication the fully reduced spectra in FITS format have been available via ftp and in the World Wide Web. However, in the VO all the spectra will be accessible using a common web interface following the standards of the International Virtual Observatory Alliance (IVOA). These libraries include F, G, K and M field stars, from dwarfs to giants. The spectral coverage is from 3800 to 10000 Å, with spectral resolution ranging from 0.09 to 3.0 Å.

The Challenges to Human Resources Development of Libraries in Times of Radical and Generational Changes.

Science.gov (United States)

Muller, Uta

Librarianship has undergone a radical change in recent years, which will be continued in the future. Whereas previously the administration of media was most important, nowadays an ever increasing willingness to provide a service is required. In addition to the essential restructuring of libraries, a generational change is taking place within the…

Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

Directory of Open Access Journals (Sweden)

Andaine Seguin-Orlando

Full Text Available Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

Directory of Open Access Journals (Sweden)

Kumar Santosh

2012-12-01

Full Text Available Abstract Background Flax (Linum usitatissimum L. is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. Results Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents. Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. Conclusions Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

Science.gov (United States)

Aigrain, Louise; Gu, Yong; Quail, Michael A

2016-06-13

The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

Generation of SCALE 6 Input Data File for Cross Section Library of PWR Spent Fuel

International Nuclear Information System (INIS)

Jeong, Chang Joon; Cho, Dong Keun

2010-11-01

In order to obtain the cross section libraries of the Korean Pressurized water reactor (PWR) spent fuel (SF), SCALE 6 code input files have been generated. The PWR fuel data were obtained from the nuclear design report (NDR) of the current operating PWRs. The input file were prepared for 16 fuel types such as 4 types of Westinghouse 14x14, 3 types of OPR-1000 16x16, 4 types of Westinghouse 16x16, and 6 types of Westinghouse 17x17. For each fuel type, 5 kinds of fuel enrichments have been considered such as 1.5, 2.0 ,3.0, 4.0 and 5.0 wt%. In the SCALE 6 calculation, a ENDF-V 44 group was used. The 25 burnup step until 72000 MWD/T was used. A 1/4 symmetry model was used for 16x16 and 17x17 fuel assembly, and 1/2 symmetry model was used for 14x14 fuel assembly The generated cross section libraries will be used for the source-term analysis of the PWR SF

Defrosting the digital library: bibliographic tools for the next generation web.

Science.gov (United States)

Hull, Duncan; Pettifer, Steve R; Kell, Douglas B

2008-10-01

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as "thought in cold storage," and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

Defrosting the digital library: bibliographic tools for the next generation web.

Directory of Open Access Journals (Sweden)

Duncan Hull

2008-10-01

Full Text Available Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as "thought in cold storage," and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

The California State Library: An Orientation Guide for Library Directors

Science.gov (United States)

California State Library, 2009

2009-01-01

The California State Library is charged with performing the following activities as defined by law. The State Library, under the direction and control of the State Librarian, an appointee of the Governor, has responsibility: (1) To collect, preserve, generate and disseminate a wide array of information; (2) To serve as the central reference and…

Integrated spectral study of small angular diameter galactic open clusters

Science.gov (United States)

Clariá, J. J.; Ahumada, A. V.; Bica, E.; Pavani, D. B.; Parisi, M. C.

2017-10-01

This paper presents flux-calibrated integrated spectra obtained at Complejo Astronómico El Leoncito (CASLEO, Argentina) for a sample of 9 Galactic open clusters of small angular diameter. The spectra cover the optical range (3800-6800 Å), with a resolution of ˜14 Å. With one exception (Ruprecht 158), the selected clusters are projected into the fourth Galactic quadrant (282o evaluate their membership status. The current cluster sample complements that of 46 open clusters previously studied by our group in an effort to gather a spectral library with several clusters per age bin. The cluster spectral library that we have been building is an important tool to tie studies of resolved and unresolved stellar content.

CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

Science.gov (United States)

Cutler, Andrew D.; Magnotti, Gaetano

2010-01-01

The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

VizieR Online Data Catalog: A library of high-S/N optical spectra of FGKM stars (Yee+, 2017)

Science.gov (United States)

Yee, S. W.; Petigura, E. A.; von Braun, K.

2017-09-01

Classification of stars, by comparing their optical spectra to a few dozen spectral standards, has been a workhorse of observational astronomy for more than a century. Here, we extend this technique by compiling a library of optical spectra of 404 touchstone stars observed with Keck/HIRES by the California Planet Search. The spectra have high resolution (R~60000), high signal-to-noise ratio (S/N~150/pixel), and are registered onto a common wavelength scale. The library stars have properties derived from interferometry, asteroseismology, LTE spectral synthesis, and spectrophotometry. To address a lack of well-characterized late-K dwarfs in the literature, we measure stellar radii and temperatures for 23 nearby K dwarfs, using modeling of the spectral energy distribution and Gaia parallaxes. This library represents a uniform data set spanning the spectral types ~M5-F1 (Teff~3000-7000K, R*~0.1-16R{Sun}). We also present "Empirical SpecMatch" (SpecMatch-Emp), a tool for parameterizing unknown spectra by comparing them against our spectral library. For FGKM stars, SpecMatch-Emp achieves accuracies of 100K in effective temperature (Teff), 15% in stellar radius (R*), and 0.09dex in metallicity ([Fe/H]). Because the code relies on empirical spectra it performs particularly well for stars ~K4 and later, which are challenging to model with existing spectral synthesizers, reaching accuracies of 70K in Teff, 10% in R*, and 0.12dex in [Fe/H]. We also validate the performance of SpecMatch-Emp, finding it to be robust at lower spectral resolution and S/N, enabling the characterization of faint late-type stars. Both the library and stellar characterization code are publicly available. (2 data files).

Generation, Testing, and Validation of a WIMS-D/4 Multigroup Cross-Section Library Based on the JENDL-3.2 Nuclear Data

International Nuclear Information System (INIS)

Rahman, Mafizur; Takano, Hideki

2001-01-01

A new 69-group library of multigroup constants for the lattice code WIMS-D/4 has been generated with an improved resonance treatment, processing nuclear data from JENDL-3.2 by NJOY91.108. A parallel ENDF/B-VI based library has also been constructed for intercomparison of results. Benchmark calculations for a number of thermal reactor critical assemblies of both uranium and plutonium fuels have been performed with the code WIMS-D/4.1 with its three different libraries: the original WIMS library (NEA-0329/10) and the new ENDF/B-VI and JENDL-3.2 based libraries. The results calculated with both ENDF and JENDL based libraries show a similar tendency and are found in better agreement with the experimental values. Benchmark parameters are further calculated with the comprehensive lattice code SRAC95. The results from SRAC95 and WIMS-D/4.1 (both using JENDL-3.2 based libraries) agree well with each other. The new library is also verified for its applicability to mixed-oxide cores of varying plutonium contents

The SpeX Prism Library Analysis Toolkit: Design Considerations and First Results

Science.gov (United States)

Burgasser, Adam J.; Aganze, Christian; Escala, Ivana; Lopez, Mike; Choban, Caleb; Jin, Yuhui; Iyer, Aishwarya; Tallis, Melisa; Suarez, Adrian; Sahi, Maitrayee

2016-01-01

Various observational and theoretical spectral libraries now exist for galaxies, stars, planets and other objects, which have proven useful for classification, interpretation, simulation and model development. Effective use of these libraries relies on analysis tools, which are often left to users to develop. In this poster, we describe a program to develop a combined spectral data repository and Python-based analysis toolkit for low-resolution spectra of very low mass dwarfs (late M, L and T dwarfs), which enables visualization, spectral index analysis, classification, atmosphere model comparison, and binary modeling for nearly 2000 library spectra and user-submitted data. The SpeX Prism Library Analysis Toolkit (SPLAT) is being constructed as a collaborative, student-centered, learning-through-research model with high school, undergraduate and graduate students and regional science teachers, who populate the database and build the analysis tools through quarterly challenge exercises and summer research projects. In this poster, I describe the design considerations of the toolkit, its current status and development plan, and report the first published results led by undergraduate students. The combined data and analysis tools are ideal for characterizing cool stellar and exoplanetary atmospheres (including direct exoplanetary spectra observations by Gemini/GPI, VLT/SPHERE, and JWST), and the toolkit design can be readily adapted for other spectral datasets as well.This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NNX15AI75G. SPLAT code can be found at https://github.com/aburgasser/splat.

Medical Library Association

Science.gov (United States)

... Next Generation Data Sciences Challenges in Health and Biomedicine Fri November 3, 2017 The Medical Library Association ... Next Generation Data Science Challenges in Health and Biomedicine. MLA's comments and recommendations will help formulate strategic ...

Influence of spectral solar radiation to the generating power of photovoltaic module; Taiyo denchi shutsuryoku eno taiyoko supekutoru eno eikyo

Energy Technology Data Exchange (ETDEWEB)

Minaki, S.; Ishihara, Y.; Todaka, T.; Harada, K. [Doshisha University, Kyoto (Japan); Oshiro, T.; Nakamura, H. [Japan quality Assurance Organization, Tokyo (Japan)

1997-11-25

As to the influence of spectral solar radiation to generating power of solar cells, a study was conducted from the aspects of season, time zone, intensity of solar radiation, etc. In the study, spectral responsive variation correction coefficients were introduced as evaluation values expressing the influence of spectral solar radiation. For the spectral distribution, an all sky spectral pyranometer by wavelength was used, and data were used which were obtained in the measurement in experimental facilities of the solar techno center. Concerning solar cell relative spectral sensitivity values, used were relative spectral sensitivity values of monocrystal and amorphous standard solar cells to the short-circuit current. Spectral response variation correction coefficients are coefficients correcting variations in conversion efficiency of solar cells due to changes in the spectral distribution. The changes of spectral responsive variation correction coefficients were studied using data obtained during April 1994 and March 1996. As a result, it was found that the coefficients showed large changes in summer and small ones in winter and that amorphous solar cells indicate this trend conspicuously. 3 refs., 6 figs., 3 tabs.

INTRIGOSS: A new Library of High Resolution Synthetic Spectra

Science.gov (United States)

Franchini, Mariagrazia; Morossi, Carlo; Di Marcancantonio, Paolo; Chavez, Miguel; GES-Builders

2018-01-01

INTRIGOSS (INaf Trieste Grid Of Synthetic Spectra) is a new High Resolution (HiRes) synthetic spectral library designed for studying F, G, and K stars. The library is based on atmosphere models computed with specified individual element abundances via ATLAS12 code. Normalized SPectra (NSP) and surface Flux SPectra (FSP), in the 4800-5400 Å wavelength range, were computed by means of the SPECTRUM code. The synthetic spectra are computed with an atomic and bi-atomic molecular line list including "bona fide" Predicted Lines (PLs) built by tuning loggf to reproduce very high SNR Solar spectrum and the UVES-U580 spectra of five cool giants extracted from the Gaia-ESO survey (GES). The astrophysical gf-values were then assessed by using more than 2000 stars with homogenous and accurate atmosphere parameters and detailed chemical composition from GES. The validity and greater accuracy of INTRIGOSS NSPs and FSPs with respect to other available spectral libraries is discussed. INTRIGOSS will be available on the web and will be a valuable tool for both stellar atmospheric parameters and stellar population studies.

Development of Neutron Energy Spectral Signatures for Passive Monitoring of Spent Nuclear Fuels in Dry Cask Storage

Science.gov (United States)

Harkness, Ira; Zhu, Ting; Liang, Yinong; Rauch, Eric; Enqvist, Andreas; Jordan, Kelly A.

2018-01-01

Demand for spent nuclear fuel dry casks as an interim storage solution has increased globally and the IAEA has expressed a need for robust safeguards and verification technologies for ensuring the continuity of knowledge and the integrity of radioactive materials inside spent fuel casks. Existing research has been focusing on "fingerprinting" casks based on count rate statistics to represent radiation emission signatures. The current research aims to expand to include neutron energy spectral information as part of the fuel characteristics. First, spent fuel composition data are taken from the Next Generation Safeguards Initiative Spent Fuel Libraries, representative for Westinghouse 17ˣ17 PWR assemblies. The ORIGEN-S code then calculates the spontaneous fission and (α,n) emissions for individual fuel rods, followed by detailed MCNP simulations of neutrons transported through the fuel assemblies. A comprehensive database of neutron energy spectral profiles is to be constructed, with different enrichment, burn-up, and cooling time conditions. The end goal is to utilize the computational spent fuel library, predictive algorithm, and a pressurized 4He scintillator to verify the spent fuel assemblies inside a cask. This work identifies neutron spectral signatures that correlate with the cooling time of spent fuel. Both the total and relative contributions from spontaneous fission and (α,n) change noticeably with respect to cooling time, due to the relatively short half-life (18 years) of the major neutron source 244Cm. Identification of this and other neutron spectral signatures allows the characterization of spent nuclear fuels in dry cask storage.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

DEFF Research Database (Denmark)

Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

2014-01-01

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries

Directory of Open Access Journals (Sweden)

Mari eNyyssönen

2013-09-01

Full Text Available Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale that matches our ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkages between genes, metabolic traits and microbial taxa and thus bridge this gap between sequence data generation and functional predictions. Here we developed high-throughput screening assays for function-based characterization of activities involved in plant polymer decomposition from environmental metagenomic libraries. The multiplexed assays use fluorogenic and chromogenic substrates, combine automated liquid handling and use a genetically modified expression host to enable simultaneous screening of 12,160 clones for 14 activities in a total of 170,240 reactions. Using this platform we identified 374 (0.26 % cellulose, hemicellulose, chitin, starch, phosphate and protein hydrolyzing clones from fosmid libraries prepared from decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by assembly and gene prediction of a subset of 95 fosmid clones, identified a broad range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme genes from 20 different glycoside hydrolase families were detected. Using tetranucleotide frequency binning of fosmid sequences, multiple enzyme activities from distinct fosmids were linked, demonstrating how biochemically-confirmed functional traits in environmental metagenomes may be attributed to groups of specific organisms. Overall, our results demonstrate how functional screening of metagenomic libraries can be used to connect microbial functionality to community composition and, as a result, complement large-scale metagenomic sequencing efforts.

The Next Generation Online Public Access Catalog in Academic Libraries

OpenAIRE

Wallis, Kim

2009-01-01

"Make it more like Google" is a refrain that is often heard by students at academic libraries when asked how library catalogs can be improved. According to the annual Beloit College Mindset list for the class of 2010, the word Google has always been a verb. It is not surprising students today turn to the web when conducting research as it is what they are familiar with and what they know. How can academic libraries handle the challenge of changing user expectations? Can open source software b...

Next-Generation Library Catalogs and the Problem of Slow Response Time

Directory of Open Access Journals (Sweden)

Margaret Brown-Sica

2010-12-01

Full Text Available Response time as defined for this study is the time that it takes for all files that constitute a single webpage to travel across the Internet from a Web server to the end user’s browser. In this study, the authors tested response times on queries for identical items in five different library catalogs, one of them a next-generation (NextGen catalog. The authors also discuss acceptable response time and how it may affect the discovery process. They suggest that librarians and vendors should develop standards for acceptable response time and use it in the product selection and development processes.

Design, construction, and characterization of a second-generation DARP in library with reduced hydrophobicity.

Science.gov (United States)

Seeger, Markus A; Zbinden, Reto; Flütsch, Andreas; Gutte, Petrus G M; Engeler, Sibylle; Roschitzki-Voser, Heidi; Grütter, Markus G

2013-09-01

Designed ankyrin repeat proteins (DARPins) are well-established binding molecules based on a highly stable nonantibody scaffold. Building on 13 crystal structures of DARPin-target complexes and stability measurements of DARPin mutants, we have generated a new DARPin library containing an extended randomized surface. To counteract the enrichment of unspecific hydrophobic binders during selections against difficult targets containing hydrophobic surfaces such as membrane proteins, the frequency of apolar residues at diversified positions was drastically reduced and substituted by an increased number of tyrosines. Ribosome display selections against two human caspases and membrane transporter AcrB yielded highly enriched pools of unique and strong DARPin binders which were mainly monomeric. We noted a prominent enrichment of tryptophan residues during binder selections. A crystal structure of a representative of this library in complex with caspase-7 visualizes the key roles of both tryptophans and tyrosines in providing target contacts. These aromatic and polar side chains thus substitute the apolar residues valine, leucine, isoleucine, methionine, and phenylalanine of the original DARPins. Our work describes biophysical and structural analyses required to extend existing binder scaffolds and simplifies an existing protocol for the assembly of highly diverse synthetic binder libraries. © 2013 The Protein Society.

Frequency interleaving towards spectrally efficient directly detected optical OFDM for next-generation optical access networks.

Science.gov (United States)

Mehedy, Lenin; Bakaul, Masuduzzaman; Nirmalathas, Ampalavanapillai

2010-10-25

In this paper, we theoretically analyze and demonstrate that spectral efficiency of a conventional direct detection based optical OFDM system (DDO-OFDM) can be improved significantly using frequency interleaving of adjacent DDO-OFDM channels where OFDM signal band of one channel occupies the spectral gap of other channel and vice versa. We show that, at optimum operating condition, the proposed technique can effectively improve the spectral efficiency of the conventional DDO-OFDM system as much as 50%. We also show that such a frequency interleaved DDO-OFDM system, with a bit rate of 48 Gb/s within 25 GHz bandwidth, achieves sufficient power budget after transmission over 25 km single mode fiber to be used in next-generation time-division-multiplexed passive optical networks (TDM-PON). Moreover, by applying 64- quadrature amplitude modulation (QAM), the system can be further scaled up to 96 Gb/s with a power budget sufficient for 1:16 split TDM-PON.

A rural virtual health sciences library project: research findings with implications for next generation library services*

OpenAIRE

Richwine, Margaret (Peggy); McGowan, Julie J.

2001-01-01

Purpose: The Shared Hospital Electronic Library of Southern Indiana (SHELSI) research project was designed to determine whether access to a virtual health sciences library and training in its use would support medical decision making in rural southern Indiana and achieve the same level of impact seen by targeted information services provided by health sciences librarians in urban hospitals.

Parameters optimization for wavelet denoising based on normalized spectral angle and threshold constraint machine learning

Science.gov (United States)

Li, Hao; Ma, Yong; Liang, Kun; Tian, Yong; Wang, Rui

2012-01-01

Wavelet parameters (e.g., wavelet type, level of decomposition) affect the performance of the wavelet denoising algorithm in hyperspectral applications. Current studies select the best wavelet parameters for a single spectral curve by comparing similarity criteria such as spectral angle (SA). However, the method to find the best parameters for a spectral library that contains multiple spectra has not been studied. In this paper, a criterion named normalized spectral angle (NSA) is proposed. By comparing NSA, the best combination of parameters for a spectral library can be selected. Moreover, a fast algorithm based on threshold constraint and machine learning is developed to reduce the time of a full search. After several iterations of learning, the combination of parameters that constantly surpasses a threshold is selected. The experiments proved that by using the NSA criterion, the SA values decreased significantly, and the fast algorithm could save 80% time consumption, while the denoising performance was not obviously impaired.

Surveying Medical Students to Gauge Library Use and Plan for a New Medical Library.

Science.gov (United States)

Aronoff, Nell

2016-01-01

In spring 2015, a 45-question survey was e-mailed to 585 medical students at the University at Buffalo (UB) in order to gauge their use of library spaces, resources, equipment, and services at UB's Health Sciences Library and plan for a library space located within a new medical school building. Students' self-reported use of the library during the academic year is presented along with the features they would like to see in their ideal library space. The responses generated in the survey are a barometer of current use and will be used in the planning process.

New WIMS library generation from ENDF/B6 and effect of resonance group structure on cell parameters

International Nuclear Information System (INIS)

Pazirandeh, Ali; Tabesh, Alireza

2002-01-01

Due to inaccessibility to NJOY, steps were taken to create WIMS library, which can be extracted from ENDF/B6 without using NJOY. In addition to using preprocessing codes few programs were written to calculate integral resonance, slowing down power per unit lethargy, potential scattering, and differential scattering cross section, scattering matrices. For neutrons with energy above 4 eV, isotropic elastic scattering was assumed. For neutrons below 4 eV the free gas model was used, except for light elements, which tabulated values of S(α,β) in ENDF/B6 used. The Goldstein-Cohen factors are taken from WIMKAL88.Lib. The integral resonance with self absorption per unit lethargy was obtained from GROUPIE output. The P 1 scattering matrices are calculated only for four elements, namely H, D, C and O at 300 K. In order to examine the created libraries, k eff , δ 28 , ρ 28 , ρ 25 and CR are calculated using new WIMS library, WIMKAL88.Lib and NEA329.Lib. The results showed general agreement. The controversial issue of WIMS library group structure, particularly in resonance region has raised the question of whether the number of resonance group i.e., 13 is optimized. We generated different WIMS libraries consisting of 5, 8, 13, 18 and 23 resonance groups. The main aim was to examine the effect to resonance group structure on calculated core parameters, mainly, k eff , δ 28 , ρ 28 , ρ 25 and CR. These parameters are also calculated and compared with those obtained using WIMKAL88, and NEA329 libraries. (author)

Generation of ENDF/B-IV based 35 group neutron cross-section library and its application in criticality studies

International Nuclear Information System (INIS)

Garg, S.B.; Sinha, A.

1985-01-01

A 35 group cross-section library with P/sub 3/-anisotropic scattering matrices and resonance self-shielding factors has been generated from the basic ENDF/B-IV cross-section files for 57 elements. This library covers the neutron energy range from 0.005 ev to 15 MeV and is well suited for the neutronics and safety analysis of fission, fusion and hybrid systems. The library is contained in two well known files, namely, ISOTXS and BRKOXS. In order to test the efficacy of this library and to bring out the importance of resonance self-shielding, a few selected fast critical assemblies representing large dilute oxide and carbide fueled uranium and plutonium based systems have been analysed. These assemblies include ZPPR/sub 2/, ZPR-3-48, ZPR-3-53, ZPR-6-6A, ZPR-6-7, ZPR-9-31 and ZEBRA-2 and are amongst those recommended by the US Nuclear Data Evaluation Working Group for testing the accuracy of cross-sections. The evaluated multiplication constants of these assemblies compare favourably with those calculated by others

Generation of the V4.2m5 and AMPX and MPACT 51 and 252-Group Libraries with ENDF/B-VII.0 and VII.1

Energy Technology Data Exchange (ETDEWEB)

Kim, Kang Seog [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Consortium for Advanced Simulation of LWRs (CASL)

2016-12-12

The evaluated nuclear data file (ENDF)/B-7.0 v4.1m3 MPACT 47-group library has been used as a main library for the Consortium for Advanced Simulation of Light Water Reactors (CASL) neutronics simulator in simulating pressurized water reactor (PWR) problems. Recent analysis for the high void boiling water reactor (BWR) fuels and burnt fuels indicates that the 47-group library introduces relatively large reactivity bias. Since the 47- group structure does not match with the SCALE 6.2 252-group boundaries, the CASL Virtual Environment for Reactor Applications Core Simulator (VERA-CS) MPACT library must be maintained independently, which causes quality assurance concerns. In order to address this issue, a new 51-group structure has been proposed based on the MPACT 47- g and SCALE 252-g structures. In addition, the new CASL library will include a 19-group structure for gamma production and interaction cross section data based on the SCALE 19- group structure. New AMPX and MPACT 51-group libraries have been developed with the ENDF/B-7.0 and 7.1 evaluated nuclear data. The 19-group gamma data also have been generated for future use, but they are only available on the AMPX 51-g library. In addition, ENDF/B-7.0 and 7.1 MPACT 252-g libraries have been generated for verification purposes. Various benchmark calculations have been performed to verify and validate the newly developed libraries.

Generation of the V4.2m5 and AMPX and MPACT 51 and 252-Group Libraries with ENDF/B-VII.0 and VII.1

International Nuclear Information System (INIS)

Kim, Kang Seog

2016-01-01

The evaluated nuclear data file (ENDF)/B-7.0 v4.1m3 MPACT 47-group library has been used as a main library for the Consortium for Advanced Simulation of Light Water Reactors (CASL) neutronics simulator in simulating pressurized water reactor (PWR) problems. Recent analysis for the high void boiling water reactor (BWR) fuels and burnt fuels indicates that the 47-group library introduces relatively large reactivity bias. Since the 47- group structure does not match with the SCALE 6.2 252-group boundaries, the CASL Virtual Environment for Reactor Applications Core Simulator (VERA-CS) MPACT library must be maintained independently, which causes quality assurance concerns. In order to address this issue, a new 51-group structure has been proposed based on the MPACT 47- g and SCALE 252-g structures. In addition, the new CASL library will include a 19-group structure for gamma production and interaction cross section data based on the SCALE 19- group structure. New AMPX and MPACT 51-group libraries have been developed with the ENDF/B-7.0 and 7.1 evaluated nuclear data. The 19-group gamma data also have been generated for future use, but they are only available on the AMPX 51-g library. In addition, ENDF/B-7.0 and 7.1 MPACT 252-g libraries have been generated for verification purposes. Various benchmark calculations have been performed to verify and validate the newly developed libraries.

