Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

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

Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.

2009-04-21

We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists.

PubMed

Miersch, Shane; Maruthachalam, Bharathikumar Vellalore; Geyer, C Ronald; Sidhu, Sachdev S

2017-05-19

We tested whether grafting an interaction domain into the hypervariable loop of a combinatorial antibody library could promote targeting to a specific epitope. Formation of the epidermal growth factor receptor (EGFR) signaling heterodimer involves extensive contacts mediated by a "dimerization loop." We grafted the dimerization loop into the third hypervariable loop of a synthetic antigen-binding fragment (Fab) library and diversified other loops using a tailored diversity strategy. This structure-directed Fab library and a naı̈ve synthetic Fab library were used to select Fabs against EGFR. Both libraries yielded high affinity Fabs that bound to overlapping epitopes on cell-surface EGFR, inhibited receptor activation, and targeted epitopes distinct from those of cetuximab and panitumumab. Epitope mapping experiments revealed complex sites of interaction, comprised of domains I and II but not exclusively localized to the receptor dimerization loop. These results validate the grafting approach for designing Fab libraries and also underscore the versatility of naı̈ve synthetic libraries.

Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

DTIC Science & Technology

2012-06-14

implemented a prototype DFT simulation software using two different open source Finite Element (FE) libraries: DEALII and FENICS . These two libraries have been...ATK. In the first part of this Phase I project we investigated two different candidate finite element libraries, DEAL II and FENICS . Although both...element libraries, Deal.II and FEniCS /dolfin, for use as back-ends to a finite element DFT in ATK, Quantum Insight and QuantumWise A/S, October 2011.

Management of scientific information with Google Drive.

PubMed

Kubaszewski, Łukasz; Kaczmarczyk, Jacek; Nowakowski, Andrzej

2013-09-20

The amount and diversity of scientific publications requires a modern management system. By "management" we mean the process of gathering interesting information for the purpose of reading and archiving for quick access in future clinical practice and research activity. In the past, such system required physical existence of a library, either institutional or private. Nowadays in an era dominated by electronic information, it is natural to migrate entire systems to a digital form. In the following paper we describe the structure and functions of an individual electronic library system (IELiS) for the management of scientific publications based on the Google Drive service. Architecture of the system. Architecture system consists of a central element and peripheral devices. Central element of the system is virtual Google Drive provided by Google Inc. Physical elements of the system include: tablet with Android operating system and a personal computer, both with internet access. Required software includes a program to view and edit files in PDF format for mobile devices and another to synchronize the files. Functioning of the system. The first step in creating a system is collection of scientific papers in PDF format and their analysis. This step is performed most frequently on a tablet. At this stage, after being read, the papers are cataloged in a system of folders and subfolders, according to individual demands. During this stage, but not exclusively, the PDF files are annotated by the reader. This allows the user to quickly track down interesting information in review or research process. Modification of the document title is performed at this stage, as well. Second element of the system is creation of a mirror database in the Google Drive virtual memory. Modified and cataloged papers are synchronized with Google Drive. At this stage, a fully functional scientific information electronic library becomes available online. The third element of the system is a periodic two-way synchronization of data between Google Drive and tablet, as occasional modification of the files with annotation or recataloging may be performed at both locations. The system architecture is designed to gather, catalog and analyze scientific publications. All steps are electronic, eliminating paper forms. Indexed files are available for re-reading and modification. The system allows for fast access to full-text search with additional features making research easier. Team collaboration is also possible with full control of user privileges. Particularly important is the safety of collected data. In our opinion, the system exceeds many commercially available applications in terms of functionality and versatility.

Revised Extended Grid Library

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

Martz, Roger L.

The Revised Eolus Grid Library (REGL) is a mesh-tracking library that was developed for use with the MCNP6TM computer code so that (radiation) particles can track on an unstructured mesh. The unstructured mesh is a finite element representation of any geometric solid model created with a state-of-the-art CAE/CAD tool. The mesh-tracking library is written using modern Fortran and programming standards; the library is Fortran 2003 compliant. The library was created with a defined application programmer interface (API) so that it could easily integrate with other particle tracking/transport codes. The library does not handle parallel processing via the message passing interfacemore » (mpi), but has been used successfully where the host code handles the mpi calls. The library is thread-safe and supports the OpenMP paradigm. As a library, all features are available through the API and overall a tight coupling between it and the host code is required. Features of the library are summarized with the following list: Can accommodate first and second order 4, 5, and 6-sided polyhedra; any combination of element types may appear in a single geometry model; parts may not contain tetrahedra mixed with other element types; pentahedra and hexahedra can be together in the same part; robust handling of overlaps and gaps; tracks element-to-element to produce path length results at the element level; finds element numbers for a given mesh location; finds intersection points on element faces for the particle tracks; produce a data file for post processing results analysis; reads Abaqus .inp input (ASCII) files to obtain information for the global mesh-model; supports parallel input processing via mpi; and support parallel particle transport by both mpi and OpenMP.« less

Titanium(IV) isopropoxide mediated solution phase reductive amination on an automated platform: application in the generation of urea and amide libraries.

PubMed

Bhattacharyya, S; Fan, L; Vo, L; Labadie, J

2000-04-01

Amine libraries and their derivatives are important targets for high throughput synthesis because of their versatility as medicinal agents and agrochemicals. As a part of our efforts towards automated chemical library synthesis, a titanium(IV) isopropoxide mediated solution phase reductive amination protocol was successfully translated to automation on the Trident(TM) library synthesizer of Argonaut Technologies. An array of 24 secondary amines was prepared in high yield and purity from 4 primary amines and 6 carbonyl compounds. These secondary amines were further utilized in a split synthesis to generate libraries of ureas, amides and sulfonamides in solution phase on the Trident(TM). The automated runs included 192 reactions to synthesize 96 ureas in duplicate and 96 reactions to synthesize 48 amides and 48 sulfonamides. A number of polymer-assisted solution phase protocols were employed for parallel work-up and purification of the products in each step.

The Surge of Micro-computers

NASA Astrophysics Data System (ADS)

Morita, Written By Ichiko; Matsumura, Translated By Tamiko

Libraries in the United States are now experiencing another phase of rapid change brought by the sudden invasion of micro-computers. Their versatility has made available not only capabilities for word processing and producing spread sheets but also introduced new approaches to large research libraries’ information networks. OCLC’s microenhancers are one example of what is now available. They can be used for retrospective conversion, provide instruction for the use of and function as front end terminals for large online catalogs. Various new ideas for the application of micro-computers will bring interesting developments in library automation.

Naval Law Review. Volume 48

DTIC Science & Technology

2001-01-01

from airports and hotels, Internet cafes , libraries, and even cellular phones. This unmatched versatility has made e-mail the preferred method of...8217 contention, however, was not that the Franchise Tax Board applied the wrong section of the code; it was that the code “unfairly taxed the wife’s

DNA-Compatible Nitro Reduction and Synthesis of Benzimidazoles.

PubMed

Du, Huang-Chi; Huang, Hongbing

2017-10-18

DNA-encoded chemical libraries have emerged as a cost-effective alternative to high-throughput screening (HTS) for hit identification in drug discovery. A key factor for productive DNA-encoded libraries is the chemical diversity of the small molecule moiety attached to an encoding DNA oligomer. The library structure diversity is often limited to DNA-compatible chemical reactions in aqueous media. Herein, we describe a facile process for reducing aryl nitro groups to aryl amines. The new protocol offers simple operation and circumvents the pyrophoric potential of the conventional method (Raney nickel). The reaction is performed in aqueous solution and does not compromise DNA structural integrity. The utility of this method is demonstrated by the versatile synthesis of benzimidazoles on DNA.

Parallel and automated library synthesis of 2-long alkyl chain benzoazoles and azole[4,5-b]pyridines under microwave irradiation.

PubMed

Martínez-Palou, Rafael; Zepeda, L Gerardo; Höpfl, Herbert; Montoya, Ascensión; Guzmán-Lucero, Diego J; Guzmán, Javier

2005-01-01

A versatile route to 40-membered library of 2-long alkyl chain substituted benzoazoles (1 and 2) and azole[4,5-b]pyridines (3 and 4) via microwave-assisted combinatorial synthesis was developed. The reactions were carried out in both monomode and multimode microwave oven. With the latter, all reactions were performed in high-throughput experimental settings consisting of an 8 x 5 combinatorial library designed to synthesize 40 compounds. Each step, from the addition of reagents to the recovery of final products, was automated. The microwave-assisted N-long chain alkylation reactions of 2-alkyl-1H-benzimidazole (1) and 2-alkyl-1H-benzimidazole[4,5-b] pyridines (3) were also studied.

A Versatile, User-Oriented, Computerized Library System.

ERIC Educational Resources Information Center

Neuron, Eric

This paper deals with the problem of the referencing or storing methods in information systems which must be designed to allow for rapid retrieval of the key data leading to the desired information or the recovery of the information directly. Considered as a secondary, but frequently desirable, feature for the system is the ability to determine…

Pedigreed mutant library- a unique resource for sorghum improvement and genomics

USDA-ARS?s Scientific Manuscript database

Sorghum (Sorghum bicolor L. Moench) is a versatile crop used for food, feeder, fodder, and biofuel. Due to its superior resilience to drought and high temperature stresses and low soil fertility, sorghum is becoming increasingly important in meeting the growing need for food and energy in face of de...

ORF phage display to identify cellular proteins with different functions.

PubMed

Li, Wei

2012-09-01

Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages. Copyright © 2012 Elsevier Inc. All rights reserved.

A Multidimensional Diversity‐Oriented Synthesis Strategy for Structurally Diverse and Complex Macrocycles

PubMed Central

Nie, Feilin; Kunciw, Dominique L.; Wilcke, David; Stokes, Jamie E.; Galloway, Warren R. J. D.; Bartlett, Sean; Sore, Hannah F.

2016-01-01

Abstract Synthetic macrocycles are an attractive area in drug discovery. However, their use has been hindered by a lack of versatile platforms for the generation of structurally (and thus shape) diverse macrocycle libraries. Herein, we describe a new concept in library synthesis, termed multidimensional diversity‐oriented synthesis, and its application towards macrocycles. This enabled the step‐efficient generation of a library of 45 novel, structurally diverse, and highly‐functionalized macrocycles based around a broad range of scaffolds and incorporating a wide variety of biologically relevant structural motifs. The synthesis strategy exploited the diverse reactivity of aza‐ylides and imines, and featured eight different macrocyclization methods, two of which were novel. Computational analyses reveal a broad coverage of molecular shape space by the library and provides insight into how the various diversity‐generating steps of the synthesis strategy impact on molecular shape. PMID:27484830

Modeling the missile-launch tube problem in DYSCO

NASA Technical Reports Server (NTRS)

Berman, Alex; Gustavson, Bruce A.

1989-01-01

DYSCO is a versatile, general purpose dynamic analysis program which assembles equations and solves dynamics problems. The executive manages a library of technology modules which contain routines that compute the matrix coefficients of the second order ordinary differential equations of the components. The executive performs the coupling of the equations of the components and manages the solution of the coupled equations. Any new component representation may be added to the library if, given the state vector, a FORTRAN program can be written to compute M, C, K, and F. The problem described demonstrates the generality of this statement.

Versatile digital micromirror device-based method for the recording of multilevel optical diffractive elements in photosensitive chalcogenide layers (AMTIR-1).

PubMed

Joerg, Alexandre; Vignaux, Mael; Lumeau, Julien

2016-08-01

A new alternative and versatile method for the production of diffractive optical elements (DOEs) with up to four phase levels in AMTIR-1 (Ge₃₃As₁₂Se₅₅) layers is demonstrated. The developed method proposes the use of the photosensitive properties of the layers and a specific in situ optical monitoring coupled with a reverse engineering algorithm to control the trigger points of the writing of the different diffractive patterns. Examples of various volume DOEs are presented.

Library Optimization in EDXRF Spectral Deconvolution for Multi-element Analysis of Ambient Aerosols

EPA Science Inventory

In multi-element analysis of atmospheric aerosols, attempts are made to fit overlapping elemental spectral lines for many elements that may be undetectable in samples due to low concentrations. Fitting with many library reference spectra has the unwanted effect of raising the an...

Object-oriented design and implementation of CFDLab: a computer-assisted learning tool for fluid dynamics using dual reciprocity boundary element methodology

NASA Astrophysics Data System (ADS)

Friedrich, J.

1999-08-01

As lecturers, our main concern and goal is to develop more attractive and efficient ways of communicating up-to-date scientific knowledge to our students and facilitate an in-depth understanding of physical phenomena. Computer-based instruction is very promising to help both teachers and learners in their difficult task, which involves complex cognitive psychological processes. This complexity is reflected in high demands on the design and implementation methods used to create computer-assisted learning (CAL) programs. Due to their concepts, flexibility, maintainability and extended library resources, object-oriented modeling techniques are very suitable to produce this type of pedagogical tool. Computational fluid dynamics (CFD) enjoys not only a growing importance in today's research, but is also very powerful for teaching and learning fluid dynamics. For this purpose, an educational PC program for university level called 'CFDLab 1.1' for Windows™ was developed with an interactive graphical user interface (GUI) for multitasking and point-and-click operations. It uses the dual reciprocity boundary element method as a versatile numerical scheme, allowing to handle a variety of relevant governing equations in two dimensions on personal computers due to its simple pre- and postprocessing including 2D Laplace, Poisson, diffusion, transient convection-diffusion.

Development library of finite elements for computer-aided design system of reed sensors

NASA Astrophysics Data System (ADS)

Kozlov, A. S.; Shmakov, N. A.; Tkalich, V. L.; Labkovskaia, R. I.; Kalinkina, M. E.; Pirozhnikova, O. I.

2018-05-01

The article is devoted to the development of a modern highly reliable element base of devices for security and fire alarm systems, in particular, to the improvement of the quality of contact cores (reed and membrane) of reed sensors. Modeling of elastic sensitive elements uses quadrangular elements of plates and shells, considered in the system of curvilinear orthogonal coordinates. The developed mathematical models and the formed finite element library are designed for systems of automated design of reed switch detectors to create competitive devices alarms. The finite element library is used for the automated system production of reed switch detectors both in series production and in the implementation of individual orders.

Status of MAPA (Modular Accelerator Physics Analysis) and the Tech-X Object-Oriented Accelerator Library

NASA Astrophysics Data System (ADS)

Cary, J. R.; Shasharina, S.; Bruhwiler, D. L.

1998-04-01

The MAPA code is a fully interactive accelerator modeling and design tool consisting of a GUI and two object-oriented C++ libraries: a general library suitable for treatment of any dynamical system, and an accelerator library including many element types plus an accelerator class. The accelerator library inherits directly from the system library, which uses hash tables to store any relevant parameters or strings. The GUI can access these hash tables in a general way, allowing the user to invoke a window displaying all relevant parameters for a particular element type or for the accelerator class, with the option to change those parameters. The system library can advance an arbitrary number of dynamical variables through an arbitrary mapping. The accelerator class inherits this capability and overloads the relevant functions to advance the phase space variables of a charged particle through a string of elements. Among other things, the GUI makes phase space plots and finds fixed points of the map. We discuss the object hierarchy of the two libraries and use of the code.

A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

PubMed Central

Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

2015-01-01

A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961

A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules.

PubMed

Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

2015-01-01

A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.

Using Internet Primary Sources to Teach Critical Thinking Skills in the Sciences. Libraries Unlimited Professional Guides in School Librarianship

ERIC Educational Resources Information Center

Johnson, Carolyn

2003-01-01

Take a cyber journey through the world of science! Presenting more than 150 websites with primary source documents and authoritative data, this versatile book helps educators guide students on virtual scientific fieldtrips in all areas of science, from astronomy, biology, and chemistry to genetics, physics, and space science. Students can meet…

Library Homepage Design at Smaller Bachelor of Arts Institutions

ERIC Educational Resources Information Center

Jones, Scott L.; Leonard, Kirsten

2011-01-01

This study examined the homepages of the libraries of 175 smaller bachelor of arts institutions, coding for the presence of 98 design elements. By reporting and examining the frequency of these features, the authors noted what is and is not common practice at these libraries. They found that only fourteen elements were present on at least half of…

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

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

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

A robust gene-stacking method utilizing yeast assembly for plant synthetic biology

DOE PAGES

Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim; ...

2016-10-26

The advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. But, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. We describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We also demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies formore » stacking genes and traits to address many impending environmental and agricultural challenges.« less

Targeting mammalian organelles with internalizing phage (iPhage) libraries

PubMed Central

Rangel, Roberto; Dobroff, Andrey S.; Guzman-Rojas, Liliana; Salmeron, Carolina C.; Gelovani, Juri G.; Sidman, Richard L.; Pasqualini, Renata; Arap, Wadih

2015-01-01

Techniques largely used for protein interaction studies and discovery of intracellular receptors, such as affinity capture complex purification and yeast two-hybrid, may produce inaccurate datasets due to protein insolubility, transient or weak protein interactions, or irrelevant intracellular context. A versatile tool to overcome these limitations as well as to potentially create vaccines and engineer peptides and antibodies as targeted diagnostic and therapeutic agents, is the phage display technique. We have recently developed a new technology for screening internalizing phage (iPhage) vectors and libraries utilizing a ligand/receptor-independent mechanism to penetrate eukaryotic cells. iPhage particles provide a unique discovery platform for combinatorial intracellular targeting of organelle ligands along with their corresponding receptors and to fingerprint functional protein domains in living cells. Here we explain the design, cloning, construction, and production of iPhage-based vectors and libraries, along with basic ligand-receptor identification and validation methodologies for organelle receptors. An iPhage library screening can be performed in ~8 weeks. PMID:24030441

The Business of Running a Special Library

ERIC Educational Resources Information Center

Waldron, Helen J.

1971-01-01

This paper, a lecture to library school students, presents in detail four elements that make a special library special," as background for a discussion of suggested approaches to follow in managing a special library. (Author/AB)

The Once and Future Publishing Library

ERIC Educational Resources Information Center

Okerson, Ann; Holzman, Alex

2015-01-01

The report explores the revitalization of library publishing and its possible future, and examines elements that influence the success and sustainability of library publishing initiatives. The authors trace the history of library publishing and factors that have transformed the publishing landscape, and describe several significant library-press…

OpenFOAM: Open source CFD in research and industry

NASA Astrophysics Data System (ADS)

Jasak, Hrvoje

2009-12-01

The current focus of development in industrial Computational Fluid Dynamics (CFD) is integration of CFD into Computer-Aided product development, geometrical optimisation, robust design and similar. On the other hand, in CFD research aims to extend the boundaries ofpractical engineering use in "non-traditional " areas. Requirements of computational flexibility and code integration are contradictory: a change of coding paradigm, with object orientation, library components, equation mimicking is proposed as a way forward. This paper describes OpenFOAM, a C++ object oriented library for Computational Continuum Mechanics (CCM) developed by the author. Efficient and flexible implementation of complex physical models is achieved by mimicking the form ofpartial differential equation in software, with code functionality provided in library form. Open Source deployment and development model allows the user to achieve desired versatility in physical modeling without the sacrifice of complex geometry support and execution efficiency.

Epitope selection from an uncensored peptide library displayed on avian leukosis virus.

PubMed

Khare, Pranay D; Rosales, Ana G; Bailey, Kent R; Russell, Stephen J; Federspiel, Mark J

2003-10-25

Phage display libraries have provided an extraordinarily versatile technology to facilitate the isolation of peptides, growth factors, single chain antibodies, and enzymes with desired binding specificities or enzymatic activities. The overall diversity of peptides in phage display libraries can be significantly limited by Escherichia coli protein folding and processing machinery, which result in sequence censorship. To achieve an optimal diversity of displayed eukaryotic peptides, the library should be produced in the endoplasmic reticulum of eukaryotic cells using a eukaryotic display platform. In the accompanying article, we presented experiments that demonstrate that polypeptides of various sizes could be efficiently displayed on the envelope glycoproteins of a eukaryotic virus, avian leukosis virus (ALV), and the displayed polypeptides could efficiently attach to cognate receptors without interfering with viral attachment and entry into susceptible cells. In this study, methods were developed to construct a model library of randomized eight amino acid peptides using the ALV eukaryotic display platform and screen the library for specific epitopes using immobilized antibodies. A virus library with approximately 2 x 10(6) different members was generated from a plasmid library of approximately 5 x 10(6) diversity. The sequences of the randomized 24 nucleotide/eight amino acid regions of representatives of the plasmid and virus libraries were analyzed. No significant sequence censorship was observed in producing the virus display library from the plasmid library. Different populations of peptide epitopes were selected from the virus library when different monoclonal antibodies were used as the target. The results of these two studies clearly demonstrate the potential of ALV as a eukaryotic platform for the display and selection of eukaryotic polypeptides libraries.

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

Van Der Marck, S. C.

Three nuclear data libraries have been tested extensively using criticality safety benchmark calculations. The three libraries are the new release of the US library ENDF/B-VII.1 (2011), the new release of the Japanese library JENDL-4.0 (2011), and the OECD/NEA library JEFF-3.1 (2006). All calculations were performed with the continuous-energy Monte Carlo code MCNP (version 4C3, as well as version 6-beta1). Around 2000 benchmark cases from the International Handbook of Criticality Safety Benchmark Experiments (ICSBEP) were used. The results were analyzed per ICSBEP category, and per element. Overall, the three libraries show similar performance on most criticality safety benchmarks. The largest differencesmore » are probably caused by elements such as Be, C, Fe, Zr, W. (authors)« less

Robotics and Automation Education: Developing the Versatile, Practical Lab.

ERIC Educational Resources Information Center

Stenerson, Jon

1986-01-01

Elements of the development of a robotics and automation laboratory are discussed. These include the benefits of upgrading current staff, ways to achieve this staff development, formation of a robotics factory automation committee, topics to be taught with a robot, elements of a laboratory, laboratory funding, and design safety. (CT)

Building with a Line

ERIC Educational Resources Information Center

Hubbert, Beth

2011-01-01

Architecture is a versatile, multifaceted area to study in the artroom with multiple age levels. It can easily stimulate a study of basic line, shape, and various other art elements and principles. It can then be extended into a more extensive study of architectural elements, styles, specific architects, architecture of different cultures, and…

EMI datalib - joining the best of ARC and gLite data libraries

NASA Astrophysics Data System (ADS)

Nilsen, J. K.; Cameron, D.; Devresse, A.; Molnar, Zs; Nagy, Zs; Salichos, M.

2012-12-01

To manage data in the grid, with its jungle of protocols and enormous amount of data in different storage solutions, it is important to have a strong, versatile and reliable data management library. While there are several data management tools and libraries available, they all have different strengths and weaknesses, and it can be hard to decide which tool to use for which purpose. EMI is a collaboration between the European middleware providers aiming to take the best out of each middleware to create one consolidated, all-purpose grid middleware. When EMI started there were two main tools for managing data - gLite had lcg util and the GFAL library, ARC had the ARC data tools and libarcdata2. While different in design and purpose, they both have the same goal; to manage data in the grid. The design of the new EMI datalib was ready by the end of 2011, and a first prototype is now implemented and going through a thorough testing phase. This presentation will give the latest results of the consolidated library together with an overview of the design, test plan and roadmap of EMI datalib.

A Monte Carlo Library Least Square approach in the Neutron Inelastic-scattering and Thermal-capture Analysis (NISTA) process in bulk coal samples

NASA Astrophysics Data System (ADS)

Reyhancan, Iskender Atilla; Ebrahimi, Alborz; Çolak, Üner; Erduran, M. Nizamettin; Angin, Nergis

2017-01-01

A new Monte-Carlo Library Least Square (MCLLS) approach for treating non-linear radiation analysis problem in Neutron Inelastic-scattering and Thermal-capture Analysis (NISTA) was developed. 14 MeV neutrons were produced by a neutron generator via the 3H (2H , n) 4He reaction. The prompt gamma ray spectra from bulk samples of seven different materials were measured by a Bismuth Germanate (BGO) gamma detection system. Polyethylene was used as neutron moderator along with iron and lead as neutron and gamma ray shielding, respectively. The gamma detection system was equipped with a list mode data acquisition system which streams spectroscopy data directly to the computer, event-by-event. A GEANT4 simulation toolkit was used for generating the single-element libraries of all the elements of interest. These libraries were then used in a Linear Library Least Square (LLLS) approach with an unknown experimental sample spectrum to fit it with the calculated elemental libraries. GEANT4 simulation results were also used for the selection of the neutron shielding material.