Comparison of techniques for quantification of next-generation sequencing libraries

DEFF Research Database (Denmark)

Hussing, Christian; Kampmann, Marie-Louise; Mogensen, Helle Smidt

2015-01-01

by quantifying NGS libraries for the Ion TorrentTM and Illumina1 platforms as well as dsDNA oligos with known DNA concentrations. Rather large variations in library concentration estimates were observed. The differences between the highest and lowest concentration estimates varied with a factor of 5...

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

Science.gov (United States)

Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

2015-09-21

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

A wave generation toolbox for the open‐source CFD library: OpenFoam

DEFF Research Database (Denmark)

Jacobsen, Niels Gjøl; Fuhrman, David R.; Fredsøe, Jørgen

2012-01-01

The open‐source CFD library OpenFoam® contains a method for solving free surface Newtonian flows using the Reynolds averaged Navier–Stokes equations coupled with a volume of fluid method. In this paper, it is demonstrated how this has been extended with a generic wave generation and absorption...... method termed ‘wave relaxation zones’, on which a detailed account is given. The ability to use OpenFoam for the modelling of waves is demonstrated using two benchmark test cases, which show the ability to model wave propagation and wave breaking. Furthermore, the reflection coefficient from outlet...... made freely available through the OpenFoam‐Extend Community....

The LAW library

International Nuclear Information System (INIS)

Green, N.M.; Parks, C.V.; Arwood, J.W.

1989-01-01

The 238 group LAW library is a new multigroup library based on ENDF/B-V data. It contains data for 302 materials and will be distributed by the Radiation Shielding Information Center, located at Oak Ridge National Laboratory. It was generated for use in neutronics calculations required in radioactive waste analyses, though it has equal utility in any study requiring multigroup neutron cross sections

Petasis/Diels-Alder/Cyclization Cascade Reactions for the Generation of Scaffolds with Multiple Stereogenic Centers and Orthogonal Handles for Library Production

DEFF Research Database (Denmark)

Flagstad, Thomas; Azevedo, Carlos M. G.; Min, Geanna

2018-01-01

A new effective strategy for the synthesis of sp3‐rich small molecules for library production is presented. The key steps to generate complexity highlight Petasis 3‐component reaction followed by an intramolecular Diels‐Alder and cyclization to generate a densely enriched tricyclic or tetracyclic...

Estimation of dimensions and orientation of multiple riverine dune generations using spectral moments

Science.gov (United States)

Lisimenka, Aliaksandr; Kubicki, Adam

2017-02-01

A new spectral analysis technique is proposed for rhythmic bedform quantification, based on the 2D Fourier transform involving the calculation of a set of low-order spectral moments. The approach provides a tool for efficient quantification of bedform length and height as well as spatial crest-line alignment. Contrary to the conventional method, it not only describes the most energetic component of an undulating seabed surface but also retrieves information on its secondary structure without application of any band-pass filter of which the upper and lower cut-off frequencies are a priori unknown. Validation is based on bathymetric data collected in the main Vistula River mouth area (Przekop Wisły), Poland. This revealed two generations (distinct groups) of dunes which are migrating seawards along distinct paths, probably related to the hydrological regime of the river. The data enable the identification of dune divergence and convergence zones. The approach proved successful in the parameterisation of topographic roughness, an essential aspect in numerical modelling studies.

Broadband light generation at ~1300 nm through spectrally recoiled solitons and dispersive waves

DEFF Research Database (Denmark)

Falk, Peter Andreas; Frosz, Michael Henoch; Bang, Ole

2008-01-01

We experimentally study the generation of broadband light at ~1300 nm from an 810 nm Ti:sapphire femtosecond pump laser. We use two photonic crystal fibers with a second infrared zero-dispersion wavelength (λZ2) and compare the efficiency of two schemes: in one fiber λZ2=1400 nm and the light...... at 1300 nm is composed of spectrally recoiled solitons; in the other fiber λZ2=1200 nm and the light at 1300 nm is composed of dispersive waves....

High-throughput expression of animal venom toxins in Escherichia coli to generate a large library of oxidized disulphide-reticulated peptides for drug discovery.

Science.gov (United States)

Turchetto, Jeremy; Sequeira, Ana Filipa; Ramond, Laurie; Peysson, Fanny; Brás, Joana L A; Saez, Natalie J; Duhoo, Yoan; Blémont, Marilyne; Guerreiro, Catarina I P D; Quinton, Loic; De Pauw, Edwin; Gilles, Nicolas; Darbon, Hervé; Fontes, Carlos M G A; Vincentelli, Renaud

2017-01-17

Animal venoms are complex molecular cocktails containing a wide range of biologically active disulphide-reticulated peptides that target, with high selectivity and efficacy, a variety of membrane receptors. Disulphide-reticulated peptides have evolved to display improved specificity, low immunogenicity and to show much higher resistance to degradation than linear peptides. These properties make venom peptides attractive candidates for drug development. However, recombinant expression of reticulated peptides containing disulphide bonds is challenging, especially when associated with the production of large libraries of bioactive molecules for drug screening. To date, as an alternative to artificial synthetic chemical libraries, no comprehensive recombinant libraries of natural venom peptides are accessible for high-throughput screening to identify novel therapeutics. In the accompanying paper an efficient system for the expression and purification of oxidized disulphide-reticulated venom peptides in Escherichia coli is described. Here we report the development of a high-throughput automated platform, that could be adapted to the production of other families, to generate the largest ever library of recombinant venom peptides. The peptides were produced in the periplasm of E. coli using redox-active DsbC as a fusion tag, thus allowing the efficient formation of correctly folded disulphide bridges. TEV protease was used to remove fusion tags and recover the animal venom peptides in the native state. Globally, within nine months, out of a total of 4992 synthetic genes encoding a representative diversity of venom peptides, a library containing 2736 recombinant disulphide-reticulated peptides was generated. The data revealed that the animal venom peptides produced in the bacterial host were natively folded and, thus, are putatively biologically active. Overall this study reveals that high-throughput expression of animal venom peptides in E. coli can generate large

Public library consumer health information pilot project: results of a National Library of Medicine evaluation.

Science.gov (United States)

Wood, F B; Lyon, B; Schell, M B; Kitendaugh, P; Cid, V H; Siegel, E R

2000-10-01

In October 1998, the National Library of Medicine (NLM) launched a pilot project to learn about the role of public libraries in providing health information to the public and to generate information that would assist NLM and the National Network of Libraries of Medicine (NN/LM) in learning how best to work with public libraries in the future. Three regional medical libraries (RMLs), eight resource libraries, and forty-one public libraries or library systems from nine states and the District of Columbia were selected for participation. The pilot project included an evaluation component that was carried out in parallel with project implementation. The evaluation ran through September 1999. The results of the evaluation indicated that participating public librarians were enthusiastic about the training and information materials provided as part of the project and that many public libraries used the materials and conducted their own outreach to local communities and groups. Most libraries applied the modest funds to purchase additional Internet-accessible computers and/or upgrade their health-reference materials. However, few of the participating public libraries had health information centers (although health information was perceived as a top-ten or top-five topic of interest to patrons). Also, the project generated only minimal usage of NLM's consumer health database, known as MEDLINEplus, from the premises of the monitored libraries (patron usage from home or office locations was not tracked). The evaluation results suggested a balanced follow-up by NLM and the NN/LM, with a few carefully selected national activities, complemented by a package of targeted activities that, as of January 2000, are being planned, developed, or implemented. The results also highlighted the importance of building an evaluation component into projects like this one from the outset, to assure that objectives were met and that evaluative information was available on a timely basis, as was

Advanced Neutron Source Cross Section Libraries (ANSL-V): ENDF/B-V based multigroup cross-section libraries for advanced neutron source (ANS) reactor studies

International Nuclear Information System (INIS)

Ford, W.E. III; Arwood, J.W.; Greene, N.M.; Moses, D.L.; Petrie, L.M.; Primm, R.T. III; Slater, C.O.; Westfall, R.M.; Wright, R.Q.

1990-09-01

Pseudo-problem-independent, multigroup cross-section libraries were generated to support Advanced Neutron Source (ANS) Reactor design studies. The ANS is a proposed reactor which would be fueled with highly enriched uranium and cooled with heavy water. The libraries, designated ANSL-V (Advanced Neutron Source Cross Section Libraries based on ENDF/B-V), are data bases in AMPX master format for subsequent generation of problem-dependent cross-sections for use with codes such as KENO, ANISN, XSDRNPM, VENTURE, DOT, DORT, TORT, and MORSE. Included in ANSL-V are 99-group and 39-group neutron, 39-neutron-group 44-gamma-ray-group secondary gamma-ray production (SGRP), 44-group gamma-ray interaction (GRI), and coupled, 39-neutron group 44-gamma-ray group (CNG) cross-section libraries. The neutron and SGRP libraries were generated primarily from ENDF/B-V data; the GRI library was generated from DLC-99/HUGO data, which is recognized as the ENDF/B-V photon interaction data. Modules from the AMPX and NJOY systems were used to process the multigroup data. Validity of selected data from the fine- and broad-group neutron libraries was satisfactorily tested in performance parameter calculations

Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

Science.gov (United States)

Marine, Rachel; Polson, Shawn W; Ravel, Jacques; Hatfull, Graham; Russell, Daniel; Sullivan, Matthew; Syed, Fraz; Dumas, Michael; Wommack, K Eric

2011-11-01

Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.

Budgeting for efficient school library services in Nigeria: Proposal for ...

African Journals Online (AJOL)

Varioussources of generating income for school libraries were also discussed and they include internally generated revenue and external sources which include over due library charges, P TA, Library Development Levy (LDL), schoolfees as well as donor agencies. To ensure adequate funding by the management, school ...

CitEST libraries

Directory of Open Access Journals (Sweden)

Maria Luísa P. Natividade Targon

2007-01-01

Full Text Available In order to obtain a better understanding of what is citrus, 33 cDNA libraries were constructed from different citrus species and genera. Total RNA was extracted from fruits, leaves, flowers, bark, seeds and roots, and subjected or not to different biotic and abiotic stresses (pathogens and drought and at several developmental stages. To identify putative promoter sequences, as well as molecular markers that could be useful for breeding programs, one shotgun library was prepared from sweet orange (Citrus sinensis var. Olimpia. In addition, EST libraries were also constructed for a citrus pathogen, the oomycete Phythophthora parasitica in either virulent or avirulent form. A total of 286,559 cDNA clones from citrus were sequenced from their 5’ end, generating 242,790 valid reads of citrus. A total of 9,504 sequences were produced in the shotgun library and the valid reads were assembled using CAP3. In this procedure, we obtained 1,131 contigs and 4,083 singletons. A total of 19,200 cDNA clones from P. parasitica were sequenced, resulting in 16,400 valid reads. The number of ESTs generated in this project is, to our knowledge, the largest citrus sequence database in the world.

Automation of library system: A study of John Harris library ...

African Journals Online (AJOL)

Information Technologist (The) ... and querying library records, maintains defaulting patrons overdue fines account while the OPAC empl oy ... The automated system generates reports necessary for an informed management decision making.

Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery.

Science.gov (United States)

Kiljunen, Saija; Pajunen, Maria I; Dilks, Kieran; Storf, Stefanie; Pohlschroder, Mechthild; Savilahti, Harri

2014-12-09

Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea.

MCNP4c JEFF-3.1 Based Libraries. Eccolib-Jeff-3.1 libraries; Les bibliotheques Eccolib-Jeff-3.1

Energy Technology Data Exchange (ETDEWEB)

Sublet, J.Ch

2006-07-01

Continuous-energy and multi-temperatures MCNP Ace types libraries, derived from the Joint European Fusion-Fission JEFF-3.1 evaluations, have been generated using the NJOY-99.111 processing code system. They include the continuous-energy neutron JEFF-3.1/General Purpose, JEFF-3.1/Activation-Dosimetry and thermal S({alpha},{beta}) JEFF-3.1/Thermal libraries and data tables. The processing steps and features are explained together with the Quality Assurance processes and records linked to the generation of such multipurpose libraries. (author)

Mineral Potential in India Using Airborne Visible/Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) Data

Science.gov (United States)

Oommen, T.; Chatterjee, S.

2017-12-01

NASA and the Indian Space Research Organization (ISRO) are generating Earth surface features data using Airborne Visible/Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) within 380 to 2500 nm spectral range. This research focuses on the utilization of such data to better understand the mineral potential in India and to demonstrate the application of spectral data in rock type discrimination and mapping for mineral exploration by using automated mapping techniques. The primary focus area of this research is the Hutti-Maski greenstone belt, located in Karnataka, India. The AVIRIS-NG data was integrated with field analyzed data (laboratory scaled compositional analysis, mineralogy, and spectral library) to characterize minerals and rock types. An expert system was developed to produce mineral maps from AVIRIS-NG data automatically. The ground truth data from the study areas was obtained from the existing literature and collaborators from India. The Bayesian spectral unmixing algorithm was used in AVIRIS-NG data for endmember selection. The classification maps of the minerals and rock types were developed using support vector machine algorithm. The ground truth data was used to verify the mineral maps.

A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

Science.gov (United States)

Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C.; Quake, Stephen R.; Burkholder, William F.

2013-01-01

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation. PMID:23894273

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

Directory of Open Access Journals (Sweden)

Swee Jin Tan

Full Text Available Library preparation for next-generation DNA sequencing (NGS remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

Automated recycling of chemistry for virtual screening and library design.

Science.gov (United States)

Vainio, Mikko J; Kogej, Thierry; Raubacher, Florian

2012-07-23

An early stage drug discovery project needs to identify a number of chemically diverse and attractive compounds. These hit compounds are typically found through high-throughput screening campaigns. The diversity of the chemical libraries used in screening is therefore important. In this study, we describe a virtual high-throughput screening system called Virtual Library. The system automatically "recycles" validated synthetic protocols and available starting materials to generate a large number of virtual compound libraries, and allows for fast searches in the generated libraries using a 2D fingerprint based screening method. Virtual Library links the returned virtual hit compounds back to experimental protocols to quickly assess the synthetic accessibility of the hits. The system can be used as an idea generator for library design to enrich the screening collection and to explore the structure-activity landscape around a specific active compound.

Extending Supernova Spectral Templates for Next Generation Space Telescope Observations

Science.gov (United States)

Roberts-Pierel, Justin; Rodney, Steven A.; Steven Rodney

2018-01-01

Widely used empirical supernova (SN) Spectral Energy Distributions (SEDs) have not historically extended meaningfully into the ultraviolet (UV), or the infrared (IR). However, both are critical for current and future aspects of SN research including UV spectra as probes of poorly understood SN Ia physical properties, and expanding our view of the universe with high-redshift James Webb Space Telescope (JWST) IR observations. We therefore present a comprehensive set of SN SED templates that have been extended into the UV and IR, as well as an open-source software package written in Python that enables a user to generate their own extrapolated SEDs. We have taken a sampling of core-collapse (CC) and Type Ia SNe to get a time-dependent distribution of UV and IR colors (U-B,r’-[JHK]), and then generated color curves are used to extrapolate SEDs into the UV and IR. The SED extrapolation process is now easily duplicated using a user’s own data and parameters via our open-source Python package: SNSEDextend. This work develops the tools necessary to explore the JWST’s ability to discriminate between CC and Type Ia SNe, as well as provides a repository of SN SEDs that will be invaluable to future JWST and WFIRST SN studies.

Identity of a brand new library

KAUST Repository

Vijayakumar, J.K.

2017-01-01

King Abdullah University of Science and Technology (KAUST) Library in Saudi Arabia aspires to be one of the great new-generation libraries in the field of scientific research. Its services and systems support a digitally born collection, 97

Accurate, fully-automated NMR spectral profiling for metabolomics.

Directory of Open Access Journals (Sweden)

Siamak Ravanbakhsh

Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

Extensible numerical library in JAVA

International Nuclear Information System (INIS)

Aso, T.; Okazawa, H.; Takashimizu, N.

2001-01-01

The authors present the current status of the project for developing the numerical library in JAVA. The authors have presented how object-oriented techniques improve usage and also development of numerical libraries compared with the conventional way at previous conference. The authors need many functions for data analysis which is not provided within JAVA language, for example, good random number generators, special functions and so on. Authors' development strategy is focused on easiness of implementation and adding new features by users themselves not only by developers. In HPC field, there are other focus efforts to develop numerical libraries in JAVA. However, their focus is on the performance of execution, not easiness of extension. Following the strategy, the authors have designed and implemented more classes for random number generators and so on

COMPETENCES OF THE LIBRARY SPECIALIST OF NEW GENERATION IN THE CONTEXT OF MARKETING COMMUNICATIONS DEVELOPMENT

Directory of Open Access Journals (Sweden)

Т. М. Костирко

2017-10-01

Full Text Available Recently, there are dynamic changes in the activities of university libraries. It requires an appropriate response in the university library professionals. The study «Competencies module library and information professional future» was conducted by specialists of Library Marketing, innovation and technical work Objective: Updating and visualization of data on «Competencies module library and information professional future». Objectives: To conduct the survey and analyze the knowledge, skills of Mykolaiv university libraries experts in the modernization of research and information activities of modern libraries. Members: 100 professionals of six Mykolaiv university libraries of methodical association. Methodology – closed questionnaire. Question was formed capable of meeting requirements for the competence of information professionals (librarians, scientists, teachers of library science, information science and presented by global Special Libraries Association (SLA, the document «Competencies for information Professionals», which was adopted in April 2016. Conclusions: The results of complex sociological research «Competences module library and information professional future» allow: • get an objective picture of the attitude of library professionals to changes in the university libraries • determine the level of information culture of Mykolaiv university libraries specialists; • to adjust plan of in-plant training in university libraries of the city.

ENDF/B-VII.0: Next Generation Evaluated Nuclear Data Library for Nuclear Science and Technology

Energy Technology Data Exchange (ETDEWEB)

Chadwick, M B; Oblozinsky, P; Herman, M; Greene, N M; McKnight, R D; Smith, D L; Young, P G; MacFarlane, R E; Hale, G M; Haight, R C; Frankle, S; Kahler, A C; Kawano, T; Little, R C; Madland, D G; Moller, P; Mosteller, R; Page, P; Talou, P; Trellue, H; White, M; Wilson, W B; Arcilla, R; Dunford, C L; Mughabghab, S F; Pritychenko, B; Rochman, D; Sonzogni, A A; Lubitz, C; Trumbull, T H; Weinman, J; Brown, D; Cullen, D E; Heinrichs, D; McNabb, D; Derrien, H; Dunn, M; Larson, N M; Leal, L C; Carlson, A D; Block, R C; Briggs, B; Cheng, E; Huria, H; Kozier, K; Courcelle, A; Pronyaev, V; der Marck, S

2006-10-02

We describe the next generation general purpose Evaluated Nuclear Data File, ENDF/B-VII.0, of recommended nuclear data for advanced nuclear science and technology applications. The library, released by the U.S. Cross Section Evaluation Working Group (CSEWG) in December 2006, contains data primarily for reactions with incident neutrons, protons, and photons on almost 400 isotopes. The new evaluations are based on both experimental data and nuclear reaction theory predictions. The principal advances over the previous ENDF/B-VI library are the following: (1) New cross sections for U, Pu, Th, Np and Am actinide isotopes, with improved performance in integral validation criticality and neutron transmission benchmark tests; (2) More precise standard cross sections for neutron reactions on H, {sup 6}Li, {sup 10}B, Au and for {sup 235,238}U fission, developed by a collaboration with the IAEA and the OECD/NEA Working Party on Evaluation Cooperation (WPEC); (3) Improved thermal neutron scattering; (4) An extensive set of neutron cross sections on fission products developed through a WPEC collaboration; (5) A large suite of photonuclear reactions; (6) Extension of many neutron- and proton-induced reactions up to an energy of 150 MeV; (7) Many new light nucleus neutron and proton reactions; (8) Post-fission beta-delayed photon decay spectra; (9) New radioactive decay data; and (10) New methods developed to provide uncertainties and covariances, together with covariance evaluations for some sample cases. The paper provides an overview of this library, consisting of 14 sublibraries in the same, ENDF-6 format, as the earlier ENDF/B-VI library. We describe each of the 14 sublibraries, focusing on neutron reactions. Extensive validation, using radiation transport codes to simulate measured critical assemblies, show major improvements: (a) The long-standing underprediction of low enriched U thermal assemblies is removed; (b) The {sup 238}U, {sup 208}Pb, and {sup 9}Be reflector

Generation of a new spectral format, the lifetime synchronous spectrum (LiSS), using phase-resolved fluorescence spectroscopy

International Nuclear Information System (INIS)

Shaver, J.M.; McGown, L.B.

1994-01-01

A new fluorescence spectral format is introduced in which fluorescence lifetime is shown as a function of synchronously scanned wavelength to generate a Lifetime Synchronous Spectrum (LiSS). Lifetimes are determined in the frequency domain with the use of Phase-Resolved Fluorescence Spectroscopy (PRFS) to obtain the phase of the fluorescence signal. Theory and construction of the LiSS are presented and experimental results are shown for solutions of single components and simple binary and ternary mixtures. These results show how the lifetime information in the LiSS augments the steady-state intensity information of a standard synchronous spectrum, providing unique information for identification of components and resolution of overlapping spectral peaks. The LiSS technique takes advantage of noise reduction inherent in the extraction of lifetime from PRFS in addition to standard spectral smoothing techniques. The precision of phase determination through PRFS is found to be comparable to that of direct phase measurements at normal fluorescence intensities and superior for low-intensity signals

Generation, Validation, and Application of Abundance Map Reference Data for Spectral Unmixing

Science.gov (United States)

Williams, McKay D.

Reference data ("ground truth") maps traditionally have been used to assess the accuracy of imaging spectrometer classification algorithms. However, these reference data can be prohibitively expensive to produce, often do not include sub-pixel abundance estimates necessary to assess spectral unmixing algorithms, and lack published validation reports. Our research proposes methodologies to efficiently generate, validate, and apply abundance map reference data (AMRD) to airborne remote sensing scenes. We generated scene-wide AMRD for three different remote sensing scenes using our remotely sensed reference data (RSRD) technique, which spatially aggregates unmixing results from fine scale imagery (e.g., 1-m Ground Sample Distance (GSD)) to co-located coarse scale imagery (e.g., 10-m GSD or larger). We validated the accuracy of this methodology by estimating AMRD in 51 randomly-selected 10 m x 10 m plots, using seven independent methods and observers, including field surveys by two observers, imagery analysis by two observers, and RSRD using three algorithms. Results indicated statistically-significant differences between all versions of AMRD, suggesting that all forms of reference data need to be validated. Given these significant differences between the independent versions of AMRD, we proposed that the mean of all (MOA) versions of reference data for each plot and class were most likely to represent true abundances. We then compared each version of AMRD to MOA. Best case accuracy was achieved by a version of imagery analysis, which had a mean coverage area error of 2.0%, with a standard deviation of 5.6%. One of the RSRD algorithms was nearly as accurate, achieving a mean error of 3.0%, with a standard deviation of 6.3%, showing the potential of RSRD-based AMRD generation. Application of validated AMRD to specific coarse scale imagery involved three main parts: 1) spatial alignment of coarse and fine scale imagery, 2) aggregation of fine scale abundances to produce

Mixture-based combinatorial libraries from small individual peptide libraries: a case study on α1-antitrypsin deficiency.

Science.gov (United States)

Chang, Yi-Pin; Chu, Yen-Ho

2014-05-16

The design, synthesis and screening of diversity-oriented peptide libraries using a "libraries from libraries" strategy for the development of inhibitors of α1-antitrypsin deficiency are described. The major buttress of the biochemical approach presented here is the use of well-established solid-phase split-and-mix method for the generation of mixture-based libraries. The combinatorial technique iterative deconvolution was employed for library screening. While molecular diversity is the general consideration of combinatorial libraries, exquisite design through systematic screening of small individual libraries is a prerequisite for effective library screening and can avoid potential problems in some cases. This review will also illustrate how large peptide libraries were designed, as well as how a conformation-sensitive assay was developed based on the mechanism of the conformational disease. Finally, the combinatorially selected peptide inhibitor capable of blocking abnormal protein aggregation will be characterized by biophysical, cellular and computational methods.

Using a digital multimeter to capture spectral information generated by a spectrophotometer broadcast / atomic absorption

International Nuclear Information System (INIS)

Villalobos Chaves, Alberto E.

2006-01-01

Spectral analysis capability of the information generated by a spectrophotometer broadcast / shimadzu AA 640-13 atomic absorption has increased, through the capture of data, using a digital multimeter as the interface between the spectrophotometer and a computer. To facilitate the identification of analytes was created Chromulan format files for the 99 chemical elements reported in the literature, and covering the region between 200 nm and 900 nm, the subject of this study. (author) [es

Comparison of neutron fluxes obtained by 2-D and 3-D geometry with different shielding libraries in biological shield of the TRIGA MARK II reactor

International Nuclear Information System (INIS)

Bozic, M.; Zagar, T.; Ravnik, M.

2003-01-01

Neutron fluxes in different spatial locations in biological shield are obtained with TORT code (TORT-Three Dimensional Oak Ridge Discrete Ordinates Neutron/Photon Transport Code). Libraries used with TORT code were BUGLE-96 library (coupled library with 47 neutron groups and 20 gamma groups) and VITAMIN-B6 library (coupled library with 199 neutron groups and 42 gamma groups). BUGLE-96 library is derived from VITAMIN-B6 library. 2-D and 3-D models for homogeneous type of problem (without inserted beam port 4) and problem with asymmetry (non-homogeneous problem; inserted beam port 4, filled with different materials) were of interest for neutron flux calculation. The main purpose is to verify the possibility for using 2-D approximation model instead of large 3-D model in some calculations. Another purpose of this paper was to compare neutron spectral constants obtained from neutron fluxes (3-D model) determined with smaller BUGLE-96 library with new constants obtained from fluxes calculated with bigger VITAMIN-B6 library. These neutron spectral constants are used in isotopic calculation with SCALE code package (ORIGEN-S). In past only neutron spectral constants determined by neutron fluxes from BUGLE-96 library were used. Experimental results used for isotopic composition comparison are available from irradiation experiment with selected type of concrete and other materials in beam port 4 (irradiation channel 4) in TRIGA Mark II reactor. These experimental results were used as a benchmark in this paper. (author)

Bandwidth scalable, coherent transmitter based on the parallel synthesis of multiple spectral slices using optical arbitrary waveform generation.

Science.gov (United States)

Geisler, David J; Fontaine, Nicolas K; Scott, Ryan P; He, Tingting; Paraschis, Loukas; Gerstel, Ori; Heritage, Jonathan P; Yoo, S J B

2011-04-25

We demonstrate an optical transmitter based on dynamic optical arbitrary waveform generation (OAWG) which is capable of creating high-bandwidth (THz) data waveforms in any modulation format using the parallel synthesis of multiple coherent spectral slices. As an initial demonstration, the transmitter uses only 5.5 GHz of electrical bandwidth and two 10-GHz-wide spectral slices to create 100-ns duration, 20-GHz optical waveforms in various modulation formats including differential phase-shift keying (DPSK), quaternary phase-shift keying (QPSK), and eight phase-shift keying (8PSK) with only changes in software. The experimentally generated waveforms showed clear eye openings and separated constellation points when measured using a real-time digital coherent receiver. Bit-error-rate (BER) performance analysis resulted in a BER < 9.8 × 10(-6) for DPSK and QPSK waveforms. Additionally, we experimentally demonstrate three-slice, 4-ns long waveforms that highlight the bandwidth scalable nature of the optical transmitter. The various generated waveforms show that the key transmitter properties (i.e., packet length, modulation format, data rate, and modulation filter shape) are software definable, and that the optical transmitter is capable of acting as a flexible bandwidth transmitter.

Spectral analysis of coolant activity from a commercial nuclear generating station

International Nuclear Information System (INIS)

Swann, J.D.; Lewis, B.J.; Ip, M.

2008-01-01

In support of the development of a real-time on-line fuel failure monitoring system for the CANDU reactor, actual gamma spectroscopy data files from the gaseous fission product (GFP) monitoring system were acquired from almost four years of operation at a commercial Nuclear Generating Station (NGS). Several spectral analysis techniques were used to process the data files. Radioisotopic activity from the plant information (PI) system was compared to an in-house C++ code that was used to determine the photopeak area and to a separate analysis with commercial software from Canberra-Aptec. These various techniques provided for a calculation of the coolant activity concentration of the noble gas and iodine species in the primary heat transport system. These data were then used to benchmark the Visual DETECT code, a user friendly software tool which can be used to characterize the defective fuel state based on a coolant activity analysis. Acceptable agreement was found with the spectral techniques when compared to the known defective bundle history at the commercial reactor. A more generalized method of assessing the fission product release data was also considered with the development of a pre-processor to evaluate the radioisotopic release rate from mass balance considerations. The release rate provided a more efficient means to characterize the occurrence of a defect and was consistent with the actual defect situation at the power plant as determined from in-bay examination of discharged fuel bundles. (author)

Development of the CANDU 66-group SN transport library

International Nuclear Information System (INIS)

Tsang, K.T.

2001-01-01

The design of the shield configuration around a nuclear reactor is strongly dependent on the neutron and photon spatial and energy distributions. The nuclear heat deposition and material damage in and surrounding the reactor core are also a function of the neutron and photon distributions. Therefore, to ensure a suitable configuration of materials for shielding or heat transfer, an accurate calculation of the particle fluxes in the reactor systems is essential. The CANDU 66-group library was developed to update the cross sections that are needed to assess the performance of CANDU bulk shields. Since about 1980, shielding analysts at Atomic Energy of Canada Limited (AECL) and Ontario Power Generation Inc. (OPGI) have been using a 38-group CANDU-specific library to perform S N transport calculations. In 1994, a new CANDU 67-group cross-section library was developed. The 67-group cross-section library was developed to provide radiation-physics analysts with up-to-date nuclear data to correct deficiencies with documentation of the old library. Although there were improvements over the 38-group library, initial use showed there were some deficiencies in the 67-group library. To correct these deficiencies, the CANDU 66-group S N transport cross-section library was developed. The 66-group library is based on the 241-group cross-section library VITAMIN-B6. Collapsing and weighting of the 241-group cross sections into 66 groups were performed using the modular code system SCALE 4.4. This paper describes how the modules in the SCALE system were applied to generate the 66-group library. The CANDU 66-group library includes both core-weighted and lattice-weighted cross sections of 235 U, 238 U, and 239 Pu with, and without, delayed fission-product photons. In addition, the 66-group library contains more response functions than did the 67-group library. Finally, the CANDU 66-group library has been validated against one-dimensional benchmark problems. The results generated with

Spectral beam combining of diode lasers with high efficiency

DEFF Research Database (Denmark)

Müller, André; Vijayakumar, Deepak; Jensen, Ole Bjarlin

2012-01-01

Based on spectral beam combining we obtain 16 W of output power, combining two 1063 nm DBR-tapered diode lasers. The spectral separation within the combined beam can be used for subsequent sum-frequency generation.......Based on spectral beam combining we obtain 16 W of output power, combining two 1063 nm DBR-tapered diode lasers. The spectral separation within the combined beam can be used for subsequent sum-frequency generation....

MacroEvoLution: A New Method for the Rapid Generation of Novel Scaffold-Diverse Macrocyclic Libraries.

Science.gov (United States)

Saupe, Jörn; Kunz, Oliver; Haustedt, Lars Ole; Jakupovic, Sven; Mang, Christian

2017-09-04

Macrocycles are a structural class bearing great promise for future challenges in medicinal chemistry. Nevertheless, there are few flexible approaches for the rapid generation of structurally diverse macrocyclic compound collections. Here, an efficient method for the generation of novel macrocyclic peptide-based scaffolds is reported. The process, named here as "MacroEvoLution", is based on a cyclization screening approach that gives reliable access to novel macrocyclic architectures. Classification of building blocks into specific pools ensures that scaffolds with orthogonally addressable functionalities are generated, which can easily be used for the generation of structurally diverse compound libraries. The method grants rapid access to novel scaffolds with scalable synthesis (multi gram scale) and the introduction of further diversity at a late stage. Despite being developed for peptidic systems, the approach can easily be extended for the synthesis of systems with a decreased peptidic character. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Collection and spectral control of high-order harmonics generated with a 50 W high-repetition rate Ytterbium femtosecond laser system

International Nuclear Information System (INIS)

Cabasse, A; Hazera, Ch; Quintard, L; Cormier, E; Petit, S; Constant, E

2016-01-01

We generate high-order harmonics with a 50 W, Yb femtosecond fiber laser system operating at 100 kHz in a tight focusing configuration. We achieve a high photon flux even with pulses longer than 500 fs. We collect the diverging extreme ultraviolet (XUV) harmonic beam in a 35 mrad wide solid angle by using a spectrometer designed to handle the high thermal load under vacuum and refocus the XUV beam onto a detector where the beam is characterised or can alternatively be used for experiments. This setup is designed for a 50 eV XUV bandwidth and offers the possibility to perform XUV-IR pump probe experiments with both temporal and spectral resolution. The high-order harmonics were generated and optimized at 100 kHz by using several gas target geometries (a gas jet and a semi-infinite gas cell) and several gases (argon, krypton, xenon) that provide XUV beams with different characteristics. After the spectrometer and for high-order harmonic generation (HHG) in xenon, we detect more than 4 × 10 10 photons per second over four harmonics, that is a useful XUV power on target of 0.1 μW. This corresponds to the emission of more than 1 μW per harmonic at the source and we achieved a similar flux with both the semi-infinite cell and the jet. In addition, we observe a strong spectral selectivity when generating harmonics in a semi-infinite gas cell as few harmonics clearly dominate the neighbouring harmonics. We attribute this spectral selectivity to phase matching effects. (paper)

SpectralNET – an application for spectral graph analysis and visualization

Directory of Open Access Journals (Sweden)

Schreiber Stuart L

2005-10-01

Full Text Available Abstract Background Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices and interactions (edges that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Results Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors. Conclusion SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from http://chembank.broad.harvard.edu/resources/. Source code is

Architectural Optimization of Digital Libraries

Science.gov (United States)

Biser, Aileen O.

1998-01-01

This work investigates performance and scaling issues relevant to large scale distributed digital libraries. Presently, performance and scaling studies focus on specific implementations of production or prototype digital libraries. Although useful information is gained to aid these designers and other researchers with insights to performance and scaling issues, the broader issues relevant to very large scale distributed libraries are not addressed. Specifically, no current studies look at the extreme or worst case possibilities in digital library implementations. A survey of digital library research issues is presented. Scaling and performance issues are mentioned frequently in the digital library literature but are generally not the focus of much of the current research. In this thesis a model for a Generic Distributed Digital Library (GDDL) and nine cases of typical user activities are defined. This model is used to facilitate some basic analysis of scaling issues. Specifically, the calculation of Internet traffic generated for different configurations of the study parameters and an estimate of the future bandwidth needed for a large scale distributed digital library implementation. This analysis demonstrates the potential impact a future distributed digital library implementation would have on the Internet traffic load and raises questions concerning the architecture decisions being made for future distributed digital library designs.

Procedure for normalization of cDNA libraries

Science.gov (United States)

Bonaldo, Maria DeFatima; Soares, Marcelo Bento

1997-01-01

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

Up-date of the BCG code library

International Nuclear Information System (INIS)

Caldeira, A.D.; Garcia, R.D.M.

1990-01-01

Procedures for generating an up-date material library for the BCG code were established. A new library was generated by processing ENDF/B-IV data with the 89-1 version of the LINEAR, RECENT and SIGMA1 programs. The effect of library change in the neutron spectrum and effective multiplication factor of a fast reactor cell was analized. During the course of this study, an error was detected in the BCG code. Although localized in a narrow energy range, the discrepancies in neutron spectrum caused by the error were large enough to yield a difference of about 1% in the effective multiplication factor of the test cell. (author)

Parallel Programming Application to Matrix Algebra in the Spectral Method for Control Systems Analysis, Synthesis and Identification

Directory of Open Access Journals (Sweden)

V. Yu. Kleshnin

2016-01-01

Full Text Available The article describes the matrix algebra libraries based on the modern technologies of parallel programming for the Spectrum software, which can use a spectral method (in the spectral form of mathematical description to analyse, synthesise and identify deterministic and stochastic dynamical systems. The developed matrix algebra libraries use the following technologies for the GPUs: OmniThreadLibrary, OpenMP, Intel Threading Building Blocks, Intel Cilk Plus for CPUs nVidia CUDA, OpenCL, and Microsoft Accelerated Massive Parallelism.The developed libraries support matrices with real elements (single and double precision. The matrix dimensions are limited by 32-bit or 64-bit memory model and computer configuration. These libraries are general-purpose and can be used not only for the Spectrum software. They can also find application in the other projects where there is a need to perform operations with large matrices.The article provides a comparative analysis of the libraries developed for various matrix operations (addition, subtraction, scalar multiplication, multiplication, powers of matrices, tensor multiplication, transpose, inverse matrix, finding a solution of the system of linear equations through the numerical experiments using different CPU and GPU. The article contains sample programs and performance test results for matrix multiplication, which requires most of all computational resources in regard to the other operations.

Novel non-viral vectors for gene delivery: synthesis of a second-generation library of mono-functionalized poly-(guanidinium)amines and their introduction into cationic lipids.

Science.gov (United States)

Byk, G; Soto, J; Mattler, C; Frederic, M; Scherman, D

1998-01-01

The development of new gene delivery technologies is a prerequisite towards gene therapy clinical trials. Because gene delivery mediated by viral vectors remains of limited scope due to immunological and propagation risks, the development of new non-viral gene delivery systems is of crucial importance. We have synthesized a secondary library of mono-functionalized poly-(guanidinium)amines generated from a library of mono-functionalized polyamines applying the concept of "libraries from libraries." The method allows a quick and easy access to mono-functionalized geometrically varied poly-(guanidinium)amines. The new building blocks were introduced into cationic lipids to obtain novel poly-(guanidinium)amine lipids, which are potential DNA vectors for gene delivery. Copyright 1998 John Wiley & Sons, Inc.

Using a spatial and tabular database to generate statistics from terrain and spectral data for soil surveys

Science.gov (United States)

Horvath , E.A.; Fosnight, E.A.; Klingebiel, A.A.; Moore, D.G.; Stone, J.E.; Reybold, W.U.; Petersen, G.W.

1987-01-01

A methodology has been developed to create a spatial database by referencing digital elevation, Landsat multispectral scanner data, and digitized soil premap delineations of a number of adjacent 7.5-min quadrangle areas to a 30-m Universal Transverse Mercator projection. Slope and aspect transformations are calculated from elevation data and grouped according to field office specifications. An unsupervised classification is performed on a brightness and greenness transformation of the spectral data. The resulting spectral, slope, and aspect maps of each of the 7.5-min quadrangle areas are then plotted and submitted to the field office to be incorporated into the soil premapping stages of a soil survey. A tabular database is created from spatial data by generating descriptive statistics for each data layer within each soil premap delineation. The tabular data base is then entered into a data base management system to be accessed by the field office personnel during the soil survey and to be used for subsequent resource management decisions.Large amounts of data are collected and archived during resource inventories for public land management. Often these data are stored as stacks of maps or folders in a file system in someone's office, with the maps in a variety of formats, scales, and with various standards of accuracy depending on their purpose. This system of information storage and retrieval is cumbersome at best when several categories of information are needed simultaneously for analysis or as input to resource management models. Computers now provide the resource scientist with the opportunity to design increasingly complex models that require even more categories of resource-related information, thus compounding the problem.Recently there has been much emphasis on the use of geographic information systems (GIS) as an alternative method for map data archives and as a resource management tool. Considerable effort has been devoted to the generation of tabular

Nuclide radioactive decay data uncertainties library

International Nuclear Information System (INIS)

Barabanova, D S; Zherdev, G M

2017-01-01

The results of the developing the library of uncertainties of radioactive decay data in the ABBN data library format are described. Different evaluations of uncertainties were compared and their effects on the results of calculations of residual energy release were determined using the test problems and experiment. Tables were generated in the ABBN format with the data obtained on the basis of libraries in ENDF-6 format. 3821 isotopes from the ENDF/B-7 data library, 3852 isotopes from the JEFF-3.11 data library and 1264 isotopes from the JENDL-4.0 data library were processed. It was revealed that the differences in the evaluations accepted in different decay data libraries are not so big, although they sometimes exceed the uncertainties assigned to the data in the ENDF/B-7 and JEFF-3.11 libraries, which as a rule, they agree with each other. On the basis of developed method it is supposed to create a library of data uncertainties for radioactive decay within the constant data system in FSUE RFNC-VNIIEF with its further connection with CRYSTAL module. (paper)

Potential of VIS-NIR-SWIR Spectroscopy from the Chinese Soil Spectral Library for Assessment of Nitrogen Fertilization Rates in the Paddy-Rice Region, China

Directory of Open Access Journals (Sweden)

Shuo Li

2015-05-01

Full Text Available To meet growing food demand with limited land and reduced environmental impact, soil testing and formulated fertilization methods have been widely adopted around the world. However, conventional technology for investigating nitrogen fertilization rates (NFR is time consuming and expensive. Here, we evaluated the use of visible near-infrared shortwave-infrared (VIS-NIR-SWIR: 400–2500 nm spectroscopy for the assessment of NFR to provide necessary information for fast, cost-effective and precise fertilization rating. Over 2000 samples were collected from paddy-rice fields in 10 Chinese provinces; samples were added to the Chinese Soil Spectral Library (CSSL. Two kinds of modeling strategies for NFR, quantitative estimation of soil N prior to classification and qualitative by classification, were employed using partial least squares regression (PLSR, locally weighted regression (LWR, and support vector machine discriminant analogy (SVMDA. Overall, both LWR and SVMDA had moderate accuracies with Cohen’s kappa coefficients of 0.47 and 0.48, respectively, while PLSR had fair accuracy (0.37. We conclude that VIS-NIR-SWIR spectroscopy coupled with the CSSL appears to be a viable, rapid means for the assessment of NFR in paddy-rice soil. Based on qualitative classification of soil spectral data only, it is recommended that the SVMDA be adopted for rapid implementation.

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries*

Science.gov (United States)

Wu, Jemma X.; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P.

2016-01-01

The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. PMID:27161445

AER working group A on improvement extension and validation of parametrized few-group libraries for VVER-440 and VVER-1000

International Nuclear Information System (INIS)

Svarny, J.

1998-01-01

The AER Working Groups A and B held its sixth meeting at SKODA JS, Plzen in April 28 and 29, 1998. There were altogether 13 participants from 6 member organizations. The list of participants and the list of papers are attached. Main topics of the meeting were: A few-group cross-section library preparation methodology (standard few-group libraries, kinetics parameters, SPND signal interpretation parametrization) and its validation; Participation on intercomparisons of spectral codes (spectral codes benchmark); of kinetics parameters calculations (kinetics parameters benchmark). (author)

BUILDING A NEW GENERATION SCIENCE LIBRARY: THE KAUST STORY

KAUST Repository

Al Zahrani, Rashed; Branin, Joseph; Yu, Yi

2012-01-01

will describe the major characteristics in contemporary science research, education, and information management that guided the design of our library facility, technical infrastructure, and services. We will give concrete examples and evaluations of our

Automatic Generation of Agents using Reusable Soft Computing Code Libraries to develop Multi Agent System for Healthcare

OpenAIRE

Priti Srinivas Sajja

2015-01-01

This paper illustrates architecture for a multi agent system in healthcare domain. The architecture is generic and designed in form of multiple layers. One of the layers of the architecture contains many proactive, co-operative and intelligent agents such as resource management agent, query agent, pattern detection agent and patient management agent. Another layer of the architecture is a collection of libraries to auto-generate code for agents using soft computing techni...

Nuclear data libraries for gamma analysis programs, including special purpose libraries

International Nuclear Information System (INIS)

Westmeier, W.; Reus, U.; Siemon, K.; Westmeier, H.

2002-01-01

A complete set of gamma ray and other data relating to the decay of all known nuclides has been compiled from the literature and electronic sources. The data were critically reviewed, evaluated and the consistency was checked. The total catalogue is comprised of data-sets for 3841 nuclides and isomers with 106,355 gamma ray and 19,347 X ray entries. A subset of 1,627 nuclides with 32,456 gamma ray entries is extracted into a database, which provides the basis for the generation of nuclide libraries for the application in spectrometry programmes. The WINDOWS based program NUC M AN was developed which serves for the updating and editing of the database as well as the generation of task-specific user libraries for special purposes. The literature cut-off date for this catalogue is January 1, 1998. (author)

Construction of High-Quality Camel Immune Antibody Libraries.

Science.gov (United States)

Romão, Ema; Poignavent, Vianney; Vincke, Cécile; Ritzenthaler, Christophe; Muyldermans, Serge; Monsion, Baptiste

2018-01-01

Single-domain antibodies libraries of heavy-chain only immunoglobulins from camelids or shark are enriched for high-affinity antigen-specific binders by a short in vivo immunization. Thus, potent binders are readily retrieved from relatively small-sized libraries of 10 7 -10 8 individual transformants, mostly after phage display and panning on a purified target. However, the remaining drawback of this strategy arises from the need to generate a dedicated library, for nearly every envisaged target. Therefore, all the procedures that shorten and facilitate the construction of an immune library of best possible quality are definitely a step forward. In this chapter, we provide the protocol to generate a high-quality immune VHH library using the Golden Gate Cloning strategy employing an adapted phage display vector where a lethal ccdB gene has to be substituted by the VHH gene. With this procedure, the construction of the library can be shortened to less than a week starting from bleeding the animal. Our libraries exceed 10 8 individual transformants and close to 100% of the clones harbor a phage display vector having an insert with the length of a VHH gene. These libraries are also more economic to make than previous standard approaches using classical restriction enzymes and ligations. The quality of the Nanobodies that are retrieved from immune libraries obtained by Golden Gate Cloning is identical to those from immune libraries made according to the classical procedure.

ENDF/B-VII.0: Next Generation Evaluated Nuclear Data Library for Nuclear Science and Technology

International Nuclear Information System (INIS)

Chadwick, M.B.; Oblozinsky, P.; Herman, M.

2006-01-01

We describe the next generation general purpose Evaluated Nuclear Data File, ENDF/B-VII.0, of recommended nuclear data for advanced nuclear science and technology applications. The library, released by the U.S. Cross Section Evaluation Working Group (CSEWG) in December 2006, contains data primarily for reactions with incident neutrons, protons, and photons on almost 400 isotopes, based on experimental data and theory predictions. The principal advances over the previous ENDF/B-VI library are the following: (1) New cross sections for U, Pu, Th, Np and Am actinide isotopes, with improved performance in integral validation criticality and neutron transmission benchmark tests; (2) More precise standard cross sections for neutron reactions on H, 6 Li, 10 B, Au and for 235,238 U fission, developed by a collaboration with the IAEA and the OECD/NEA Working Party on Evaluation Cooperation (WPEC); (3) Improved thermal neutron scattering; (4) An extensive set of neutron cross sections on fission products developed through a WPEC collaboration; (5) A large suite of photonuclear reactions; (6) Extension of many neutron- and proton-induced evaluations up to 150 MeV; (7) Many new light nucleus neutron and proton reactions; (8) Post-fission beta-delayed photon decay spectra; (9) New radioactive decay data; (10) New methods for uncertainties and covariances, together with covariance evaluations for some sample cases; and (11) New actinide fission energy deposition. The paper provides an overview of this library, consisting of 14 sublibraries in the same ENDF-6 format as the earlier ENDF/B-VI library. We describe each of the 14 sublibraries, focusing on neutron reactions. Extensive validation, using radiation transport codes to simulate measured critical assemblies, show major improvements: (a) The long-standing underprediction of low enriched uranium thermal assemblies is removed; (b) The 238 U and 208 Pb reflector biases in fast systems are largely removed; (c) ENDF/B-VI.8 good

Construction of CRISPR Libraries for Functional Screening.

Science.gov (United States)

Carstens, Carsten P; Felts, Katherine A; Johns, Sarah E

2018-01-01

Identification of gene function has been aided by the ability to generate targeted gene knockouts or transcriptional repression using the CRISPR/CAS9 system. Using pooled libraries of guide RNA expression vectors that direct CAS9 to a specific genomic site allows identification of genes that are either enriched or depleted in response to a selection scheme, thus linking the affected gene to the chosen phenotype. The quality of the data generated by the screening is dependent on the quality of the guide RNA delivery library with regards to error rates and especially evenness of distribution of the guides. Here, we describe a method for constructing complex plasmid libraries based on pooled designed oligomers with high representation and tight distributions. The procedure allows construction of plasmid libraries of >60,000 members with a 95th/5th percentile ratio of less than 3.5.

DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

Science.gov (United States)

Franzini, Raphael M; Neri, Dario; Scheuermann, Jörg

2014-04-15

DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target

Generation of doublet spectral lines at self-seeded X-ray FELs

Energy Technology Data Exchange (ETDEWEB)

Geloni, Gianluca [European XFEL GmbH, Hamburg (Germany); Kocharyan, Vitali; Saldin, Evgeni [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2010-11-15

Self-seeding schemes, consisting of two undulators with a monochromator in between, aim to reduce the bandwidth of SASE X-ray FELs. We recently proposed to use a new method of monochromatization exploiting a single crystal in Braggtransmission geometry for self-seeding in the hard X-ray range. The obvious and technically possible extension is to use such kind of monochromator setup with two -or more- crystals arranged in a series to spectrally filter the SASE radiation at two -or more- closely-spaced wavelengths within the FEL gain band. This allows for the production of doublet- or multiplet-spectral lines. Applications exist over a broad range of hard X-ray wavelengths involving any process where there is a large change in cross section over a narrow wavelength range, as in multiple wavelength anomalous diffraction techniques (MAD). In this paper we consider the simultaneous operation of the LCLS hard X-ray FEL at two closely spaced wavelengths. We present simulation results for the LCLS baseline, and we show that this method can produce fully coherent radiation shared between two longitudinal modes. Mode spacing can be easily tuned within the FEL gain band, i.e. within 10 eV. An interesting aspect of the proposed scheme is a way of modulating the electron bunch at optical frequencies without a seed quantum laser. In fact, the XFEL output intensity contains an oscillating ''mode-beat'' component whose frequency is related to the frequency difference between the pair of longitudinal modes considered. Thus, at saturation one obtains FEL-induced modulations of energy loss and energy spread in the electron bunch at optical frequency. These modulations can be converted into density modulation at the same optical frequency with the help of a weak chicane installed behind the baseline undulator. Powerful coherent radiation can then be generated with the help of an optical transition radiation (OTR) station,which have important applications. In this paper we briefly

Generation of doublet spectral lines at self-seeded X-ray FELs

International Nuclear Information System (INIS)

Geloni, Gianluca; Kocharyan, Vitali; Saldin, Evgeni

2010-11-01

Self-seeding schemes, consisting of two undulators with a monochromator in between, aim to reduce the bandwidth of SASE X-ray FELs. We recently proposed to use a new method of monochromatization exploiting a single crystal in Braggtransmission geometry for self-seeding in the hard X-ray range. The obvious and technically possible extension is to use such kind of monochromator setup with two -or more- crystals arranged in a series to spectrally filter the SASE radiation at two -or more- closely-spaced wavelengths within the FEL gain band. This allows for the production of doublet- or multiplet-spectral lines. Applications exist over a broad range of hard X-ray wavelengths involving any process where there is a large change in cross section over a narrow wavelength range, as in multiple wavelength anomalous diffraction techniques (MAD). In this paper we consider the simultaneous operation of the LCLS hard X-ray FEL at two closely spaced wavelengths. We present simulation results for the LCLS baseline, and we show that this method can produce fully coherent radiation shared between two longitudinal modes. Mode spacing can be easily tuned within the FEL gain band, i.e. within 10 eV. An interesting aspect of the proposed scheme is a way of modulating the electron bunch at optical frequencies without a seed quantum laser. In fact, the XFEL output intensity contains an oscillating ''mode-beat'' component whose frequency is related to the frequency difference between the pair of longitudinal modes considered. Thus, at saturation one obtains FEL-induced modulations of energy loss and energy spread in the electron bunch at optical frequency. These modulations can be converted into density modulation at the same optical frequency with the help of a weak chicane installed behind the baseline undulator. Powerful coherent radiation can then be generated with the help of an optical transition radiation (OTR) station,which have important applications. In this paper we briefly

MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides

International Nuclear Information System (INIS)

Yang, Xu; Lazar, Iulia M

2009-01-01

The discovery of novel protein biomarkers is essential in the clinical setting to enable early disease diagnosis and increase survivability rates. To facilitate differential expression analysis and biomarker discovery, a variety of tandem mass spectrometry (MS/MS)-based protein profiling techniques have been developed. For achieving sensitive detection and accurate quantitation, targeted MS screening approaches, such as multiple reaction monitoring (MRM), have been implemented. MCF-7 breast cancer protein cellular extracts were analyzed by 2D-strong cation exchange (SCX)/reversed phase liquid chromatography (RPLC) separations interfaced to linear ion trap MS detection. MS data were interpreted with the Sequest-based Bioworks software (Thermo Electron). In-house developed Perl-scripts were used to calculate the spectral counts and the representative fragment ions for each peptide. In this work, we report on the generation of a library of 9,677 peptides (p < 0.001), representing ~1,572 proteins from human breast cancer cells, that can be used for MRM/MS-based biomarker screening studies. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum (p-value, DeltaM, Xcorr, DeltaCn, Sp, no. of matching a, b, y ions in the spectrum), the retention time, and the top 10 most intense product ions that correspond to a given peptide. Only proteins identified by at least two spectral counts are listed. The experimental distribution of protein frequencies, as a function of molecular weight, closely matched the theoretical distribution of proteins in the human proteome, as provided in the SwissProt database. The amino acid sequence coverage of the identified proteins ranged from 0.04% to 98.3%. The highest-abundance proteins in the cellular extract had a molecular weight (MW)<50,000. Preliminary experiments have

A library of IUE white dwarf spectra for stellar population analyses.

Science.gov (United States)

Bica, E.; Bonatto, C.; Giovannini, O.

1996-10-01

We present high Signal to Noise ratio IUE spectra of different classes of white dwarfs, to be used as templates for stellar population analyses in the ultraviolet region. We present average stellar parameters associated to each group. The library contains 6 groups for DA's, 2 for DO's and 5 for DB's. We also present equivalent widths of spectral features, and continuum measurements. We call attention to the spectral characteristics which are promising indicators of the presence of white dwarfs in the spectra of composite stellar populations.

Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library.

Science.gov (United States)

Lachaud, Laurence; Fernández-Arévalo, Anna; Normand, Anne-Cécile; Lami, Patrick; Nabet, Cécile; Donnadieu, Jean Luc; Piarroux, Martine; Djenad, Farid; Cassagne, Carole; Ravel, Christophe; Tebar, Silvia; Llovet, Teresa; Blanchet, Denis; Demar, Magalie; Harrat, Zoubir; Aoun, Karim; Bastien, Patrick; Muñoz, Carmen; Gállego, Montserrat; Piarroux, Renaud

2017-10-01

Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani , L. guyanensis , and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers. Copyright © 2017 American Society for Microbiology.

Enhanced digital library system that supports sustainable knowledge

African Journals Online (AJOL)

Enhanced digital library system that supports sustainable knowledge: A focus ... This research work provides a Web-Based University library, ability to access the ... and generates pins to authorize bonafide students and staff of the University.

Application of RSS in Special Libraries

Directory of Open Access Journals (Sweden)

Shima Moradi

2007-07-01

Full Text Available Despite of ever increasing scope and volume of online information content and the constant need for easy accessibility to these contents, experts in various subject matters always face time constraints when searching for information or looking up their intended resource. Meanwhile, special libraries are faced with diminishing resources, time and human resource needed for providing services and meeting the information need of the said experts. Nowadays Push Technologies, in form of RSS could be used to speed up on-time information dissemination. RSS feeds could spontaneously deliver information to the users. These could be posted on webpages or read by RSS readers. RSS has numerous applications such as web page content update, reading lists, table of contents, current awareness, guides etc. The present paper while outlining RSS as one of the next generation web tools, would point out its various advantages and applications in the new generation of libraries (Lib 2.0,particularly the special libraries. It would also offer pointers to its application in meeting the information needs of experts and users in such libraries.

Characterization of Passive Spectral Regrowth in Radio Frequency Systems

Science.gov (United States)

2013-01-01

as using RF absorber and Faraday cages around sensi- tive spots. To ensure maximum radiated isolation, each cable or component should be shielded...nonlinear effects of spectral-regrowth-generating phenomena on an RF signal. Detection of low-level passive spectral regrowth close in frequency to a...experimentally and analytically characterize the nonlinear effects of spectral- regrowth-generating phenomena on an RF signal. Detection of low-level passive

Production of spectrally reconstructed uv-radiation by means of a nonlinear conversion of the generation frequency of a dye laser with lamp pumping

Energy Technology Data Exchange (ETDEWEB)

Anufrik, S S; Mostovnikov, V A; Rubinov, A N

1976-03-01

By doubling the generation frequency of an organic dye laser with lamp pumping, radiation is obtained in the spectral region of 285 to 305 nm. Depending on the mode of operation of a given laser the spectral width of the uv-radiation was 0.5 or approximately 0.003 nm. The maximum energy of second harmonic pulses was equal to approximately 0.01 J. (SJR)

Theoretical extension and experimental demonstration of spectral compression in second-harmonic generation by Fresnel-inspired binary phase shaping

Science.gov (United States)

Li, Baihong; Dong, Ruifang; Zhou, Conghua; Xiang, Xiao; Li, Yongfang; Zhang, Shougang

2018-05-01

Selective two-photon microscopy and high-precision nonlinear spectroscopy rely on efficient spectral compression at the desired frequency. Previously, a Fresnel-inspired binary phase shaping (FIBPS) method was theoretically proposed for spectral compression of two-photon absorption and second-harmonic generation (SHG) with a square-chirped pulse. Here, we theoretically show that the FIBPS can introduce a negative quadratic frequency phase (negative chirp) by analogy with the spatial-domain phase function of Fresnel zone plate. Thus, the previous theoretical model can be extended to the case where the pulse can be transformed limited and in any symmetrical spectral shape. As an example, we experimentally demonstrate spectral compression in SHG by FIBPS for a Gaussian transform-limited pulse and show good agreement with the theory. Given the fundamental pulse bandwidth, a narrower SHG bandwidth with relatively high intensity can be obtained by simply increasing the number of binary phases. The experimental results also verify that our method is superior to that proposed in [Phys. Rev. A 46, 2749 (1992), 10.1103/PhysRevA.46.2749]. This method will significantly facilitate the applications of selective two-photon microscopy and spectroscopy. Moreover, as it can introduce negative dispersion, hence it can also be generalized to other applications in the field of dispersion compensation.

The Steacie Library Dungeon Hackfest: Hackers in the Library Coding, Collaborating and Creating

Directory of Open Access Journals (Sweden)

Sarah Shujah

2013-12-01

Full Text Available The Steacie Science and Engineering Library at York University hosted its first annual Steacie Library Dungeon Hackfest in February 2013. The purpose of a hackfest is to spend a day (or longer using computer programming skills to collaborate on a particular software project and, hopefully, bring the project to reality. The project may be an app, widget, or website. It is evident that hackfests, as a form of engaged learning, help to reinforce the relevance of the library since it has implications for information literacy, open access, faculty liaison, and the changing perception of library as place. Twenty-five participants that included students, faculty, and staff hacked on Open York Data: York University’s openly accessible records and data such as course codes, lab stats of computers available in various libraries, subject headings, and research interests of faculty. The Hackfest produced several innovative ideas including a “Class Optimizer” program to help students generate a course schedule, and a mobile android app “YU Labs” that informs students of the computers available in a specific library. Library instruction was informally imparted during the Hackfest. There were discussions about open source, developing a research idea, and recommended tools to help students complete their projects. This article encapsulates the inspiration behind the Hackfest, discusses the library as the host, the resources used, the theme, achievements, and assessment. To summarize, the library Hackfest provided a space for literacy, life-long learning, and support of the open source pedagogy.

Digital Libraries: The Next Generation in File System Technology.

Science.gov (United States)

Bowman, Mic; Camargo, Bill

1998-01-01

Examines file sharing within corporations that use wide-area, distributed file systems. Applications and user interactions strongly suggest that the addition of services typically associated with digital libraries (content-based file location, strongly typed objects, representation of complex relationships between documents, and extrinsic…

Collision-induced stimulated photon echo generated at transition 0-1 on broad spectral line conditions

Science.gov (United States)

Rubtsova, N. N.; Gol'dort, V. G.; Ishchenko, V. N.; Khvorostov, E. B.; Kochubei, S. A.; Borisov, G. M.; Ledovskikh, D. V.; Reshetov, V. A.

2018-04-01

For the first time, the collision induced stimulated photon echo generated at transition 1S0 → 3 P1 of 174Yb (type 0-1) in the mixture of gases Yb  +  Xe was investigated in the presence of weak longitudinal magnetic field, with experimental parameters corresponding to broad spectral line conditions. Comparison of the experimental echo amplitude versus magnetic field strength dependence with the theoretical curve shows a very good agreement, giving rise to an improved estimate for the difference between alignment and orientation decay rates.

An ensemble training scheme for machine-learning classification of Hyperion satellite imagery with independent hyperspectral libraries

Science.gov (United States)

Friedel, Michael; Buscema, Massimo

2016-04-01

A training scheme is proposed for the real-time classification of soil and vegetation (landscape) components in EO-1 Hyperion hyperspectral images. First, an auto-contractive map is used to compute connectivity of reflectance values for spectral bands (N=200) from independent laboratory spectral library components. Second, a minimum spanning tree is used to identify optimal grouping of training components from connectivity values. Third, the reflectance values for optimal landscape component signatures are sorted. Fourth, empirical distribution functions (EDF) are computed for each landscape component. Fifth, the Monte-Carlo technique is used to generate realizations (N=30) for each landscape EDF. The correspondence of component realizations to original signatures validates the stochastic procedure. Presentation of the realizations to the self-organizing map (SOM) is done using three different map sizes: 14x10, 28x20, and 40 x 30. In each case, the SOM training proceeds first with a rough phase (20 iterations using a Gaussian neighborhood with an initial and final radius of 11 units and 3 units) and then fine phase (400 iterations using a Gaussian neighborhood with an initial and final radius of 3 units and 1 unit). The initial and final learning rates of 0.5 and 0.05 decay linearly down to 10-5, and the Gaussian neighborhood function decreases exponentially (decay rate of 10-3 iteration-1) providing reasonable convergence. Following training of the three networks, each corresponding SOM is used to independently classify the original spectral library signatures. In comparing the different SOM networks, the 28x20 map size is chosen for independent reproducibility and processing speed. The corresponding universal distance matrix reveals separation of the seven component classes for this map size thereby supporting it use as a Hyperion classifier.

Influence of spectral history on PWR full core calculation results

International Nuclear Information System (INIS)

Bilodid, Y.; Mittag, S.

2011-01-01

The few-group cross section libraries, used by reactor dynamics codes, are affected by the spectral history effect-a dependence of fuel cross sections not only on burnup, but also on local spectral conditions during burnup. A cross section correction method based on Pu-239 concentration was implemented in the reactor dynamic code DYN3D. This paper describes the influence of a cross section correction on full-core calculation results. Steady-state and burnup characteristics of a PWR equilibrium cycle, calculated by DYN3D with and without cross section corrections, are compared. A study has shown a significant influence of spectral history on axial power and burnup distributions as well as on calculated cycle length. An impact of the correction on transient calculations is studied for a control rod ejection example. (Authors)

Using R and the Tidyverse to Generate Library Usage Reports

Directory of Open Access Journals (Sweden)

Andy Meyer

2018-02-01

Full Text Available Gathering, analyzing, and communicating library usage data provides a foundation for thoughtful assessment. However, the amount of time and expertise required creates a barrier to actually using this data. By using the statistical programming language R and the tools and approach of the Tidyverse, the process of gathering, analyzing, and communicating data can be automated in ways that reduce the amount of time and energy required. At the same time, this approach increases staff capacity for other data science projects and creates a shareable model and framework for other libraries. This article focuses on electronic resource usage reports - especially Counter DB1 Reports - but this approach could be extended to other data sources and needs.

Next Generation UAV Based Spectral Systems for Environmental Monitoring

Data.gov (United States)

National Aeronautics and Space Administration — At present, UAVs used in environmental monitoring mostly collect low spectral resolution imagery, capable of retrieving canopy greenness or properties related water...

Building a better fragment library for de novo protein structure prediction.

Directory of Open Access Journals (Sweden)

Saulo H P de Oliveira

Full Text Available Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10. We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. "Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources".

Building a Better Fragment Library for De Novo Protein Structure Prediction

Science.gov (United States)

de Oliveira, Saulo H. P.; Shi, Jiye; Deane, Charlotte M.

2015-01-01

Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10). We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. “Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources”. PMID:25901595

MCNP and MATXS cross section libraries based on JENDL-3.3

International Nuclear Information System (INIS)

Kosako, Kazuaki; Konno, Chikara; Fukahori, Tokio; Shibata, Keiichi

2003-01-01

The continuous energy cross section library for the Monte Carlo transport code MCNP-4C, FSXLIB-J33, has been generated from the latest version of JENDL-3.3. The multigroup cross section library with the MATXS format, MATXS-J33, has been generated also from JENDL-3.3. Both libraries contain all nuclides in JENDL-3.3 and are processed at 300 K by the nuclear data processing system NJOY99. (author)

What's New in the Library Automation Arena?

Science.gov (United States)

Breeding, Marshall

1998-01-01

Reviews trends in library automation based on vendors at the 1998 American Library Association Annual Conference. Discusses the major industry trend, a move from host-based computer systems to the new generation of client/server, object-oriented, open systems-based automation. Includes a summary of developments for 26 vendors. (LRW)

Validation of a new library of nuclear constants of the WIMS code

International Nuclear Information System (INIS)

Aguilar H, F.

1991-10-01

The objective of the present work is to reproduce the experimental results of the thermal reference problems (benchmarks) TRX-1, TRX-2 and BAPL-1 to BAPL-3 with the WIMS code. It was proceeded in two stages, the first one consisted on using the original library of the code, while in the second one, a library that only contains the present elements in the benchmarks: H 1 , O 16 , Al 27 , U 235 and U 238 was generated. To generate the present nuclear data in the WIMS library, it was used the ENDF/B-IV database and the Data processing system of Nuclear Data NJOY, the library was generated using the FIXER code. (Author)

NJOY processed multigroup library for fast reactor applications and point data library for MCNP - Experience and validation

International Nuclear Information System (INIS)

Kim Jung-Do; Gil Choong-Sup

1996-01-01

JEF-1-based 50-group cross section library for fast reactor applications and point data library for continuous-energy Monte Carlo code MCNP have been generated using NJOY91.38 system. They have been examined by analyzing measured integral quantities such as criticality and central reaction rate ratios for 8 small fast critical assemblies. (author). 9 refs, 2 figs, 10 tabs

Generation of a library of two-group diffusion and kinetics parameters for DYN3D

International Nuclear Information System (INIS)

Petkov, P.T.; Christoskov, I.D.; Kamenov, K.; Antov, A.

2002-01-01

A library of two-group diffusion and kinetics parameters has been generated for the neutron kinetics code DYN3D for analysis of reactivity initiated accidents for the WWER-440 reactors, based on the MAGRU approximation methodology for the diffusion and kinetics parameters. The accuracy of this methodology has been tested and the conclusion is that it is not adequate. A new approximation methodology, based on interpolation for the most widely varying parameters, i.e. the moderator temperature and density, and on approximation for all other independent parameters, is presented. The methodology of calculation of the kinetics parameters using primary data from ENDF-B/VI is described in detail (Authors)

Library of neutron cross sections of the Thermos code

International Nuclear Information System (INIS)

Alonso V, G.; Hernandez L, H.

1991-10-01

The present work is the complement of the IT.SN/DFR-017 report in which the structure and the generation of the library of the Thermos code is described. In this report the comparison among the values of the cross sections that has the current library of the Thermos code and those generated by means of the ENDF-B/NJOY it is shown. (Author)

Silhouette and spectral line profiles in the special modification of the Kerr black hole geometry generated by quintessential fields

Energy Technology Data Exchange (ETDEWEB)

Schee, Jan; Stuchlik, Zdenek [Silesian University in Opava, Faculty of Philosophy and Science, Institute of Physics and Research Centre for Theoretical Physics and Astrophysics, Opava (Czech Republic)

2016-11-15

We study optical effects in quintessential Kerr black hole spacetimes corresponding to the limiting case of the equation-of-state parameter ω{sub q} = -1/3 of the quintessence. In dependence on the dimensionless quintessential field parameter c, we determine the black hole silhouette and the spectral line profiles of Keplerian disks generated in this special quintessential Kerr geometry, representing an extension of the general modifications of the Kerr geometry introduced recently by Ghasemi-Nodehi and Bambi (Eur. Phys. J. C 56:290, 2016). We demonstrate that due to the influence of the parameter c, the silhouette is almost homogeneously enlarged, and the spectral line profiles are redshifted with almost conserved shape. (orig.)

Public Libraries, Digital Literacy and Participatory Culture

Science.gov (United States)

McShane, Ian

2011-01-01

In recent years public libraries have experimented with user-generated or community-contributed content through the interactive tools of Web 2.0. For some commentators this not just establishes a new relationship between libraries and their publics, but signals the end of information hegemony and an "expert paradigm". Such claims need to…

The Effect of Epidermal Structures on Leaf Spectral Signatures of Ice Plants (Aizoaceae

Directory of Open Access Journals (Sweden)

René Hans-Jürgen Heim

2015-12-01

Full Text Available Epidermal structures (ES of leaves are known to affect the functional properties and spectral responses. Spectral studies focused mostly on the effect of hairs or wax layers only. We studied a wider range of different ES and their impact on spectral properties. Additionally, we identified spectral regions that allow distinguishing different ES. We used a field spectrometer to measure ex situ leaf spectral responses from 350 nm–2500 nm. A spectral library for 25 species of the succulent family Aizoaceae was assembled. Five functional types were defined based on ES: flat epidermal cell surface, convex to papillary epidermal cell surface, bladder cells, hairs and wax cover. We tested the separability of ES using partial least squares discriminant analysis (PLS-DA based on the spectral data. Subsequently, variable importance (VIP was calculated to identify spectral regions relevant for discriminating our functional types (classes. Classification performance was high, with a kappa value of 0.9 indicating well-separable spectral classes. VIP calculations identified six spectral regions of increased importance for the classification. We confirmed and extended previous findings regarding the visible-near-infrared spectral region. Our experiments also confirmed that epidermal leaf traits can be classified due to clearly distinguishable spectral signatures across species and genera within the Aizoaceae.

Immune Antibody Libraries: Manipulating The Diverse Immune Repertoire for Antibody Discovery.

Science.gov (United States)

Lim, Theam Soon; Chan, Soo Khim

2016-01-01

Antibody phage display is highly dependent on the availability of antibody libraries. There are several forms of libraries depending mainly on the origin of the source materials. There are three major classes of libraries, mainly the naïve, immune and synthetic libraries. Immune antibody libraries are designed to isolate specific and high affinity antibodies against disease antigens. The pre-exposure of the host to an infection results in the production of a skewed population of antibodies against the particular infection. This characteristic takes advantage of the in vivo editing machinery to generate bias and specific immune repertoire. The skewed but diverse repertoire of immune libraries has been adapted successfully in the generation of antibodies against a wide range of diseases. We envisage immune antibody libraries to play a greater role in the discovery of antibodies for diseases in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Peak fitting and identification software library for high resolution gamma-ray spectra

International Nuclear Information System (INIS)

Uher, Josef; Roach, Greg; Tickner, James

2010-01-01

A new gamma-ray spectral analysis software package is under development in our laboratory. It can be operated as a stand-alone program or called as a software library from Java, C, C++ and MATLAB TM environments. It provides an advanced graphical user interface for data acquisition, spectral analysis and radioisotope identification. The code uses a peak-fitting function that includes peak asymmetry, Compton continuum and flexible background terms. Peak fitting function parameters can be calibrated as functions of energy. Each parameter can be constrained to improve fitting of overlapping peaks. All of these features can be adjusted by the user. To assist with peak identification, the code can automatically measure half-lives of single or multiple overlapping peaks from a time series of spectra. It implements library-based peak identification, with options for restricting the search based on radioisotope half-lives and reaction types. The software also improves the reliability of isotope identification by utilizing Monte-Carlo simulation results.

Identity of a brand new library

KAUST Repository

Vijayakumar, J.K.

2017-03-16

King Abdullah University of Science and Technology (KAUST) Library in Saudi Arabia aspires to be one of the great new-generation libraries in the field of scientific research. Its services and systems support a digitally born collection, 97% of their collection is electronic. The spectacular library facility with lots of space for collaboration and its collections remains open twenty-four hours, every day of the year and is facilitated by a staff coming from 12 different nationalities. It has an Open Access mandate, the first in the Middle East region, and runs a successful digital research repository.

Global Convergence of a Spectral Conjugate Gradient Method for Unconstrained Optimization

Directory of Open Access Journals (Sweden)

Jinkui Liu

2012-01-01

Full Text Available A new nonlinear spectral conjugate descent method for solving unconstrained optimization problems is proposed on the basis of the CD method and the spectral conjugate gradient method. For any line search, the new method satisfies the sufficient descent condition gkTdk<−∥gk∥2. Moreover, we prove that the new method is globally convergent under the strong Wolfe line search. The numerical results show that the new method is more effective for the given test problems from the CUTE test problem library (Bongartz et al., 1995 in contrast to the famous CD method, FR method, and PRP method.