A versatile system for the rapid collection, handling and graphics analysis of multidimensional data

NASA Astrophysics Data System (ADS)

O'Brien, P. M.; Moloney, G.; O'Connor, A.; Legge, G. J. F.

1993-05-01

The aim of this work was to provide a versatile system for handling multiparameter data that may arise from a variety of experiments — nuclear, AMS, microprobe elemental analysis, 3D microtomography etc. Some of the most demanding requirements arise in the application of microprobes to quantitative elemental mapping and to microtomography. A system to handle data from such experiments had been under continuous development and use at MARC for the past 15 years. It has now been made adaptable to the needs of multiparameter (or single parameter) experiments in general. The original system has been rewritten, greatly expanded and made much more powerful and faster, by use of modern computer technology — a VME bus computer with a real time operating system and a RISC workstation running Unix and the X Window system. This provides the necessary (i) power, speed and versatility, (ii) expansion and updating capabilities (iii) standardisation and adaptability, (iv) coherent modular programming structures, (v) ability to interface to other programs and (vi) transparent operation with several levels, involving the use of menus, programmed function keys and powerful macro programming facilities.

Parallel Element Agglomeration Algebraic Multigrid and Upscaling Library

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

Barker, Andrew T.; Benson, Thomas R.; Lee, Chak Shing

ParELAG is a parallel C++ library for numerical upscaling of finite element discretizations and element-based algebraic multigrid solvers. It provides optimal complexity algorithms to build multilevel hierarchies and solvers that can be used for solving a wide class of partial differential equations (elliptic, hyperbolic, saddle point problems) on general unstructured meshes. Additionally, a novel multilevel solver for saddle point problems with divergence constraint is implemented.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

PubMed

Koo, Byoung-Mo; Kritikos, George; Farelli, Jeremiah D; Todor, Horia; Tong, Kenneth; Kimsey, Harvey; Wapinski, Ilan; Galardini, Marco; Cabal, Angelo; Peters, Jason M; Hachmann, Anna-Barbara; Rudner, David Z; Allen, Karen N; Typas, Athanasios; Gross, Carol A

2017-03-22

A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Special Section: Library Equipment and Furniture.

ERIC Educational Resources Information Center

Michaels, Andrea; And Others

1992-01-01

Five articles discuss designing library interiors for ergonomic needs and requirements of the Americans with Disabilities Act. Highlights include elements of library furnishings for use with technology; directories of vendors that supply libraries and distributors of technological devices for the blind and physically handicapped; adaptive…

YAP Version 4.0

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

Nelson, Eric M.

2004-05-20

The YAP software library computes (1) electromagnetic modes, (2) electrostatic fields, (3) magnetostatic fields and (4) particle trajectories in 2d and 3d models. The code employs finite element methods on unstructured grids of tetrahedral, hexahedral, prism and pyramid elements, with linear through cubic element shapes and basis functions to provide high accuracy. The novel particle tracker is robust, accurate and efficient, even on unstructured grids with discontinuous fields. This software library is a component of the MICHELLE 3d finite element gun code.

Appropriate Use Policies for Computers in College/University Libraries. CLIP Note.

ERIC Educational Resources Information Center

Tuten, Jane, Comp.; Junker, Karen, Comp.

The purpose of this College Library Information Packet (CLIP) Note is to help libraries identify desirable elements found in computer use policies and to provide guidelines for college and small university libraries that want to develop policies or have been directed to implement policies for computer usage in their libraries. In January 2001, a…

The Role and Function of Presidential Libraries.

ERIC Educational Resources Information Center

Fischer, Linda

This paper identifies various elements of presidential libraries. The advantages and disadvantages of the libraries' centralization or decentralization are discussed, and some common misconceptions held by the public as to the role and function of presidential libraries are identified. Criticism and debate from the professional community about…

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

H4DAQ: a modern and versatile data-acquisition package for calorimeter prototypes test-beams

NASA Astrophysics Data System (ADS)

Marini, A. C.

2018-02-01

The upgrade of the particle detectors for the HL-LHC or for future colliders requires an extensive program of tests to qualify different detector prototypes with dedicated test beams. A common data-acquisition system, H4DAQ, was developed for the H4 test beam line at the North Area of the CERN SPS in 2014 and it has since been adopted in various applications for the CMS experiment and AIDA project. Several calorimeter prototypes and precision timing detectors have used our system from 2014 to 2017. H4DAQ has proven to be a versatile application and has been ported to many other beam test environments. H4DAQ is fast, simple, modular and can be configured to support various kinds of setup. The functionalities of the DAQ core software are split into three configurable finite state machines: data readout, run control, and event builder. The distribution of information and data between the various computers is performed using ZEROMQ (0MQ) sockets. Plugins are available to read different types of hardware, including VME crates with many types of boards, PADE boards, custom front-end boards and beam instrumentation devices. The raw data are saved as ROOT files, using the CERN C++ ROOT libraries. A Graphical User Interface, based on the python gtk libraries, is used to operate the H4DAQ and an integrated data quality monitoring (DQM), written in C++, allows for fast processing of the events for quick feedback to the user. As the 0MQ libraries are also available for the National Instruments LabVIEW program, this environment can easily be integrated within H4DAQ applications.

One-Year Plan for Library Services.

ERIC Educational Resources Information Center

Caroline County Public Library, Denton, MD.

This action plan for the Caroline County (MD) Public Library describes the key elements of library service for the 1985-86 fiscal year, derived from the library's long range plan for 1985-90. Objectives, strategies, activities, and timetables for accomplishing the following goals are outlined: (1) citizens of the county will increasingly meet…

Design Principles for the Information Architecture of a SMET Education Digital Library.

ERIC Educational Resources Information Center

Dong, Andy; Agogino, Alice M.

This implementation paper introduces principles for the information architecture of an educational digital library, principles that address the distinction between designing digital libraries for education and designing digital libraries for information retrieval in general. Design is a key element of any successful product. Good designers and…

Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection.

PubMed

Castañón, Jesús; Román, José Pablo; Jessop, Theodore C; de Blas, Jesús; Haro, Rubén

2018-06-01

DNA-encoded libraries (DELs) have emerged as an efficient and cost-effective drug discovery tool for the exploration and screening of very large chemical space using small-molecule collections of unprecedented size. Herein, we report an integrated automation and informatics system designed to enhance the quality, efficiency, and throughput of the production and affinity selection of these libraries. The platform is governed by software developed according to a database-centric architecture to ensure data consistency, integrity, and availability. Through its versatile protocol management functionalities, this application captures the wide diversity of experimental processes involved with DEL technology, keeps track of working protocols in the database, and uses them to command robotic liquid handlers for the synthesis of libraries. This approach provides full traceability of building-blocks and DNA tags in each split-and-pool cycle. Affinity selection experiments and high-throughput sequencing reads are also captured in the database, and the results are automatically deconvoluted and visualized in customizable representations. Researchers can compare results of different experiments and use machine learning methods to discover patterns in data. As of this writing, the platform has been validated through the generation and affinity selection of various libraries, and it has become the cornerstone of the DEL production effort at Lilly.

User Requirements Analysis For Digital Library Application Using Quality Function Deployment.

NASA Astrophysics Data System (ADS)

Wulandari, Lily; Sularto, Lana; Yusnitasari, Tristyanti; Ikasari, Diana

2017-03-01

This study attemp to build Smart Digital Library to be used by the wider community wherever they are. The system is built in the form of Smart Digital Library portal which uses semantic similarity method (Semantic Similarity) to search journals, articles or books by title or author name. This method is also used to determine the recommended books to be read by visitors of Smart Digital Library based on testimony from a previous reader automatically. Steps being taken in the development of Smart Digital Library system is the analysis phase, design phase, testing and implementation phase. At this stage of the analysis using WebQual for the preparation of the instruments to be distributed to the respondents and the data obtained from the respondents will be processed using Quality Function Deployment. In the analysis phase has the purpose of identifying consumer needs and technical requirements. The analysis was performed to a digital library on the web digital library Gunadarma University, Bogor Institute of Agriculture, University of Indonesia, etc. The questionnaire was distributed to 200 respondents. The research methodology begins with the collection of user requirements and analyse it using QFD. Application design is funded by the government through a program of Featured Universities Research by the Directorate General of Higher Education (DIKTI). Conclusions from this research are identified which include the Consumer Requirements of digital library application. The elements of the consumers requirements consists of 13 elements and 25 elements of Engineering Characteristics digital library requirements. Therefore the design of digital library applications that will be built, is designed according to the findings by eliminating features that are not needed by restaurant based on QFD House of Quality.

The Extended and Experimenting College Library. Appendixes 1 - 3.

ERIC Educational Resources Information Center

Taylor, Robert S.; Trueswell, Richard W.

There were four objectives in this first phase in developing the concept of the experimenting and extended college library: (1) exploration of the configurations, functions, and operations of the academic library in transition; (2) initial analysis of the elements of such a library in the context of an experimenting institution, i.e. Hampshire…

Analyses of the 1981-82 Illinois Public Library Statistics.

ERIC Educational Resources Information Center

Wallace, Danny P.

Using data provided by the annual reports of Illinois public libraries and by the Illinois state library, this publication is a companion to the November 1982 issue of "Illinois Libraries," which enumerated the 16 data elements upon which the analyses are based. Three additional types of information are provided for each of six…

The t-Butylsulfinamide Lynchpin in Transition Metal-Mediated Multiscaffold Library Synthesis

PubMed Central

Bauer, Renato A.; DiBlasi, Christine M.; Tan, Derek S.

2010-01-01

A unified synthetic approach to diverse polycyclic scaffolds has been developed using transition metal-mediated cycloaddition and cyclization reactions of enynes and diynes. The t-butylsulfinamide group has been identified as a particularly versatile lynchpin in these reactions, with a reactivity profile uniquely suited for efficient, stereoselective substrate synthesis and downstream transformations. This approach provides ten distinct, functionalized scaffold classes related to common core structures in alkaloid and terpenoid natural products. PMID:20356070

FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.

PubMed

Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

2017-05-15

MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM. The software and the datasets are available at http://www.di.unisa.it/FASTdoop/ . umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Jeddah Historical Building Information Modelling "JHBIM" - Object Library

NASA Astrophysics Data System (ADS)

Baik, A.; Alitany, A.; Boehm, J.; Robson, S.

2014-05-01

The theory of using Building Information Modelling "BIM" has been used in several Heritage places in the worldwide, in the case of conserving, documenting, managing, and creating full engineering drawings and information. However, one of the most serious issues that facing many experts in order to use the Historical Building Information Modelling "HBIM", is creating the complicated architectural elements of these Historical buildings. In fact, many of these outstanding architectural elements have been designed and created in the site to fit the exact location. Similarly, this issue has been faced the experts in Old Jeddah in order to use the BIM method for Old Jeddah historical Building. Moreover, The Saudi Arabian City has a long history as it contains large number of historic houses and buildings that were built since the 16th century. Furthermore, the BIM model of the historical building in Old Jeddah always take a lot of time, due to the unique of Hijazi architectural elements and no such elements library, which have been took a lot of time to be modelled. This paper will focus on building the Hijazi architectural elements library based on laser scanner and image survey data. This solution will reduce the time to complete the HBIM model and offering in depth and rich digital architectural elements library to be used in any heritage projects in Al-Balad district, Jeddah City.

KAOS/LIB-V: A library of nuclear response functions generated by KAOS-V code from ENDF/B-V and other data files

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

Farawila, Y.; Gohar, Y.; Maynard, C.

1989-04-01

KAOS/LIB-V: A library of processed nuclear responses for neutronics analyses of nuclear systems has been generated. The library was prepared using the KAOS-V code and nuclear data from ENDF/B-V. The library includes kerma (kinetic energy released in materials) factors and other nuclear response functions for all materials presently of interest in fusion and fission applications for 43 nonfissionable and 15 fissionable isotopes and elements. The nuclear response functions include gas production and tritium-breeding functions, and all important reaction cross sections. KAOS/LIB-V employs the VITAMIN-E weighting function and energy group structure of 174 neutron groups. Auxiliary nuclear data bases, e.g., themore » Japanese evaluated nuclear data library JENDL-2 were used as a source of isotopic cross sections when these data are not provided in ENDF/B-V files for a natural element. These are needed mainly to estimate average quantities such as effective Q-values for the natural element. This analysis of local energy deposition was instrumental in detecting and understanding energy balance deficiencies and other problems in the ENDF/B-V data. Pertinent information about the library and a graphical display of the main nuclear response functions for all materials in the library are given. 35 refs.« less

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

Numerical tool development of fluid-structure interactions for investigation of obstructive sleep apnea

NASA Astrophysics Data System (ADS)

Huang, Chien-Jung; White, Susan; Huang, Shao-Ching; Mallya, Sanjay; Eldredge, Jeff

2016-11-01

Obstructive sleep apnea (OSA) is a medical condition characterized by repetitive partial or complete occlusion of the airway during sleep. The soft tissues in the upper airway of OSA patients are prone to collapse under the low pressure loads incurred during breathing. The ultimate goal of this research is the development of a versatile numerical tool for simulation of air-tissue interactions in the patient specific upper airway geometry. This tool is expected to capture several phenomena, including flow-induced vibration (snoring) and large deformations during airway collapse of the complex airway geometry in respiratory flow conditions. Here, we present our ongoing progress toward this goal. To avoid mesh regeneration, for flow model, a sharp-interface embedded boundary method is used on Cartesian grids for resolving the fluid-structure interface, while for the structural model, a cut-cell finite element method is used. Also, to properly resolve large displacements, non-linear elasticity model is used. The fluid and structure solvers are connected with the strongly coupled iterative algorithm. The parallel computation is achieved with the numerical library PETSc. Some two- and three- dimensional preliminary results are shown to demonstrate the ability of this tool.

Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

PubMed Central

Ji, Haitao; Stanton, Benjamin Z.; Igarashi, Jotaro; Li, Huiying; Martásek, Pavel; Roman, Linda J.; Poulos, Thomas L.; Silverman, Richard B.

2010-01-01

Fragment hopping, a new fragment-based approach for de novo inhibitor design focusing on ligand diversity and isozyme selectivity, is described. The core of this approach is the derivation of the minimal pharmacophoric element for each pharmacophore. Sites for both ligand binding and isozyme selectivity are considered in deriving the minimal pharmacophoric elements. Five general-purpose libraries are established: the basic fragment library, the bioisostere library, the rules for metabolic stability, the toxicophore library, and the side chain library. These libraries are employed to generate focused fragment libraries to match the minimal pharmacophoric elements for each pharmacophore and then to link the fragment to the desired molecule. This method was successfully applied to neuronal nitric oxide synthase (nNOS), which is implicated in stroke and neurodegenerative diseases. Starting with the nitroarginine-containing dipeptide inhibitors we developed previously, a small organic molecule with a totally different chemical structure was designed, which showed nanomolar nNOS inhibitory potency and more than 1000-fold nNOS selectivity. The crystallographic analysis confirms that the small organic molecule with a constrained conformation can exactly mimic the mode of action of the dipeptide nNOS inhibitors. Therefore, a new peptidomimetic strategy, referred to as fragment hopping, which creates small organic molecules that mimic the biological function of peptides by a pharmacophore-driven strategy for fragment-based de novo design, has been established as a new type of fragment-based inhibitor design. As an open system, the newly established approach efficiently incorporates the concept of early “ADME/Tox” considerations and provides a basic platform for medicinal chemistry-driven efforts. PMID:18321097

Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep).

PubMed

Guellouz, Asma; Valerio-Lepiniec, Marie; Urvoas, Agathe; Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.

Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep)

PubMed Central

Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a “filtration” procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×109 independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties. PMID:24014183

The Elements of Library Research: What Every Student Needs to Know

ERIC Educational Resources Information Center

George, Mary W.

2008-01-01

To do solid academic research, college students need to look beyond the computer search engine. This short, practical book introduces students to the important components of the information-seeking process. "The Elements of Library Research" provides a foundation for success in any research assignment, from a freshman paper to a senior thesis.…

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

Defining Elemental Imitation Mechanisms: A Comparison of Cognitive and Motor-Spatial Imitation Learning across Object- and Computer-Based Tasks

ERIC Educational Resources Information Center

Subiaul, Francys; Zimmermann, Laura; Renner, Elizabeth; Schilder, Brian; Barr, Rachel

2016-01-01

During the first 5 years of life, the versatility, breadth, and fidelity with which children imitate change dramatically. Currently, there is no model to explain what underlies such significant changes. To that end, the present study examined whether task-independent but domain-specific--elemental--imitation mechanism explains performance across…

Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements.

PubMed

Crivianu-Gaita, Victor; Thompson, Michael

2016-11-15

The choice of biosensing elements is crucial for the development of the optimal biosensor. Three of the most versatile biosensing elements are antibody single-chain Fv fragments (scFv), antibody fragment-antigen binding (Fab') units, and aptamers. This article provides an overview of these three biorecognition elements with respects to their synthesis/engineering, various immobilization techniques, and examples of their use in biosensors. Furthermore, the final section of the review compares and contrasts their characteristics (time/cost of development, ease and variability of immobilization, affinity, stability) illustrating their advantages and disadvantages. Overall, scFv fragments are found to display the highest customizability (i.e. addition of functional groups, immobilizing peptides, etc.) due to recombinant synthesis techniques. If time and cost are an issue in the development of the biosensor, Fab' fragments should be chosen as they are relatively cheap and can be developed quickly from whole antibodies (several days). However, if there are sufficient funds and time is not a factor, aptamers should be utilized as they display the greatest affinity towards their target analytes and are extremely stable (excellent biosensor regenerability). Copyright © 2016 Elsevier B.V. All rights reserved.

The Marketing of Special Libraries to Their Parent Organisations: A Study of Selected Melbourne Institutions.

ERIC Educational Resources Information Center

Kelso, Helena

1995-01-01

A survey of corporate and government libraries in Victoria, Australia, revealed that many are in favor of marketing services to their parent organizations, but in practice very few undertake formal marketing planning. Highlights elements of marketing processes in use by libraries and examines why more libraries are not preparing and implementing…

The Carnegie Mellon/Sirsi Corporation Alliance.

ERIC Educational Resources Information Center

Troll, Denise A.; Depellegrin, Tracey A.; Myers, Melanie D.

1999-01-01

Describes the relationship between Carnegie Mellon University libraries and Sirsi Corporation, their integrated library-management system vendor. Topics include Carnegie Mellon's expertise in library automation research and development; and three primary elements of the alliance: research, including user protocols, surveys, and focus groups;…

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

The Human Element in the Virtual Library.

ERIC Educational Resources Information Center

Saunders, Laverna M.

1999-01-01

Introduces the concept of the virtual library and explores how the increasing reliance on computers and digital information has affected library users and staff. Discusses users' expectations, democratization of access, human issues, organizational change, technostress, ergonomics, assessment, and strategies for success and survival. Contains 35…

More arrows in the quiver: new pathways and old problems with heavy alkaline earth metal diphenylmethanides.

PubMed

Alexander, Jacob S; Ruhlandt-Senge, Karin

2004-03-05

Progress in the field of sigma-bonded alkaline earth organometallics has been handicapped by numerous complications, such as high reactivity, low solubility, and the limited availability of suitable starting materials. Here we present two synthetic methods, hydrocarbon elimination and desilylation, as alternative routes into this chemistry. A novel barium diphenylmethanide was prepared using these routes delineating that both methods provide a powerful, versatile synthetic access route to an extended library of organometallic alkaline earth derivatives.

Engineering of Transition Metal Catalysts Confined in Zeolites

PubMed Central

2018-01-01

Transition metal–zeolite composites are versatile catalytic materials for a wide range of industrial and lab-scale processes. Significant advances in fabrication and characterization of well-defined metal centers confined in zeolite matrixes have greatly expanded the library of available materials and, accordingly, their catalytic utility. In this review, we summarize recent developments in the field from the perspective of materials chemistry, focusing on synthesis, postsynthesis modification, (operando) spectroscopy characterization, and computational modeling of transition metal–zeolite catalysts. PMID:29861546

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'.

PubMed

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.

A versatile transfection assay system to evaluate the biological effects of diverse industrial chemicals.

PubMed

Koizumi, Shinji; Ohno, Shotaro; Otsuka, Fuminori

2012-01-01

Gene expression processes are now recognized as important targets of the toxic effects exerted by industrial chemicals. The transient transfection assay is a powerful tool to evaluate such effects. Thus, we developed a versatile assay system by constructing a basic reporter plasmid in which the regulatory DNA sequence to be studied can easily be substituted. To verify the performance of this system, reporter plasmids carrying any of the three distinct regulatory sequences, estrogen responsive element (ERE), glucocorticoid responsive element (GRE) and xenobiotic responsive element (XRE) were constructed. After transfection of human cells, these plasmids successfully expressed the relevant reporter genes in response to specific inducers, β-estradiol, dexamethasone and 3-methylcholanthrene, respectively. Several industrial chemicals were assayed using these reporter plasmids, and the ability of p-dimethylaminoazobenzene to elevate GRE- and XRE-mediated transcription was detected. α-Naphthylamine and o-tolidine were also observed to increase the XRE-mediated response. The transfection assay system established here will be useful to evaluate the effects of a wide variety of industrial chemicals.

Exploring the Chemistry of Bicyclic Isoxazolidines for the Multicomponent Synthesis of Glycomimetic Building Blocks.

PubMed

Hoogenboom, Jorin; Lutz, Martin; Zuilhof, Han; Wennekes, Tom

2016-10-07

Starting from a chiral furanone, the nitrone-olefin [3 + 2] cycloaddition can be used to obtain bicyclic isoxazolidines for which we report a set of reactions to selectively modify each functional position. These synthetically versatile bicyclic isoxazolidines allowed us to obtain complex glycomimetic building blocks, like iminosugars, via multicomponent chemistry. For example, a library of 20 pipecolic acid derivatives, a recurring motif in various prescription drugs, could be obtained via a one-pot Staudinger/aza-Wittig/Ugi three-component reaction of a bicyclic isoxazolidine-derived azido-hemiacetal. Notably, specific pipecolic acids in this library were obtained via hydrolysis of an unique tricyclic imidate side product of the Ugi reaction. The azido-hemiacetal was also converted into an aza-C-glycoside iminosugar via an unprecendented one-pot Staudinger/aza-Wittig/Mannich reaction.

Implementing a Systematic Planning Process in Two Very Small Rural Public Libraries.

ERIC Educational Resources Information Center

Senkevitch, Judith J.

1985-01-01

Describes a pilot project by a regional library system in central New York State to implement systematic planning activities in rural public libraries serving populations under 5,000. Motivations for the adoption of innovation and key elements in the decision making process during implementation are examined. (CLB)

Internet Policy Handbook for Libraries. Neal-Schuman NetGuide Series.

ERIC Educational Resources Information Center

Smith, Mark

This book is intended to guide library administrators--directors and departmental managers in public, school, and academic libraries--through the many complex decisions inherent in managing public Internet access. The handbook systematically deals with each possible element of an Internet policy. It identifies the options available at each…

Expanding Library Support of Faculty Research: Exploring Readiness

ERIC Educational Resources Information Center

Brown, Jeanne M.; Tucker, Cory

2013-01-01

The changing research and information environment requires a reexamination of library support for research. This study considers research-related attitudes and practices to identify elements indicating readiness or resistance to expanding the library's role in research support. A survey of faculty conducted at the University of Nevada Las Vegas…

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

Clinedinst, Winston C.; Slominski, Christopher J.; Dickson, Richard W.; Wolverton, David A.

1993-01-01

The individual software processes used in the flight computers on-board the Advanced Transport Operating System (ATOPS) aircraft have many common functional elements. A library of commonly used software modules was created for general uses among the processes. The library includes modules for mathematical computations, data formatting, system database interfacing, and condition handling. The modules available in the library and their associated calling requirements are described.

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

NASA Astrophysics Data System (ADS)

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.

A Dynamic Finite Element Method for Simulating the Physics of Faults Systems

NASA Astrophysics Data System (ADS)

Saez, E.; Mora, P.; Gross, L.; Weatherley, D.

2004-12-01

We introduce a dynamic Finite Element method using a novel high level scripting language to describe the physical equations, boundary conditions and time integration scheme. The library we use is the parallel Finley library: a finite element kernel library, designed for solving large-scale problems. It is incorporated as a differential equation solver into a more general library called escript, based on the scripting language Python. This library has been developed to facilitate the rapid development of 3D parallel codes, and is optimised for the Australian Computational Earth Systems Simulator Major National Research Facility (ACcESS MNRF) supercomputer, a 208 processor SGI Altix with a peak performance of 1.1 TFlops. Using the scripting approach we obtain a parallel FE code able to take advantage of the computational efficiency of the Altix 3700. We consider faults as material discontinuities (the displacement, velocity, and acceleration fields are discontinuous at the fault), with elastic behavior. The stress continuity at the fault is achieved naturally through the expression of the fault interactions in the weak formulation. The elasticity problem is solved explicitly in time, using the Saint Verlat scheme. Finally, we specify a suitable frictional constitutive relation and numerical scheme to simulate fault behaviour. Our model is based on previous work on modelling fault friction and multi-fault systems using lattice solid-like models. We adapt the 2D model for simulating the dynamics of parallel fault systems described to the Finite-Element method. The approach uses a frictional relation along faults that is slip and slip-rate dependent, and the numerical integration approach introduced by Mora and Place in the lattice solid model. In order to illustrate the new Finite Element model, single and multi-fault simulation examples are presented.

Creation of a Radiation Hard 0.13 Micron CMOS Library at IHP

NASA Astrophysics Data System (ADS)

Jagdhold, U.

2010-08-01

To support space applications we will develop an 0.13 micron CMOS library which should be radiation hard up to 200 krad. By introducing new radiation hard design rules we will minimize IC-level leakage and single event latchup (SEL). To reduce single event upset (SEU) we will add two p-MOS transistors to all flip flops. For reliability reasons we will use double contacts in all library elements. The additional rules and the library elements will then be integrated in our Cadence mixed signal designkit, Virtuoso IC6.1 [1]. A test chip will be produced with our in house 0.13 micron BiCMOS technology, see Ref. [2].Thereafter we will doing radiation tests according the ESA specifications, see Ref. [3], [4].

A versatile setup using femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman scattering

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

Shen, Yujie, E-mail: styojm@physics.tamu.edu; Voronine, Dmitri V.; Sokolov, Alexei V.

2015-08-15

We report a versatile setup based on the femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman scattering. The setup uses a femtosecond Ti:Sapphire oscillator source and a folded 4f pulse shaper, in which the pulse shaping is carried out through conventional optical elements and does not require a spatial light modulator. Our setup is simple in alignment, and can be easily switched between the collinear single-beam and the noncollinear two-beam configurations. We demonstrate the capability for investigating both transparent and highly scattering samples by detecting transmitted and reflected signals, respectively.

Tagmentation on Microbeads: Restore Long-Range DNA Sequence Information Using Next Generation Sequencing with Library Prepared by Surface-Immobilized Transposomes.

PubMed

Chen, He; Yao, Jiacheng; Fu, Yusi; Pang, Yuhong; Wang, Jianbin; Huang, Yanyi

2018-04-11

The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but they often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient, and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically label adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing. In our proof-of-principle experiment, more than 4.5% of the reads are linked with their adjacent reads, and the longest linkage is over 1112 bp. We demonstrate TOM with eight barcodes, but the number of barcodes can be scaled up by an ultrahigh complexity construction. We also show this method has low amplification bias and effectively fits the applications to identify copy number variations.

Being There is Only the Beginning: Toward More Effective Web 2.0 Use in Academic Libraries

DTIC Science & Technology

2010-01-02

Google is Our Friend,” and “ Plagiarism 101.” Also unlike the hard-to-find blogs, many academic libraries, including both Hollins University and Urbana...Effective Web 2.0 Use in Academic Libraries by Hanna C. Bachrach Pratt Institute...5a. CONTRACT NUMBER 2.0 Use in Academic Libraries 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Bachrach

Library of Michigan FY 2000 LSTA Subgrant Program Guidelines.

ERIC Educational Resources Information Center

Michigan Library, Lansing.

This handbook provides FY (fiscal year) 2000 guidelines developed by the Library of Michigan for applying for LSTA (Library Services and Technology Act) subgrant funding. The handbook includes the following sections: (1) overview of the LSTA subgrant program; (2) general application guidelines for all funding areas; (3) required elements of the…

Printers' Devices as Decorative Elements in Library Architecture

ERIC Educational Resources Information Center

Nipps, Karen

2013-01-01

As has been described in the editorials of the past two issues, "The Library Quarterly" has changed in appearance and content to better reflect contemporary research on library-related issues. As the newly dubbed "History of the Book" editor, Karen Nipps is excited that the cover article segment of the journal is being expanded…

Measures for Electronic Resources (E-Metrics). Complete Set.

ERIC Educational Resources Information Center

Association of Research Libraries, Washington, DC.

The Association of Research Libraries (ARL) E-Metrics study was designed as an 18-month project in three phases: an inventory of what libraries were already doing about data collection for electronic resources and an identification of any libraries that could provide best practice; identifying and testing data elements that could be collected and…

Creating Electronic Tutorials: On Your Mark, Get Set, Go!

ERIC Educational Resources Information Center

Plumb, Tawnya K.

2010-01-01

As library patrons move online, librarians must move instructional content online to join them. One means of educating library users is to meet them on their computers with electronic tutorials. Electronic tutorials may be used for various instructional tasks such as teaching users about the basic elements of a library catalog, pointing out the…

New York State's School Library Evaluation

ERIC Educational Resources Information Center

Jaeger, Paige

2012-01-01

The New York State's School Library Media Program Evaluation (SLMPE) rubric provides a window of opportunity for a librarian to talk with his/her administrators about library program elements that may be out of the librarian's control. There are three areas of focus on the SLMPE Rubric: (1) Teaching and Learning; (2) Building and Learning…

Toward a versatile toolbox for cucurbit[n]uril-based supramolecular hydrogel networks through in situ polymerization.

PubMed

Liu, Ji; Soo Yun Tan, Cindy; Lan, Yang; Scherman, Oren A

2017-09-15

The success of exploiting cucurbit[ n ]uril (CB[ n ])-based molecular recognition in self-assembled systems has sparked a tremendous interest in polymer and materials chemistry. In this study, polymerization in the presence of host-guest complexes is applied as a modular synthetic approach toward a diverse set of CB[8]-based supramolecular hydrogels with desirable properties, such as mechanical strength, toughness, energy dissipation, self-healing, and shear-thinning. A range of vinyl monomers, including acrylamide-, acrylate-, and imidazolium-based hydrophilic monomers, could be easily incorporated as the polymer backbones, leading to a library of CB[8] hydrogel networks. This versatile strategy explores new horizons for the construction of supramolecular hydrogel networks and materials with emergent properties in wearable and self-healable electronic devices, sensors, and structural biomaterials. © 2017 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 3105-3109.

General-Purpose Electronic System Tests Aircraft

NASA Technical Reports Server (NTRS)

Glover, Richard D.

1989-01-01

Versatile digital equipment supports research, development, and maintenance. Extended aircraft interrogation and display system is general-purpose assembly of digital electronic equipment on ground for testing of digital electronic systems on advanced aircraft. Many advanced features, including multiple 16-bit microprocessors, pipeline data-flow architecture, advanced operating system, and resident software-development tools. Basic collection of software includes program for handling many types of data and for displays in various formats. User easily extends basic software library. Hardware and software interfaces to subsystems provided by user designed for flexibility in configuration to meet user's requirements.

Assessment of antibody library diversity through next generation sequencing and technical error compensation

PubMed Central

Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error. PMID:28505201

Assessment of antibody library diversity through next generation sequencing and technical error compensation.

PubMed

Fantini, Marco; Pandolfini, Luca; Lisi, Simonetta; Chirichella, Michele; Arisi, Ivan; Terrigno, Marco; Goracci, Martina; Cremisi, Federico; Cattaneo, Antonino

2017-01-01

Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity. Quantitative evaluation of antibody library complexity and quality has been for a long time inadequately addressed, due to the high similarity and length of the sequences of the library. Complexity was usually inferred by the transformation efficiency and tested either by fingerprinting and/or sequencing of a few hundred random library elements. Inferring complexity from such a small sampling is, however, very rudimental and gives limited information about the real diversity, because complexity does not scale linearly with sample size. Next-generation sequencing (NGS) has opened new ways to tackle the antibody library complexity quality assessment. However, much remains to be done to fully exploit the potential of NGS for the quantitative analysis of antibody repertoires and to overcome current limitations. To obtain a more reliable antibody library complexity estimate here we show a new, PCR-free, NGS approach to sequence antibody libraries on Illumina platform, coupled to a new bioinformatic analysis and software (Diversity Estimator of Antibody Library, DEAL) that allows to reliably estimate the complexity, taking in consideration the sequencing error.

pH-programmable DNA logic arrays powered by modular DNAzyme libraries.

PubMed

Elbaz, Johann; Wang, Fuan; Remacle, Francoise; Willner, Itamar

2012-12-12

Nature performs complex information processing circuits, such the programmed transformations of versatile stem cells into targeted functional cells. Man-made molecular circuits are, however, unable to mimic such sophisticated biomachineries. To reach these goals, it is essential to construct programmable modular components that can be triggered by environmental stimuli to perform different logic circuits. We report on the unprecedented design of artificial pH-programmable DNA logic arrays, constructed by modular libraries of Mg(2+)- and UO(2)(2+)-dependent DNAzyme subunits and their substrates. By the appropriate modular design of the DNA computation units, pH-programmable logic arrays of various complexities are realized, and the arrays can be erased, reused, and/or reprogrammed. Such systems may be implemented in the near future for nanomedical applications by pH-controlled regulation of cellular functions or may be used to control biotransformations stimulated by bacteria.

The carnegie protein trap library: a versatile tool for Drosophila developmental studies.

PubMed

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D; Nystul, Todd G; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E; Murphy, Terence D; Levis, Robert W; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A; Spradling, Allan C

2007-03-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.

Construction and Screening of Marine Metagenomic Large Insert Libraries.

PubMed

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

76 FR 5145 - Notice of Availability of the Final Long-Term Management and Storage of Elemental Mercury...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-28

... are available for public review at the locations listed below. Colorado Mesa County Library, 530 Grand..., Washington, DC 20585, (202) 586-5955. Georgia Augusta State University, Reese Library, 2500 Walton Way, Augusta, GA 30904, (706) 737-1745. Savannah State University, Asa H. Gordon Library, 2200 Tompkins Road...

Listening to Students: Customer Journey Mapping at Birmingham City University Library and Learning Resources

ERIC Educational Resources Information Center

Andrews, Judith; Eade, Eleanor

2013-01-01

Birmingham City University's Library and Learning Resources' strategic aim is to improve student satisfaction. A key element is the achievement of the Customer Excellence Standard. An important component of the standard is the mapping of services to improve quality. Library and Learning Resources has developed a methodology to map these…

Getting Started with The Math Forum Problems of the Week Library. Teacher's Guide

ERIC Educational Resources Information Center

Math Forum @ Drexel, 2009

2009-01-01

The Math Forum Problems of the Week Library is designed to leverage the power of interactive technology to hold student interest while increasing their success as strategic thinkers. The Math Forum Library is an online source of non-routine challenges in which problem solving and mathematical communication are key elements of every problem. This…

Strategic Alignment at the University of Manchester Library: Ambitions, Transitions, and New Values

ERIC Educational Resources Information Center

Jeal, Yvette

2014-01-01

The University of Manchester Library (UML) is embarking on an ambitious new strategy that aims to align the library more closely to the work of the University--to contribute to the University's strategic success. This article describes elements of the strategy development and content, focusing on methods used; how the service has worked…

Effective Communication: An Essential Tool To Cope with the Challenge of Technological Change.

ERIC Educational Resources Information Center

Coing, Marga

For a library to function effectively, it is essential that it fosters an open management style, which encourages communication of ideas and objectives both within the library itself and, by example, in other elements in the overall administration of which the library is a part. This paper describes the improvement in morale, efficiency, and…

Library Spaces for Urban, Diverse Commuter Students: A Participatory Action Research Project

ERIC Educational Resources Information Center

Brown-Sica, Margaret S.

2012-01-01

A data-gathering project using elements of Participatory Action Research was conducted at the Auraria Library, which serves the University of Colorado Denver, the Metropolitan State College of Denver and the Community College of Denver. The project was administered in order to shape a plan to develop a Learning Commons environment at the library.…

Four Versatile Metal Reactions.

ERIC Educational Resources Information Center

Hearn, Barbara C.

1988-01-01

Presents several strategies to teach the reactivity of metal elements. Stresses the safety aspects of these demonstrations using an overhead projector and a plexiglass safety shield. Lists some of the essential learnings desired in these activities. Includes a chart of the activity series of metals. (CW)

Transverse-structure electrostatic charged particle beam lens

DOEpatents

Moran, M.J.

1998-10-13

Electrostatic particle-beam lenses using a concentric co-planar array of independently biased rings can be advantageous for some applications. Traditional electrostatic lenses often consist of axial series of biased rings, apertures, or tubes. The science of lens design has devoted much attention to finding axial arrangements that compensate for the substantial optical aberrations of the individual elements. Thus, as with multi-element lenses for light, a multi-element charged-particle lens can have optical behavior that is far superior to that of the individual elements. Transverse multiple-concentric-ring lenses achieve high performance, while also having advantages in terms of compactness and optical versatility. 7 figs.

Transverse-structure electrostatic charged particle beam lens

DOEpatents

Moran, Michael J.

1998-01-01

Electrostatic particle-beam lenses using a concentric co-planar array of independently biased rings can be advantageous for some applications. Traditional electrostatic lenses often consist of axial series of biased rings, apertures, or tubes. The science of lens design has devoted much attention to finding axial arrangements that compensate for the substantial optical aberrations of the individual elements. Thus, as with multi-element lenses for light, a multi-element charged-particle lens can have optical behavior that is far superior to that of the individual elements. Transverse multiple-concentric-ring lenses achieve high performance, while also having advantages in terms of compactness and optical versatility.

Analytical performance of a versatile laboratory microscopic X-ray fluorescence system for metal uptake studies on argillaceous rocks

NASA Astrophysics Data System (ADS)

Gergely, Felicián; Osán, János; Szabó, B. Katalin; Török, Szabina

2016-02-01

Laboratory-scale microscopic X-ray fluorescence (micro-XRF) plays an increasingly important role in various fields where multielemental investigations of samples are indispensable. In case of geological samples, the reasonable detection limits (LOD) and spatial resolutions are necessary to identify the trace element content in microcrystalline level. The present study focuses on the analytical performance of a versatile laboratory-scale micro-XRF system with various options of X-ray sources and detectors to find the optimal experimental configuration in terms of sensitivities and LOD for selected elements in loaded petrographic thin sections. The method was tested for sorption studies involving thin sections prepared from cores of Boda Claystone Formation, which is a potential site for a high-level radioactive waste repository. Loaded ions in the sorption measurements were Cs(I) and Ni(II) chemically representing fission and corrosion products. Based on the collected elemental maps, the correlation between the elements representative of main rock components and the selected loaded ion was studied. For the elements of interest, Cs(I) and Ni(II) low-power iMOXS source with polycapillary and silicon drift detector was found to be the best configuration to reach the optimal LOD values. Laboratory micro-XRF was excellent to identify the responsible key minerals for the uptake of Cs(I). In case of nickel, careful corrections were needed because of the relatively high Ca content of the rock samples. The results were compared to synchrotron radiation micro-XRF.

Mainstreaming the New Library.

ERIC Educational Resources Information Center

Keeler, Elizabeth

1982-01-01

This discussion of methods of integrating the corporate library into the mainstream of affairs highlights three major elements of the process: marketing, production, and advertising. Professionalism and the information seeking behavior of clients are noted. Five references are provided. (EJS)

Radiation Hard 0.13 Micron CMOS Library at IHP

NASA Astrophysics Data System (ADS)

Jagdhold, U.

2013-08-01

To support space applications we have developed an 0.13 micron CMOS library which should be radiation hard up to 200 krad. The article describes the concept to come to a radiation hard digital circuit and was introduces in 2010 [1]. By introducing new radiation hard design rules we will minimize IC-level leakage and single event latch-up (SEL). To reduce single event upset (SEU) we add two p-MOS transistors to all flip flops. For reliability reasons we use double contacts in all library elements. The additional rules and the library elements are integrated in our Cadence mixed signal design kit, “Virtuoso” IC6.1 [2]. A test chip is produced with our in house 0.13 micron BiCMOS technology, see Ref. [3]. As next step we will doing radiation tests according the european space agency (ESA) specifications, see Ref. [4], [5].

Ethics Instruction in Library and Information Science: The Role of "Ethics across the Curriculum"

ERIC Educational Resources Information Center

Smith, Bernie Todd

2010-01-01

Ethics is an important element of most graduate professional training programs. In the field of Library and Information Science (LIS) the inclusion of ethics in the curriculum is supported by a position paper by library educators and is monitored in the accreditation of graduate programs. Despite the many LIS programs which claim to integrate…

A stochastic method for computing hadronic matrix elements

DOE PAGES

Alexandrou, Constantia; Constantinou, Martha; Dinter, Simon; ...

2014-01-24

In this study, we present a stochastic method for the calculation of baryon 3-point functions which is an alternative to the typically used sequential method offering more versatility. We analyze the scaling of the error of the stochastically evaluated 3-point function with the lattice volume and find a favorable signal to noise ratio suggesting that the stochastic method can be extended to large volumes providing an efficient approach to compute hadronic matrix elements and form factors.

Foundations for Effective School Library Media Programs.

ERIC Educational Resources Information Center

Haycock, Ken, Ed.

This collection of 38 articles, reprinted from "Emergency Librarian," addresses critical elements of school library media program development and implementation, organized by seven areas: foundations; the school context; role clarification; information literacy; collaborative program planning and teaching; program development; and…

Tour Robot Dance

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

Cleary, Geoff

2014-09-08

This program exercises the robotic elements in Oracle Storage Tek tape libraries. This is useful for two known cases: 1.) shaking out marginal or new hardware by ensuring hardware robustness under high-duty usage. 2.) ensuring tape libraries are visually interesting during datacenter tours

Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

PubMed Central

Wu, Chengcang; Proestou, Dina; Carter, Dorothy; Nicholson, Erica; Santos, Filippe; Zhao, Shaying; Zhang, Hong-Bin; Goldsmith, Marian R

2009-01-01

Background Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences. Conclusion The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes. PMID:19558662

Verification of a Finite Element Model for Pyrolyzing Ablative Materials

NASA Technical Reports Server (NTRS)

Risch, Timothy K.

2017-01-01

Ablating thermal protection system (TPS) materials have been used in many reentering spacecraft and in other applications such as rocket nozzle linings, fire protection materials, and as countermeasures for directed energy weapons. The introduction of the finite element model to the analysis of ablation has arguably resulted in improved computational capabilities due the flexibility and extended applicability of the method, especially to complex geometries. Commercial finite element codes often provide enhanced capability compared to custom, specially written programs based on versatility, usability, pre- and post-processing, grid generation, total life-cycle costs, and speed.

Experience in Using a Finite Element Stress and Vibration Package on a Minicomputer,

DTIC Science & Technology

1982-01-01

as the Gra’phics Oricntat.ed Interactive Finite Element Time Sharing Pacl’age ( GIFTS ). This packge has been running on a PDP11/60 minicomputer...Unlike many other FEM packages, GIFTS consists of a collecticon E of fully compatible special purpose programns operating on a se. ef files on disk known...matrix is initiated by running the appropriate ptrojrF:’. from the GIFTS library. The following if, a list of the major (IFtS library programs with a

Development and Synthesis of DNA-Encoded Benzimidazole Library.

PubMed

Ding, Yun; Chai, Jing; Centrella, Paolo A; Gondo, Chenaimwoyo; DeLorey, Jennifer L; Clark, Matthew A

2018-04-25

Encoded library technology (ELT) is an effective approach to the discovery of novel small-molecule ligands for biological targets. A key factor for the success of the technology is the chemical diversity of the libraries. Here we report the development of DNA-conjugated benzimidazoles. Using 4-fluoro-3-nitrobenzoic acid as a key synthon, we synthesized a 320 million-member DNA-encoded benzimidazole library using Fmoc-protected amino acids, amines and aldehydes as diversity elements. Affinity selection of the library led to the discovery of a novel, potent and specific antagonist of the NK3 receptor.

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

PubMed Central

Hennig, Bianca P.; Velten, Lars; Racke, Ines; Tu, Chelsea Szu; Thoms, Matthias; Rybin, Vladimir; Besir, Hüseyin; Remans, Kim; Steinmetz, Lars M.

2017-01-01

Efficient preparation of high-quality sequencing libraries that well represent the biological sample is a key step for using next-generation sequencing in research. Tn5 enables fast, robust, and highly efficient processing of limited input material while scaling to the parallel processing of hundreds of samples. Here, we present a robust Tn5 transposase purification strategy based on an N-terminal His6-Sumo3 tag. We demonstrate that libraries prepared with our in-house Tn5 are of the same quality as those processed with a commercially available kit (Nextera XT), while they dramatically reduce the cost of large-scale experiments. We introduce improved purification strategies for two versions of the Tn5 enzyme. The first version carries the previously reported point mutations E54K and L372P, and stably produces libraries of constant fragment size distribution, even if the Tn5-to-input molecule ratio varies. The second Tn5 construct carries an additional point mutation (R27S) in the DNA-binding domain. This construct allows for adjustment of the fragment size distribution based on enzyme concentration during tagmentation, a feature that opens new opportunities for use of Tn5 in customized experimental designs. We demonstrate the versatility of our Tn5 enzymes in different experimental settings, including a novel single-cell polyadenylation site mapping protocol as well as ultralow input DNA sequencing. PMID:29118030

A Cost Analysis and Utilization Study of the Stanford University Library System, Prepared for Stanford University, Stanford, California. Memorandum Report.

ERIC Educational Resources Information Center

Densmore, Glen; Bourne, Charles

This study was conducted to determine what fraction of the total cost of the Stanford University library system can properly be charged to each of the four major groups of users: undergraduate students, graduate students, faculty and staff, and non-Stanford users. Eight separate cost elements were developed for each of the library's cost centers…

Trends and Innovations in North American Libraries with an Emphasis on Developments in Canada, Especially Ontario. A Course Outline and Bibliographies.

ERIC Educational Resources Information Center

Palmer, Joseph W.

This outline for a graduate library school course at the State University of New York at Buffalo emphasizes trends and developments in North American librarianship with primary emphasis on Canada (especially Ontario). The participation of Canadian authorities as guest lecturers and field trips to Canadian libraries are important elements in the…

PLANS; a finite element program for nonlinear analysis of structures. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Pifko, A.; Armen, H., Jr.; Levy, A.; Levine, H.

1977-01-01

The PLANS system, rather than being one comprehensive computer program, is a collection of finite element programs used for the nonlinear analysis of structures. This collection of programs evolved and is based on the organizational philosophy in which classes of analyses are treated individually based on the physical problem class to be analyzed. Each of the independent finite element computer programs of PLANS, with an associated element library, can be individually loaded and used to solve the problem class of interest. A number of programs have been developed for material nonlinear behavior alone and for combined geometric and material nonlinear behavior. The usage, capabilities, and element libraries of the current programs include: (1) plastic analysis of built-up structures where bending and membrane effects are significant, (2) three dimensional elastic-plastic analysis, (3) plastic analysis of bodies of revolution, and (4) material and geometric nonlinear analysis of built-up structures.

Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening.

PubMed

Velagapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P; French, Jonathan M; Disney, Matthew D

2012-11-16

There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.