Next-generation applications in healthcare digital libraries using semantic service composition and coordination.

Science.gov (United States)

Möller, Thorsten; Schuldt, Heiko; Gerber, Andreas; Klusch, Matthias

2006-06-01

Healthcare digital libraries (DLs) increasingly make use of dedicated services to access functionality and/or data. Semantic (web) services enhance single services and facilitate compound services, thereby supporting advanced applications on top of a DL. The traditional process management approach tends to focus on process definition at build time rather than on actual service events in run time, and to anticipate failures in order to define appropriate strategies. This paper presents a novel approach where service coordination is distributed among a set of agents. A dedicated component plans compound semantic services on demand for a particular application. In failure, the planner is reinvoked to define contin- gency strategies. Finally, matchmaking is effected at runtime by choosing the appropriate service provider. These combined technologies will provide key support for highly flexible next-generation DL applications. Such technologies are under development within CASCOM.

Automated design of degenerate codon libraries.

Science.gov (United States)

Mena, Marco A; Daugherty, Patrick S

2005-12-01

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.

Rapid mutation of Spirulina platensis by a new mutagenesis system of atmospheric and room temperature plasmas (ARTP and generation of a mutant library with diverse phenotypes.

Directory of Open Access Journals (Sweden)

Mingyue Fang

Full Text Available In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.

An optical modulation format generation scheme based on spectral filtering and frequency-to-time mapping

Institute of Scientific and Technical Information of China (English)

ZHANG Ai-ling; ZHANG Yue; SONG Hong-yun; YAO Yuan; PAN Hong-gang

2018-01-01

An optical modulation format generation scheme based on spectral filtering and frequency-to-time mapping is experimentally demonstrated.Many modulation formats with continuously adjustable duty radio and bit rate can be formed by changing the dispersion of dispersion element and the bandwidth of shaped spectrum in this scheme.In the experiment,non-return-to-zero (NRZ) signal with bit rate of 29.41 Gbit/s and 1/2 duty ratio return-to-zero (RZ) signal with bit rate of 13.51 Gbit/s are obtained.The maximum bit rate of modulation format signal is also analyzed.

Criticality and safety parameter studies for upgrading 3 MW TRIGA MARK II research reactor and validation of generated cross section library and computational method

International Nuclear Information System (INIS)

Bhuiyan, S.I.; Mondal, M.A.W.; Sarker, M.M.; Rahman, M.; Shahdatullah, M.S.; Huda, M.Q.; Chakrroborty, T.K.; Khan, M.J.H.

2000-01-01

This study deals with the neutronic and thermal hydraulic analysis of the 3MW TRIGA MARK II research reactor to upgrade it to a higher flux. The upgrading will need a major reshuffling and reconfiguration of the current core. To reshuffle the current core configuration, the chain of NJOY94.10 - WIMSD-5A - CITATION - PARET - MCNP4B2 codes has been used for the overall analysis. The computational methods, tools and techniques, customisation of cross section libraries, various models for cells and super cells, and a lot of associated utilities have been standardised and established/validated for the overall core analysis. Analyses using the 4-group and 7-group libraries of macroscopic cross sections generated from the 69-group WIMSD-5 library showed that a 7-group structure is more suitable for TRIGA calculations considering its LEU fuel composition. The MCNP calculations established that the CITATION calculations and the generated cross section library are reasonably good for neutronic analysis of TRIGA reactors. Results obtained from PARET demonstrated that the flux upgrade will not cause the temperature limit on the fuel to be exceeded. Also, the maximum power density remains, by a substantial margin below the level at which the departure from nucleate boiling could occur. A possible core with two additional irradiation channels around the CT is projected where almost identical thermal fluxes as in the CT are obtained. The reconfigured core also shows 7.25% thermal flux increase in the Lazy Susan. (author)

The LAW Library -- A multigroup cross-section library for use in radioactive waste analysis calculations

International Nuclear Information System (INIS)

Greene, N.M.; Arwood, J.W.; Wright, R.Q.; Parks, C.V.

1994-08-01

The 238-group LAW Library is a new multigroup neutron cross-section library based on ENDF/B-V data, with five sets of data taken from ENDF/B-VI ( 14 N 7 , 15 N 7 , 16 O 8 , 154Eu 63 , and 155 Eu 63 ). These five nuclides are included because the new evaluations are thought to be superior to those in Version 5. The LAW Library contains data for over 300 materials and will be distributed by the Radiation Shielding Information Center, located at Oak Ridge National Laboratory. It was generated for use in neutronics calculations required in radioactive waste analyses, although it has equal utility in any study requiring multigroup neutron cross sections

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Directory of Open Access Journals (Sweden)

Bendahmane Abdelhafid

2011-05-01

Full Text Available Abstract Background Melon (Cucumis melo, an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. Result We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs and 3,073 single nucleotide polymorphisms (SNPs in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but

A Lightweight Compact Multi-Spectral Imager Using Novel Computer-Generated Micro-Optics and Spectral-Extraction Algorithms

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this NASA Early-stage research proposal is to demonstrate an ultra-compact, lightweight broadband hyper- and multi-spectral imaging system that is...

Rapid access to compound libraries through flow technology: fully automated synthesis of a 3-aminoindolizine library via orthogonal diversification.

Science.gov (United States)

Lange, Paul P; James, Keith

2012-10-08

A novel methodology for the synthesis of druglike heterocycle libraries has been developed through the use of flow reactor technology. The strategy employs orthogonal modification of a heterocyclic core, which is generated in situ, and was used to construct both a 25-membered library of druglike 3-aminoindolizines, and selected examples of a 100-member virtual library. This general protocol allows a broad range of acylation, alkylation and sulfonamidation reactions to be performed in conjunction with a tandem Sonogashira coupling/cycloisomerization sequence. All three synthetic steps were conducted under full automation in the flow reactor, with no handling or isolation of intermediates, to afford the desired products in good yields. This fully automated, multistep flow approach opens the way to highly efficient generation of druglike heterocyclic systems as part of a lead discovery strategy or within a lead optimization program.

Maximum spectral demands in the near-fault region

Science.gov (United States)

Huang, Yin-Nan; Whittaker, Andrew S.; Luco, Nicolas

2008-01-01

The Next Generation Attenuation (NGA) relationships for shallow crustal earthquakes in the western United States predict a rotated geometric mean of horizontal spectral demand, termed GMRotI50, and not maximum spectral demand. Differences between strike-normal, strike-parallel, geometric-mean, and maximum spectral demands in the near-fault region are investigated using 147 pairs of records selected from the NGA strong motion database. The selected records are for earthquakes with moment magnitude greater than 6.5 and for closest site-to-fault distance less than 15 km. Ratios of maximum spectral demand to NGA-predicted GMRotI50 for each pair of ground motions are presented. The ratio shows a clear dependence on period and the Somerville directivity parameters. Maximum demands can substantially exceed NGA-predicted GMRotI50 demands in the near-fault region, which has significant implications for seismic design, seismic performance assessment, and the next-generation seismic design maps. Strike-normal spectral demands are a significantly unconservative surrogate for maximum spectral demands for closest distance greater than 3 to 5 km. Scale factors that transform NGA-predicted GMRotI50 to a maximum spectral demand in the near-fault region are proposed.

About the Library - Betty Petersen Memorial Library

Science.gov (United States)

branch library of the NOAA Central Library. The library serves the NOAA Science Center in Camp Springs , Maryland. History and Mission: Betty Petersen Memorial Library began as a reading room in the NOAA Science Science Center staff and advises the library on all aspects of the library program. Library Newsletters

Architectures for Collaboration: Roles and Expectations for Digital Libraries

Science.gov (United States)

Brantley, Peter

2008-01-01

Libraries are successful to the extent that they can bridge communities and can leverage the diversity of the quest, the research, and the discovery. By building bridges among various sectors, libraries will be able to define themselves in the next generation.

America's Star Libraries, 2010: Top-Rated Libraries

Science.gov (United States)

Lyons, Ray; Lance, Keith Curry

2010-01-01

The "LJ" Index of Public Library Service 2010, "Library Journal"'s national rating of public libraries, identifies 258 "star" libraries. Created by Ray Lyons and Keith Curry Lance, and based on 2008 data from the IMLS, it rates 7,407 public libraries. The top libraries in each group get five, four, or three stars. All included libraries, stars or…

Featured Library: Parrish Library

OpenAIRE

Kirkwood, Hal P, Jr

2015-01-01

The Roland G. Parrish Library of Management & Economics is located within the Krannert School of Management at Purdue University. Between 2005 - 2007 work was completed on a white paper that focused on a student-centered vision for the Management & Economics Library. The next step was a massive collection reduction and a re-envisioning of both the services and space of the library. Thus began a 3 phase renovation from a 2 floor standard, collection-focused library into a single floor, 18,000s...

Atmospheric parameters, spectral indexes and their relation to CPV spectral performance

Energy Technology Data Exchange (ETDEWEB)

Núñez, Rubén, E-mail: ruben.nunez@ies-def.upm.es; Antón, Ignacio, E-mail: ruben.nunez@ies-def.upm.es; Askins, Steve, E-mail: ruben.nunez@ies-def.upm.es; Sala, Gabriel, E-mail: ruben.nunez@ies-def.upm.es [Instituto de Energía Solar - Universidad Politécnica de Madrid, Instituto de Energía Solar, ETSI Telecomunicación, Ciudad Universitaria 28040 Madrid (Spain)

2014-09-26

Air Mass and atmosphere components (basically aerosol (AOD) and precipitable water (PW)) define the absorption of the sunlight that arrive to Earth. Radiative models such as SMARTS or MODTRAN use these parameters to generate an equivalent spectrum. However, complex and expensive instruments (as AERONET network devices) are needed to obtain AOD and PW. On the other hand, the use of isotype cells is a convenient way to characterize spectrally a place for CPV considering that they provide the photocurrent of the different internal subcells individually. Crossing data from AERONET station and a Tri-band Spectroheliometer, a model that correlates Spectral Mismatch Ratios and atmospheric parameters is proposed. Considering the amount of stations of AERONET network, this model may be used to estimate the spectral influence on energy performance of CPV systems close to all the stations worldwide.

Open Source Solutions for Libraries: ABCD vs Koha

Science.gov (United States)

Macan, Bojan; Fernandez, Gladys Vanesa; Stojanovski, Jadranka

2013-01-01

Purpose: The purpose of this study is to present an overview of the two open source (OS) integrated library systems (ILS)--Koha and ABCD (ISIS family), to compare their "next-generation library catalog" functionalities, and to give comparison of other important features available through ILS modules. Design/methodology/approach: Two open source…

Multigroup cross section library; WIMS library

International Nuclear Information System (INIS)

Kannan, Umasankari

2000-01-01

The WIMS library has been extensively used in thermal reactor calculations. This multigroup constants library was originally developed from the UKNDL in the late 60's and has been updated in 1986. This library has been distributed with the WIMS-D code by NEA data bank. The references to WIMS library in literature are the 'old' which is the original as developed by the AEA Winfrith and the 'new' which is the current 1986 WIMS library. IAEA has organised a CRP where a new and fully updated WIMS library will soon be available. This paper gives an overview of the definitions of the group constants that go into any basic nuclear data library used for reactor calculations. This paper also outlines the contents of the WIMS library and some of its shortcomings

The Handheld Library: Developments at the Rector Gabriel Ferraté Library, UPC

Directory of Open Access Journals (Sweden)

Beatriz Benítez Juan

2011-10-01

Full Text Available The purpose of this paper is to highlight the mobile services developed by the Rector Gabriel Ferraté Library (BRGF of the Universitat Politècnica de Catalunya (UPC-Barcelona Tech in Barcelona, Spain. We hope this paper will be of use to other libraries exploring new technologies for communicating and delivering their services to users at a time when mobile services are an emerging topic in librarianship and information science literature. By setting out the successive steps involved in the as yet unfinished process of building our mobile services portfolio, we aim to offer a detailed picture of the mobile services and features offered by a university library from a case study perspective. The main topics to be discussed include: The BRGF’s mobile website, including the information available, its interactive capabilities and the services it provides to its users. The mobile-friendly version of UP Commons(the UPC Library Service’s institutional repositories. The UPC Library Service’s mobile OPAC. The mobile version of u-win(BRGF’s videogame service. The use of QR codes to deliver information to mobile devices. Text message notifications. Additional topics for discussion include: The library’s organisation and the organisational concepts that underpin and make possible its technological developments (including mobile. BRGF’s concern regarding the reduction of investment in the development of mobile services. The criteria and tools used to guide the library’s decisions regarding the design and orientation of current and future mobile services. How mobile services can help to improve the image of the library as a leading technology site. Selected mobile features that BRGF plans to offer in the near future. Ultimately, this paper aims to delineate the effectiveness and potential of delivering library services by the preferred means of communication of a new generation of students and teachers.

The Leadership Dimension in Information and Communication Technology Adoption in African Libraries

Directory of Open Access Journals (Sweden)

Adetoun A. Oyelude

2014-02-01

Full Text Available The article focuses on leadership challenges in adaptation to Information and Communication Technologies (ICTs in African libraries. It identifies and discusses the need for adequate leadership styles and behavior in the bid to adapt effectively to new technologies. Online survey, observation arising from personal professional practice experience, personal communication, and interview methods were used to gather data for the study. Older library professionals, many of whom are still very visible across the leadership strata of libraries, were found to exhibit diverse attitude to the adaptation to ICTs deployment and use in their libraries. Some library leaders and older generation professionals were discovered to react somewhat negatively to changes in technology used in their libraries, preventing the younger professionals from performing to full capacity, and generally showing nonchalance to new technologies. Proper training and retraining, mentoring, and harnessing the synergy of ideas, with respectful communication from new generation library professionals, was found to be desirable. Change management workshops and implementation of standard ethics of the profession are recommended, while emphasis is put on the need for library professionals to overcome their technophobia and take leadership in adapting to move the library and information profession forward.

The spectral imaging facility: Setup characterization

Energy Technology Data Exchange (ETDEWEB)

De Angelis, Simone, E-mail: simone.deangelis@iaps.inaf.it; De Sanctis, Maria Cristina; Manzari, Paola Olga [Institute for Space Astrophysics and Planetology, INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome (Italy); Ammannito, Eleonora [Institute for Space Astrophysics and Planetology, INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome (Italy); Department of Earth, Planetary and Space Sciences, University of California, Los Angeles, Los Angeles, California 90095-1567 (United States); Di Iorio, Tatiana [ENEA, UTMEA-TER, Rome (Italy); Liberati, Fabrizio [Opto Service SrL, Campagnano di Roma (RM) (Italy); Tarchi, Fabio; Dami, Michele; Olivieri, Monica; Pompei, Carlo [Selex ES, Campi Bisenzio (Italy); Mugnuolo, Raffaele [Italian Space Agency, ASI, Spatial Geodesy Center, Matera (Italy)

2015-09-15

The SPectral IMager (SPIM) facility is a laboratory visible infrared spectrometer developed to support space borne observations of rocky bodies of the solar system. Currently, this laboratory setup is used to support the DAWN mission, which is in its journey towards the asteroid 1-Ceres, and to support the 2018 Exo-Mars mission in the spectral investigation of the Martian subsurface. The main part of this setup is an imaging spectrometer that is a spare of the DAWN visible infrared spectrometer. The spectrometer has been assembled and calibrated at Selex ES and then installed in the facility developed at the INAF-IAPS laboratory in Rome. The goal of SPIM is to collect data to build spectral libraries for the interpretation of the space borne and in situ hyperspectral measurements of planetary materials. Given its very high spatial resolution combined with the imaging capability, this instrument can also help in the detailed study of minerals and rocks. In this paper, the instrument setup is first described, and then a series of test measurements, aimed to the characterization of the main subsystems, are reported. In particular, laboratory tests have been performed concerning (i) the radiation sources, (ii) the reference targets, and (iii) linearity of detector response; the instrumental imaging artifacts have also been investigated.

Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.

Science.gov (United States)

Boone, Morgane; De Koker, Andries; Callewaert, Nico

2018-04-06

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.

Validation of the 172 group ENDFB7GX library

International Nuclear Information System (INIS)

Khan, Suhail Ahmad; Raj, Devesh; Karthikeyan, R.; Jagannathan, V.

2007-01-01

Full text: Five 172 group libraries, viz., IAEAGX, ENDFB6GX, JENDL3GX, JEFF31GX, and LWRPSGX were obtained as a part of the IAEA WIMS Library Update Project (WLUP). The first four libraries have data available for 173 nuclides up to 244 Cm. The LWRPSGX library based on JEFF3.1 point dataset is an extended library up to 252 Cf. Data for 12 more actinides and the related burnup chain were added. The five libraries were validated against known experiments in an earlier work. In general the LWRPSGX was found to be giving better results. Recently another version of 172 group library 'ENDFB7GX' has been released. In the present work we provide the results of validation of the ENDFB7GX library against the same set of experimental data and a comparison with results of other libraries. The experimental configuration data include a variety of uniform lattices with enriched UO 2 , U- metal, mixed oxide (UO 2 -PuO 2 ) fuels with H 2 O and D 2 O moderators for a wide range of enrichment, fuel diameter and ratio of moderator to fuel volume (V m /V f ). The calculations have been done using the code LATTEST which solves the single pin lattice cell problem by 1-D multi-group transport theory after cylindricalising the square or hexagonal cell boundary. The LATTEST code is an improved version of the MURLI code and is capable of providing a ready testing of any new cross section library against a set of experimental benchmark lattices collected from various sources. The calculated k eff values and certain spectral indices, where available, have been compared for all the libraries for more than hundred critical lattices. There is a general under prediction of k eff values by all libraries. The maximum under prediction is for ENDFB6GX library and the least is for JENDL3GX library. The ENDFB7GX library, in general, is found to over predict in comparison to the k eff values obtained using LWRPSGX library. While scrutinizing the basic nuclear data it was noted that the slowing down cross

Neutron cross section libraries for analysis of fusion neutronics experiments

International Nuclear Information System (INIS)

Kosako, Kazuaki; Oyama, Yukio; Maekawa, Hiroshi; Nakamura, Tomoo

1988-03-01

We have prepared two computer code systems producing neutron cross section libraries to analyse fusion neutronics experiments. First system produces the neutron cross section library in ANISN format, i.e., the multi-group constants in group independent format. This library can be obtained by using the multi-group constant processing code system MACS-N and the ANISN format cross section compiling code CROKAS. Second system is for the continuous energy cross section library for the MCNP code. This library can be obtained by the nuclear data processing system NJOY which generates pointwise energy cross sections and the cross section compiling code MACROS for the MCNP library. In this report, we describe the production procedures for both types of the cross section libraries, and show six libraries with different conditions in ANISN format and a library for the MCNP code. (author)

Intersection numbers of spectral curves

CERN Document Server

Eynard, B.

2011-01-01

We compute the symplectic invariants of an arbitrary spectral curve with only 1 branchpoint in terms of integrals of characteristic classes in the moduli space of curves. Our formula associates to any spectral curve, a characteristic class, which is determined by the laplace transform of the spectral curve. This is a hint to the key role of Laplace transform in mirror symmetry. When the spectral curve is y=\\sqrt{x}, the formula gives Kontsevich--Witten intersection numbers, when the spectral curve is chosen to be the Lambert function \\exp{x}=y\\exp{-y}, the formula gives the ELSV formula for Hurwitz numbers, and when one chooses the mirror of C^3 with framing f, i.e. \\exp{-x}=\\exp{-yf}(1-\\exp{-y}), the formula gives the Marino-Vafa formula, i.e. the generating function of Gromov-Witten invariants of C^3. In some sense this formula generalizes ELSV, Marino-Vafa formula, and Mumford formula.

Estimation of sub-pixel water area on Tibet plateau using multiple endmembers spectral mixture spectral analysis from MODIS data

Science.gov (United States)

Cui, Qian; Shi, Jiancheng; Xu, Yuanliu

2011-12-01

Water is the basic needs for human society, and the determining factor of stability of ecosystem as well. There are lots of lakes on Tibet Plateau, which will lead to flood and mudslide when the water expands sharply. At present, water area is extracted from TM or SPOT data for their high spatial resolution; however, their temporal resolution is insufficient. MODIS data have high temporal resolution and broad coverage. So it is valuable resource for detecting the change of water area. Because of its low spatial resolution, mixed-pixels are common. In this paper, four spectral libraries are built using MOD09A1 product, based on that, water body is extracted in sub-pixels utilizing Multiple Endmembers Spectral Mixture Analysis (MESMA) using MODIS daily reflectance data MOD09GA. The unmixed result is comparing with contemporaneous TM data and it is proved that this method has high accuracy.

Development of libraries for ORIGEN2 code based on JENDL-3.2

Energy Technology Data Exchange (ETDEWEB)

Suyama, Kenya; Katakura, Jun-ichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Ishikawa, Makoto; Ohkawachi, Yasushi

1998-03-01

The working Group of JNDC `Nuclide Generation Evaluation` has launched a project to make libraries for ORIGEN2 code based on the latest nuclear data library `JENDL-3.2` for current design of LWR and FBR fuels. Many of these libraries are under validation. (author)

UMPHE: A Library for Effective Computing On Encrypted Data

Directory of Open Access Journals (Sweden)

Philipp Borisovich Burtyka

2016-03-01

Full Text Available The paper describes the design and implementation of a new software library that implements fully homomorphic encryption schemes based on unilateral matrix polynomials. The library is written in C++ using the NTL mathematical library and has multilayer structure. The main focus is on optimizations and batching techniques. The paper presents novel encryption and key generation algorithms for matrix polynomial based cryptosystems and techniques for data movement between the slots of the ciphertext.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

Science.gov (United States)

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

Iterative optimization of performance libraries by hierarchical division of codes

International Nuclear Information System (INIS)

Donadio, S.

2007-09-01

The increasing complexity of hardware features incorporated in modern processors makes high performance code generation very challenging. Library generators such as ATLAS, FFTW and SPIRAL overcome this issue by empirically searching in the space of possible program versions for the one that performs the best. This thesis explores fully automatic solution to adapt a compute-intensive application to the target architecture. By mimicking complex sequences of transformations useful to optimize real codes, we show that generative programming is a practical tool to implement a new hierarchical compilation approach for the generation of high performance code relying on the use of state-of-the-art compilers. As opposed to ATLAS, this approach is not application-dependant but can be applied to fairly generic loop structures. Our approach relies on the decomposition of the original loop nest into simpler kernels. These kernels are much simpler to optimize and furthermore, using such codes makes the performance trade off problem much simpler to express and to solve. Finally, we propose a new approach for the generation of performance libraries based on this decomposition method. We show that our method generates high-performance libraries, in particular for BLAS. (author)

Croatian library leaders’ views on (their library quality

Directory of Open Access Journals (Sweden)

Kornelija Petr Balog

2014-04-01

Full Text Available The purpose of this paper is to determine and describe the library culture in Croatian public libraries. Semi-structured interviews with 14 library directors (ten public and four academic were conducted. The tentative discussion topics were: definition of quality, responsibility for quality, satisfaction with library services, familiarization with user perspective of library and librarians, monitoring of user expectations and opinions. These interviews incorporate some of the findings of the project Evaluation of library and information services: public and academic libraries. The project investigates library culture in Croatian public and academic libraries and their preparedness for activities of performance measurement. The interviews reveal that library culture has changed positively in the past few years and that library leaders have positive attitude towards quality and evaluation activities. Library culture in Croatian libraries is a relatively new concept and as such was not actively developed and/or created. This article looks into the library culture of Croatian libraries, but at the same time investigates whether there is any trace of culture of assessment in them. Also, this article brings the latest update on views, opinions and atmosphere in Croatian public and academic libraries.

A Validated MCNP(X) Cross Section Library based on JEFF 3.1

International Nuclear Information System (INIS)

Haeck, W.; Verboomen, B.

2006-01-01

ALEPH-LIB is a multi-temperature neutron transport library for standard use by MCNP(X) and ALEPH generated with ALEPH-DLG. This is an auxiliary computer code to ALEPH, the Monte Carlo burn-up code under development at SCK-CEN in collaboration with Ghent university. ALEPH-DLG automates the entire process of generating library files with NJOY and takes care of the first requirement of a validated application library: verify the processing. It produces tailor made NJOY input files using data from the original ENDF file (initial temperature, the fact if the nuclide is fissile or if it has unresolved resonances, etc.) When the library files have been generated, ALEPH-DLG will also process the output from NJOY by extracting all messages and warnings. If ALEPH-DLG finds anything out of the ordinary, it will either warn the user or perform corrective actions. The temperatures included in the ALEPH-LIB library are 300, 600, 900, 1200, 1500 and 1800 K. Library files were produced for the JEF 2.2, JEFF 3.0, JEFF 3.1, JENDL 3.3 and ENDF/B-VI.8 nuclear data libraries. This will be extended with ENDF/B-VII when it becomes available. This report deals with the JEFF 3.1 files included in ALEPH-LIB that are now released by the NEA-OECD.