Three-Dimensional Finite Element Analysis of Sheet-Pile Cellular Cofferdams

DTIC Science & Technology

1992-04-01

requirements were in selecting the shell element for this study: * Nodes only at the midsurface of the element. * Higher-order shape functions to...on orthogonal curvilinear coordinate (shell coordinates) system with the ref- erence surface of the element midsurface (Figure 4.13). The formulation...element was selected which allows for: * Nodes at the midsurface of the element only. 150 CHAPTER 4. ADDITIONS TO THE ELEMENT LIBRARY " Higher-order

Three-Dimensional Plasma-Based Stall Control Simulations with Coupled First-Principles Approaches

DTIC Science & Technology

2006-07-01

flow code, developed at the Computational Plasma Dynamics Laboratory at Kettering University. The method is based on a versatile finite-element ( FE ...McLaughlin, T., and Baughn, J., 2005. “Acoustic testing of the dielectric barrier dis- charge ( dbd ) plasma actuator”. AIAA Paper 2005-0565, Jan

Telescoping Mechanics: A New Paradigm for Composite Behavior Simulation

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Murthy, P. L. N.; Gotsis, P. K.; Mital. S. K.

2004-01-01

This report reviews the application of telescoping mechanics to composites using recursive laminate theory. The elemental scale is the fiber-matrix slice, the behavior of which propagates to laminate. The results from using applications for typical, hybrid, and smart composites and composite-enhanced reinforced concrete structures illustrate the versatility and generality of telescoping scale mechanics. Comparisons with approximate, single-cell, and two- and three-dimensional finite-element methods demonstrate the accuracy and computational effectiveness of telescoping scale mechanics for predicting complex composite behavior.

Technology's Impact on Library Interior Planning.

ERIC Educational Resources Information Center

Michaels, David Leroy

1987-01-01

Discusses issues to be considered in planning a library that will anticipate the needs of the future. Power and telecommunications capacity are stressed, and a checklist of items requiring specific writing services is included. Recommendations for workstation design and structural elements are offered. (MES)

Introduction.

ERIC Educational Resources Information Center

Dain, Phyllis; Steig, Margaret F.

1979-01-01

While libraries have the basic responsibility of collecting, documenting, and organizing information, they also have a bigger responsibility to societal elements of public policy, political theory, social trends, and cultural values. This article introduces the theme of this issue, which discusses libraries and society in relation to these bigger…

Versatile microbial surface-display for environmental remediation and biofuels production

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

Wu, Cindy H.; Mulchandani, Ashok; Chen, wilfred

2008-02-14

Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production.

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities' libraries.

PubMed

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries' Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers to achieve faster and more accurate information resources. Therefore, the influence of librarians' ideas on the awareness of web designers and developers will be important for using metadata elements as general, and specifically for applying such standards.

Marrow Derived Antibody Library for the Treatment of Neuroblastoma

DTIC Science & Technology

2015-12-01

Award Number: W81XWH-12-1-0332 TITLE: Marrow-Derived Antibody Library for the Treatment of Neuroblastoma PRINCIPAL INVESTIGATOR: Giselle...Marrow-Derived Antibody Library for Treatment of Neuroblastoma 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...to Spectrum Health. 14. ABSTRACT Neuroblastoma (NB) is the most common solid tumor in children, which accounts for 15% of all pediatric cancer deaths

Simulation Comparisons of Three Different Meander Line Dipoles

DTIC Science & Technology

2015-01-01

Paez C I. Design formulas for a meandered dipole. IEEE Xplore Digital Library, 2014: n. pag. Web. 2 September 2014. 2. Nguyen, VH, Phan, HP, Hoang...MH. Improving radiation characteristics of UHF RFID antennas by zigzag structures. IEEE Xplore Digital Library, 2014: n. pag. Web. 2 September 2014...geometry-based, frequency-independent lumped element model. IEEE Xplore Digital Library, 2014: n. pag. Web. 2 September 2014. 5. Olaode OO, Palmer WD

Using graph approach for managing connectivity in integrative landscape modelling

NASA Astrophysics Data System (ADS)

Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger

2013-04-01

In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). OpenFLUID-landr library has been developed in order i) to be used with no GIS expert skills needed (common gis formats can be read and simplified spatial management is provided), ii) to easily develop adapted rules of landscape discretization and graph creation to follow spatialized model requirements and iii) to allow model developers to manage dynamic and complex spatial topology. Graph management in OpenFLUID are shown with i) examples of hydrological modelizations on complex farmed landscapes and ii) the new implementation of Geo-MHYDAS tool based on the OpenFLUID-landr library, which allows to discretize a landscape and create graph structure for the MHYDAS model requirements.

Marketing the hospital library.

PubMed

Bridges, Jane

2005-01-01

Many librarians do not see themselves as marketers, but marketing is an essential role for hospital librarians. Library work involves education, and there are parallels between marketing and education as described in this article. It is incumbent upon hospital librarians actively to pursue ways of reminding their customers about library services. This article reinforces the idea that marketing is an element in many of the things that librarians already do, and includes a list of suggested marketing strategies intended to remind administrators, physicians, and other customers that they have libraries in their organizations.

Client value models provide a framework for rational library planning (or, phrasing the answer in the form of a question).

PubMed

Van Moorsel, Guillaume

2005-01-01

Libraries often do not know how clients value their product/ service offerings. Yet at a time when the mounting costs for library support are increasingly difficult to justify to the parent institution, the library's ability to gauge the value of its offerings to clients has never been more critical. Client Value Models (CVMs) establish a common definition of value elements-or a "value vocabulary"-for libraries and their clients, thereby providing a basis upon which to make rational planning decisions regarding product/service acquisition and development. The CVM concept is borrowed from business and industry, but its application has a natural fit in libraries. This article offers a theoretical consideration and practical illustration of CVM application in libraries.

Virtual Reality and the Virtual Library.

ERIC Educational Resources Information Center

Oppenheim, Charles

1993-01-01

Explains virtual reality, including proper and improper uses of the term, and suggests ways that libraries might be affected by it. Highlights include elements of virtual reality systems; possible virtual reality applications, including architecture, the chemical industry, transport planning, armed forces, and entertainment; and the virtual…

A Survey of Campus Coordinators of Undergraduate Research Programs

ERIC Educational Resources Information Center

Hensley, Merinda Kaye; Shreeves, Sarah L.; Davis-Kahl, Stephanie

2015-01-01

Interest in supporting undergraduate research programs continues to grow within academic librarianship. This article presents how undergraduate research program coordinators perceive and value library support of their programs. Undergraduate research coordinators from a variety of institutions were surveyed on which elements of libraries and…

A new hybrid transfinite element computational methodology for applicability to conduction/convection/radiation heat transfer

NASA Technical Reports Server (NTRS)

Tamma, Kumar K.; Railkar, Sudhir B.

1988-01-01

This paper describes new and recent advances in the development of a hybrid transfinite element computational methodology for applicability to conduction/convection/radiation heat transfer problems. The transfinite element methodology, while retaining the modeling versatility of contemporary finite element formulations, is based on application of transform techniques in conjunction with classical Galerkin schemes and is a hybrid approach. The purpose of this paper is to provide a viable hybrid computational methodology for applicability to general transient thermal analysis. Highlights and features of the methodology are described and developed via generalized formulations and applications to several test problems. The proposed transfinite element methodology successfully provides a viable computational approach and numerical test problems validate the proposed developments for conduction/convection/radiation thermal analysis.

High temperature electrically conducting ceramic heating element and control system

NASA Technical Reports Server (NTRS)

Halbach, C. R.; Page, R. J.

1975-01-01

Improvements were made in both electrode technology and ceramic conductor quality to increase significantly the lifetime and thermal cycling capability of electrically conducting ceramic heater elements. These elements were operated in vacuum, inert and reducing environments as well as oxidizing atmospheres adding to the versatility of the conducting ceramic as an ohmic heater. Using stabilized zirconia conducting ceramic heater elements, a furnace was fabricated and demonstrated to have excellent thermal response and cycling capability. The furnace was used to melt platinum-20% rhodium alloy (melting point 1904 C) with an isothermal ceramic heating element having a nominal working cavity size of 2.5 cm diameter by 10.0 cm long. The furnace was operated to 1940 C with the isothermal ceramic heating element. The same furnace structure was fitted with a pair of main heater elements to provide axial gradient temperature control over a working cavity length of 17.8 cm.

Four-terminal circuit element with photonic core

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

Sampayan, Stephen

A four-terminal circuit element is described that includes a photonic core inside of the circuit element that uses a wide bandgap semiconductor material that exhibits photoconductivity and allows current flow through the material in response to the light that is incident on the wide bandgap material. The four-terminal circuit element can be configured based on various hardware structures using a single piece or multiple pieces or layers of a wide bandgap semiconductor material to achieve various designed electrical properties such as high switching voltages by using the photoconductive feature beyond the breakdown voltages of semiconductor devices or circuits operated basedmore » on electrical bias or control designs. The photonic core aspect of the four-terminal circuit element provides unique features that enable versatile circuit applications to either replace the semiconductor transistor-based circuit elements or semiconductor diode-based circuit elements.« less

Developments in boundary element methods - 2

NASA Astrophysics Data System (ADS)

Banerjee, P. K.; Shaw, R. P.

This book is a continuation of the effort to demonstrate the power and versatility of boundary element methods which began in Volume 1 of this series. While Volume 1 was designed to introduce the reader to a selected range of problems in engineering for which the method has been shown to be efficient, the present volume has been restricted to time-dependent problems in engineering. Boundary element formulation for melting and solidification problems in considered along with transient flow through porous elastic media, applications of boundary element methods to problems of water waves, and problems of general viscous flow. Attention is given to time-dependent inelastic deformation of metals by boundary element methods, the determination of eigenvalues by boundary element methods, transient stress analysis of tunnels and caverns of arbitrary shape due to traveling waves, an analysis of hydrodynamic loads by boundary element methods, and acoustic emissions from submerged structures.

Marketing the Health Sciences Library.

ERIC Educational Resources Information Center

Norman, O. Gene

The basic activities of marketing are discussed, including gathering information and determining needs, designing a program around the elements of the marketing mix, and managing the marketing program. Following a general discussion, applications of the marketing concepts to a health sciences library are described. The administrator of the health…

School Libraries: A Design Recipe for the Future.

ERIC Educational Resources Information Center

Myerberg, Henry

2002-01-01

Discusses design elements of a 21st century school library, including space, books and shelving, seats, tables, technology (computers, scanners, projectors), building materials (wood, metal, plastic, paint, glass, fibers), and light and color. A sidebar describes the L!BRARY initiative to creatively design, professionally staff, and…

Releasing Reservations from Isolation.

ERIC Educational Resources Information Center

Ambler, Marjane

1994-01-01

Discusses the role of the emerging tribal libraries, designed to serve as repositories of Native American history and knowledge. Indicates that the tribal libraries and archives have provided a means for recentralizing documents important to Native American history that had previously been moved to distant repositories by outside elements. (MAB)

Toward a digital library strategy for a National Information Infrastructure

NASA Technical Reports Server (NTRS)

Coyne, Robert A.; Hulen, Harry

1993-01-01

Bills currently before the House and Senate would give support to the development of a National Information Infrastructure, in which digital libraries and storage systems would be an important part. A simple model is offered to show the relationship of storage systems, software, and standards to the overall information infrastructure. Some elements of a national strategy for digital libraries are proposed, based on the mission of the nonprofit National Storage System Foundation.

The Integrated Library System Design Concepts for a Complete Serials Control Subsystem.

DTIC Science & Technology

1984-08-20

7AD-fl149 379 THE INTEGRTED LIBRARY SYSTEM DESIGN CONCEPTS FOR A 1/COMPLETE SERIALS CONTROL UBSYSTEM(U) ONLINE COMPUTER SYSTEMS INC GERMANTOWN MD 28...CONTROL SUBSYSTEM Presented to: The Pentagon Library The Pentagon Washington, DC 20310 Prepared by: Online Computer Systems, Inc. 20251 Century Blvd...MDA903-82-C-0535 9. PERFORMING ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT, PROJECT, TASK AREA & WORK UNIT NUMBERS Online Computer Systems, Inc

Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation

PubMed Central

Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

2016-01-01

Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy—combining sequential and modular concepts—enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain. PMID:27901024

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

PubMed Central

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D.; Nystul, Todd G.; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E.; Murphy, Terence D.; Levis, Robert W.; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A.; Spradling, Allan C.

2007-01-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600–900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions. PMID:17194782

Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation.

PubMed

Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

2016-11-30

Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

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

Caberoy, Nora B.; Zhou, Yixiong; Alvarado, Gabriela

To efficiently elucidate the biological roles of phosphatidylserine (PS), we developed open-reading-frame (ORF) phage display to identify PS-binding proteins. The procedure of phage panning was optimized with a phage clone expressing MFG-E8, a well-known PS-binding protein. Three rounds of phage panning with ORF phage display cDNA library resulted in {approx}300-fold enrichment in PS-binding activity. A total of 17 PS-binding phage clones were identified. Unlike phage display with conventional cDNA libraries, all 17 PS-binding clones were ORFs encoding 13 real proteins. Sequence analysis revealed that all identified PS-specific phage clones had dimeric basic amino acid residues. GST fusion proteins were expressedmore » for 3 PS-binding proteins and verified for their binding activity to PS liposomes, but not phosphatidylcholine liposomes. These results elucidated previously unknown PS-binding proteins and demonstrated that ORF phage display is a versatile technology capable of efficiently identifying binding proteins for non-protein molecules like PS.« less

Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

PubMed

Andreou, Andreas I; Nakayama, Naomi

2018-01-01

Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

Using Specific Binding DNA Capture Elements to Direct Pulsed Power Killing of Biological Agents

DTIC Science & Technology

2003-06-01

Department of the Air Force position, policy, or decision unless so designated by other documentation. VI. REFERENCES [1] V. Majidi and M. R. Joseph...Spectroscopic applications of laser-induced plasmas,” Crit. Rev. Analyt. Chem. 23, 143-162, 1992. [2] V. Majidi , “Laser-induced plasmas: A versatile tool

Analysis of Brick Masonry Wall using Applied Element Method

NASA Astrophysics Data System (ADS)

Lincy Christy, D.; Madhavan Pillai, T. M.; Nagarajan, Praveen

2018-03-01

The Applied Element Method (AEM) is a versatile tool for structural analysis. Analysis is done by discretising the structure as in the case of Finite Element Method (FEM). In AEM, elements are connected by a set of normal and shear springs instead of nodes. AEM is extensively used for the analysis of brittle materials. Brick masonry wall can be effectively analyzed in the frame of AEM. The composite nature of masonry wall can be easily modelled using springs. The brick springs and mortar springs are assumed to be connected in series. The brick masonry wall is analyzed and failure load is determined for different loading cases. The results were used to find the best aspect ratio of brick to strengthen brick masonry wall.

Organic nanofiber nanosensors

NASA Astrophysics Data System (ADS)

Madsen, M.; Schiek, M.; Thomsen, P.; Andersen, N. L.; Lützen, A.; Rubahn, H.-G.

2007-09-01

A new way of developing optical nanosensors is presented. Organic nanofibers serve as key elements in these new types of devices, which exploit both the smallness and brightness of the nanoaggregates to make new compact and sensitive optical nanosensors. On the basis of bottom up technology, we functionalize individual molecules, which are then intrinsically sensitive to specific agents. These molecules are used as building blocks for controlled growth of larger nanoscaled aggregates. The aggregates in turn can be used as sensing elements on the meso-scale in the size range from hundred nanometers to a few hundred microns. The organic nanofibers thereby might become a versatile tool within nanosensor technology, allowing sensing on the basis of individual molecules over small aggregates to large assemblies. First experiments of Bovine Serum Albumin (BSA) coupling to para-hexaphenyl (p-6P) nanofibers are presented, which could lead towards a new type of protein sensors. Besides large versatility and sensitivity, the nanofibers benefit from the fact that they can be integrated in devices, either in liquids by the use of microfluidic cavities or all in parallel.

Study of the versatility of a graphite furnace atomic absorption spectrometric method for the determination of cadmium in the environmental field.

PubMed

Rucandio, M Isabel; Petit-Domínguez, M Dolores

2002-01-01

Cadmium is a representative example of trace elements that are insidious and widespread health hazards. In contemporary environmental analysis, there is a clear trend toward its determination over a wide range of concentrations in complex matrixes. This paper describes a versatile method for the determination of Cd at various levels (0.1-500 microg/g) in several sample types, such as soils, sediments, coals, ashes, sewage sludges, animal tissues, and plants, by graphite furnace atomic absorption spectrometry with Zeeman background correction. The effect of the individual presence of about 50 elements, with an interference/analyte concentration ratio of up to 10(5), was tested; recoveries of Cd ranged from 93 to 106%. The influence of different media, such as HNO3, HCI, HF, H2SO4, HClO4, acetic acid, hydroxylammonium chloride, and ammonium acetate, in several concentrations, was also tested. From these studies it can be concluded that the analytical procedure is scarcely matrix dependent, and the results obtained for a wide diversity of reference materials are in good agreement with the certified values.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy

NASA Astrophysics Data System (ADS)

Chamberland, Marc J. P.; Taylor, Randle E. P.; Rogers, D. W. O.; Thomson, Rowan M.

2016-12-01

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm)3 voxels) and eye plaque (with (1 mm)3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy.

PubMed

Chamberland, Marc J P; Taylor, Randle E P; Rogers, D W O; Thomson, Rowan M

2016-12-07

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm) 3 voxels) and eye plaque (with (1 mm) 3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

Friends' Organizations: The Supportive Element Essential to Libraries.

ERIC Educational Resources Information Center

Progar, Dorothy

Reviewed are the history and public relations, financial and service roles of lay "Friends of the Library" groups. Programs and techniques useful in the pursuit of these roles are suggested. Guidelines for a constitution, fee schedule, and administrative structure plus a bibliography give potential friends organizations help in…

The Day Search Stood Still

ERIC Educational Resources Information Center

Sexton, Will

2010-01-01

That little rectangle with a button next to it? (Those things called search boxes but might just as well be called "resource drains.") Imagine it disappearing from a library's webpages. The intricate works behind these design elements make up a major portion of what library staff spends time and money developing, populating, supporting,…

ICT and Marketing Challenges in Latin American Libraries.

ERIC Educational Resources Information Center

Feria, Lourdes

Latin American libraries have experienced an important development in the last two decades. Telecommunications and Information Technologies (ITC) have been key elements in this process. There are leading institutions with remarkable programs; nevertheless it is necessary to design marketing strategies to improve their benefits. A case study based…

Elements, Compounds & Mixtures. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

The world contains a limited number of elements--the purest form of matter. But when these elements are combined, the possibilities are limitless! Water, carbon dioxide and salt are just a few examples of how elements can be combined to form entirely new substances. Many of these combinations occur naturally, while others are man-made. Students…

Probing a 2-Aminobenzimidazole Library for Binding to RNA Internal Loops via Two-Dimensional Combinatorial Screening

PubMed Central

Velegapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P.; French, Jonathan M.; Disney, Matthew D.

2012-01-01

There are many potential RNA drug targets in bacterial, viral, and the human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition. PMID:22958065

Visualization of protein sequence features using JavaScript and SVG with pViz.js.

PubMed

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need in Bioinformatics. Although many Web sites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. pViz.js is a JavaScript library, available on github at https://github.com/Genentech/pviz. This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The marriage of metallacycle transfer chemistry with Suzuki-Miyaura cross-coupling to give main group element-containing conjugated polymers.

PubMed

He, Gang; Kang, Le; Torres Delgado, William; Shynkaruk, Olena; Ferguson, Michael J; McDonald, Robert; Rivard, Eric

2013-04-10

A versatile and general synthetic route for the synthesis of conjugated main group element-based polymers, previously inaccessible by conventional means, is reported. These polymers contain five-membered chalcogenophene rings based on S, Se, and Te, and we demonstrate that optoelectronic properties can be readily tuned via controlled atom substitution chemistry. In addition, regioregular hybrid thiophene-selenophene-tellurophene and selenophene-fluorene copolymers were synthesized to provide a further illustration of the scope of the presented metallacycle transfer/cross-coupling polymerization method.

Reconfigurable antenna using plasma reflector

NASA Astrophysics Data System (ADS)

Jusoh, Mohd Taufik; Ahmad, Khairol Amali; Din, Muhammad Faiz Md; Hashim, Fakroul Ridzuan

2018-02-01

This paper presents the feasibility study and design of plasma implementation in industrial, scientific and medical (ISM) communication band. A reflector antenna with rounded shaped is proposed to collimate beam in particular direction radiated by a quarter wave antenna operating at 2.4GHz. The simulations result has shown that by using plasma as the reflector elements, the gain, directivity and radiation patterns are identical with metal elements with only small different in the broadside direction. The versatility of the antenna is achievable by introducing electrical reconfigurable option to change the beam pattern.

Finite element solution for energy conservation using a highly stable explicit integration algorithm

NASA Technical Reports Server (NTRS)

Baker, A. J.; Manhardt, P. D.

1972-01-01

Theoretical derivation of a finite element solution algorithm for the transient energy conservation equation in multidimensional, stationary multi-media continua with irregular solution domain closure is considered. The complete finite element matrix forms for arbitrarily irregular discretizations are established, using natural coordinate function representations. The algorithm is embodied into a user-oriented computer program (COMOC) which obtains transient temperature distributions at the node points of the finite element discretization using a highly stable explicit integration procedure with automatic error control features. The finite element algorithm is shown to posses convergence with discretization for a transient sample problem. The condensed form for the specific heat element matrix is shown to be preferable to the consistent form. Computed results for diverse problems illustrate the versatility of COMOC, and easily prepared output subroutines are shown to allow quick engineering assessment of solution behavior.

Computer program calculates gamma ray source strengths of materials exposed to neutron fluxes

NASA Technical Reports Server (NTRS)

Heiser, P. C.; Ricks, L. O.

1968-01-01

Computer program contains an input library of nuclear data for 44 elements and their isotopes to determine the induced radioactivity for gamma emitters. Minimum input requires the irradiation history of the element, a four-energy-group neutron flux, specification of an alloy composition by elements, and selection of the output.

Absolutely Write! Teaching the Craft Elements of Writing. Bill Harp Professional Teachers Library.

ERIC Educational Resources Information Center

Thomason, Tommy; York, Carol

This book discusses basic craft elements of writing, illustrates from adult and children's literature what constitutes an engaging passage of description, and then illustrates how that craft can be taught in a workshop environment. In addition, this book includes involvement experiences that help teachers experience these craft elements. After an…

Development of a versatile XRF scanner for the elemental imaging of paintworks

NASA Astrophysics Data System (ADS)

Ravaud, E.; Pichon, L.; Laval, E.; Gonzalez, V.; Eveno, M.; Calligaro, T.

2016-01-01

Scanning XRF is a powerful elemental imaging technique introduced at the synchrotron that has recently been transposed to laboratory. The growing interest in this technique stems from its ability to collect images reflecting pigment distribution within large areas on artworks by means of their elemental signature. In that sense, scanning XRF appears highly complementary to standard imaging techniques (Visible, UV, IR photography and X-ray radiography). The versatile XRF scanner presented here has been designed and built at the C2RMF in response to specific constraints: transportability, cost-effectiveness and ability to scan large areas within a single working day. The instrument is based on a standard X-ray generator with sub-millimetre collimated beam and a SDD-based spectrometer to collected X-ray spectra. The instrument head is scanned in front of the painting by means of motorised movements to cover an area up to 300 × 300 mm2 with a resolution of 0.5 mm (600 × 600 pixels). The 15-kg head is mounted on a stable photo stand for rapid positioning on paintworks and maintains a free side-access for safety; it can also be attached to a lighter tripod for field measurements. Alignment is achieved with a laser pointer and a micro-camera. With a scanning speed of 5 mm/s and 0.1 s/point, elemental maps are collected in 10 h, i.e. a working day. The X-ray spectra of all pixels are rapidly processed using an open source program to derive elemental maps. To illustrate the capabilities of this instrument, this contribution presents the results obtained on the Belle Ferronnière painted by Leonardo da Vinci (1452-1519) and conserved in the Musée du Louvre, prior to its restoration at the C2RMF.

GALARIO: a GPU accelerated library for analysing radio interferometer observations

NASA Astrophysics Data System (ADS)

Tazzari, Marco; Beaujean, Frederik; Testi, Leonardo

2018-06-01

We present GALARIO, a computational library that exploits the power of modern graphical processing units (GPUs) to accelerate the analysis of observations from radio interferometers like Atacama Large Millimeter and sub-millimeter Array or the Karl G. Jansky Very Large Array. GALARIO speeds up the computation of synthetic visibilities from a generic 2D model image or a radial brightness profile (for axisymmetric sources). On a GPU, GALARIO is 150 faster than standard PYTHON and 10 times faster than serial C++ code on a CPU. Highly modular, easy to use, and to adopt in existing code, GALARIO comes as two compiled libraries, one for Nvidia GPUs and one for multicore CPUs, where both have the same functions with identical interfaces. GALARIO comes with PYTHON bindings but can also be directly used in C or C++. The versatility and the speed of GALARIO open new analysis pathways that otherwise would be prohibitively time consuming, e.g. fitting high-resolution observations of large number of objects, or entire spectral cubes of molecular gas emission. It is a general tool that can be applied to any field that uses radio interferometer observations. The source code is available online at http://github.com/mtazzari/galario under the open source GNU Lesser General Public License v3.

Atlas : A library for numerical weather prediction and climate modelling

NASA Astrophysics Data System (ADS)

Deconinck, Willem; Bauer, Peter; Diamantakis, Michail; Hamrud, Mats; Kühnlein, Christian; Maciel, Pedro; Mengaldo, Gianmarco; Quintino, Tiago; Raoult, Baudouin; Smolarkiewicz, Piotr K.; Wedi, Nils P.

2017-11-01

The algorithms underlying numerical weather prediction (NWP) and climate models that have been developed in the past few decades face an increasing challenge caused by the paradigm shift imposed by hardware vendors towards more energy-efficient devices. In order to provide a sustainable path to exascale High Performance Computing (HPC), applications become increasingly restricted by energy consumption. As a result, the emerging diverse and complex hardware solutions have a large impact on the programming models traditionally used in NWP software, triggering a rethink of design choices for future massively parallel software frameworks. In this paper, we present Atlas, a new software library that is currently being developed at the European Centre for Medium-Range Weather Forecasts (ECMWF), with the scope of handling data structures required for NWP applications in a flexible and massively parallel way. Atlas provides a versatile framework for the future development of efficient NWP and climate applications on emerging HPC architectures. The applications range from full Earth system models, to specific tools required for post-processing weather forecast products. The Atlas library thus constitutes a step towards affordable exascale high-performance simulations by providing the necessary abstractions that facilitate the application in heterogeneous HPC environments by promoting the co-design of NWP algorithms with the underlying hardware.

BASIC: A Simple and Accurate Modular DNA Assembly Method.

PubMed

Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

2017-01-01

Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach.

PubMed

Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

2014-11-01

Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods.

PubMed

Kamoun, Choumouss; Payen, Thibaut; Hua-Van, Aurélie; Filée, Jonathan

2013-10-11

Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches. In this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300 bp) for which both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods. Compared to classical BLAST-based methods, the sensitivity of de novo and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtained by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.

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

PubMed

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.

Versatile aggressive mimicry of cicadas by an Australian predatory katydid.

PubMed

Marshall, David C; Hill, Kathy B R

2009-01-01

In aggressive mimicry, a predator or parasite imitates a signal of another species in order to exploit the recipient of the signal. Some of the most remarkable examples of aggressive mimicry involve exploitation of a complex signal-response system by an unrelated predator species. We have found that predatory Chlorobalius leucoviridis katydids (Orthoptera: Tettigoniidae) can attract male cicadas (Hemiptera: Cicadidae) by imitating the species-specific wing-flick replies of sexually receptive female cicadas. This aggressive mimicry is accomplished both acoustically, with tegminal clicks, and visually, with synchronized body jerks. Remarkably, the katydids respond effectively to a variety of complex, species-specific Cicadettini songs, including songs of many cicada species that the predator has never encountered. We propose that the versatility of aggressive mimicry in C. leucoviridis is accomplished by exploiting general design elements common to the songs of many acoustically signaling insects that use duets in pair-formation. Consideration of the mechanism of versatile mimicry in C. leucoviridis may illuminate processes driving the evolution of insect acoustic signals, which play a central role in reproductive isolation of populations and the formation of species.

Design and Construction of Versatile Experiment Spherical Torus (VEST) at Seoul National University

NASA Astrophysics Data System (ADS)

An, Younghwa; Chung, Kyoung-Jae; Jung, Bongki; Lee, Hyunyeong; Sung, Choongki; Kim, Hyun-Seok; Na, Yong-Su; Hwang, Yong-Seok

2011-10-01

A new spherical torus, named as VEST (Versatile Experiment Spherical Torus), has been built at Seoul National University to investigate versatile research topics such as double null merging start-up, divertor engineering and non-inductive current drive. VEST is characterized by two partial solenoid coils installed at both vertical ends of a center stack, which will be used for double null merging start-up schemes. A poloidal field (PF) coil system including the partial solenoids for break-down and a long solenoid for the sustainment of merged plasma has been designed by solving circuit equations for the PF coils and vacuum vessel elements in consideration of required volt-second, null configuration and eddy current. To supply required currents to the PF coils and solenoids, power supplies based on double-swing circuit have been designed and fabricated with capacitor banks and thyristor switch assemblies. Also a power supply utilizing cost-effective commercial batteries has been developed for toroidal field(TF) coils. Detailed descriptions on the design of VEST and some initial test results will be presented.

Regenerative biomaterials that "click": simple, aqueous-based protocols for hydrogel synthesis, surface immobilization, and 3D patterning.

PubMed

Nimmo, Chelsea M; Shoichet, Molly S

2011-11-16

The click chemistry era has generated a library of versatile "spring-loaded" reactions that offer high yields, regio- and stereospecificity, and outstanding functional group tolerance. These powerful transformations are particularly advantageous for the design of sophisticated biomaterials that require high levels of precision and control, namely, materials that promote tissue regeneration such as hydrogels, 2D functionalized substrates, and 3D biomimetic scaffolds. In this review, the synthesis and application of regenerative biomaterials via click chemistry are summarized. Particular emphasis is placed on the copper(I)-catalyzed alkyne-azide cycloaddition, Diels-Alder cycloadditions, and thiol-click coupling.

Modularity of a leaf moth-wing pattern and a versatile characteristic of the wing-pattern ground plan

PubMed Central

2013-01-01

Background One of the most intriguing questions in evolutionary developmental biology is how an insect acquires a mimicry pattern within its body parts. A striking example of pattern mimicry is found in the pattern diversity of moth and butterfly wings, which is thought to evolve from preexisting elements illustrated by the nymphalid ground plan (NGP). Previous studies demonstrated that individuality of the NGP facilitates the decoupling of associated common elements, leading to divergence. In contrast, recent studies on the concept of modularity have argued the importance of a combination of coupling and decoupling of the constituent elements. Here, we examine the modularity of a mimicry wing pattern in a moth and explore an evolvable characteristic of the NGP. Results This study examined the wings of the noctuid moth Oraesia excavata, which closely resemble leaves with a leaf venation pattern. Based on a comparative morphological procedure, we found that this leaf pattern was formed by the NGP common elements. Using geometric morphometrics combined with network analysis, we found that each of the modules in the leaf pattern integrates the constituent components of the leaf venation pattern (i.e., the main and lateral veins). Moreover, the detected modules were established by coupling different common elements and decoupling even a single element into different modules. The modules of the O. excavata wing pattern were associated with leaf mimicry, not with the individuality of the NGP common elements. For comparison, we also investigated the modularity of a nonmimetic pattern in the noctuid moth Thyas juno. Quantitative analysis demonstrated that the modules of the T. juno wing pattern regularly corresponded to the individuality of the NGP common elements, unlike those in the O. excavata wing pattern. Conclusions This study provides the first evidence for modularity in a leaf mimicry pattern. The results suggest that the evolution of this pattern involves coupling and decoupling processes to originate these modules, free from the individuality of the NGP system. We propose that this evolution has been facilitated by a versatile characteristic of the NGP, allowing the association of freely modifiable subordinate common elements to make modules. PMID:23890367

Significance of clustering and classification applications in digital and physical libraries

NASA Astrophysics Data System (ADS)

Triantafyllou, Ioannis; Koulouris, Alexandros; Zervos, Spiros; Dendrinos, Markos; Giannakopoulos, Georgios

2015-02-01

Applications of clustering and classification techniques can be proved very significant in both digital and physical (paper-based) libraries. The most essential application, document classification and clustering, is crucial for the content that is produced and maintained in digital libraries, repositories, databases, social media, blogs etc., based on various tags and ontology elements, transcending the traditional library-oriented classification schemes. Other applications with very useful and beneficial role in the new digital library environment involve document routing, summarization and query expansion. Paper-based libraries can benefit as well since classification combined with advanced material characterization techniques such as FTIR (Fourier Transform InfraRed spectroscopy) can be vital for the study and prevention of material deterioration. An improved two-level self-organizing clustering architecture is proposed in order to enhance the discrimination capacity of the learning space, prior to classification, yielding promising results when applied to the above mentioned library tasks.

A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Lou, John Z.; Norton, Charles D.; Cwik, Thomas A.

1999-01-01

The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.

Steel Industry Analysis Brief

EIA Publications

2009-01-01

The steel industry is critical to the U.S. economy. Steel is the material of choice for many elements of construction, transportation, manufacturing, and a variety of consumer products. It is the backbone of bridges, skyscrapers, railroads, automobiles, and appliances. Most grades of steel used today - particularly high-strength steels that are lighter and more versatile - were not available a decade ago.

Novel Laser-Based Technique is Ideal for Real-Time Environmental Analysis

ERIC Educational Resources Information Center

Journal of Chemical Education, 2005

2005-01-01

Ocean Optics offers laser-induced breakdown spectrometer systems (LIBS) that can be used to identify light to heavy metals in a variety of sample types and geometries in environmental analysis applications. LIBS are versatile, real-time, high-resolution analyzers for qualitative analysis, in less than one second, of every element in solids,…

The microcomputer scientific software series 1: the numerical information manipulation system.

Treesearch

Harold M. Rauscher

1983-01-01

The Numerical Information Manipulation System extends the versatility provided by word processing systems for textual data manipulation to mathematical or statistical data in numeric matrix form. Numeric data, stored and processed in the matrix form, may be manipulated in a wide variety of ways. The system allows operations on single elements, entire rows, or columns...

Anatomy of Advocacy: A Case Study of the White House Petition

ERIC Educational Resources Information Center

Burns, Elizabeth; Kimmel, Sue; Dickinson, Gail

2016-01-01

Little research has been conducted examining advocacy efforts in the school library field despite the fact that program advocate is a prominent role for school librarians. One element of advocacy is the engagement in political initiatives that may affect school library programs. This case study investigates the effectiveness of one advocacy effort…

The Learning Center

ERIC Educational Resources Information Center

Wernick, Laura

2010-01-01

Since the second century, libraries have been esteemed as keepers of the flame of knowledge and culture. At the stone Library of Celcus, constructed in Turkey in 1100 A.D., for example, 15,000 documents were kept safe from the elements and other destructive forces such as rodents. In places like Celcus, the knowledge of Greek philosophy, Roman…

Blade loss transient dynamics analysis, volume 1. Task 2: TETRA 2 theoretical development

NASA Technical Reports Server (NTRS)

Gallardo, Vincente C.; Black, Gerald

1986-01-01

The theoretical development of the forced steady state analysis of the structural dynamic response of a turbine engine having nonlinear connecting elements is discussed. Based on modal synthesis, and the principle of harmonic balance, the governing relations are the compatibility of displacements at the nonlinear connecting elements. There are four displacement compatibility equations at each nonlinear connection, which are solved by iteration for the principle harmonic of the excitation frequency. The resulting computer program, TETRA 2, combines the original TETRA transient analysis (with flexible bladed disk) with the steady state capability. A more versatile nonlinear rub or bearing element which contains a hardening (or softening) spring, with or without deadband, is also incorporated.

Single service point: it's all in the design.

PubMed

Bradigan, Pamela S; Rodman, Ruey L

2008-01-01

"Design thinking" principles from a leading design firm, IDEO, were key elements in the planning process for a one-desk service model, the ASK Desk, at the John A. Prior Health Sciences Library. The library administration and staff employed the methodology to enhance customer experiences, meet technology challenges, and compete in a changing education environment. The most recent renovations demonstrate how the principles were applied. The concept of "continuous design thinking" is important in the library's daily operations to serve customers most effectively.

Finite Element Peen Forming Simulation

NASA Astrophysics Data System (ADS)

Gariépy, Alexandre; Larose, Simon; Perron, Claude; Bocher, Philippe; Lévesque, Martin

Shot peening consists of projecting multiple small particles onto a ductile part in order to induce compressive residual stresses near the surface. Peen forming, a derivative of shot peening, is a process that creates an unbalanced stress state which in turn leads to a deformation to shape thin parts. This versatile and cost-effective process is commonly used to manufacture aluminum wing skins and rocket panels. This paper presents the finite element modelling approach that was developed by the authors to simulate the process. The method relies on shell elements and calculated stress profiles and uses an approximation equation to take into account the incremental nature of the process. Finite element predictions were in good agreement with experimental results for small-scale tests. The method was extended to a hypothetical wing skin model to show its potential applications.

Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum.

PubMed

Wei, Liang; Xu, Ning; Wang, Yiran; Zhou, Wei; Han, Guoqiang; Ma, Yanhe; Liu, Jun

2018-05-01

Due to the lack of efficient control elements and tools, the fine-tuning of gene expression in the multi-gene metabolic pathways is still a great challenge for engineering microbial cell factories, especially for the important industrial microorganism Corynebacterium glutamicum. In this study, the promoter library-based module combination (PLMC) technology was developed to efficiently optimize the expression of genes in C. glutamicum. A random promoter library was designed to contain the putative - 10 (NNTANANT) and - 35 (NNGNCN) consensus motifs, and refined through a three-step screening procedure to achieve numerous genetic control elements with different strength levels, including fluorescence-activated cell sorting (FACS) screening, agar plate screening, and 96-well plate screening. Multiple conventional strategies were employed for further precise characterizations of the promoter library, such as real-time quantitative PCR, sodium dodecyl sulfate polyacrylamide gel electrophoresis, FACS analysis, and the lacZ reporter system. These results suggested that the established promoter elements effectively regulated gene expression and showed varying strengths over a wide range. Subsequently, a multi-module combination technology was created based on the efficient promoter elements for combination and optimization of modules in the multi-gene pathways. Using this technology, the threonine biosynthesis pathway was reconstructed and optimized by predictable tuning expression of five modules in C. glutamicum. The threonine titer of the optimized strain was significantly improved to 12.8 g/L, an approximate 6.1-fold higher than that of the control strain. Overall, the PLMC technology presented in this study provides a rapid and effective method for combination and optimization of multi-gene pathways in C. glutamicum.

Toward performance portability of the Albany finite element analysis code using the Kokkos library

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

Demeshko, Irina; Watkins, Jerry; Tezaur, Irina K.

Performance portability on heterogeneous high-performance computing (HPC) systems is a major challenge faced today by code developers: parallel code needs to be executed correctly as well as with high performance on machines with different architectures, operating systems, and software libraries. The finite element method (FEM) is a popular and flexible method for discretizing partial differential equations arising in a wide variety of scientific, engineering, and industrial applications that require HPC. This paper presents some preliminary results pertaining to our development of a performance portable implementation of the FEM-based Albany code. Performance portability is achieved using the Kokkos library. We presentmore » performance results for the Aeras global atmosphere dynamical core module in Albany. Finally, numerical experiments show that our single code implementation gives reasonable performance across three multicore/many-core architectures: NVIDIA General Processing Units (GPU’s), Intel Xeon Phis, and multicore CPUs.« less

Toward performance portability of the Albany finite element analysis code using the Kokkos library

DOE PAGES

Demeshko, Irina; Watkins, Jerry; Tezaur, Irina K.; ...

2018-02-05

Performance portability on heterogeneous high-performance computing (HPC) systems is a major challenge faced today by code developers: parallel code needs to be executed correctly as well as with high performance on machines with different architectures, operating systems, and software libraries. The finite element method (FEM) is a popular and flexible method for discretizing partial differential equations arising in a wide variety of scientific, engineering, and industrial applications that require HPC. This paper presents some preliminary results pertaining to our development of a performance portable implementation of the FEM-based Albany code. Performance portability is achieved using the Kokkos library. We presentmore » performance results for the Aeras global atmosphere dynamical core module in Albany. Finally, numerical experiments show that our single code implementation gives reasonable performance across three multicore/many-core architectures: NVIDIA General Processing Units (GPU’s), Intel Xeon Phis, and multicore CPUs.« less

Numerical Assessment of Rockbursting.

DTIC Science & Technology

1987-05-27

static equilibrium, nonlinear elasticity, strain-softening • material , unstable propagation of pre-existing cracks , and finally - surface...structure of LINOS, which is common to most of the large finite element codes, the library of element and material subroutines can be easily expanded... material model subroutines , are tested by comparing finite element results with analytical or numerical results derived for hypo-elastic and

A Practical Guide for Personnel Management: The Essential Elements.

ERIC Educational Resources Information Center

Todaro, Julie B.

The essential elements of personnel management are outlined. Personnel management may be called by various names and may be practiced by various levels of management, but in any case it is one of the most important elements of a management position. While sample forms generally relate to Texas community colleges and libraries, the guide is written…

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition.

PubMed

Bruderer, Tobias; Varesio, Emmanuel; Hidasi, Anita O; Duchoslav, Eva; Burton, Lyle; Bonner, Ron; Hopfgartner, Gérard

2018-03-01

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H] + and 483 in negative mode [M-H] - . MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.

Secreting and sensing the same molecule allows cells to achieve versatile social behaviors

PubMed Central

Youk, Hyun; Lim, Wendell A.

2014-01-01

Cells that secrete and sense the same signaling molecule are ubiquitous. To uncover the functional capabilities of the core ‘secrete-and-sense’ circuit motif shared by these cells, we engineered yeast to secrete and sense the mating pheromone. Perturbing each circuit element revealed parameters that control the degree to which the cell communicated with itself versus with its neighbors. This tunable interplay of self- and neighbor-communication enables cells to span a diverse repertoire of cellular behaviors. These include a cell being asocial by responding only to itself, social through quorum sensing and an isogenic population of cells splitting into social and asocial subpopulations. A mathematical model explained these behaviors. The versatility of the secrete-and-sense circuit motif may explain its recurrence across species. PMID:24503857

Aeroelastic Analysis Of Versatile Thermal Insulation Panels For Launchers Applications

NASA Astrophysics Data System (ADS)

Carrera, E.; Zappino, E.; Augello, G.; Ferrarese, A.; Montabone, M.

2011-05-01

The aeroelastic behavior of a Versatile Thermal Insulation (VTI) has been investigated. Among the various loadings acting on the panels in this work the attention is payed to fluid structure interaction. e.g. panel flutter phenomena. Known available results from open literature, related to similar problems, permit to analyze the effect of various Mach regimes, including boundary layers thickness effects, in-plane mechanical and thermal loadings, nonlinear effect and amplitude of so called limit cycle oscillations. Dedicated finite element model is developed for the supersonic regime. The model used for coupling orthotropic layered structural model with to Piston Theory aerodynamic models allows the calculations of flutter conditions in case of curved panels supported in a dis- crete number of points. Through this approach the flutter boundaries of the VTI-panel have been investigated.

Are You Being Served? Designing the Customer Service Curriculum

ERIC Educational Resources Information Center

Ippoliti, Cinthya

2014-01-01

Customer service is a core component of user experience and an important element in making patrons feel welcomed and valued within our libraries. At the University of Maryland Libraries, we took on the challenging task of creating a customer service training curriculum for all staff working at public service points and offering a digital badge for…

Checklist of Library Building Design Considerations.

ERIC Educational Resources Information Center

Sannwald, William W., Ed.; Smith, Robert S., Ed.

This checklist is designed to provide librarians, architects, and other members of a building design team with a list of questions to ask during the design phase of a new or remodeled library building project. The purpose of the questions is to make sure that no element of the building is overlooked by the building design team in their programming…

Analyzing Current Serials in Virginia: An Application of the Ulrich's Serials Analysis System

ERIC Educational Resources Information Center

Metz, Paul; Gasser, Sharon

2006-01-01

VIVA (the Virtual Library of Virginia) was one of the first subscribers to R. R. Bowker's Ulrich's Serials Analysis System (USAS). Creating a database that combined a union report of current serial subscriptions within most academic libraries in the state with the data elements present in Ulrich's made possible a comprehensive analysis designed…

Efficiency Study of Implicit and Explicit Time Integration Operators for Finite Element Applications

DTIC Science & Technology

1977-07-01

cffiAciency, wherein Beta =0 provides anl exp~licit algorithm, wvhile Beta &0 provides anl implicit algorithm. Both algorithmns arc used in the same...Hlueneme CA: CO, Code C44A Port j IHuenemne, CA NAVSEC Cod,. 6034 (Library), Washington DC NAVSI*CGRUAC’I’ PWO, ’rorri Sta, OkinawaI NAVSIIIPRBFTAC Library

Myokit: A simple interface to cardiac cellular electrophysiology.

PubMed

Clerx, Michael; Collins, Pieter; de Lange, Enno; Volders, Paul G A

2016-01-01

Myokit is a new powerful and versatile software tool for modeling and simulation of cardiac cellular electrophysiology. Myokit consists of an easy-to-read modeling language, a graphical user interface, single and multi-cell simulation engines and a library of advanced analysis tools accessible through a Python interface. Models can be loaded from Myokit's native file format or imported from CellML. Model export is provided to C, MATLAB, CellML, CUDA and OpenCL. Patch-clamp data can be imported and used to estimate model parameters. In this paper, we review existing tools to simulate the cardiac cellular action potential to find that current tools do not cater specifically to model development and that there is a gap between easy-to-use but limited software and powerful tools that require strong programming skills from their users. We then describe Myokit's capabilities, focusing on its model description language, simulation engines and import/export facilities in detail. Using three examples, we show how Myokit can be used for clinically relevant investigations, multi-model testing and parameter estimation in Markov models, all with minimal programming effort from the user. This way, Myokit bridges a gap between performance, versatility and user-friendliness. Copyright © 2015 Elsevier Ltd. All rights reserved.

Monosaccharides as Versatile Units for Water-Soluble Supramolecular Polymers.

PubMed

Leenders, Christianus M A; Jansen, Gijs; Frissen, Martijn M M; Lafleur, René P M; Voets, Ilja K; Palmans, Anja R A; Meijer, E W

2016-03-18

We introduce monosaccharides as versatile water-soluble units to compatibilise supramolecular polymers based on the benzene-1,3,5-tricarboxamide (BTA) moiety with water. A library of monosaccharide-based BTAs is evaluated, varying the length of the alkyl chain (hexyl, octyl, decyl and dodecyl) separating the BTA and saccharide units, as well as the saccharide units (α-glucose, β-glucose, α-mannose and α-galactose). In all cases, the monosaccharides impart excellent water compatibility. The length of the alkyl chain is the determining factor to obtain either long, one-dimensional supramolecular polymers (dodecyl spacer), small aggregates (decyl spacer) or molecularly dissolved (octyl and hexyl) BTAs in water. For the BTAs comprising a dodecyl spacer, our results suggest that a cooperative self-assembly process is operative and that the introduction of different monosaccharides does not significantly change the self- assembly behaviour. Finally, we investigate the potential of post-assembly functionalisation of the formed supramolecular polymers by taking advantage of dynamic covalent bond formation between the monosaccharides and benzoxaboroles. We observe that the supramolecular polymers readily react with a fluorescent benzoxaborole derivative permitting imaging of these dynamic complexes by confocal fluorescence microscopy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Progress in Computational Simulation of Earthquakes

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay; Lyzenga, Gregory; Judd, Michele; Li, P. Peggy; Norton, Charles; Tisdale, Edwin; Granat, Robert

2006-01-01

GeoFEST(P) is a computer program written for use in the QuakeSim project, which is devoted to development and improvement of means of computational simulation of earthquakes. GeoFEST(P) models interacting earthquake fault systems from the fault-nucleation to the tectonic scale. The development of GeoFEST( P) has involved coupling of two programs: GeoFEST and the Pyramid Adaptive Mesh Refinement Library. GeoFEST is a message-passing-interface-parallel code that utilizes a finite-element technique to simulate evolution of stress, fault slip, and plastic/elastic deformation in realistic materials like those of faulted regions of the crust of the Earth. The products of such simulations are synthetic observable time-dependent surface deformations on time scales from days to decades. Pyramid Adaptive Mesh Refinement Library is a software library that facilitates the generation of computational meshes for solving physical problems. In an application of GeoFEST(P), a computational grid can be dynamically adapted as stress grows on a fault. Simulations on workstations using a few tens of thousands of stress and displacement finite elements can now be expanded to multiple millions of elements with greater than 98-percent scaled efficiency on over many hundreds of parallel processors (see figure).