A Validated MCNP(X) Cross Section Library based on JEFF 3.1

Energy Technology Data Exchange (ETDEWEB)

Haeck, W; Verboomen, B

2006-10-15

ALEPH-LIB is a multi-temperature neutron transport library for standard use by MCNP(X) and ALEPH generated with ALEPH-DLG. This is an auxiliary computer code to ALEPH, the Monte Carlo burn-up code under development at SCK-CEN in collaboration with Ghent university. ALEPH-DLG automates the entire process of generating library files with NJOY and takes care of the first requirement of a validated application library: verify the processing. It produces tailor made NJOY input files using data from the original ENDF file (initial temperature, the fact if the nuclide is fissile or if it has unresolved resonances, etc.) When the library files have been generated, ALEPH-DLG will also process the output from NJOY by extracting all messages and warnings. If ALEPH-DLG finds anything out of the ordinary, it will either warn the user or perform corrective actions. The temperatures included in the ALEPH-LIB library are 300, 600, 900, 1200, 1500 and 1800 K. Library files were produced for the JEF 2.2, JEFF 3.0, JEFF 3.1, JENDL 3.3 and ENDF/B-VI.8 nuclear data libraries. This will be extended with ENDF/B-VII when it becomes available. This report deals with the JEFF 3.1 files included in ALEPH-LIB that are now released by the NEA-OECD.

SNSEDextend: SuperNova Spectral Energy Distributions extrapolation toolkit

Science.gov (United States)

Pierel, Justin D. R.; Rodney, Steven A.; Avelino, Arturo; Bianco, Federica; Foley, Ryan J.; Friedman, Andrew; Hicken, Malcolm; Hounsell, Rebekah; Jha, Saurabh W.; Kessler, Richard; Kirshner, Robert; Mandel, Kaisey; Narayan, Gautham; Filippenko, Alexei V.; Scolnic, Daniel; Strolger, Louis-Gregory

2018-05-01

SNSEDextend extrapolates core-collapse and Type Ia Spectral Energy Distributions (SEDs) into the UV and IR for use in simulations and photometric classifications. The user provides a library of existing SED templates (such as those in the authors' SN SED Repository) along with new photometric constraints in the UV and/or NIR wavelength ranges. The software then extends the existing template SEDs so their colors match the input data at all phases. SNSEDextend can also extend the SALT2 spectral time-series model for Type Ia SN for a "first-order" extrapolation of the SALT2 model components, suitable for use in survey simulations and photometric classification tools; as the code does not do a rigorous re-training of the SALT2 model, the results should not be relied on for precision applications such as light curve fitting for cosmology.

Level 0 to 1 processing of the imaging Fourier transform spectrometer GLORIA: generation of radiometrically and spectrally calibrated spectra

Directory of Open Access Journals (Sweden)

A. Kleinert

2014-12-01

Full Text Available The Gimballed Limb Observer for Radiance Imaging of the Atmosphere (GLORIA is an imaging Fourier transform spectrometer that is capable of operating on various high-altitude research aircraft. It measures the atmospheric emission in the thermal infrared spectral region in limb and nadir geometry. GLORIA consists of a classical Michelson interferometer combined with an infrared camera. The infrared detector has a usable area of 128 × 128 pixels, measuring up to 16 384 interferograms simultaneously. Imaging Fourier transform spectrometers impose a number of challenges with respect to instrument calibration and algorithm development. The optical setup with extremely high optical throughput requires the development of new methods and algorithms for spectral and radiometric calibration. Due to the vast amount of data there is a high demand for scientifically intelligent optimisation of the data processing. This paper outlines the characterisation and processing steps required for the generation of radiometrically and spectrally calibrated spectra. Methods for performance optimisation of the processing algorithm are presented. The performance of the data processing and the quality of the calibrated spectra are demonstrated for measurements collected during the first deployments of GLORIA on aircraft.

SERKON program for compiling a multigroup library to be used in BETTY calculation

International Nuclear Information System (INIS)

Nguyen Phuoc Lan.

1982-11-01

A SERKON-type program was written to compile data sets generated by FEDGROUP-3 into a multigroup library for BETTY calculation. A multigroup library was generated from the ENDF/B-IV data file and tested against the TRX-1 and TRX-2 lattices with good results. (author)

Encoded libraries of chemically modified peptides.

Science.gov (United States)

Heinis, Christian; Winter, Greg

2015-06-01

The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries. Copyright © 2015. Published by Elsevier Ltd.

Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

Science.gov (United States)

O'Hagan, Steve; Kell, Douglas B

2018-01-01

Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley

BIBGTR: nuclear data libraries for the programs Unimug and Anisn

International Nuclear Information System (INIS)

Ono, S.; Caldeira, A.D.

1989-11-01

Nuclear data libraries generable by the NJOY for the programs UNIMUG and ANISN, using evaluated data from ENDF/B-IV and ENDF/B-V are described. These libraries will be used by Radioisotope Thermoelectric Generators Project of Instituto de Estudos Avancados. (author) [pt

MOX Cross-Section Libraries for ORIGEN-ARP

International Nuclear Information System (INIS)

Gauld, I.C.

2003-01-01

The use of mixed-oxide (MOX) fuel in commercial nuclear power reactors operated in Europe has expanded rapidly over the past decade. The predicted characteristics of MOX fuel such as the nuclide inventories, thermal power from decay heat, and radiation sources are required for design and safety evaluations, and can provide valuable information for non-destructive safeguards verification activities. This report describes the development of computational methods and cross-section libraries suitable for the analysis of irradiated MOX fuel with the widely-used and recognized ORIGEN-ARP isotope generation and depletion code of the SCALE (Standardized Computer Analyses for Licensing Evaluation) code system. The MOX libraries are designed to be used with the Automatic Rapid Processing (ARP) module of SCALE that interpolates appropriate values of the cross sections from a database of parameterized cross-section libraries to create a problem-dependent library for the burnup analysis. The methods in ORIGEN-ARP, originally designed for uranium-based fuels only, have been significantly upgraded to handle the larger number of interpolation parameters associated with MOX fuels. The new methods have been incorporated in a new version of the ARP code that can generate libraries for low-enriched uranium (LEU) and MOX fuel types. The MOX data libraries and interpolation algorithms in ORIGEN-ARP have been verified using a database of declared isotopic concentrations for 1042 European MOX fuel assemblies. The methods and data are validated using a numerical MOX fuel benchmark established by the Organization for Economic Cooperation and Development (OECD) Working Group on burnup credit and nuclide assay measurements for irradiated MOX fuel performed as part of the Belgonucleaire ARIANE International Program

Effective Spectral Function for Quasielastic Scattering on Nuclei

OpenAIRE

Bodek, A.; Christy, M. E.; Coopersmith, B.

2014-01-01

Spectral functions that are used in neutrino event generators to model quasielastic (QE) scattering from nuclear targets include Fermi gas, Local Thomas Fermi gas (LTF), Bodek-Ritchie Fermi gas with high momentum tail, and the Benhar-Fantoni two dimensional spectral function. We find that the $\

Simplification of gamma-ray spectral data by using Fourier transform

International Nuclear Information System (INIS)

Tominaga, Shoji; Nagata, Shojiro; Nayatani, Yoshinobu; Ueda, Isamu; Sasaki, Satoshi.

1977-01-01

A method is proposed to represent γ-ray response spectra by Fourier series for the purpose of compressing spectral data. The usefulness of the method was confirmed by applying it to a spectral library of a NaI detector. In the method, a response spectrum as a wave is described by superposition of sine (cosine) waves with low frequencies, whose coefficient parameters can be obtained by a Fast Fourier Transform program. The relation between the number of parameters and the fitting error is discussed, and as the result, it is shown that the number of parameters can be reduced to about a half. The merits and features are presented in practical application of the method to the analysis of γ-ray spectra. (auth.)

One-group constant libraries for nuclear equilibrium state

Energy Technology Data Exchange (ETDEWEB)

Mizutani, Akihiko; Sekimoto, Hiroshi [Tokyo Inst. of Tech. (Japan). Research Lab. for Nuclear Reactors

1997-03-01

One-group constant libraries for the nuclear equilibrium state were generated for both liquid sodium cooled MOX fuel type fast reactor and PWR type thermal reactor with Equilibrium Cell Iterative Calculation System (ECICS) using JENDL-3.2, -3, -2 and ENDF/B-VI nuclear data libraries. ECICS produced one-group constant sets for 129 heavy metal nuclides and 1238 fission products. (author)

ZZ ANSLV, Multigroup Cross Sections Library for ANS Reactor Design Studies

International Nuclear Information System (INIS)

2000-01-01

A - Description of program or function: - Format: AMPX Master Interface Library format. Number of groups: Fine Group (99 energy groups) General Purpose Neutron Library. Materials: H, He, Be, B, Graphite, N, O, Na, Mg, Al, Si, K, Ti, V, Cr, Mn, Fe, Co, Ni, Kr, Zr, Mo, Tc, Ru, Ag, Cd, Cs, Ce, Pr, Pm, Sm, Eu, Hf, Ta, U, C, F, Cu, Sn, Pb, Rh, I, Xe, Nd, Th, Np, Pu, Am, Cm, Bk, Cf, Es, MAFP, WAFP. Origin: ENDF/B-V. - Format: AMPX Master Interface Library format. Number of groups: Broad Group (39 energy groups) General Purpose Neutron Library. Materials: H, He, Be, B, Graphite, N, O, Na, Mg, Al, Si, K, Ti, V, Cr, Mn, Fe, Co, Ni, Kr, Zr, Mo, Tc, Ru, Ag, Cd, Cs, Ce, Pr, Pm, Sm, Eu, Hf, Ta, U, C, F, Cu, Sn, Pb, Rh, I, Xe, Nd, Th, Np, Pu, Am, Cm, Bk, Cf, Es, MAFP, WAFP. Origin: ENDF/B-V. - Format: AMPX Master Interface Library format. Number of groups: Gamma-Ray Interaction (GRI) Library in 44-groups. Materials: H, He, Be, B, C, N, O, Na, Mg, Al, Si, K, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Mo, Ag, Cd, Xe, Sm, Eu, Hf, Ta, Ir, Pb, Th, U, Pu. Origin: ENDF/B-V; LENDL-V evaluations for 12 materials. - Format: AMPX Master Interface Library format. Number of groups: Coupled Library containing (CNG) 99-group neutron and 44-group gamma-ray data. Materials: H, Be, B, C, N, O, Na, Mg, Al, Si, K, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Mo, Ag, Cd, Eu, Hf, Ta, Pb, Th, U, Pu. Origin: ENDF/B-V. - Format: AMPX Master Interface Library format. Number of groups: Coupled neutron-gamma (CNG) Library containing 39-group, and 44-group gamma-ray data. Materials: H, Be, B, C, N, O, Na, Mg, Al, Si, K, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Mo, Ag, Cd, Eu, Hf, Ta, Pb, Th, U, Pu. Origin: ENDF/B-V. Weighting spectrum: Maxwellian 300 K + 1/(E*sigma-total) + fission spectrum4 types of boundaries have been used depending isotope and library type (see report). Pseudo-problem-independent, multigroup cross section libraries were generated to support the Advanced Neutron source (ANS) reactor design studies. The ANS was

ZZ TEMPEST/MUFT, Thermal Neutron and Fast Neutron Multigroup Cross-Section Library for Program LEOPARD

International Nuclear Information System (INIS)

Kim, Jung-Do; Lee, Jong Tai

1986-01-01

Description of problem or function: Format: TEMPEST and MUFT; Number of groups: 246 thermal groups in TEMPEST Format and 54 fast groups in MUFT Format. From this library, the program SPOTS4 generates a 172-54 group library as input to the code LEOPARD. Nuclides: H, O, Zr, C, Fe, Ni, Al, Cr, Mn, U, Pu, Th, Pa, Xe, Sm, B and D. Origin: ENDF/B-4; Weighting spectrum: 1/E + U 235 fission spectrum. Data library of thermal and fast neutron group Cross sections to generate input to the program LEOPARD. The data is based on ENDF/B-4 and consists of two parts: (1) 246 thermal groups in TEMPEST Format. (2) 54 fast groups in MUFT Format. From this library, the program SPOTS4 generates a 172-54 group library as input to the code LEOPARD (NESC0279)

Library Information System Time-Sharing (LISTS) Project. Final Report.

Science.gov (United States)

Black, Donald V.

The Library Information System Time-Sharing (LISTS) experiment was based on three innovations in data processing technology: (1) the advent of computer time-sharing on third-generation machines, (2) the development of general-purpose file-management software and (3) the introduction of large, library-oriented data bases. The main body of the…

Canute Rules the Waves?: Hope for E-Library Tools Facing the Challenge of the "Google Generation"

Science.gov (United States)

Myhill, Martin

2007-01-01

Purpose: To consider the findings of a recent e-resources survey at the University of Exeter Library in the context of the dominance of web search engines in academia, balanced by the development of e-library tools such as the library OPAC, OpenURL resolvers, metasearch engines, LDAP and proxy servers, and electronic resource management modules.…

The Chandra X-ray Observatory PSF Library

Science.gov (United States)

Karovska, M.; Beikman, S. J.; Elvis, M. S.; Flanagan, J. M.; Gaetz, T.; Glotfelty, K. J.; Jerius, D.; McDowell, J. C.; Rots, A. H.

Pre-flight and on-orbit calibration of the Chandra X-Ray Observatory provided a unique base for developing detailed models of the optics and detectors. Using these models we have produced a set of simulations of the Chandra point spread function (PSF) which is available to the users via PSF library files. We describe here how the PSF models are generated and the design and content of the Chandra PSF library files.

Intrinsic Chirality and Prochirality at Air/R-(+)- and S-(-)-Limonene Interfaces: Spectral Signatures with Interference Chiral Sum-Frequency Generation Vibrational Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Fu, Li; Zhang, Yun; Wei, Zhehao; Wang, Hongfei

2014-06-04

We report in this work detailed measurements on the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800-3050cm-1) of the air/liquid interfaces of R-limonene and S-limonene, using the recently developed high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS). The achiral SFG spectra of R-limonene and S-limonene, as well as the equal amount (50/50) racemic mixture show that the enantiomers are with the same interfacial orientations. The interference chiral SFG spectra of the limonene enantiomers exhibit spectral signature from chiral response of the Cα-H stretching mode, and spectral signature from prochiral response of the CH2 asymmetric stretching mode, respectively. The chiral spectral feature of the Cα-H stretching mode changes sign from R-limonene to S-limonene, and disappears for the 50/50 racemic mixture. While the prochiral spectral feature of the CH2 asymmetric stretching mode is the same for R-limonene and S-limonene, and also surprisingly remains the same for the 50/50 racemic mixture. These results provided detail information in understanding the structure and chirality of molecular interfaces, and demonstrated the sensitivity and potential of SFG-VS as unique spectroscopic tool for chirality characterization and chiral recognition at the molecular interface.

An expert computer program for classifying stars on the MK spectral classification system

International Nuclear Information System (INIS)

Gray, R. O.; Corbally, C. J.

2014-01-01

This paper describes an expert computer program (MKCLASS) designed to classify stellar spectra on the MK Spectral Classification system in a way similar to humans—by direct comparison with the MK classification standards. Like an expert human classifier, the program first comes up with a rough spectral type, and then refines that spectral type by direct comparison with MK standards drawn from a standards library. A number of spectral peculiarities, including barium stars, Ap and Am stars, λ Bootis stars, carbon-rich giants, etc., can be detected and classified by the program. The program also evaluates the quality of the delivered spectral type. The program currently is capable of classifying spectra in the violet-green region in either the rectified or flux-calibrated format, although the accuracy of the flux calibration is not important. We report on tests of MKCLASS on spectra classified by human classifiers; those tests suggest that over the entire HR diagram, MKCLASS will classify in the temperature dimension with a precision of 0.6 spectral subclass, and in the luminosity dimension with a precision of about one half of a luminosity class. These results compare well with human classifiers.

An expert computer program for classifying stars on the MK spectral classification system

Energy Technology Data Exchange (ETDEWEB)

Gray, R. O. [Department of Physics and Astronomy, Appalachian State University, Boone, NC 26808 (United States); Corbally, C. J. [Vatican Observatory Research Group, Tucson, AZ 85721-0065 (United States)

2014-04-01

This paper describes an expert computer program (MKCLASS) designed to classify stellar spectra on the MK Spectral Classification system in a way similar to humans—by direct comparison with the MK classification standards. Like an expert human classifier, the program first comes up with a rough spectral type, and then refines that spectral type by direct comparison with MK standards drawn from a standards library. A number of spectral peculiarities, including barium stars, Ap and Am stars, λ Bootis stars, carbon-rich giants, etc., can be detected and classified by the program. The program also evaluates the quality of the delivered spectral type. The program currently is capable of classifying spectra in the violet-green region in either the rectified or flux-calibrated format, although the accuracy of the flux calibration is not important. We report on tests of MKCLASS on spectra classified by human classifiers; those tests suggest that over the entire HR diagram, MKCLASS will classify in the temperature dimension with a precision of 0.6 spectral subclass, and in the luminosity dimension with a precision of about one half of a luminosity class. These results compare well with human classifiers.

Libraries for users services in academic libraries

CERN Document Server

Alvite, Luisa

2010-01-01

This book reviews the quality and evolution of academic library services. It revises service trends offered by academic libraries and the challenge of enhancing traditional ones such as: catalogues, repositories and digital collections, learning resources centres, virtual reference services, information literacy and 2.0 tools.studies the role of the university library in the new educational environment of higher educationrethinks libraries in academic contextredefines roles for academic libraries

Generation of consistent nuclear properties of DUPIC fuel by DRAGON with ENDF/B-VI nuclear data library

International Nuclear Information System (INIS)

Shen, W.; Rozon, D.

1998-01-01

DRAGON code with 89-groups ENDF/B-VI cross section library was used in this paper to generate consistent nuclear properties of DUPIC fuel. The reference feed material used for the DUPIC fuel cycle is a 17x17 French standard 900 MWe PWR spent fuel assembly with 3.2 w/o initial enrichment and 32500 MWD/7 discharge burnup. The PWR fuel assembly was modeled by JPMT/SYBILT transport method in DRAGON to generate nuclide fields of spent PWR fuel. The resultant nuclide fields constitute the initial fuel composition files for reference DUPIC fuel which can be accessed by DRAGON for CANDU 2D cluster geometry depletion calculation and 3D supercell calculation. Because of uneven spatial power distribution in PWR assemblies and full core, unexpected transition cycle, and various fuel management strategy, the spent PWR fuel composition is expected to be different from one assembly to the next. This heterogeneity was characterized also by modeling various spent PWR fuel assembly types in the paper. (author)

Self-phase-modulation induced spectral broadening in silicon waveguides

Science.gov (United States)

Boyraz, Ozdal; Indukuri, Tejaswi; Jalali, Bahram

2004-03-01

The prospect for generating supercontinuum pulses on a silicon chip is studied. Using ~4ps optical pulses with 2.2GW/cm2 peak power, a 2 fold spectral broadening is obtained. Theoretical calculations, that include the effect of two-photon-absorption, indicate up to 5 times spectral broadening is achievable at 10x higher peak powers. Representing a nonlinear loss mechanism at high intensities, TPA limits the maximum optical bandwidth that can be generated.

ADL-3. Nuclear data library for activation and transmutation calculations

International Nuclear Information System (INIS)

Grudzevich, O.T.; Zelenetskij, A.V.; Ignatyuk, A.V.; Pashchenko, A.B.

1995-07-01

It is shown that the use of simplified approaches to calculate threshold neutron reaction cross-sections is not acceptable for the generation of cross-section libraries. Although rigorous models are complex and involve laborious calculations, they provide the only reliable means for evaluating cross-sections when no experimental data are available. A brief description is given of the new version of the library ADL-3 generated by the authors. It contains 18,200 excitation functions of reactions induced by neutrons of up to 20 MeV. The threshold reaction cross-sections have been calculated in the Hauser-Feshbach-Moldauer formalism with allowance for the contribution of non-equilibrium processes. The cross-sections obtained have been tested by comparison with experimental data and evaluations from other libraries. (author)

Updating of the LEOPARD data library

International Nuclear Information System (INIS)

Henrique Claro, L.; Cunha Menezes Filho, A. da

1984-01-01

The LEOPARD library is being updated and tested for typical PWR unit cells with enrichments ranging from 1.0 to 4.1%(W/o) and H 2 O:U ratios varying from 1.0 to 10.0. A reasonably good agreement with experimental values for some spectral indices is obtained if the fission cross-section of 235 U is reduced by 0.6% in the thermal range and by 20% in the epithermal range, the epithermal capture cross-section for 235 U is increased by about 20% and the number of neutrons per fission in the thermal range of 235 U is increased by 0.8%. (author)

The moderization of the Leopard library

International Nuclear Information System (INIS)

Claro, L.H.; Cunha Menezes Filho, A. da.

1983-07-01

The LEOPARD library is updated and tested for typical PWR unit cells with enrichment ranging from 1.0 to 4.%(W/o) and H 2 O:U ratio varying from 1.0 to 10.0. A reasonably good agreement with experimental values for some spectral indices is obtained if the fission cross section of U-235 is reduced by .6% in the thermal range and by 20% in the epithermal range; the epithermal capture cross section for U-238 is increased by about 20% and the number of neutrons per fission in the thermal range of U-235 is increased by .8%. (Author) [pt

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

Energy Technology Data Exchange (ETDEWEB)

Ting, Ying S.; Egertson, Jarrett D.; Bollinger, James G.; Searle, Brian C.; Payne, Samuel H.; Noble, William Stafford; MacCoss, Michael J.

2017-08-07

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECECAN to build a plasma proteome library from DIA data and to query known sequence variants.

Thermal reactor benchmark testing of 69 group library

International Nuclear Information System (INIS)

Liu Guisheng; Wang Yaoqing; Liu Ping; Zhang Baocheng

1994-01-01

Using a code system NSLINK, AMPX master library in WIMS 69 groups structure are made from nuclides relating to 4 newest evaluated nuclear data libraries. Some integrals of 10 thermal reactor benchmark assemblies recommended by the U.S. CSEWG are calculated using rectified PASC-1 code system and compared with foreign results, the authors results are in good agreement with others. 69 group libraries of evaluated data bases in TPFAP interface file are generated with NJOY code system. The k ∞ values of 6 cell lattice assemblies are calculated by the code CBM. The calculated results are analysed and compared

Design issues for numerical libraries on scalable multicore architectures

International Nuclear Information System (INIS)

Heroux, M A

2008-01-01

Future generations of scalable computers will rely on multicore nodes for a significant portion of overall system performance. At present, most applications and libraries cannot exploit multiple cores beyond running addition MPI processes per node. In this paper we discuss important multicore architecture issues, programming models, algorithms requirements and software design related to effective use of scalable multicore computers. In particular, we focus on important issues for library research and development, making recommendations for how to effectively develop libraries for future scalable computer systems

Voltage Spectral Structure as a Parameter of System Technical Diagnostics of Ship Diesel Engine-Synchronous Generators

Directory of Open Access Journals (Sweden)

Gasparjans Aleksandrs

2015-07-01

Full Text Available A method of technical diagnostics of ship diesel engine – generator installation – is proposed. Spectral-power diagnostic parameters of the synchronous generator voltage and currents are used. The electric machine in this case is the multipurpose sensor of diagnostic parameters. A judgment on the quality of the operational processes in diesel engine cylinders and its technical condition is possible on the basis of these parameters. This method is applicable to piston compressor installations with electric drive. On the basis of such parameters as rotating torque, angular speed and angular acceleration it is possible to estimate the quality of the operating process in the cylinders of a diesel engine, the condition of its cylinder-piston group and the crank gear mechanism. The investigation was realized on the basis of a diesel-generator with linear load. The generator operation was considered for the case of constant RL load. Together with the above mentioned, the condition of bearings of synchronous machines, uniformity of the air gap, windings of the electric machine were estimated during the experiments as well. The frequency spectrum of the stator current of the generator was researched and analyzed. In this case the synchronous machine is becoming a rather exact multipurpose diagnostic sensor. The signal of non-uniformity in the operation process of diesel engine cylinders and its technical condition is the increasing of the amplitudes of typical frequencies.