The Textalk, A Uniquely Simple, Versatile Type of Audio-Visual Module: How to Prepare and Use It.

ERIC Educational Resources Information Center

Thomas, D. Des S.; Habowsky, J. E. J.

Textbooks emphasizing visual elements in exposition can be enriched using crisp, concise, audio-taped commentaries to focus attention on essential points in each illustration. These text aids, packaged in the convenient form of cassettes (usually one per chapter), have a number of obvious advantages: (1) any teacher can prepare them; (2) they are…

A New Improved and Extended Version of the Multicell Bacterial Simulator gro.

PubMed

Gutiérrez, Martín; Gregorio-Godoy, Paula; Pérez Del Pulgar, Guillermo; Muñoz, Luis E; Sáez, Sandra; Rodríguez-Patón, Alfonso

2017-08-18

gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits and microbial consortia. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use, and provide new functionalities. The new version of gro is between 1 and 2 orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 10 5 cells in less than 10 min. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version of gro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.

SLHAplus: A library for implementing extensions of the standard model

NASA Astrophysics Data System (ADS)

Bélanger, G.; Christensen, Neil D.; Pukhov, A.; Semenov, A.

2011-03-01

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules. Program summaryProgram title: SLHAplus_1.3 Catalogue identifier: AEHX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 6283 No. of bytes in distributed program, including test data, etc.: 52 119 Distribution format: tar.gz Programming language: C Computer: IBM PC, MAC Operating system: UNIX (Linux, Darwin, Cygwin) RAM: 2000 MB Classification: 11.1 Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables. Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses. Running time: 0.001 sec

Design sensitivity analysis with Applicon IFAD using the adjoint variable method

NASA Technical Reports Server (NTRS)

Frederick, Marjorie C.; Choi, Kyung K.

1984-01-01

A numerical method is presented to implement structural design sensitivity analysis using the versatility and convenience of existing finite element structural analysis program and the theoretical foundation in structural design sensitivity analysis. Conventional design variables, such as thickness and cross-sectional areas, are considered. Structural performance functionals considered include compliance, displacement, and stress. It is shown that calculations can be carried out outside existing finite element codes, using postprocessing data only. That is, design sensitivity analysis software does not have to be imbedded in an existing finite element code. The finite element structural analysis program used in the implementation presented is IFAD. Feasibility of the method is shown through analysis of several problems, including built-up structures. Accurate design sensitivity results are obtained without the uncertainty of numerical accuracy associated with selection of a finite difference perturbation.

The finite element method in low speed aerodynamics

NASA Technical Reports Server (NTRS)

Baker, A. J.; Manhardt, P. D.

1975-01-01

The finite element procedure is shown to be of significant impact in design of the 'computational wind tunnel' for low speed aerodynamics. The uniformity of the mathematical differential equation description, for viscous and/or inviscid, multi-dimensional subsonic flows about practical aerodynamic system configurations, is utilized to establish the general form of the finite element algorithm. Numerical results for inviscid flow analysis, as well as viscous boundary layer, parabolic, and full Navier Stokes flow descriptions verify the capabilities and overall versatility of the fundamental algorithm for aerodynamics. The proven mathematical basis, coupled with the distinct user-orientation features of the computer program embodiment, indicate near-term evolution of a highly useful analytical design tool to support computational configuration studies in low speed aerodynamics.

Structural Analysis Methods for Structural Health Management of Future Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Tessler, Alexander

2007-01-01

Two finite element based computational methods, Smoothing Element Analysis (SEA) and the inverse Finite Element Method (iFEM), are reviewed, and examples of their use for structural health monitoring are discussed. Due to their versatility, robustness, and computational efficiency, the methods are well suited for real-time structural health monitoring of future space vehicles, large space structures, and habitats. The methods may be effectively employed to enable real-time processing of sensing information, specifically for identifying three-dimensional deformed structural shapes as well as the internal loads. In addition, they may be used in conjunction with evolutionary algorithms to design optimally distributed sensors. These computational tools have demonstrated substantial promise for utilization in future Structural Health Management (SHM) systems.

Microanalysis study on ancient Wiangkalong Pottery

NASA Astrophysics Data System (ADS)

Won-in, K.; Tancharakorn, S.; Dararutana, P.

2017-09-01

Wiangkalong is one of major ceramic production cities in northern of Thailand, once colonized by the ancient Lanna Kingdom (1290 A.D.). Ancient Wiangkalong potteries were produced with shapes and designs as similar as those of the Chinese Yuan and Ming Dynasties. Due to the complex nature of materials and objects, extremely sensitive, spatially resolved, multi-elemental and versatile analytical instruments using non-destructive and non-sampling methods to analyze theirs composition are need. In this work, micro-beam X-ray fluorescence spectroscopy based on synchrotron radiation was firstly used to characterize the elemental composition of the ancient Wiangkalong pottery. The results showed the variations in elemental composition of the body matrix, the glaze and the underglaze painting, such as K, Ca, Ti, V, Cr, Mn and Fe.

Scenario planning: a tool for academic health sciences libraries.

PubMed

Ludwig, Logan; Giesecke, Joan; Walton, Linda

2010-03-01

Review the International Campaign to Revitalise Academic Medicine (ICRAM) Future Scenarios as a potential starting point for developing scenarios to envisage plausible futures for health sciences libraries. At an educational workshop, 15 groups, each composed of four to seven Association of Academic Health Sciences Libraries (AAHSL) directors and AAHSL/NLM Fellows, created plausible stories using the five ICRAM scenarios. Participants created 15 plausible stories regarding roles played by health sciences librarians, how libraries are used and their physical properties in response to technology, scholarly communication, learning environments and health care economic changes. Libraries are affected by many forces, including economic pressures, curriculum and changes in technology, health care delivery and scholarly communications business models. The future is likely to contain ICRAM scenario elements, although not all, and each, if they come to pass, will impact health sciences libraries. The AAHSL groups identified common features in their scenarios to learn lessons for now. The hope is that other groups find the scenarios useful in thinking about academic health science library futures.

A facile approach to construct versatile signal amplification system for bacterial detection.

PubMed

Qi, Peng; Zhang, Dun; Wan, Yi; Lv, Dandan

2014-01-01

In this work, a facile approach to design versatile signal amplification system for bacterial detection has been presented. Bio-recognition elements and signaling molecules can be immobilized on the surface of Fe₃O₄@MnO₂ nanomaterials with the help of bioinspired polydopamine (PDA). Fe₃O₄@MnO₂ nanoplates were chosen as carrier for bio-recognizing and signaling molecules because this kind of nanomaterial was superparamagnetic and the existence of MnO₂ could enhance the polymerization of dopamine due to its strong oxidative ability. This nanocomposite system was versatile because PDA around Fe₃O₄@MnO₂ nanoplates provided a stable and convenient platform for immobilization of biological and chemical materials, and various kinds of bio-recognizing and signaling molecules could be immobilized by reaction with pendant amino groups of dopamine to meet different detection requirements. Since a substantial amount of signaling molecules were immobilized on the surface of the nanocomposites, so the sensitivity of detection would be improved when the prepared nanocomposites were selectively conjugated with target pathogen. In the experimental section, a sandwich-type electrochemical biosensor was developed to verify the amplified bacterial detection sensitivity. Concanavalin A (conA) and ferrocene (Fc) were chosen as bio-recognition elements and signaling molecules for detection of Desulforibrio caledoiensis, respectively. The conA and Fc modified nanocomposites were conjugated on electrode by the selective recognition between conA and target bacteria, and the bacterial population was obtained by quantification of the electrochemical signal of Fc moieties. The experimental results showed that the detection sensitivity for D. caledoiensis was improved by taking advantage of this signal amplification system. © 2013 Elsevier B.V. All rights reserved.

High content screening of defined chemical libraries using normal and glioma-derived neural stem cell lines.

PubMed

Danovi, Davide; Folarin, Amos A; Baranowski, Bart; Pollard, Steven M

2012-01-01

Small molecules with potent biological effects on the fate of normal and cancer-derived stem cells represent both useful research tools and new drug leads for regenerative medicine and oncology. Long-term expansion of mouse and human neural stem cells is possible using adherent monolayer culture. These cultures represent a useful cellular resource to carry out image-based high content screening of small chemical libraries. Improvements in automated microscopy, desktop computational power, and freely available image processing tools, now means that such chemical screens are realistic to undertake in individual academic laboratories. Here we outline a cost effective and versatile time lapse imaging strategy suitable for chemical screening. Protocols are described for the handling and screening of human fetal Neural Stem (NS) cell lines and their malignant counterparts, Glioblastoma-derived neural stem cells (GNS). We focus on identification of cytostatic and cytotoxic "hits" and discuss future possibilities and challenges for extending this approach to assay lineage commitment and differentiation. Copyright © 2012 Elsevier Inc. All rights reserved.

Production of the next-generation library virtual tour.

PubMed

Duncan, J M; Roth, L K

2001-10-01

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.

Synergy: Creating a Library Website with Social Interaction and a Collection Focus

ERIC Educational Resources Information Center

Kiyotake, Cynthia

2010-01-01

Since launching its first website in 1997, the Arapahoe Library District (ALD) has constantly looked at ways to review and renew this vital tool for patrons. This article focuses on the process of redesigning the ALD website--the steps taken and decisions made in order to create a site that incorporates interactive elements and patron input and…

Java Source Code Analysis for API Migration to Embedded Systems

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

Winter, Victor; McCoy, James A.; Guerrero, Jonathan

Embedded systems form an integral part of our technological infrastructure and oftentimes play a complex and critical role within larger systems. From the perspective of reliability, security, and safety, strong arguments can be made favoring the use of Java over C in such systems. In part, this argument is based on the assumption that suitable subsets of Java’s APIs and extension libraries are available to embedded software developers. In practice, a number of Java-based embedded processors do not support the full features of the JVM. For such processors, source code migration is a mechanism by which key abstractions offered bymore » APIs and extension libraries can made available to embedded software developers. The analysis required for Java source code-level library migration is based on the ability to correctly resolve element references to their corresponding element declarations. A key challenge in this setting is how to perform analysis for incomplete source-code bases (e.g., subsets of libraries) from which types and packages have been omitted. This article formalizes an approach that can be used to extend code bases targeted for migration in such a manner that the threats associated the analysis of incomplete code bases are eliminated.« less

New Adventures in Screencasting

ERIC Educational Resources Information Center

Flynn, Stephen X.

2013-01-01

There are universal elements to great videos and games that drive large audiences: beautiful cinematography and graphics, engaging and purposeful screenplays and storylines, unforgettable soundtracks, and a brand name that makes viewers and players want to return for more. Libraries can, and should, employ these elements in their own videos to…

A Study on Urban Road Traffic Safety Based on Matter Element Analysis

PubMed Central

Hu, Qizhou; Zhou, Zhuping; Sun, Xu

2014-01-01

This paper examines a new evaluation of urban road traffic safety based on a matter element analysis, avoiding the difficulties found in other traffic safety evaluations. The issue of urban road traffic safety has been investigated through the matter element analysis theory. The chief aim of the present work is to investigate the features of urban road traffic safety. Emphasis was placed on the construction of a criterion function by which traffic safety achieved a hierarchical system of objectives to be evaluated. The matter element analysis theory was used to create the comprehensive appraisal model of urban road traffic safety. The technique was used to employ a newly developed and versatile matter element analysis algorithm. The matter element matrix solves the uncertainty and incompatibility of the evaluated factors used to assess urban road traffic safety. The application results showed the superiority of the evaluation model and a didactic example was included to illustrate the computational procedure. PMID:25587267

PyOperators: Operators and solvers for high-performance computing

NASA Astrophysics Data System (ADS)

Chanial, P.; Barbey, N.

2012-12-01

PyOperators is a publicly available library that provides basic operators and solvers for small-to-very large inverse problems ({http://pchanial.github.com/pyoperators}). It forms the backbone of the package PySimulators, which implements specific operators to construct an instrument model and means to conveniently represent a map, a timeline or a time-dependent observation ({http://pchanial.github.com/pysimulators}). Both are part of the Tamasis (Tools for Advanced Map-making, Analysis and SImulations of Submillimeter surveys) toolbox, aiming at providing versatile, reliable, easy-to-use, and optimal map-making tools for Herschel and future generation of sub-mm instruments. The project is a collaboration between 4 institutes (ESO Garching, IAS Orsay, CEA Saclay, Univ. Leiden).

Artificially Expanded Genetic Information Systems for New Aptamer Technologies.

PubMed

Biondi, Elisa; Benner, Steven A

2018-05-09

Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”.

Balancing gene expression without library construction via a reusable sRNA pool.

PubMed

Ghodasara, Amar; Voigt, Christopher A

2017-07-27

Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt 'target' sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations. This pool can simultaneously optimize up to six genes in a system. This requires building only a single system-specific construct by placing a target sequence upstream of each gene and transforming it with the pre-built sRNA pool. The resulting library is screened and the top clone is sequenced to determine the promoter controlling each sRNA, from which the fold-repression of the genes can be inferred. The system is then rebuilt by rationally selecting parts that implement the optimal expression of each gene. We demonstrate the versatility of this approach by using the same pool to optimize a metabolic pathway (β-carotene) and genetic circuit (XNOR logic gate). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Vertical distribution of major sulfate-reducing bacteria in a shallow eutrophic meromictic lake.

PubMed

Kubo, Kyoko; Kojima, Hisaya; Fukui, Manabu

2014-10-01

The vertical distribution of sulfate-reducing bacteria was investigated in a shallow, eutrophic, meromictic lake, Lake Harutori, located in a residential area of Kushiro, Japan. A steep chemocline, characterized by gradients of oxygen, sulfide and salinity, was found at a depth of 3.5-4.0 m. The sulfide concentration at the bottom of the lake was high (up to a concentration of 10.7 mM). Clone libraries were constructed using the aprA gene, which encodes adenosine-5'-phosphosulfate reductase subunit A, in order to monitor sulfate-reducing bacteria. In the aprA clone libraries, the most abundant sequences were those from the Desulfosarcina-Desulfococcus (DSS) group. A primer set for a DSS group-specific 16S rRNA gene was used to construct another clone library, analysis of which revealed that the uncultured group of sulfate-reducing bacteria, SEEP SRB-1, accounted for nearly half of the obtained sequences. Quantification of the major bacterial groups by catalyzed reporter deposition-fluorescence in situ hybridization demonstrated that the DSS group accounted for 3.2-4.8% of the total bacterial community below the chemocline. The results suggested that the DSS group was one of the major groups of sulfate-reducing bacteria and that these presumably metabolically versatile bacteria might play an important role in sulfur cycling in Lake Harutori. Copyright © 2014 Elsevier GmbH. All rights reserved.

The structural bioinformatics library: modeling in biomolecular science and beyond.

PubMed

Cazals, Frédéric; Dreyfus, Tom

2017-04-01

Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. 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

Versatile Aggressive Mimicry of Cicadas by an Australian Predatory Katydid

PubMed Central

Marshall, David C.; Hill, Kathy B. R.

2009-01-01

Background In aggressive mimicry, a predator or parasite imitates a signal of another species in order to exploit the recipient of the signal. Some of the most remarkable examples of aggressive mimicry involve exploitation of a complex signal-response system by an unrelated predator species. Methodology/Principal Findings We have found that predatory Chlorobalius leucoviridis katydids (Orthoptera: Tettigoniidae) can attract male cicadas (Hemiptera: Cicadidae) by imitating the species-specific wing-flick replies of sexually receptive female cicadas. This aggressive mimicry is accomplished both acoustically, with tegminal clicks, and visually, with synchronized body jerks. Remarkably, the katydids respond effectively to a variety of complex, species-specific Cicadettini songs, including songs of many cicada species that the predator has never encountered. Conclusions/Significance We propose that the versatility of aggressive mimicry in C. leucoviridis is accomplished by exploiting general design elements common to the songs of many acoustically signaling insects that use duets in pair-formation. Consideration of the mechanism of versatile mimicry in C. leucoviridis may illuminate processes driving the evolution of insect acoustic signals, which play a central role in reproductive isolation of populations and the formation of species. PMID:19142230

Simulation of magnetic active polymers for versatile microfluidic devices

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Özelt, Harald; Fischbacher, Johann; Reichel, Franz; Exl, Lukas; Bance, Simon; Kataeva, Nadezhda; Binder, Claudia; Brückl, Hubert; Schrefl, Thomas

2013-01-01

We propose to use a compound of magnetic nanoparticles (20-100 nm) embedded in a flexible polymer (Polydimethylsiloxane PDMS) to filter circulating tumor cells (CTCs). The analysis of CTCs is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. The combination of experiments and simulations lead to a versatile microfluidic lab-on-chip device. Simulations are essential to understand the influence of the embedded nanoparticles in the elastic PDMS when applying a magnetic gradient field. It combines finite element calculations of the polymer, magnetic simulations of the embedded nanoparticles and the fluid dynamic calculations of blood plasma and blood cells. With the use of magnetic active polymers a wide range of tunable microfluidic structures can be created. The method can help to increase the yield of needed isolated CTCs.

Benzyl Alcohol-Mediated Versatile Method to Fabricate Nonstoichiometric Metal Oxide Nanostructures.

PubMed

Qamar, Mohammad; Adam, Alaaldin; Azad, Abdul-Majeed; Kim, Yong-Wah

2017-11-22

Nanostructured metal oxides with cationic or anionic deficiency find applications in a wide range of technological areas including the energy sector and environment. However, a facile route to prepare such materials in bulk with acceptable reproducibility is still lacking; many synthesis techniques are still only bench-top and cannot be easily scaled-up. Here, we report that the benzyl alcohol (BA)-mediated method is capable of producing a host of nanostructured metal oxides (MO x , where M = Ti, Zn, Ce, Sn, In, Ga, or Fe) with inherent nonstoichiometry. It employs multifunctional BA as a solvent, a reducing agent, and a structure-directing agent. Depending on the oxidation states of metal, elemental or nonstoichiometric oxide forms are obtained. Augmented photoelectrochemical oxidation of water under visible light by some of these nonstoichiometric oxides highlights the versatility of the BA-mediated synthesis protocol.

Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool.

PubMed

Kim, Adele; Pyykko, Ilmari

2011-08-01

Transposons have been promising elements for gene integration, and the Sleeping Beauty (SB) system has been the major one for many years, although there have been several other transposon systems available, for example, Tol2. However, recently another system known as PiggyBac (PB) has been introduced and developed for fulfilling the same purposes, for example, mutagenesis, transgenesis and gene therapy and in some cases with improved transposition efficiency and advantages over the Sleeping Beauty transposon system, although improved hyperactive transposase has highly increased the transposition efficacy for SB. The PB systems have been used in many different scientific research fields; therefore, the purpose of this review is to describe some of these versatile uses of the PiggyBac system to give readers an overview on the usage of PiggyBac system.

SimTrack: A compact c++ library for particle orbit and spin tracking in accelerators

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

Luo, Yun

2015-06-24

SimTrack is a compact c++ library of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam-beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam-beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam-beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture,more » physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.« less

Low-cost ultrasonic lamb-wave transducer

NASA Technical Reports Server (NTRS)

Kammerer, C. C.

1978-01-01

Transducer propagates Lamb wave through thin aluminum sheet material. Model includes two elements that measure effects of damping and loading which, in turn, are indirectly equated to bond integrity. Transducer has been used to evaluate bond integrity of aluminum facing adhesively bonded to aluminum facing. Because of versatility, it is now possible to inspect many objects of different configurations that could not be reached with earlier transducers.

Passively mode-locked Raman fiber laser with 100 GHz repetition rate

NASA Astrophysics Data System (ADS)

Schröder, Jochen; Coen, Stéphane; Vanholsbeeck, Frédérique; Sylvestre, Thibaut

2006-12-01

We experimentally demonstrate the operation of a passively mode-locked Raman fiber ring laser with an ultrahigh repetition rate of 100GHz and up to 430mW of average output power. This laser constitutes a simple wavelength versatile pulsed optical source. Stable mode locking is based on dissipative four-wave mixing with a single fiber Bragg grating acting as the mode-locking element.

Adult Services in the Third Millennium.

ERIC Educational Resources Information Center

Monroe, Margaret E.

1979-01-01

Presents a four-step model for "planning" or "forecasting" future of adult services in public libraries: (1) identification of forces at work; (2) analysis of probable impacts of one force upon another; (3) identification of preferred (and rejected) elements of future with forces that control elements; and (4) strategies to be…

Application Reuse Library for Software, Requirements, and Guidelines

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Thronesbery, Carroll

1994-01-01

Better designs are needed for expert systems and other operations automation software, for more reliable, usable and effective human support. A prototype computer-aided Application Reuse Library shows feasibility of supporting concurrent development and improvement of advanced software by users, analysts, software developers, and human-computer interaction experts. Such a library expedites development of quality software, by providing working, documented examples, which support understanding, modification and reuse of requirements as well as code. It explicitly documents and implicitly embodies design guidelines, standards and conventions. The Application Reuse Library provides application modules with Demo-and-Tester elements. Developers and users can evaluate applicability of a library module and test modifications, by running it interactively. Sub-modules provide application code and displays and controls. The library supports software modification and reuse, by providing alternative versions of application and display functionality. Information about human support and display requirements is provided, so that modifications will conform to guidelines. The library supports entry of new application modules from developers throughout an organization. Example library modules include a timer, some buttons and special fonts, and a real-time data interface program. The library prototype is implemented in the object-oriented G2 environment for developing real-time expert systems.

MINITEX (Minnesota Interlibrary Teletype Experiment); Report Covering the First 18 Months of Project Operation, January 1, 1969 through June 30, 1970...

ERIC Educational Resources Information Center

Stanford, Edward B.

In 1968, a two-year pilot project, called the Minnesota Interlibrary Teletype Experiment (MINITEX) was undertaken to test the feasibility of sharing the University of Minnesota's library resources with patrons of outstate libraries. This report presents the definitive evaluation for the MINITEX project. The four elements in the design of the…

A Study of Periodical Literature Searching at an Urban Research Library: Problems and Patterns.

ERIC Educational Resources Information Center

Carey, Kevin

Patron use of periodical indexes at an urban academic research library was studied over a 7-week period in the summer of 1982. A total of 98 patrons were interviewed on a random basis as they used various periodical and newspaper indexes. The questionnaire was designed to gather information on citation elements, the methods patrons use to locate…

Production of the next-generation library virtual tour

PubMed Central

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

LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

NASA Astrophysics Data System (ADS)

Zhou, J.; Deyhim, A.; Krueger, S.; Gregurick, S. K.

2005-08-01

A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling. Program summaryTitle of program:LORES Catalogue identifier: ADVC Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PC Operating systems:UNIX64 6.5 and LINUX 2.4.7 Programming language used:C Memory required to execute with typical data:8 MB No. of lines in distributed program, including test data, etc.:2270 No. of bytes in distributed program, including test data, etc.:13 302 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MATH library

Quantitative elemental analysis of an industrial mineral talc, using accelerator-based analytical technique

NASA Astrophysics Data System (ADS)

Olabanji, S. O.; Ige, A. O.; Mazzoli, C.; Ceccato, D.; Ajayi, E. O. B.; De Poli, M.; Moschini, G.

2005-10-01

Accelerator-based technique of PIXE was employed for the determination of the elemental concentration of an industrial mineral, talc. Talc is a very versatile mineral in industries with several applications. Due to this, there is a need to know its constituents to ensure that the workers are not exposed to health risks. Besides, microscopic tests on some talc samples in Nigeria confirm that they fall within the BP British Pharmacopoeia standard for tablet formation. However, for these samples to become a local source of raw material for pharmaceutical grade talc, the precise elemental compositions should be established which is the focus of this work. Proton beam produced by the 2.5 MV AN 2000 Van de Graaff accelerator at INFN, LNL, Legnaro, Padova, Italy was used for the PIXE measurements. The results which show the concentration of different elements in the talc samples, their health implications and metabolic roles are presented and discussed.

Design of a high-speed digital processing element for parallel simulation

NASA Technical Reports Server (NTRS)

Milner, E. J.; Cwynar, D. S.

1983-01-01

A prototype of a custom designed computer to be used as a processing element in a multiprocessor based jet engine simulator is described. The purpose of the custom design was to give the computer the speed and versatility required to simulate a jet engine in real time. Real time simulations are needed for closed loop testing of digital electronic engine controls. The prototype computer has a microcycle time of 133 nanoseconds. This speed was achieved by: prefetching the next instruction while the current one is executing, transporting data using high speed data busses, and using state of the art components such as a very large scale integration (VLSI) multiplier. Included are discussions of processing element requirements, design philosophy, the architecture of the custom designed processing element, the comprehensive instruction set, the diagnostic support software, and the development status of the custom design.

Thin film ceramic thermocouples

NASA Technical Reports Server (NTRS)

Gregory, Otto (Inventor); Fralick, Gustave (Inventor); Wrbanek, John (Inventor); You, Tao (Inventor)

2011-01-01

A thin film ceramic thermocouple (10) having two ceramic thermocouple (12, 14) that are in contact with each other in at least on point to form a junction, and wherein each element was prepared in a different oxygen/nitrogen/argon plasma. Since each element is prepared under different plasma conditions, they have different electrical conductivity and different charge carrier concentration. The thin film thermocouple (10) can be transparent. A versatile ceramic sensor system having an RTD heat flux sensor can be combined with a thermocouple and a strain sensor to yield a multifunctional ceramic sensor array. The transparent ceramic temperature sensor that could ultimately be used for calibration of optical sensors.

Optimization of Wireless Power Transfer Systems Enhanced by Passive Elements and Metasurfaces

NASA Astrophysics Data System (ADS)

Lang, Hans-Dieter; Sarris, Costas D.

2017-10-01

This paper presents a rigorous optimization technique for wireless power transfer (WPT) systems enhanced by passive elements, ranging from simple reflectors and intermedi- ate relays all the way to general electromagnetic guiding and focusing structures, such as metasurfaces and metamaterials. At its core is a convex semidefinite relaxation formulation of the otherwise nonconvex optimization problem, of which tightness and optimality can be confirmed by a simple test of its solutions. The resulting method is rigorous, versatile, and general -- it does not rely on any assumptions. As shown in various examples, it is able to efficiently and reliably optimize such WPT systems in order to find their physical limitations on performance, optimal operating parameters and inspect their working principles, even for a large number of active transmitters and passive elements.

On the treatment of ill-conditioned cases in the Monte Carlo library least-squares approach for inverse radiation analyzers

NASA Astrophysics Data System (ADS)

Meric, Ilker; Johansen, Geir A.; Holstad, Marie B.; Mattingly, John; Gardner, Robin P.

2012-05-01

Prompt gamma-ray neutron activation analysis (PGNAA) has been and still is one of the major methods of choice for the elemental analysis of various bulk samples. This is mostly due to the fact that PGNAA offers a rapid, non-destructive and on-line means of sample interrogation. The quantitative analysis of the prompt gamma-ray data could, on the other hand, be performed either through the single peak analysis or the so-called Monte Carlo library least-squares (MCLLS) approach, of which the latter has been shown to be more sensitive and more accurate than the former. The MCLLS approach is based on the assumption that the total prompt gamma-ray spectrum of any sample is a linear combination of the contributions from the individual constituents or libraries. This assumption leads to, through the minimization of the chi-square value, a set of linear equations which has to be solved to obtain the library multipliers, a process that involves the inversion of the covariance matrix. The least-squares solution may be extremely uncertain due to the ill-conditioning of the covariance matrix. The covariance matrix will become ill-conditioned whenever, in the subsequent calculations, two or more libraries are highly correlated. The ill-conditioning will also be unavoidable whenever the sample contains trace amounts of certain elements or elements with significantly low thermal neutron capture cross-sections. In this work, a new iterative approach, which can handle the ill-conditioning of the covariance matrix, is proposed and applied to a hydrocarbon multiphase flow problem in which the parameters of interest are the separate amounts of the oil, gas, water and salt phases. The results of the proposed method are also compared with the results obtained through the implementation of a well-known regularization method, the truncated singular value decomposition. Final calculations indicate that the proposed approach would be able to treat ill-conditioned cases appropriately.

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities’ libraries

PubMed Central

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Introduction: Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries’ Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. Materials and Methods: The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. Results: The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). Conclusion: It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers to achieve faster and more accurate information resources. Therefore, the influence of librarians’ ideas on the awareness of web designers and developers will be important for using metadata elements as general, and specifically for applying such standards. PMID:24741646

A standard library for modeling satellite orbits on a microcomputer

NASA Astrophysics Data System (ADS)

Beutel, Kenneth L.

1988-03-01

Introductory students of astrodynamics and the space environment are required to have a fundamental understanding of the kinematic behavior of satellite orbits. This thesis develops a standard library that contains the basic formulas for modeling earth orbiting satellites. This library is used as a basis for implementing a satellite motion simulator that can be used to demonstrate orbital phenomena in the classroom. Surveyed are the equations of orbital elements, coordinate systems and analytic formulas, which are made into a standard method for modeling earth orbiting satellites. The standard library is written in the C programming language and is designed to be highly portable between a variety of computer environments. The simulation draws heavily on the standards established by the library to produce a graphics-based orbit simulation program written for the Apple Macintosh computer. The simulation demonstrates the utility of the standard library functions but, because of its extensive use of the Macintosh user interface, is not portable to other operating systems.

Geomega: MEGAlib's Uniform Geometry and Detector Description Tool for Geant3, MGGPOD, and Geant4

NASA Astrophysics Data System (ADS)

Zoglauer, Andreas C.; Andritschke, R.; Schopper, F.; Wunderer, C. B.

2006-09-01

The Medium Energy Gamma-ray Astronomy library MEGAlib is a set of software tools for the analysis of low to medium energy gamma-ray telescopes, especially Compton telescopes. It comprises all necessary data analysis steps from simulation/measurements via event reconstruction to image reconstruction and enables detailed performance assessments. In the energy range of Compton telescopes (with energy deposits from a few keV up to hundreds of MeV), the Geant Monte-Carlo software packages (Geant3 with its MGGPOD extension as well as Geant4) are widely used. Since each tool has its unique advantages, MEGAlib contains a geometry and detector description library, called Geomega, which allows to use those tools in a uniform way. It incorporates the versatile 3D display facilities available within the ROOT libraries. The same geometry, material, trigger, and detector description can be used for all simulation tools as well as for the later event analysis in the MEGAlib framework. This is done by converting the MEGAlib geometry into the Geant3 or MGGPOD format or directly linking the Geomega library into Geant4. The geometry description can handle most (and can be extended to handle all) volumes common to Geant3, Geant4 and ROOT. In Geomega a list of features is implemented which are especially useful for optimizing detector geometries: It allows to define constants, can handle mathematical operations, enables volume scaling, checks for overlaps of detector volumes, does mass calculations, etc. Used in combination with MEGAlib, Geomega enables discretization, application of detector noise, thresholds, various trigger conditions, defective pixels, etc. The highly modular and completely object-oriented library is written in C++ and based on ROOT. It has been originally developed for the tracking Compton scattering and Pair creation telescope MEGA and has been successfully applied to a wide variety of telescopes, such as ACT, NuSTAR, or GRI.

Penicillin binding protein 3 of Staphylococcus aureus NCTC 8325-4 binds and activates human plasminogen.

PubMed

Kylväjä, Riikka; Ojalehto, Tuomas; Kainulainen, Veera; Virkola, Ritva; Westerlund-Wikström, Benita

2016-08-04

Staphylococcus aureus is a versatile pathogen expressing a number of virulence-associated adhesive molecules. In a previous study, we generated in a secretion-competent Escherichia coli strain a library of random FLAG-tag positive (FTP) polypeptides of S. aureus. To identify adhesive proteins and gain additional knowledge on putative virulence factors of S. aureus, we here screened the FTP library against human serum proteins. Staphylococcus aureus NCTC 8325-4, origin of the FTP library, adhered to immobilized plasminogen in vitro. In an enzyme-linked immunoassay a C-terminal part of penicillin binding protein 3 (PBP3), included in the FTP library, bound to immobilized plasminogen. We expressed and purified full-length PBP3 and its C-terminal fragments as recombinant proteins. In a time-resolved fluorometry-based assay the PBP3 polypeptides bound to immobilized plasminogen. The polypeptides enhanced formation of plasmin from plasminogen as analyzed by cleavage of a chromogenic plasmin substrate. The present findings, although preliminary, demonstrate reliably that S. aureus NCTC 8325-4 adheres to immobilized plasminogen in vitro and that the adhesion may be mediated by a C-terminal fragment of the PBP3 protein. The full length PBP3 and the penicillin binding C-terminal domain of PBP3 expressed as recombinant proteins bound plasminogen and activated plasminogen to plasmin. These phenomena were inhibited by the lysine analogue ε-aminocaproic acid suggesting that the binding is mediated by lysine residues. A detailed molecular description of surface molecules enhancing the virulence of S. aureus will aid in understanding of its pathogenicity and help in design of antibacterial drugs in the future.

Elements of Information Inquiry, Evolution of Models & Measured Reflection

ERIC Educational Resources Information Center

Callison, Daniel; Baker, Katie

2014-01-01

In 2003 Paula Montgomery, founding editor of School Library Media Activities Monthly and former branch chief of school media services for the Maryland State Department of Education, published a guide to teaching information inquiry. Her staff also illustrated the elements of information inquiry as a recursive cycle with interaction among the…

Map Metadata: Essential Elements for Search and Storage

ERIC Educational Resources Information Center

Beamer, Ashley

2009-01-01

Purpose: The purpose of this paper is to develop an understanding of the issues surrounding the cataloguing of maps in archives and libraries. An investigation into appropriate metadata formats, such as MARC21, EAD and Dublin Core with RDF, shows how particular map data can be stored. Mathematical map elements, specifically co-ordinates, are…

Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.

PubMed

Xing, Li; McDonald, Joseph J; Kolodziej, Steve A; Kurumbail, Ravi G; Williams, Jennifer M; Warren, Chad J; O'Neal, Janet M; Skepner, Jill E; Roberds, Steven L

2011-03-10

Structure-based virtual screening was applied to design combinatorial libraries to discover novel and potent soluble epoxide hydrolase (sEH) inhibitors. X-ray crystal structures revealed unique interactions for a benzoxazole template in addition to the conserved hydrogen bonds with the catalytic machinery of sEH. By exploitation of the favorable binding elements, two iterations of library design based on amide coupling were employed, guided principally by the docking results of the enumerated virtual products. Biological screening of the libraries demonstrated as high as 90% hit rate, of which over two dozen compounds were single digit nanomolar sEH inhibitors by IC(50) determination. In total the library design and synthesis produced more than 300 submicromolar sEH inhibitors. In cellular systems consistent activities were demonstrated with biochemical measurements. The SAR understanding of the benzoxazole template provides valuable insights into discovery of novel sEH inhibitors as therapeutic agents.

Building Communities of Engineers to Share Technical Expertise

NASA Technical Reports Server (NTRS)

Topousis, Daria E.; Dennehy, Cornelius J.; Fesq, Lorraine M.

2012-01-01

Developed by the core community to describe our vision of an approach to ensure a sufficiently technically advanced and affordable AR&D technology base is available to support future NASA missions. The goal of this strategy is to create an environment exploiting reusable technology elements for an AR&D system design and development process which is: a) Lower-Risk. b) More Versatile/Scalable. c) Reliable & Crew-Safe. d) More Affordable.

Family Expense Manager Application in Android

NASA Astrophysics Data System (ADS)

Rajaprabha, M. N.

2017-11-01

FAMILY EXPENSES MANAGER is an android application. This monitors your own costs, family costs and incidental costs. This resembles a present day costs day book in your versatile. This application helps you to monitor your every day costs, settlement points of interest, general rundown, report in detail and periodic costs subtle elements. Every one of the information is put away in database and can be recovered by the client and their relatives.

Progress in Finite Element Modeling of the Lower Extremities

DTIC Science & Technology

2015-06-01

bending and subsequent injury , e.g., the distal tibia motion results in bending of the tibia rather than the tibia rotating about the knee joint...layers, rich anisotropy, and wide variability. Developing a model for predictive injury capability, therefore, needs to be versatile and flexible to... injury capability presents many challenges, the first of which is identifying the types of conditions where injury prediction is needed. Our focus

Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs.

PubMed

Chetverina, Darya; Savitskaya, Ekaterina; Maksimenko, Oksana; Melnikova, Larisa; Zaytseva, Olga; Parshikov, Alexander; Galkin, Alexander V; Georgiev, Pavel

2008-02-01

Much of the research on insulators in Drosophila has been done with transgenic constructs using the white gene (mini-white) as reporter. Hereby we report that the sequence between the white and CG32795 genes in Drosophila melanogaster contains an insulator of a novel kind. Its functional core is within a 368 bp segment almost contiguous to the white 3'UTR, hence we name it as Wari (white-abutting resident insulator). Though Wari contains no binding sites for known insulator proteins and does not require Su(Hw) or Mod(mdg4) for its activity, it can equally well interact with another copy of Wari and with unrelated Su(Hw)-dependent insulators, gypsy or 1A2. In its natural downstream position, Wari reinforces enhancer blocking by any of the three insulators placed between the enhancer and the promoter; again, Wari-Wari, Wari-gypsy or 1A2-Wari pairing results in mutual neutralization (insulator bypass) when they precede the promoter. The distressing issue is that this element hides in all mini-white constructs employed worldwide to study various insulators and other regulatory elements as well as long-range genomic interactions, and its versatile effects could have seriously influenced the results and conclusions of many works.

Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs

PubMed Central

Chetverina, Darya; Savitskaya, Ekaterina; Maksimenko, Oksana; Melnikova, Larisa; Zaytseva, Olga; Parshikov, Alexander; Galkin, Alexander V.; Georgiev, Pavel

2008-01-01

Much of the research on insulators in Drosophila has been done with transgenic constructs using the white gene (mini-white) as reporter. Hereby we report that the sequence between the white and CG32795 genes in Drosophila melanogaster contains an insulator of a novel kind. Its functional core is within a 368 bp segment almost contiguous to the white 3′UTR, hence we name it as Wari (white-abutting resident insulator). Though Wari contains no binding sites for known insulator proteins and does not require Su(Hw) or Mod(mdg4) for its activity, it can equally well interact with another copy of Wari and with unrelated Su(Hw)-dependent insulators, gypsy or 1A2. In its natural downstream position, Wari reinforces enhancer blocking by any of the three insulators placed between the enhancer and the promoter; again, Wari–Wari, Wari–gypsy or 1A2–Wari pairing results in mutual neutralization (insulator bypass) when they precede the promoter. The distressing issue is that this element hides in all mini-white constructs employed worldwide to study various insulators and other regulatory elements as well as long-range genomic interactions, and its versatile effects could have seriously influenced the results and conclusions of many works. PMID:18086699

Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment.

PubMed

Davin-Regli, Anne; Pagès, Jean-Marie

2015-01-01

Enterobacter aerogenes and E. cloacae have been reported as important opportunistic and multiresistant bacterial pathogens for humans during the last three decades in hospital wards. These Gram-negative bacteria have been largely described during several outbreaks of hospital-acquired infections in Europe and particularly in France. The dissemination of Enterobacter sp. is associated with the presence of redundant regulatory cascades that efficiently control the membrane permeability ensuring the bacterial protection and the expression of detoxifying enzymes involved in antibiotic degradation/inactivation. In addition, these bacterial species are able to acquire numerous genetic mobile elements that strongly contribute to antibiotic resistance. Moreover, this particular fitness help them to colonize several environments and hosts and rapidly and efficiently adapt their metabolism and physiology to external conditions and environmental stresses. Enterobacter is a versatile bacterium able to promptly respond to the antibiotic treatment in the colonized patient. The balance of the prevalence, E. aerogenes versus E. cloacae, in the reported hospital infections during the last period, questions about the horizontal transmission of mobile elements containing antibiotic resistance genes, e.g., the efficacy of the exchange of resistance genes Klebsiella pneumoniae to Enterobacter sp. It is also important to mention the possible role of antibiotic use in the treatment of bacterial infectious diseases in this E. aerogenes/E. cloacae evolution.

Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment

PubMed Central

Davin-Regli, Anne; Pagès, Jean-Marie

2015-01-01

Enterobacter aerogenes and E. cloacae have been reported as important opportunistic and multiresistant bacterial pathogens for humans during the last three decades in hospital wards. These Gram-negative bacteria have been largely described during several outbreaks of hospital-acquired infections in Europe and particularly in France. The dissemination of Enterobacter sp. is associated with the presence of redundant regulatory cascades that efficiently control the membrane permeability ensuring the bacterial protection and the expression of detoxifying enzymes involved in antibiotic degradation/inactivation. In addition, these bacterial species are able to acquire numerous genetic mobile elements that strongly contribute to antibiotic resistance. Moreover, this particular fitness help them to colonize several environments and hosts and rapidly and efficiently adapt their metabolism and physiology to external conditions and environmental stresses. Enterobacter is a versatile bacterium able to promptly respond to the antibiotic treatment in the colonized patient. The balance of the prevalence, E. aerogenes versus E. cloacae, in the reported hospital infections during the last period, questions about the horizontal transmission of mobile elements containing antibiotic resistance genes, e.g., the efficacy of the exchange of resistance genes Klebsiella pneumoniae to Enterobacter sp. It is also important to mention the possible role of antibiotic use in the treatment of bacterial infectious diseases in this E. aerogenes/E. cloacae evolution. PMID:26042091

Introduction of Information Science into Library Training in Eastern Africa. Expert Meeting (Dar es Salaam, Tanzania, February 26-29, 1980).

ERIC Educational Resources Information Center

Abidi, S. A. H.; Moeller, T.

In 1978 a team of three people was formed to survey the existing library training facilities in East Africa and to suggest possibilities as to how the elements of information science could be introduced either into existing programs or into special courses organized for the purpose. The team submitted its report to a joint meeting of the…

TAP 1: A Finite Element Program for Steady-State Thermal Analysis of Convectively Cooled Structures

NASA Technical Reports Server (NTRS)

Thornton, E. A.

1976-01-01

The program has a finite element library of six elements: two conduction/convection elements to model heat transfer in a solid, two convection elements to model heat transfer in a fluid, and two integrated conduction/convection elements to represent combined heat transfer in tubular and plate/fin fluid passages. Nonlinear thermal analysis due to temperature dependent thermal parameters is performed using the Newton-Raphson iteration method. Program output includes nodal temperatures and element heat fluxes. Pressure drops in fluid passages may be computed as an option. A companion plotting program for displaying the finite element model and predicted temperature distributions is presented. User instructions and sample problems are presented in appendixes.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

PubMed

Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

2006-05-03

Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Hijazi Architectural Object Library (haol)

NASA Astrophysics Data System (ADS)

Baik, A.; Boehm, J.

2017-02-01

As with many historical buildings around the world, building façades are of special interest; moreover, the details of such windows, stonework, and ornaments give each historic building its individual character. Each object of these buildings must be classified in an architectural object library. Recently, a number of researches have been focusing on this topic in Europe and Canada. From this standpoint, the Hijazi Architectural Objects Library (HAOL) has reproduced Hijazi elements as 3D computer models, which are modelled using a Revit Family (RFA). The HAOL will be dependent on the image survey and point cloud data. The Hijazi Object such as Roshan and Mashrabiyah, become as vocabulary of many Islamic cities in the Hijazi region such as Jeddah in Saudi Arabia, and even for a number of Islamic historic cities such as Istanbul and Cairo. These architectural vocabularies are the main cause of the beauty of these heritage. However, there is a big gap in both the Islamic architectural library and the Hijazi architectural library to provide these unique elements. Besides, both Islamic and Hijazi architecture contains a huge amount of information which has not yet been digitally classified according to period and styles. Due to this issue, this paper will be focusing on developing of Heritage BIM (HBIM) standards and the HAOL library to reduce the cost and the delivering time for heritage and new projects that involve in Hijazi architectural styles. Through this paper, the fundamentals of Hijazi architecture informatics will be provided via developing framework for HBIM models and standards. This framework will provide schema and critical information, for example, classifying the different shapes, models, and forms of structure, construction, and ornamentation of Hijazi architecture in order to digitalize parametric building identity.

Self-Oscillating Josephson Quantum Heat Engine

NASA Astrophysics Data System (ADS)

Marchegiani, G.; Virtanen, P.; Giazotto, F.; Campisi, M.

2016-11-01

The design of a mesoscopic self-oscillating heat engine that works thanks to purely quantum effects is presented. The proposed scheme is amenable to experimental implementation with current state-of-the-art nanotechnology and materials. One of the main features of the structure is its versatility: The engine can deliver work to a generic load without galvanic contact. This versatility makes it a promising building block for low-temperature on-chip energy-management applications. The heat engine consists of a circuit featuring a thermoelectric element based on a ferromagnetic insulator-superconductor tunnel junction and a Josephson weak link that realizes a purely quantum dc-ac converter. This makeup enables the contactless transfer of work to the load (a generic RL circuit). The performance of the heat engine is investigated as a function of the thermal gradient applied to the thermoelectric junction. Power up to 1 pW can be delivered to a load RL=10 Ω .

Generalised syntheses of ordered mesoporous oxides: the atrane route

NASA Astrophysics Data System (ADS)

Cabrera, Saúl; El Haskouri, Jamal; Guillem, Carmen; Latorre, Julio; Beltrán-Porter, Aurelio; Beltrán-Porter, Daniel; Marcos, M. Dolores; Amorós *, Pedro

2000-06-01

A new simple and versatile technique to obtain mesoporous oxides is presented. While implying surfactant-assisted formation of mesostructured intermediates, the original chemical contribution of this approach lies in the use of atrane complexes as precursors. Without prejudice to their inherent unstability in aqueous solution, the atranes show a marked inertness towards hydrolysis. Bringing kinetic factors into play, it becomes possible to control the processes involved in the formation of the surfactant-inorganic phase composite micelles, which constitute the elemental building blocks of the mesostructures. Independent of the starting compositional complexity, both the mesostructured intermediates and the final mesoporous materials are chemically homogeneous. The final ordered mesoporous materials are thermally stable and show unimodal porosity, as well as homogeneous microstructure and texture. Examples of materials synthesised on account of the versatility of this new method, including siliceous, non siliceous and mixed oxides, are presented and discussed.

A method for using solid modeling CAD software to create an implant library for the fabrication of a custom abutment.

PubMed

Zhang, Jing; Zhang, Rimei; Ren, Guanghui; Zhang, Xiaojie

2017-02-01

This article describes a method that incorporates the solid modeling CAD software Solidworks with a dental milling machine to fabricate individual abutments in house. This process involves creating an implant library with 3-dimensional (3D) models and manufacturing a base, scan element, abutment, and crown anatomy. The 3D models can be imported into any dental computer-aided design and computer-aided (CAD-CAM) manufacturing system. This platform increases abutment design flexibility, as the base and scan elements can be designed to fit several shapes as needed to meet clinical requirements. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

\\Space: A new code to estimate \\temp, \\logg, and elemental abundances

NASA Astrophysics Data System (ADS)

Boeche, C.

2016-09-01

\\Space is a FORTRAN95 code that derives stellar parameters and elemental abundances from stellar spectra. To derive these parameters, \\Space does not measure equivalent widths of lines nor it uses templates of synthetic spectra, but it employs a new method based on a library of General Curve-Of-Growths. To date \\Space works on the wavelength range 5212-6860 Å and 8400-8921 Å, and at the spectral resolution R=2000-20000. Extensions of these limits are possible. \\Space is a highly automated code suitable for application to large spectroscopic surveys. A web front end to this service is publicly available at http://dc.g-vo.org/SP_ACE together with the library and the binary code.

Isolation of a peptide from Ph.D.-C7C phage display library for detection of Cry1Ab.