SCHOOL COMMUNITY PERCEPTION OF LIBRARY APPS AGAINTS LIBRARY EMPOWERMENT

Directory of Open Access Journals (Sweden)

Achmad Riyadi Alberto

2017-07-01

Full Text Available Abstract. This research is motivated by the development of information and communication technology (ICT in the library world so rapidly that allows libraries in the present to develop its services into digital-based services. This study aims to find out the school community’s perception of library apps developed by Riche Cynthia Johan, Hana Silvana, and Holin Sulistyo and its influence on library empowerment at the library of SD Laboratorium Percontohan UPI Bandung. Library apps in this research belong to the context of m-libraries, which is a library that meets the needs of its users by using mobile platforms such as smartphones,computers, and other mobile devices. Empowerment of library is the utilization of all aspects of the implementation of libraries to the best in order to achieve the expected goals. An analysis of the schoolcommunity’s perception of library apps using the Technology Acceptance Model (TAM includes: ease of use, usefulness, usability, usage trends, and real-use conditions. While the empowerment of the library includes aspects: information empowerment, empowerment of learning resources, empowerment of human resources, empowerment of library facilities, and library promotion. The research method used in this research is descriptive method with quantitative approach. Population and sample in this research is school community at SD Laboratorium Percontohan UPI Bandung. Determination of sample criteria by using disproportionate stratified random sampling with the number of samples of 83 respondents. Data analysis using simple linear regression to measure the influence of school community perception about library apps to library empowerment. The result of data analysis shows that there is influence between school community perception about library apps to library empowerment at library of SD Laboratorium Percontohan UPI Bandung which is proved by library acceptance level and library empowerment improvement.

cDNA library information - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Dicty_cDB cDNA library information Data detail Data name cDNA library information DOI 10.189...s Data item Description cDNA library name Names of cDNA libraries (AF, AH, CF, CH, FC, FC-IC, FCL, SF, SH, S...(C) 5) sexually fusion-competent KAX3 cells (Gamete phase) (F) cDNA library construction method How to construct cDNA library...dir) 2) Full-length cDNA libraries (oligocapped method)(fl) 3) Gamete-specific subtraction library (sub) cDNA library... construction protocol Link to the webpage describing the protocol for generating cDNA library Size

Spectrally- and Time-Resolved Sum Frequency Generation (STiR-SFG): a new tool for ultrafast hydrogen bond dynamics at interfaces.

Science.gov (United States)

Benderskii, Alexander; Bordenyuk, Andrey; Weeraman, Champika

2006-03-01

The recently developed spectrally- and time-resolved Sum Frequency Generation (STiR-SFG) is a surface-selective 3-wave mixing (IR+visible) spectroscopic technique capable of measuring ultrafast spectral evolution of vibrational coherences. A detailed description of this measurement will be presented, and a noniterative method or deconvolving the laser pulses will be introduced to obtain the molecular response function. STiR-SFG, combined with the frequency-domain SFG spectroscopy, was applied to study hydrogen bonding dynamics at aqueous interfaces (D2O/CaF2). Spectral dynamics of the OD-stretch on the 50-150 fs time scale provides real-time observation of ultrafast H-bond rearrangement. Tuning the IR wavelength to the blue or red side of the OD-stretch transition, we selectively monitor the dynamics of different sub-ensembles in the distribution of the H-bond structures. The blue-side excitation (weaker H-bonding) shows monotonic red-shift of the OD-frequency. In contrast, the red-side excitation (stronger H-bonding structures) produces a blue-shift and a recursion, which may indicate the presence of an underdamped intermolecular mode of interfacial water. Effect of electrolyte concentration on the H-bond dynamics will be discussed.

ℓ0 -based sparse hyperspectral unmixing using spectral information and a multi-objectives formulation

Science.gov (United States)

Xu, Xia; Shi, Zhenwei; Pan, Bin

2018-07-01

Sparse unmixing aims at recovering pure materials from hyperpspectral images and estimating their abundance fractions. Sparse unmixing is actually ℓ0 problem which is NP-h ard, and a relaxation is often used. In this paper, we attempt to deal with ℓ0 problem directly via a multi-objective based method, which is a non-convex manner. The characteristics of hyperspectral images are integrated into the proposed method, which leads to a new spectra and multi-objective based sparse unmixing method (SMoSU). In order to solve the ℓ0 norm optimization problem, the spectral library is encoded in a binary vector, and a bit-wise flipping strategy is used to generate new individuals in the evolution process. However, a multi-objective method usually produces a number of non-dominated solutions, while sparse unmixing requires a single solution. How to make the final decision for sparse unmixing is challenging. To handle this problem, we integrate the spectral characteristic of hyperspectral images into SMoSU. By considering the spectral correlation in hyperspectral data, we improve the Tchebycheff decomposition function in SMoSU via a new regularization item. This regularization item is able to enforce the individual divergence in the evolution process of SMoSU. In this way, the diversity and convergence of population is further balanced, which is beneficial to the concentration of individuals. In the experiments part, three synthetic datasets and one real-world data are used to analyse the effectiveness of SMoSU, and several state-of-art sparse unmixing algorithms are compared.

Design criteria for the 218-group criticality safety reference library

International Nuclear Information System (INIS)

Westfall, R.M.; Ford, W.E. III; Webster, C.C.

1978-01-01

The generation of a 218-group neutron cross-section library from ENDF/B-IV data is described. Experience in selecting broad-group subsets and applying them in the analysis of critical experiments is related. Recommendations on the use of the 218-group library are made. 3 figures, 5 tables

Scientific writing and editing: a new role for the library.

Science.gov (United States)

Stephens, P A; Campbell, J M

1995-10-01

Traditional library instruction programs teach scientists how to find and manage information, but not how to report their research findings effectively. Since 1990, the William H. Welch Medical Library has sponsored classes on scientific writing and, since 1991, has offered a fee-based editing service for affiliates of the Johns Hopkins Medical Institutions. These programs were designed to fill an educational gap: Although formal instruction was offered to support other phases of the scientific communication process, the medical institutions had no central resource designed to help scientists develop and improve their writing skills. The establishment of such a resource at Welch has been well received by the community. Attendance at classes has grown steadily, and in 1993 a credit course on biomedical writing was added to the curriculum. The editing service, introduced in late 1991, has generated more requests for assistance than can be handled by the library's editor. This service not only extends the library's educational outreach but also generates a revenue stream. The Welch program in scientific writing and editing, or elements of it, could provide a model for other academic medical libraries interested in moving in this new direction.

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

Science.gov (United States)

Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

2012-01-01

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

Are You Building Your Library with the Right Stuff?

Science.gov (United States)

Abram, Stephen

1999-01-01

Outlines technology trends affecting library marketing: change is too slow; education is out/learning is in; the next generation are "NextHeads"; the next generation is different; change cannot be managed generationally; "virtual" is place, not format; communities of interest are not bounded by geography; new brands are…

The even and the odd spectral flows on the N=2 superconformal algebras

International Nuclear Information System (INIS)

Gato-Rivera, B.

1998-01-01

There are two different spectral flows on the N=2 superconformal algebras (four in the case of the topological algebra). The usual spectral flow, first considered by Schwimmer and Seiberg, is an even transformation, whereas the spectral flow previously considered by the author and Rosado is an odd transformation. We show that the even spectral flow is generated by the odd spectral flow, and therefore only the latter is fundamental. We also analyze thoroughly the four ''topological'' spectral flows, writing two of them here for the first time. Whereas the even and the odd spectral flows have quasi-mirrored properties acting on the antiperiodic or the periodic algebras, the topological even and odd spectral flows have drastically different properties acting on the topological algebra. The other two topological spectral flows have mixed even and odd properties. We show that the even and the even-odd topological spectral flows are generated by the odd and the odd-even topological spectral flows, and therefore only the latter are fundamental. (orig.)

Spectral Feature Analysis of Minerals and Planetary Surfaces in an Introductory Planetary Science Course

Science.gov (United States)

Urban, Michael J.

2013-01-01

Using an ALTA II reflectance spectrometer, the USGS digital spectral library, graphs of planetary spectra, and a few mineral hand samples, one can teach how light can be used to study planets and moons. The author created the hands-on, inquiry-based activity for an undergraduate planetary science course consisting of freshman to senior level…

Substitution dynamical systems spectral analysis

CERN Document Server

Queffélec, Martine

2010-01-01

This volume mainly deals with the dynamics of finitely valued sequences, and more specifically, of sequences generated by substitutions and automata. Those sequences demonstrate fairly simple combinatorical and arithmetical properties and naturally appear in various domains. As the title suggests, the aim of the initial version of this book was the spectral study of the associated dynamical systems: the first chapters consisted in a detailed introduction to the mathematical notions involved, and the description of the spectral invariants followed in the closing chapters. This approach, combined with new material added to the new edition, results in a nearly self-contained book on the subject. New tools - which have also proven helpful in other contexts - had to be developed for this study. Moreover, its findings can be concretely applied, the method providing an algorithm to exhibit the spectral measures and the spectral multiplicity, as is demonstrated in several examples. Beyond this advanced analysis, many...

ANITA-2000 activation code package - updating of the decay data libraries and validation on the experimental data of the 14 MeV Frascati Neutron Generator

Directory of Open Access Journals (Sweden)

Frisoni Manuela

2016-01-01

Full Text Available ANITA-2000 is a code package for the activation characterization of materials exposed to neutron irradiation released by ENEA to OECD-NEADB and ORNL-RSICC. The main component of the package is the activation code ANITA-4M that computes the radioactive inventory of a material exposed to neutron irradiation. The code requires the decay data library (file fl1 containing the quantities describing the decay properties of the unstable nuclides and the library (file fl2 containing the gamma ray spectra emitted by the radioactive nuclei. The fl1 and fl2 files of the ANITA-2000 code package, originally based on the evaluated nuclear data library FENDL/D-2.0, were recently updated on the basis of the JEFF-3.1.1 Radioactive Decay Data Library. This paper presents the results of the validation of the new fl1 decay data library through the comparison of the ANITA-4M calculated values with the measured electron and photon decay heats and activities of fusion material samples irradiated at the 14 MeV Frascati Neutron Generator (FNG of the NEA-Frascati Research Centre. Twelve material samples were considered, namely: Mo, Cu, Hf, Mg, Ni, Cd, Sn, Re, Ti, W, Ag and Al. The ratios between calculated and experimental values (C/E are shown and discussed in this paper.

Vision Egg: an open-source library for realtime visual stimulus generation

Directory of Open Access Journals (Sweden)

Andrew D Straw

2008-11-01

Full Text Available Modern computer hardware makes it possible to produce visual stimuli in ways not previously possible. Arbitrary scenes, from traditional sinusoidal gratings to naturalistic 3D scenes can now be specified on a frame-by-frame basis in realtime. I have developed a programming library called the Vision Egg that aims to make it easy to take advantage of these innovations. The Vision Egg is a free, open-source library making use of OpenGL and written in the high-level language Python with extensions in C. Careful attention has been paid to the issues of luminance and temporal calibration, and several interfacing techniques to input devices such as mice, movement tracking systems, and digital triggers are discussed. Together, these make the Vision Egg suitable for many psychophysical, electrophysiological, and behavioral experiments. This software is available for free download at http://www.visionegg.org/.

Planetary Image Geometry Library

Science.gov (United States)

Deen, Robert C.; Pariser, Oleg

2010-01-01

The Planetary Image Geometry (PIG) library is a multi-mission library used for projecting images (EDRs, or Experiment Data Records) and managing their geometry for in-situ missions. A collection of models describes cameras and their articulation, allowing application programs such as mosaickers, terrain generators, and pointing correction tools to be written in a multi-mission manner, without any knowledge of parameters specific to the supported missions. Camera model objects allow transformation of image coordinates to and from view vectors in XYZ space. Pointing models, specific to each mission, describe how to orient the camera models based on telemetry or other information. Surface models describe the surface in general terms. Coordinate system objects manage the various coordinate systems involved in most missions. File objects manage access to metadata (labels, including telemetry information) in the input EDRs and RDRs (Reduced Data Records). Label models manage metadata information in output files. Site objects keep track of different locations where the spacecraft might be at a given time. Radiometry models allow correction of radiometry for an image. Mission objects contain basic mission parameters. Pointing adjustment ("nav") files allow pointing to be corrected. The object-oriented structure (C++) makes it easy to subclass just the pieces of the library that are truly mission-specific. Typically, this involves just the pointing model and coordinate systems, and parts of the file model. Once the library was developed (initially for Mars Polar Lander, MPL), adding new missions ranged from two days to a few months, resulting in significant cost savings as compared to rewriting all the application programs for each mission. Currently supported missions include Mars Pathfinder (MPF), MPL, Mars Exploration Rover (MER), Phoenix, and Mars Science Lab (MSL). Applications based on this library create the majority of operational image RDRs for those missions. A

Generation of response functions of a NaI detector by using an interpolation technique

International Nuclear Information System (INIS)

Tominaga, Shoji

1983-01-01

A computer method is developed for generating response functions of a NaI detector to monoenergetic γ-rays. The method is based on an interpolation between measured response curves by a detector. The computer programs are constructed for Heath's response spectral library. The principle of the basic mathematics used for interpolation, which was reported previously by the author, et al., is that response curves can be decomposed into a linear combination of intrinsic-component patterns, and thereby the interpolation of curves is reduced to a simple interpolation of weighting coefficients needed to combine the component patterns. This technique has some advantages of data compression, reduction in computation time, and stability of the solution, in comparison with the usual functional fitting method. The processing method of segmentation of a spectrum is devised to generate useful and precise response curves. A spectral curve, obtained for each γ-ray source, is divided into some regions defined by the physical processes, such as the photopeak area, the Compton continuum area, the backscatter peak area, and so on. Each segment curve then is processed separately for interpolation. Lastly the estimated curves to the respective areas are connected on one channel scale. The generation programs are explained briefly. It is shown that the generated curve represents the overall shape of a response spectrum including not only its photopeak but also the corresponding Compton area, with a sufficient accuracy. (author)

Generation and evaluation of mammalian secreted and membrane protein expression libraries for high-throughput target discovery.

Science.gov (United States)

Panavas, Tadas; Lu, Jin; Liu, Xuesong; Winkis, Ann-Marie; Powers, Gordon; Naso, Michael F; Amegadzie, Bernard

2011-09-01

Expressed protein libraries are becoming a critical tool for new target discovery in the pharmaceutical industry. In order to get the most meaningful and comprehensive results from protein library screens, it is essential to have library proteins in their native conformation with proper post-translation modifications. This goal is achieved by expressing untagged human proteins in a human cell background. We optimized the transfection and cell culture conditions to maximize protein expression in a 96-well format so that the expression levels were comparable with the levels observed in shake flasks. For detection purposes, we engineered a 'tag after stop codon' system. Depending on the expression conditions, it was possible to express either native or tagged proteins from the same expression vector set. We created a human secretion protein library of 1432 candidates and a small plasma membrane protein set of about 500 candidates. Utilizing the optimized expression conditions, we expressed and analyzed both libraries by SDS-PAGE gel electrophoresis and Western blotting. Two thirds of secreted proteins could be detected by Western-blot analyses; almost half of them were visible on Coomassie stained gels. In this paper, we describe protein expression libraries that can be easily produced in mammalian expression systems in a 96-well format, with one protein expressed per well. The libraries and methods described allow for the development of robust, high-throughput functional screens designed to assay for protein specific functions associated with a relevant disease-specific activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Photonic linear chirped microwave signal generation based on the ultra-compact spectral shaper using the slow light effect

DEFF Research Database (Denmark)

Yan, Siqi; Gao, Shengqian; Zhou, Feng

2017-01-01

A novel concept to generate a linear chirped microwave signal is proposed and experimentally demonstrated. The frequency to time mapping method is employed, where the photonic crystal waveguide Mach-Zehnder interferometer structure acts as the spectral shaper thanks to the slow light effect. By o....... The utilization of the slow light effect brings in significant advantages, including the ultra-small footprint of 0.096 mm(2) and simple structure to our scheme, which may be of great importance towards its potential applications. (C) 2017 Optical Society of America...

FCXSEC: multigroup cross-section libraries for nuclear fuel cycle shielding calculations

International Nuclear Information System (INIS)

Ford, W.E. III; Webster, C.C.; Diggs, B.R.; Pevey, R.E.; Croff, A.G.

1980-05-01

Starting with the pseudo-composition-independent VITAMIN-C cross-sectin library, composition-dependent fine-(171n-36γ) and broad-group (22n-21γ) self-shielded AMPX master, broad-group microscopic ANISN-formatted, and broad-group macroscopic ANISN-formatted cross-section libraries were generated to be used for nuclear fuel cycle shielding calculations. The specifications for the data and the procedure used to prepare the libraries are described

Reanalysis of the gas-cooled fast reactor experiments at the zero power facility proteus - Spectral indices

Energy Technology Data Exchange (ETDEWEB)

Perret, G.; Pattupara, R. M. [Paul Scherrer Inst., 5232 Villigen (Switzerland); Girardin, G. [Ecole Polytechnique Federale de Lausanne, 1015 Lausanne (Switzerland); Chawla, R. [Paul Scherrer Inst., 5232 Villigen (Switzerland); Ecole Polytechnique Federale de Lausanne, 1015 Lausanne (Switzerland)

2012-07-01

The gas-cooled fast reactor (GCFR) concept was investigated experimentally in the PROTEUS zero power facility at the Paul Scherrer Inst. during the 1970's. The experimental program was aimed at neutronics studies specific to the GCFR and at the validation of nuclear data in fast spectra. A significant part of the program used thorium oxide and thorium metal fuel either distributed quasi-homogeneously in the reference PuO{sub 2}/UO{sub 2} lattice or introduced in the form of radial and axial blanket zones. Experimental results obtained at the time are still of high relevance in view of the current consideration of the Gas-cooled Fast Reactor (GFR) as a Generation-IV nuclear system, as also of the renewed interest in the thorium cycle. In this context, some of the experiments have been modeled with modern Monte Carlo codes to better account for the complex PROTEUS whole-reactor geometry and to allow validating recent continuous neutron cross-section libraries. As a first step, the MCNPX model was used to test the JEFF-3.1, JEFF-3.1.1, ENDF/B-VII.0 and JENDL-3.3 libraries against spectral indices, notably involving fission and capture of {sup 232}Th and {sup 237}Np, measured in GFR-like lattices. (authors)

Self-referencing, spectrally, or spatially encoded spectral interferometry for the complete characterization of attosecond electromagnetic pulses

International Nuclear Information System (INIS)

Cormier, Eric; Walmsley, Ian A.; Wyatt, Adam S.; Corner, Laura; Kosik, Ellen M.; DiMauro, Louis F.

2005-01-01

We propose a method for the complete characterization of attosecond duration electromagnetic pulses produced by high harmonic generation in an atomic gas. Our method is based on self-referencing spectral interferometry of two spectrally sheared extreme ultraviolet pulses, which is achieved by pumping the harmonic source with two sheared optical driving pulses. The resulting interferogram contains sufficient information to completely reconstruct the temporal behavior of the electric field. We demonstrate that such a method is feasible, and outline two possible experimental configurations

Welcome to the National Wetlands Research Center Library: Not Just Another Library-A Special Library

Science.gov (United States)

Broussard, Linda

2007-01-01

Libraries are grouped into four major types: public, school, academic, and special. The U.S. Geological Survey's (USGS) National Wetlands Research Center (NWRC) library is classified as a special library because it is sponsored by the Federal government, and the collections focus on a specific subject. The NWRC library is the only USGS library dedicated to wetland science. Library personnel offer expert research services to meet the informational needs of NWRC scientists, managers, and support personnel. The NWRC library participates in international cataloging and resource sharing, which allows libraries from throughout the world to borrow from its collections. This sharing facilitates the research of other governmental agencies, universities, and those interested in the study of wetlands.

An in silico MS/MS library for automatic annotation of novel FAHFA lipids.

Science.gov (United States)

Ma, Yan; Kind, Tobias; Vaniya, Arpana; Gennity, Ingrid; Fahrmann, Johannes F; Fiehn, Oliver

2015-01-01

A new lipid class named 'fatty acid esters of hydroxyl fatty acids' (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens, a tandem mass spectra (MS/MS) library is needed. Due to the limitation of the commercial available standard compounds, we proposed building an in silico MS/MS library to extend the coverage of molecules. We developed a computer-generated library with 3267 tandem mass spectra (MS/MS) for 1089 FAHFA species. FAHFA spectra were generated based on authentic standards with negative mode electrospray ionization and 10, 20, and 40 V collision induced dissociation at 4 spectra/s as used in in ultra-high performance liquid chromatography-QTOF mass spectrometry studies. However, positional information of the hydroxyl group is only obtained either at lower QTOF spectra acquisition rates of 1 spectrum/s or at the MS(3) level in ion trap instruments. Therefore, an additional set of 4290 fragment-rich MS/MS spectra was created to enable distinguishing positional FAHFA isomers. The library was generated based on ion fragmentations and ion intensities of FAHFA external reference standards, developing a heuristic model for fragmentation rules and extending these rules to large swaths of computer-generated structures of FAHFAs with varying chain lengths, degrees of unsaturation and hydroxyl group positions. Subsequently, we validated the new in silico library by discovering several new FAHFA species in egg yolk, showing that this library enables high-throughput screening of FAHFA lipids in various biological matrices. The developed library and templates are freely available for commercial or noncommercial use at http://fiehnlab.ucdavis.edu/staff/yanma/fahfa-lipid-library. This in silico MS/MS library allows users to annotate FAHFAs from accurate mass tandem mass spectra in an easy and fast manner

Endf/B-VII.0 Based Library for Paragon - 313

International Nuclear Information System (INIS)

Huria, H.C.; Kucukboyaci, V.N.; Ouisloumen, M.

2010-01-01

A new 70-group library has been generated for the Westinghouse lattice physics code PARAGON using the ENDF/B-VII.0 nuclear data files. The new library retains the major features of the current library, including the number of energy groups and the reduction in the U-238 resonance integral. The upper bound for the up-scattering effects in the new library, however, has been moved to 4.0 eV from 2.1 eV for better MOX fuel predictions. The new library has been used to analyze standard benchmarks and also to compare the measured and predicted parameters for different types of Westinghouse and Combustion Engineering (CE) type operating reactor cores. Results indicate that the new library will not impact the reactivity, power distribution and the temperature coefficient predictions over a wide range of physics design parameters; however, will improve the MOX core predictions. In other words, the ENDF/B-VI.3 and ENDF/B-VII.0 produce similar results for reactor core calculations. (authors)

Assessing Library Automation and Virtual Library Development in Four Academic Libraries in Oyo, Oyo State, Nigeria

Science.gov (United States)

Gbadamosi, Belau Olatunde

2011-01-01

The paper examines the level of library automation and virtual library development in four academic libraries. A validated questionnaire was used to capture the responses from academic librarians of the libraries under study. The paper discovers that none of the four academic libraries is fully automated. The libraries make use of librarians with…

Spectral correlations in Anderson insulating wires

Science.gov (United States)

Marinho, M.; Micklitz, T.

2018-01-01

We calculate the spectral level-level correlation function of Anderson insulating wires for all three Wigner-Dyson classes. A measurement of its Fourier transform, the spectral form factor, is within reach of state-of-the-art cold atom quantum quench experiments, and we find good agreement with recent numerical simulations of the latter. Our derivation builds on a representation of the level-level correlation function in terms of a local generating function which may prove useful in other contexts.

ANSL-V: ENDF/B-V based multigroup cross-section libraries for Advanced Neutron Source (ANS) reactor studies

International Nuclear Information System (INIS)

Ford, W.E. III; Arwood, J.W.; Greene, N.M.; Petrie, L.M.; Primm, R.T. III; Waddell, M.W.; Webster, C.C.; Westfall, R.M.; Wright, R.Q.

1987-01-01

Multigroup P3 neutron, P0-P3 secondary gamma ray production (SGRP), and P6 gamma ray interaction (GRI) cross section libraries have been generated to support design work on the Advanced Neutron Source (ANS) reactor. The libraries, designated ANSL-V (Advanced Neutron Source Cross-Section Libraries), are data bases in a format suitable for subsequent generation of problem dependent cross sections. The ANSL-V libraries are available on magnetic tape from the Radiation Shielding Information Center at Oak Ridge National Laboratory

FUNCTIONAL VALUES OF VILLAGE LIBRARY IN INHERITANCE WORKS OF LOCAL CULTURE

Directory of Open Access Journals (Sweden)

Pawit M Yusup

2017-12-01

books, magazines, newspapers, maps, brochures, and the like, both in print and digital format. These works contain a benefit for knowledge and education. Meanwhile, the library as an institution in charge of managing printed and recorded works, including ancient works, continues to contribute in this work with storage for wider dissemination. This study examines the existence of public libraries and village libraries in West Java related to its role as referred to above. The method used is direct observation to the field. The result illustrates that public libraries and village libraries already participate to provide this type of collection for the benefit of the public on the current generation and the future. Keywords: Printed Materials, Paper records, Ancient manuscripts,Cultural Values, Public Library.

A Study of Early Learning Services in Museums and Libraries

Science.gov (United States)

Sirinides, P.; Fink, R.; DuBois, T.

2017-01-01

Museums and libraries can play a role in providing opportunities for early learning, and there is clear momentum and infrastructure already in place to help make this happen. Researchers conducted a mixed-methods descriptive study to generate new evidence about the availability of services for young children in museums and libraries, and the…

Design of a modified endoscope illuminator for spectral imaging of colorectal tissues

Science.gov (United States)

Browning, Craig M.; Mayes, Samuel; Rich, Thomas C.; Leavesley, Silas J.

2017-02-01

The gold standard for locating colonic polyps is a white light endoscope in a colonoscopy, however, polyps smaller than 5 mm can be easily missed. Modified procedures such as narrow band imaging have shown only marginal increases in detection rates. Spectral imaging is a potential solution to improve the sensitivity and specificity of colonoscopies by providing the ability to distinguish molecular fluorescence differences in tissues. The goal of this work is to implement a spectral endoscopic light source to acquire spectral image data of colorectal tissues. A beta-version endoscope light source was developed, by retrofitting a white light endoscope light source (Olympus, CLK-4) with 16 narrow band LEDs. This redesigned, beta-prototype uses high-power LEDs with a minimum output of 500 mW to provide sufficient spectral output (0.5 mW) through the endoscope. A mounting apparatus was designed to provide sufficient heat dissipation. Here, we report recent results of our tests to characterize the intensity output through the light source and endoscope to determine the flat spectral output for imaging and intensity losses through the endoscope. We also report preliminary spectral imaging data from transverse pig colon that demonstrates the ability to result in working practical spectral data. Preliminary results of this revised prototype spectral endoscope system demonstrate that there is sufficient power to allow the imaging process to continue and potentially determine spectral differences in cancerous and normal tissue from imaging ex vivo pairs. Future work will focus on building a spectral library for the colorectal region and refining the user interface the system for in vivo use.

Aftereffects of Spectrally Similar and Dissimilar Spectral Motion Adaptors in the Tritone Paradox

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Stephanie Malek

2018-05-01

Full Text Available Shepard tones consist of octave-spaced components, whose amplitudes are generated under a fixed bell-shaped spectral envelope. They are well defined in pitch chroma, but generate octave confusions that in turn can produce ambiguities in the perceived relative pitch heights when their chromas are exactly a tritone apart (the tritone paradox. This study examined the effects of tonal context on relative pitch height judgments using adaptor sequences followed by target sequences (pairs of Shepard tones of different chromas separated by a tritone. Listeners judged whether the second target Shepard tone was higher or lower than the first. Adaptor sequences consisted of rising or falling scales (43 s at the beginning of each block, 4 s before each target sequence. Two sets of Shepard tones were used for adaptors and targets that were generated under spectral envelopes centered at either A3 (220 Hz and C6 (1,046 Hz. Pitch direction judgments (rising vs. falling to spectrally consistent (A3–A3, C6–C6 and inconsistent (A3–C6, C6–A3 adaptor-target combinations were studied. Large significant contrastive aftereffects (0.08–0.21 change in fraction of pitch direction responses were only found for the Shepard tones that were judged as higher in the control condition (judgments about the target sequences without adaptor sequences for the consistent adaptor-target conditions (A3–A3, C6–C6. The experiments rule out explanations based on non-sensory decision making processes. Possible explanations in terms of perceptual aftereffects caused by adaptation in central auditory frequency-motion detectors are discussed.

Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order.

Science.gov (United States)

Aron, Miles; Browning, Richard; Carugo, Dario; Sezgin, Erdinc; Bernardino de la Serna, Jorge; Eggeling, Christian; Stride, Eleanor

2017-05-12

Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes. Here we present a MATLAB spectral imaging toolbox with the aim of overcoming these limitations. In addition to common operations, such as the calculation of distributions of GP values, generation of pseudo-colored GP maps, and spectral analysis, a key highlight of this tool is reliable membrane segmentation for probes that are rapidly internalized. Furthermore, handling for hyperstacks, 3D reconstruction and batch processing facilitates analysis of data sets generated by time series, z-stack, and area scan microscope operations. Finally, the object size distribution is determined, which can provide insight into the mechanisms underlying changes in membrane properties and is desirable for e.g. studies involving model membranes and surfactant coated particles. Analysis is demonstrated for cell membranes, cell-derived vesicles, model membranes, and microbubbles with environmentally-sensitive probes Laurdan, carboxyl-modified Laurdan (C-Laurdan), Di-4-ANEPPDHQ, and Di-4-AN(F)EPPTEA (FE), for quantification of the local lateral density of lipids or lipid packing. The Spectral Imaging Toolbox is a powerful tool for the segmentation and processing of large spectral imaging datasets with a reliable method for membrane segmentation and no ability in programming required. The

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

Directory of Open Access Journals (Sweden)

Brad Thomas Townsley

2015-05-01

Full Text Available Next Generation Sequencing (NGS is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE libraries and can easily extend to full transcript coverage shotgun (SHO type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Multicultural dialogue in the school library

Directory of Open Access Journals (Sweden)

Barbara Hanuš

2009-01-01

Full Text Available Nowadays many countries are confronted with the sudden and increased number of child immigrants which has a strong impact on education systems. A school library plays an important role in the development of intercultural dialogue as it keeps materials in many languages and develops different ways of youth activity. Fiction and non fiction show the abundance of habits and cultures in the world, they reveal different life stories and encourage the idea of diversity. A youth library encourages the inter-generational and intercultural dialogue. In the environment with a lot of immigrants it is very important for the library to consider the needs of the youth and to cooperate with their parents, too. The school in which most of the pupils do not speak Slovenian as their mother tongue is described. Library activities encourage their interest in learning the language of their new environment. Well developed literacy has a great impact on their educational results, but it is true that people can not understand other cultures unless they are aware of their own cultural identity.

In situ epoxide generation by dimethyldioxirane oxidation and the use of epichlorohydrin in the flow synthesis of a library of β-amino alcohols.

Science.gov (United States)

Cossar, Peter J; Baker, Jennifer R; Cain, Nicholas; McCluskey, Adam

2018-04-01

The flow coupling of epichlorohydrin with substituted phenols, while efficient, limits the nature of the epoxide available for the development of focused libraries of β-amino alcohols. This limitation was encountered in the production of analogues of 1-(4-nitrophenoxy)-3-((2-((4-(trifluoromethyl)pyrimidin-2-yl)amino)ethyl)amino)propan-2-ol 1 , a potential antibiotic lead. The in situ (flow) generation of dimethyldoxirane (DMDO) and subsequent flow olefin epoxidation abrogates this limitation and afforded facile access to structurally diverse β-amino alcohols. Analogues of 1 were readily accessed either via (i) a flow/microwave hybrid approach, or (ii) a sequential flow approach. Key steps were the in situ generation of DMDO, with olefin epoxidation in typically good yields and a flow-mediated ring opening aminolysis to form an expanded library of β-amino alcohols 1 and 10a - 18g , resulting in modest ( 11a , 21%) to excellent ( 12g , 80%) yields. Alternatively flow coupling of epichlorohydrin with phenols 4a - 4m (22%-89%) and a Bi(OTf) 3 catalysed microwave ring opening with amines afforded a select range of β-amino alcohols, but with lower levels of aminolysis regiocontrol than the sequential flow approach.

MARKETING LIBRARY SERVICES IN ACADEMIC LIBRARIES: A ...

African Journals Online (AJOL)

MARKETING LIBRARY SERVICES IN ACADEMIC LIBRARIES: A TOOL FOR SURVIVAL IN THE ... This article discusses the concept of marketing library and information services as an ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

Sensitivity analysis of critical experiments with evaluated nuclear data libraries

International Nuclear Information System (INIS)

Fujiwara, D.; Kosaka, S.

2008-01-01

Criticality benchmark testing was performed with evaluated nuclear data libraries for thermal, low-enriched uranium fuel rod applications. C/E values for k eff were calculated with the continuous-energy Monte Carlo code MVP2 and its libraries generated from Endf/B-VI.8, Endf/B-VII.0, JENDL-3.3 and JEFF-3.1. Subsequently, the observed k eff discrepancies between libraries were decomposed to specify the source of difference in the nuclear data libraries using sensitivity analysis technique. The obtained sensitivity profiles are also utilized to estimate the adequacy of cold critical experiments to the boiling water reactor under hot operating condition. (authors)

Libraries and Accessibility: Istanbul Public Libraries Case

Directory of Open Access Journals (Sweden)

Gül Yücel

2016-12-01

Full Text Available In the study; the assessment of accessibility has been conducted in Istanbul public libraries within the scope of public area. Public libraries commonly serve with its user of more than 20 million in total, spread to the general of Turkey, having more than one thousand branches in the centrums and having more than one million registered members. The building principles and standards covering the subjects such as the selection of place, historical and architectural specification of the region, distance to the centre of population and design in a way that the disabled people could benefit from the library services fully have been determined with regulations in the construction of new libraries. There are works for the existent libraries such as access for the disabled, fire safety precautions etc. within the scope of the related standards. Easy access by everyone is prioritized in the public libraries having a significant role in life-long learning. The purpose of the study is to develop solution suggestions for the accessibility problems in the public libraries. The study based on the eye inspection and assessments carried out within the scope of accessibility in the public libraries subsidiary to Istanbul Culture and Tourism Provincial Directorate Library and Publications Department within the provincial borders of Istanbul. The arrangements such as reading halls, study areas, book shelves etc. have been examined within the frame of accessible building standards. Building entrances, ramps and staircases, horizontal and vertical circulation of building etc. have been taken into consideration within the scope of accessible building standards. The subjects such as the reading and studying areas and book shelf arrangements for the library have been assessed within the scope of specific buildings. There are a total of 34 public libraries subsidiary to Istanbul Culture and Tourism Provincial Directorate on condition that 20 ea. of them are in the

Production of application libraries for WIMS

International Nuclear Information System (INIS)

Dean, C.J.

1996-01-01

The WIMS codes have been developed over a period of 30 years to include sophisticated modelling of many thermal reactor lattices. WIMS6 is currently being developed to include the flexibility of WIMSE together with the case of use seen in LWRWIMS. A new cross-section library is to be released with WIMS6. For the first time since the original WIMSD was written, the library is being generated from completely new differential data based mainly on JEF2.2. Quality Assurance into the XMAS library is achieved in three levels; through general procedures during assembly, by validation studies and by verification. The main general procedure involves forming overall physics quantities (Thermal average cross section, resonance integrals and fission spectrum average values) from the point evaluations and comparing them with similar quantities from the XMAS library. Examples of validation are studies optimizing the background cross-sections at which resonance integrals are tabulated and comparing reaction rates from homogeneous calculations with those formed in Monte Carlo and deterministic codes which represent energy variation of cross-section on a hyperfine energy mesh. Verification involves performing benchmark calculations and comparing results with experiment and calculations with the Apollo code. The current XMAS library contains 140 nuclides based on JEF2.2 evaluations. (author)

Nuclear data processing and multigroup cross section generation

International Nuclear Information System (INIS)

Kim, Jeong Do; Kil, Chung Sub

1996-01-01

The multigroup constants for WIMS/CASMO were updated with ENDF/B-VI and were tested. The continuous energy MCNP library developed last year was validated against the LWR-simulated critical experiments. The MCNP library will be used to design and analyze nuclear and shielding facilities. The system for generation of MATXS multigroup library and TRANSX code, which is able to prepare the data for the discrete ordinates and diffusion codes from the MATXS library, was established. The MATXS libraries for analyses of thermal and fast critical experiments were generated and tested. The MATXS/TRANSX system for the discrete ordinates and diffusion codes will be useful for nuclear analyses. 10 tabs., 5 figs., 17 refs. (Author)

Public libraries in the library regions in the year 2009

Directory of Open Access Journals (Sweden)

Milena Bon

2011-01-01

Full Text Available Purpose: Regional public libraries were initiated in 2003 to connect professional activities of libraries within regional networks and to ensure coordinated library development in a region in cooperation with the Library System Development Centre at the National and University Library performing a coordinating role. The article analyses the performance of public libraries and their integration in regional library networks in order to find out the level of development of conditions of performance of public libraries.Methodology/approach: Statistical data for the year 2009 were the basis for the overview of library activities of ten library regions with regard to applicable legislation and library standards. The level of regional library activities is compared to the socio-economic situation of statistical regions thus representing a new approach to the presentation of Slovenian’s public libraries’ development.Results: Absolute values indicate better development of nine libraries in the central Slovenia region while relative values offer a totally different picture. Four libraries in the region of Nova Gorica prove the highest level of development.Research limitation: Research is limited to the year 2009 and basic statistical analysis.Originality/practical implications: Findings of the analysis are useful for public libraries to plan their development strategy within a region and for financial bodies to provide for adequate financing for library activities in a specific region. The basic condition for successful public library performance is the even and harmonized development of conditions of performance as recommended by library standards.

Development of new ORIGEN2 data library sets for research reactors with light water cooled oxide and silicide LEU (20 w/o) fuels based on JENDL-3.3 nuclear data

International Nuclear Information System (INIS)

Liem, Peng Hong; Sembiring, Tagor Malem

2013-01-01

Highlights: • We developed new ORIGEN2 data library sets for research reactors based on JENDL-3.3. • The sets cover oxide and silicide LEU fuels with meat density up to 4.74 g U/cm 3 . • Two kinds of data library sets are available: fuel region and non-fuel regions. • We verified the new data library sets with other codes. • We validated the new data library against a non-destructive test. -- Abstract: New sets of ORIGEN2 data library dedicated to research/testing reactors with light water cooled oxide and silicide LEU fuel plates based on JENDL-3.3 nuclear data were developed, verified and validated. The new sets are considered to be an extension of the most recent release of ORIGEN2.2UPJ code, i.e. the ORLIBJ33 library sets. The newly generated ORIGEN2 data library sets cover both oxide and silicide LEU fuels with fuel meat density range from 2.96 to 4.74 g U/cm 3 used in the present and future operation of the Indonesian 30 MWth RSG GAS research reactor. The new sets are expected applicable also for other research/testing reactors which utilize similar fuels or have similar neutron spectral indices. In addition to the traditional ORIGEN2 library sets for fuel depletion analyses in fuel regions, in the new data library sets, new ORIGEN2 library sets for irradiation/activation analyses were also prepared which cover all representative non-fuel regions of RSG GAS such as reflector elements, irradiation facilities, etc. whose neutron spectra are significantly softer than fuel regions. Verification with other codes as well as validation with a non-destructive test result showed promising results where a good agreement was confirmed

The high throughput virtual slit enables compact, inexpensive Raman spectral imagers

Science.gov (United States)

Gooding, Edward; Deutsch, Erik R.; Huehnerhoff, Joseph; Hajian, Arsen R.

2018-02-01

Raman spectral imaging is increasingly becoming the tool of choice for field-based applications such as threat, narcotics and hazmat detection; air, soil and water quality monitoring; and material ID. Conventional fiber-coupled point source Raman spectrometers effectively interrogate a small sample area and identify bulk samples via spectral library matching. However, these devices are very slow at mapping over macroscopic areas. In addition, the spatial averaging performed by instruments that collect binned spectra, particularly when used in combination with orbital raster scanning, tends to dilute the spectra of trace particles in a mixture. Our design, employing free space line illumination combined with area imaging, reveals both the spectral and spatial content of heterogeneous mixtures. This approach is well suited to applications such as detecting explosives and narcotics trace particle detection in fingerprints. The patented High Throughput Virtual Slit1 is an innovative optical design that enables compact, inexpensive handheld Raman spectral imagers. HTVS-based instruments achieve significantly higher spectral resolution than can be obtained with conventional designs of the same size. Alternatively, they can be used to build instruments with comparable resolution to large spectrometers, but substantially smaller size, weight and unit cost, all while maintaining high sensitivity. When used in combination with laser line imaging, this design eliminates sample photobleaching and unwanted photochemistry while greatly enhancing mapping speed, all with high selectivity and sensitivity. We will present spectral image data and discuss applications that are made possible by low cost HTVS-enabled instruments.

Japanese evaluated nuclear data library version 3, JENDL-3

International Nuclear Information System (INIS)

Asami, Tetsuo; Igarashi, Shun-ichi; Ihara, Hitoshi

1989-01-01

The third version of Japanese Evaluated Nuclear Data Library, JENDL-3, has recently been compiled and issued. The major features of JENDL-3 are that it covers a much larger number of nuclides than the previous versions, that evaluation is made over the all energy regions from 10 -5 eV to 20 MeV using proper nuclear theories for each of the energy regions, and that it contains data on gamma ray generation. The present report first gives an outline of JENDL-3, and then describes the evaluation of nuclear data covering light nuclides, nuclides in structural materials, fission product nuclides, major actinide nuclides, transplutonium nuclides, and gamma ray generation. The applicability of JENDL-3 is examined through a variety of bench mark tests covering the fast reactor, thermal neutron reactor, shielding, neutronics of nuclear fusion reactor, dosimetry, and gamma ray generation data. The report also describes a library for calculation of decay heat, which has close relations with JENDL-3. It has been demonstrated that the experimental data given in this library are very reliable with high reproducibility. Additional activities planned for the future are also outlined briefly. (N.K.)

FOND-2.2-evaluated nuclear data library for constants sets generation at ABBN constants providing system

International Nuclear Information System (INIS)

Koscheev, V.N.; Nikolaev, M.N.; Tsiboulia, A.M.

2002-01-01

The library FOND-2.2 of evaluated nuclear data files, which was created at the ABBN laboratory of IPPE, is described. FOND-2 library is the basic nuclear data source used for the preparation of group data sets with different energy structures. ABBN-93.1 group data set was retrieved from the FOND-2 data library and nowadays it is widely used in different applications, in neutronics calculations of different nuclear energetic installations with different kinds of neutron spectra, in radiation shielding calculation, and so on. (author)

Evaluation of WIMS-D/4 nuclear data library used on TRIGA reactor calculation

International Nuclear Information System (INIS)

Chen Wei; Xie Zhongsheng; Jiang Xinbiao; Chen Da

1997-01-01

The 69 groups constants of H in ZrH, 166 Er and 167 Er generated by NJOY and GASKET codes are inserted into WIMS nuclear data library WIMS-CNDC and WIMS-NINT libraries used on RTIGA reactor calculation are obtained. In order to check WIMS-CNDC and WIMS-NINT libraries, the scattering cross-section is compared with that in WIMS-IJS library. The group constant, K ∞ and temperature coefficient are calculated by using WIMS-CNDC, WIMS-NINT and WIMS-IJS. The results show the both libraries are suitable for calculation of TRIGA reactor

Computer-assisted spectral design and synthesis

Science.gov (United States)

Vadakkumpadan, Fijoy; Wang, Qiqi; Sun, Yinlong

2005-01-01

In this paper, we propose a computer-assisted approach for spectral design and synthesis. This approach starts with some initial spectrum, modifies it interactively, evaluates the change, and decides the optimal spectrum. Given a requested change as function of wavelength, we model the change function using a Gaussian function. When there is the metameric constraint, from the Gaussian function of request change, we propose a method to generate the change function such that the result spectrum has the same color as the initial spectrum. We have tested the proposed method with different initial spectra and change functions, and implemented an interactive graphics environment for spectral design and synthesis. The proposed approach and graphics implementation for spectral design and synthesis can be helpful for a number of applications such as lighting of building interiors, textile coloration, and pigment development of automobile paints, and spectral computer graphics.

VITAMIN E: a multipurpose ENDF/B-V coupled neutron-gamma cross section library

International Nuclear Information System (INIS)

Barhen, J.; Cacuci, D.G.; Ford, W.E. III; Roussin, R.W.; Wagschal, J.J.; Weisbin, C.R.; White, J.E.; Wright, R.Q.

1979-01-01

The US Department of Energy Office of Fusion Energy and the Division of Reactor Research and Technology jointly sponsored the development of a coupled fine-group cross section library (VITAMIN-C). The experience gained in the generation, validation, and utilization of the VITAMIN-C library along with its broad range of applicability has led to the request for updating this data set using ENDF/B-V. Additional support in this regard has been provided by the Defense Nuclear Agency (DNA) and by EPRI in support of weapons analyses and light water reactor shielding and dosimetry problems, respectively. The rationale for developing the multipurpose ENDF/B-V-based VITAMIN-E library is presented, with special emphasis on new models used in the data generation algorithms. The library specifications and testing procedures are also discussed in detail. The distribution of the VITAMIN-E library is currently subject to the same restrictions as the distribution of the ENDF/B-V data. 2 tables

COMBS: open source python library for RVE generation - Application to microscale diffusion simulations in cementitious materials

International Nuclear Information System (INIS)

Bourcier, C.; Laucoin, E.; Dridi, W.; Chomat, L.; Bary, B.; Adam, E.

2013-01-01

In the context of radioactive waste storage and disposal, the knowledge of the concrete diffusivity is primordial in the numerical simulations of the long term behavior of these materials. COMBS is an open source python library, it is used to define the shapes of the inclusions, to insert them in the box featuring the representative volume element (RVE) of the cementitious medium, and to assess their diffusive properties. The algorithms developed in COMBS target a fast placement of the inclusions and a fast generation of the RVE shape and mesh. Two application cases are considered: the unaltered material diffusivity and the degraded material diffusivity. The first case of application focuses on the description of the capillary porosity. The second application case focuses on the description of the degradation of cementitious material (mineral and porosity) and the diffusive properties associated. The reliability of the analytical effective medium approximations (MT and SC) is confirmed from 3D finite elements (FE) calculations performed on a matrix-inclusions microstructure obtained by RVE generation with Combs. The results also show the need to take into account the percolation behavior

Spectrally-isolated violet to blue wavelength generation by cascaded degenerate four-wave mixing in a photonic crystal fiber.

Science.gov (United States)

Yuan, Jinhui; Kang, Zhe; Li, Feng; Zhang, Xianting; Zhou, Guiyao; Sang, Xinzhu; Wu, Qiang; Yan, Binbin; Zhou, Xian; Wang, Liang; Zhong, Kangping; Wang, Kuiru; Yu, Chongxiu; Tam, Hwa Yaw; Wai, P K A

2016-06-01

Generation of spectrally-isolated wavelengths in the violet to blue region based on cascaded degenerate four-wave mixing (FWM) is experimentally demonstrated for the first time in a tailor-made photonic crystal fiber, which has two adjacent zero dispersion wavelengths (ZDWs) at 696 and 852 nm in the fundamental mode. The influences of the wavelength λp and the input average power Pav of the femtosecond pump pulses on the phase-matched frequency conversion process are studied. When femtosecond pump pulses at λp of 880, 870, and 860 nm and Pav of 500 mW are coupled into the normal dispersion region close to the second ZDW, the first anti-Stokes waves generated near the first ZDW act as a secondary pump for the next FWM process. The conversion efficiency ηas2 of the second anti-Stokes waves, which are generated at the violet to blue wavelengths of 430, 456, and 472 nm, are 4.8, 6.48, and 9.66%, for λp equalling 880, 870, and 860 nm, respectively.

Libraries Today, Libraries Tomorrow: Contemporary Library Practices and the Role of Library Space in the L

Directory of Open Access Journals (Sweden)

Ana Vogrinčič Čepič

2013-09-01

Full Text Available ABSTRACTPurpose: The article uses sociological concepts in order to rethink the changes in library practices. Contemporary trends are discussed with regard to the changing nature of working habits, referring mostly to the new technology, and the (emergence of the third space phenomenon. The author does not regard libraries only as concrete public service institutions, but rather as complex cultural forms, taking in consideration wider social context with a stress on users’ practices in relation to space.Methodology/approach: The article is based on the (self- observation of the public library use, and on the (discourse analysis of internal library documents (i.e. annual reports and plans and secondary sociological literature. As such, the cultural form approach represents a classic method of sociology of culture.Results: The study of relevant material in combination with direct personal experiences reveals socio-structural causes for the change of users’ needs and habits, and points at the difficulty of spatial redefinition of libraries as well as at the power of the discourse.Research limitations: The article is limited to an observation of users’ practices in some of the public libraries in Ljubljana and examines only a small number of annual reports – the discoveries are then further debated from the sociological perspective.Originality/practical implications: The article offers sociological insight in the current issues of the library science and tries to suggest a wider explanation that could answer some of the challenges of the contemporary librarianship.

Updating Photonuclear Data Library and Generating a Reference Database for Photon Strength Functions. 1st Research Coordination Meeting. Summary Report