PubMed

Wang, Yun; Wang, Qian; Wu, Ai-Hua; Hao, Zhen-Ping; Liu, Xian-Jin

2017-12-15

Traditional ELISA methods of using animal immunity yield antibodies for detection Cry toxin. Not only is this incredibly harmful to the animals, but is also time-intensive. Here we developed a simple method to yield the recognition element. Using a critical selection strategy and immunoassay we confirmed a clone from the Ph.D-C7C phage library, which has displayed the most interesting Cry1Ab-binding characteristics examined in this study (Fig. 1). The current study indicates that isolating peptide is an alternative method for the preparation of a recognition element, and that the developed assay is a potentially useful tool for detecting Cry1Ab. Copyright © 2017. Published by Elsevier Inc.

Student-Built High-Altitude Balloon Payload with Sensor Array and Flight Computer

NASA Astrophysics Data System (ADS)

Jeffery, Russell; Slaton, William

A payload was designed for a high-altitude weather balloon. The flight controller consisted of a Raspberry Pi running a Python 3.4 program to collect and store data. The entire payload was designed to be versatile and easy to modify so that it could be repurposed for other projects: The code was written with the expectation that more sensors and other functionality would be added later, and a Raspberry Pi was chosen as the processor because of its versatility, its active support community, and its ability to interface easily with sensors, servos, and other such hardware. For this project, extensive use was made of the Python 3.4 libraries gps3, PiCamera, and RPi.GPIO to collect data from a GPS breakout board, a Raspberry Pi camera, a geiger counter, two thermocouples, and a pressure sensor. The data collected clearly shows that pressure and temperature decrease as altitude increases, while β-radiation and γ-radiation increase as altitude increases. These trends in the data follow those predicted by theoretical calculations made for comparison. This payload was developed in such a way that future students could easily alter it to include additional sensors, biological experiments, and additional error monitoring and management. Arkansas Space Grant Consortium (ASGC) Workforce Development Grant.

An update on the LIM and SH3 domain protein 1 (LASP1): a versatile structural, signaling, and biomarker protein

PubMed Central

Orth, Martin F.; Cazes, Alex; Butt, Elke; Grunewald, Thomas G. P.

2015-01-01

The gene encoding the LIM and SH3 domain protein (LASP1) was cloned two decades ago from a cDNA library of breast cancer metastases. As the first protein of a class comprising one N-terminal LIM and one C-terminal SH3 domain, LASP1 founded a new LIM-protein subfamily of the nebulin group. Since its discovery LASP1 proved to be an extremely versatile protein because of its exceptional structure allowing interaction with various binding partners, its ubiquitous expression in normal tissues, albeit with distinct expression patterns, and its ability to transmit signals from the cytoplasm into the nucleus. As a result, LASP1 plays key roles in cell structure, physiological processes, and cell signaling. Furthermore, LASP1 overexpression contributes to cancer aggressiveness hinting to a potential value of LASP1 as a cancer biomarker. In this review we summarize published data on structure, regulation, function, and expression pattern of LASP1, with a focus on its role in human cancer and as a biomarker protein. In addition, we provide a comprehensive transcriptome analysis of published microarrays (n=2,780) that illustrates the expression profile of LASP1 in normal tissues and its overexpression in a broad range of human cancer entities. PMID:25622104

Large Format Multifunction 2-Terabyte Optical Disk Storage System

NASA Technical Reports Server (NTRS)

Kaiser, David R.; Brucker, Charles F.; Gage, Edward C.; Hatwar, T. K.; Simmons, George O.

1996-01-01

The Kodak Digital Science OD System 2000E automated disk library (ADL) base module and write-once drive are being developed as the next generation commercial product to the currently available System 2000 ADL. Under government sponsorship with the Air Force's Rome Laboratory, Kodak is developing magneto-optic (M-O) subsystems compatible with the Kodak Digital Science ODW25 drive architecture, which will result in a multifunction (MF) drive capable of reading and writing 25 gigabyte (GB) WORM media and 15 GB erasable media. In an OD system 2000 E ADL configuration with 4 MF drives and 100 total disks with a 50% ration of WORM and M-O media, 2.0 terabytes (TB) of versatile near line mass storage is available.

Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

NASA Astrophysics Data System (ADS)

Lahinta, A.; Haris, I.; Abdillah, T.

2017-03-01

The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

Polyelemental nanoparticle libraries.

PubMed

Chen, Peng-Cheng; Liu, Xiaolong; Hedrick, James L; Xie, Zhuang; Wang, Shunzhi; Lin, Qing-Yuan; Hersam, Mark C; Dravid, Vinayak P; Mirkin, Chad A

2016-06-24

Multimetallic nanoparticles are useful in many fields, yet there are no effective strategies for synthesizing libraries of such structures, in which architectures can be explored in a systematic and site-specific manner. The absence of these capabilities precludes the possibility of comprehensively exploring such systems. We present systematic studies of individual polyelemental particle systems, in which composition and size can be independently controlled and structure formation (alloy versus phase-separated state) can be understood. We made libraries consisting of every combination of five metallic elements (Au, Ag, Co, Cu, and Ni) through polymer nanoreactor-mediated synthesis. Important insight into the factors that lead to alloy formation and phase segregation at the nanoscale were obtained, and routes to libraries of nanostructures that cannot be made by conventional methods were developed. Copyright © 2016, American Association for the Advancement of Science.

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements.

PubMed

Richard, D; Ravigné, V; Rieux, A; Facon, B; Boyer, C; Boyer, K; Grygiel, P; Javegny, S; Terville, M; Canteros, B I; Robène, I; Vernière, C; Chabirand, A; Pruvost, O; Lefeuvre, P

2017-04-01

Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated with mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family. © 2017 John Wiley & Sons Ltd.

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

PubMed

Smith, Robin P; Riesenfeld, Samantha J; Holloway, Alisha K; Li, Qiang; Murphy, Karl K; Feliciano, Natalie M; Orecchia, Lorenzo; Oksenberg, Nir; Pollard, Katherine S; Ahituv, Nadav

2013-07-18

Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.

Structured grid technology to enable flow simulation in an integrated system environment

NASA Astrophysics Data System (ADS)

Remotigue, Michael Gerard

An application-driven Computational Fluid Dynamics (CFD) environment needs flexible and general tools to effectively solve complex problems in a timely manner. In addition, reusable, portable, and maintainable specialized libraries will aid in rapidly developing integrated systems or procedures. The presented structured grid technology enables the flow simulation for complex geometries by addressing grid generation, grid decomposition/solver setup, solution, and interpretation. Grid generation is accomplished with the graphical, arbitrarily-connected, multi-block structured grid generation software system (GUM-B) developed and presented here. GUM-B is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a solid-modeling data structure that utilizes a structured grid generation library and a geometric library based on Non-Uniform Rational B-Splines (NURBS). A presented modification of the solid-modeling data structure provides the capability for arbitrarily-connected regions between the grid blocks. The presented grid generation library provides algorithms that are reliable and accurate. GUM-B has been utilized to generate numerous structured grids for complex geometries in hydrodynamics, propulsors, and aerodynamics. The versatility of the libraries that compose GUM-B is also displayed in a prototype to automatically regenerate a grid for a free-surface solution. Grid decomposition and solver setup is accomplished with the graphical grid manipulation and repartition software system (GUMBO) developed and presented here. GUMBO is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a structured grid-tools library. The described functions within the grid-tools library reduce the possibility of human error during decomposition and setup for the numerical solver by accounting for boundary conditions and connectivity. GUMBO is linked with a flow solver interface, to the parallel UNCLE code, to provide load balancing tools and solver setup. Weeks of boundary condition and connectivity specification and validation has been reduced to hours. The UNCLE flow solver is utilized for the solution of the flow field. To accelerate convergence toward a quick engineering answer, a full multigrid (FMG) approach coupled with UNCLE, which is a full approximation scheme (FAS), is presented. The prolongation operators used in the FMG-FAS method are compared. The procedure is demonstrated on a marine propeller in incompressible flow. Interpretation of the solution is accomplished by vortex feature detection. Regions of "Intrinsic Swirl" are located by interrogating the velocity gradient tensor for complex eigenvalues. The "Intrinsic Swirl" parameter is visualized on a solution of a marine propeller to determine if any vortical features are captured. The libraries and the structured grid technology presented herein are flexible and general enough to tackle a variety of complex applications. This technology has significantly enabled the capability of the ERC personnel to effectively calculate solutions for complex geometries.

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

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

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

Identification of Useful Nanobodies by Phage Display of Immune Single Domain Libraries Derived from Camelid Heavy Chain Antibodies.

PubMed

Romao, Ema; Morales-Yanez, Francisco; Hu, Yaozhong; Crauwels, Maxine; De Pauw, Pieter; Hassanzadeh, Gholamreza Ghassanzadeh; Devoogdt, Nick; Ackaert, Chloe; Vincke, Cecile; Muyldermans, Serge

2016-01-01

The discovery of functional heavy chain-only antibodies devoid of light chains in sera of camelids and sharks in the early nineties provided access to the generation of minimal-sized, single-domain, in vivo affinity-matured, recombinant antigenbinding fragments, also known as Nanobodies. Recombinant DNA technology and adaptation of phage display vectors form the basis to construct large naïve, synthetic or medium sized immune libraries from where multiple Nanobodies have been retrieved. Alternative selection methods (i.e. bacterial display, bacterial two-hybrid, Cis-display and ribosome display) have also been developed to identify Nanobodies. The antigen affinity, stability, expression yields and structural details of the Nanobodies have been determined by standard technology. Nanobodies were subsequently engineered for higher stability and affinity, to have a sequence closer to that of human immunoglobulin domains, or to add designed effector functions. Antigen specific Nanobodies recognizing with high affinity their cognate antigen were retrieved from various libraries. High expression yields are obtained from microorganisms, even when expressed in the cytoplasm. The purified Nanobodies are shown to possess beneficial biochemical and biophysical properties. The crystal structure of Nanobody::antigen complexes reveal the preference of Nanobodies for cavities on the antigen surface. Thanks to the properties described above, Nanobodies became a highly valued and versatile tool for biomolecular research. Moreover, numerous diagnostic and therapeutic Nanobody-based applications have been developed in the past decade. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Activity-Based Profiling of a Physiologic Aglycone Library Reveals Sugar Acceptor Promiscuity of Family 1 UDP-Glucosyltransferases from Grape1[W

PubMed Central

Bönisch, Friedericke; Frotscher, Johanna; Stanitzek, Sarah; Rühl, Ernst; Wüst, Matthias; Bitz, Oliver; Schwab, Wilfried

2014-01-01

Monoterpenols serve various biological functions and accumulate in grape (Vitis vinifera), where a major fraction occurs as nonvolatile glycosides. We have screened the grape genome for sequences with similarity to terpene URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASES (UGTs) from Arabidopsis (Arabidopsis thaliana). A ripening-related expression pattern was shown for three candidates by spatial and temporal expression analyses in five grape cultivars. Transcript accumulation correlated with the production of monoterpenyl β-d-glucosides in grape exocarp during ripening and was low in vegetative tissue. Targeted functional screening of the recombinant UGTs for their biological substrates was performed by activity-based metabolite profiling (ABMP) employing a physiologic library of aglycones built from glycosides isolated from grape. This approach led to the identification of two UDP-glucose:monoterpenol β-d-glucosyltransferases. Whereas VvGT14a glucosylated geraniol, R,S-citronellol, and nerol with similar efficiency, the three allelic forms VvGT15a, VvGT15b, and VvGT15c preferred geraniol over nerol. Kinetic resolution of R,S-citronellol and R,S-linalool was shown for VvGT15a and VvGT14a, respectively. ABMP revealed geraniol as the major biological substrate but also disclosed that these UGTs may add to the production of further glycoconjugates in planta. ABMP of aglycone libraries provides a versatile tool to uncover novel biologically relevant substrates of small-molecule glycosyltransferases that often show broad sugar acceptor promiscuity. PMID:25073706

Development of a Focused Library of Triazole-Linked Privileged-Structure-Based Conjugates Leading to the Discovery of Novel Phenotypic Hits against Protozoan Parasitic Infections.

PubMed

Uliassi, Elisa; Piazzi, Lorna; Belluti, Federica; Mazzanti, Andrea; Kaiser, Marcel; Brun, Reto; Moraes, Carolina B; Freitas-Junior, Lucio H; Gul, Sheraz; Kuzikov, Maria; Ellinger, Bernhard; Borsari, Chiara; Costi, Maria Paola; Bolognesi, Maria Laura

2018-04-06

Protozoan infections caused by Plasmodium, Leishmania, and Trypanosoma spp. contribute significantly to the burden of infectious diseases worldwide, causing severe morbidity and mortality. The inadequacy of available treatments calls for cost- and time-effective drug discovery endeavors. To this end, we envisaged the triazole linkage of privileged structures as an effective drug design strategy to generate a focused library of high-quality compounds. The versatility of this approach was combined with the feasibility of a phenotypic assay, integrated with early ADME-tox profiling. Thus, an 18-membered library was efficiently assembled via Huisgen cycloaddition of phenothiazine, biphenyl, and phenylpiperazine scaffolds. The resulting 18 compounds were then tested against seven parasite strains, and counter-screened for selectivity against two mammalian cell lines. In parallel, hERG and cytochrome P450 (CYP) inhibition, and mitochondrial toxicity were assessed. Remarkably, 10-((1-(3-([1,1'-biphenyl]-3-yloxy)propyl)-1H-1,2,3-triazol-5-yl)methyl)-10H-phenothiazine (7) and 10-(3-(1-(3-([1,1'-biphenyl]-3-yloxy)propyl)-1H-1,2,3-triazol-4-yl)propyl)-10H-phenothiazine (12) showed respective IC 50 values of 1.8 and 1.9 μg mL -1 against T. cruzi, together with optimal selectivity. In particular, compound 7 showed a promising ADME-tox profile. Thus, hit 7 might be progressed as an antichagasic lead. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microplates with adaptive surfaces.

PubMed

Akbulut, Meshude; Lakshmi, Dhana; Whitcombe, Michael J; Piletska, Elena V; Chianella, Iva; Güven, Olgun; Piletsky, Sergey A

2011-11-14

Here we present a new and versatile method for the modification of the well surfaces of polystyrene microtiter plates (microplates) with poly(N-phenylethylene diamine methacrylamide), (poly-NPEDMA). The chemical grafting of poly-NPEDMA to the surface of microplates resulted in the formation of thin layers of a polyaniline derivative bearing pendant methacrylamide double bonds. These were used as the attachment point for various functional polymers through photochemical grafting of various, for example, acrylate and methacrylate, polymers with different functionalities. In a model experiment, we have modified poly-NPEDMA-coated microplates with a small library of polymers containing different functional groups using a two-step approach. In the first step, double bonds were activated by UV irradiation in the presence of N,N-diethyldithiocarbamic acid benzyl ester (iniferter). This enabled grafting of the polymer library in the second step by UV irradiation of solutions of the corresponding monomers in the microplate wells. The uniformity of coatings was confirmed spectrophotometrically, by microscopic imaging and by contact angle measurements (CA). The feasibility of the current technology has been shown by the generation of a small library of polymers grafted to the microplate well surfaces and screening of their affinity to small molecules, such as atrazine, a trio of organic dyes, and a model protein, bovine serum albumin (BSA). The stability of the polymers, reproducibility of measurement, ease of preparation, and cost-effectiveness make this approach suitable for applications in high-throughput screening in the area of materials research.

Evaluation of a Nonlinear Finite Element Program - ABAQUS.

DTIC Science & Technology

1983-03-15

anisotropic properties. * MATEXP - Linearly elastic thermal expansions with isotropic, orthotropic and anisotropic properties. * MATELG - Linearly...elastic materials for general sections (options available for beam and shell elements). • MATEXG - Linearly elastic thermal expansions for general...decomposition of a matrix. * Q-R algorithm • Vector normalization, etc. Obviously, by consolidating all the utility subroutines in a library, ABAQUS has

Design and Field Test of a Mass Efficient Crane for Lunar Payload Handling and Inspection: The Lunar Surface Manipulation System

NASA Technical Reports Server (NTRS)

Doggett, William R.; King, Bruce D.; Jones, Thomas Carno; Dorsey, John T.; Mikulas, Martin M.

2008-01-01

Devices for lifting, translating and precisely placing payloads are critical for efficient Earthbased construction operations. Both recent and past studies have demonstrated that devices with similar functionality will be needed to support lunar outpost operations. Lunar payloads include: a) prepackaged hardware and supplies which must be unloaded from landers and then accurately located at their operational site, b) sensor packages used for periodic inspection of landers, habitat surfaces, etc., and c) local materials such as regolith which require grading, excavation and placement. Although several designs have been developed for Earth based applications, these devices lack unique design characteristics necessary for transport to and use on the harsh lunar surface. These design characteristics include: a) composite components, b) compact packaging for launch, c) simple in-field reconfiguration and repair, and d) support for tele-operated or automated operations. Also, in contrast to Earth-based construction, where special purpose devices dominate a construction site, a lunar outpost will require versatile devices which provide operational benefit from initial construction through sustained operations. This paper will detail the design of a unique, high performance, versatile lifting device designed for operations on the lunar surface. The device is called the Lunar Surface Manipulation System to highlight the versatile nature of the device which supports conventional cable suspended crane operations as well as operations usually associated with a manipulator such as precise positioning where the payload is rigidly grappled by a tool attached to the tip of the device. A first generation test-bed to verify design methods and operational procedures is under development at the NASA Langley Research Center and recently completed field tests at Moses Lake Washington. The design relied on non-linear finite element analysis which is shown to correlate favorably with laboratory experiments. A key design objective, reviewed in this paper, is the device s simplicity, resulting from a focus on the minimum set of functions necessary to perform payload offload. Further development of the device has the potential for significant mass savings, with a high performance device incorporating composite elements estimated to have a mass less than 3% of the mass of the maximum lunar payload lifted at the tip. The paper will conclude with future plans for expanding the operational versatility of the device.

Advance finite element modeling of rotor blade aeroelasticity

NASA Technical Reports Server (NTRS)

Straub, F. K.; Sangha, K. B.; Panda, B.

1994-01-01

An advanced beam finite element has been developed for modeling rotor blade dynamics and aeroelasticity. This element is part of the Element Library of the Second Generation Comprehensive Helicopter Analysis System (2GCHAS). The element allows modeling of arbitrary rotor systems, including bearingless rotors. It accounts for moderately large elastic deflections, anisotropic properties, large frame motion for maneuver simulation, and allows for variable order shape functions. The effects of gravity, mechanically applied and aerodynamic loads are included. All kinematic quantities required to compute airloads are provided. In this paper, the fundamental assumptions and derivation of the element matrices are presented. Numerical results are shown to verify the formulation and illustrate several features of the element.

Mammary Cancer and Activation of Transposable Elements

DTIC Science & Technology

2015-03-01

regularly hold meetings. • Completed Y1 4-6 6. • Preliminary Methyl-MAPS analysis of pilot virgin samples • This material was never received. Based...construct the libraries for sequencing. A strategic decision was made to hold the material for validation, rather than attempt library construction. Y2 10...derived adipo- cytes and ADS-derived induced pluripotent stem cells (ADS-iPSCs) (19) and primary mouse ES cells to isolated sperm and oocytes (20). We

Developing parallel GeoFEST(P) using the PYRAMID AMR library

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Tisdale, Robert E.

2004-01-01

The PYRAMID parallel unstructured adaptive mesh refinement (AMR) library has been coupled with the GeoFEST geophysical finite element simulation tool to support parallel active tectonics simulations. Specifically, we have demonstrated modeling of coseismic and postseismic surface displacement due to a simulated Earthquake for the Landers system of interacting faults in Southern California. The new software demonstrated a 25-times resolution improvement and a 4-times reduction in time to solution over the sequential baseline milestone case. Simulations on workstations using a few tens of thousands of stress displacement finite elements can now be expanded to multiple millions of elements with greater than 98% scaled efficiency on various parallel platforms over many hundreds of processors. Our most recent work has demonstrated that we can dynamically adapt the computational grid as stress grows on a fault. In this paper, we will describe the major issues and challenges associated with coupling these two programs to create GeoFEST(P). Performance and visualization results will also be described.

High-throughput screens in mammalian cells using the CRISPR-Cas9 system.

PubMed

Peng, Jingyu; Zhou, Yuexin; Zhu, Shiyou; Wei, Wensheng

2015-06-01

As a powerful genome-editing tool, the clustered regularly interspaced short palindromic repeats (CRISPR)-clustered regularly interspaced short palindromic repeats-associated protein 9 (Cas9) system has been quickly developed into a large-scale function-based screening strategy in mammalian cells. This new type of genetic library is constructed through the lentiviral delivery of single-guide RNA collections that direct Cas9 or inactive dead Cas9 fused with effectors to interrogate gene function or regulate gene transcription in targeted cells. Compared with RNA interference screening, the CRISPR-Cas9 system demonstrates much higher levels of effectiveness and reliability with respect to both loss-of-function and gain-of-function screening. Unlike the RNA interference strategy, a CRISPR-Cas9 library can target both protein-coding sequences and regulatory elements, including promoters, enhancers and elements transcribing microRNAs and long noncoding RNAs. This powerful genetic tool will undoubtedly accelerate the mechanistic discovery of various biological processes. In this mini review, we summarize the general procedure of CRISPR-Cas9 library mediated functional screening, system optimization strategies and applications of this new genetic toolkit. © 2015 FEBS.

Modular assembly of optical nanocircuits.

PubMed

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-29

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic 'lumped' circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

Modular assembly of optical nanocircuits

NASA Astrophysics Data System (ADS)

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-01

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic ‘lumped’ circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

Boundary element based multiresolution shape optimisation in electrostatics

NASA Astrophysics Data System (ADS)

Bandara, Kosala; Cirak, Fehmi; Of, Günther; Steinbach, Olaf; Zapletal, Jan

2015-09-01

We consider the shape optimisation of high-voltage devices subject to electrostatic field equations by combining fast boundary elements with multiresolution subdivision surfaces. The geometry of the domain is described with subdivision surfaces and different resolutions of the same geometry are used for optimisation and analysis. The primal and adjoint problems are discretised with the boundary element method using a sufficiently fine control mesh. For shape optimisation the geometry is updated starting from the coarsest control mesh with increasingly finer control meshes. The multiresolution approach effectively prevents the appearance of non-physical geometry oscillations in the optimised shapes. Moreover, there is no need for mesh regeneration or smoothing during the optimisation due to the absence of a volume mesh. We present several numerical experiments and one industrial application to demonstrate the robustness and versatility of the developed approach.

Ordered versus Unordered Map for Primitive Data Types

DTIC Science & Technology

2015-09-01

mapped to some element. C++ provides two types of map containers within the standard template library, the std ::map and the std ::unordered_map...classes. As the name implies, the containers main functional difference is that the elements in the std ::map are ordered by the key, and the std ...unordered_map are not ordered based on their key. The std ::unordered_map elements are placed into “buckets” based on a hash value computed for their key

Mineral resource of the month: molybdenum

USGS Publications Warehouse

Magyar, Michael J.

2004-01-01

Molybdenum is a metallic element that is most frequently used in alloy and stainless steels, which together represent the single largest market for molybdenum. Molybdenum has also proven invaluable in carbon steel, cast iron and superalloys. Its alloying versatility is unmatched because its addition enhances material performance under high-stress conditions in expanded temperature ranges and in highly corrosive environments. The metal is also used in catalysts, other chemicals, lubricants and many other applications.

Series Fault Limiting Resistors for Atlas Marx Modules

DTIC Science & Technology

1995-07-01

use Reticulated Vitreous Carbon (RVC)2 foam blocks for the series resistor element. The blocks will serve as a resistive transmission line on the...3,4. 2. Joseph Wang, (Department of Chemistry, New Mexico State University, Las Cruces NM 88003, USA), " Reticulated Vitreous Carbon -A New Versatile...0.08 Ohm-em fitting our requirements well. The process of producing RVC results in a reproducibly refined form of continuous-fiber, vitreous Carbon

A mobility based vibroacoustic energy transmission simulation into an enclosure through a double-wall panel.

PubMed

Sahu, Atanu; Bhattacharya, Partha; Niyogi, Arup Guha; Rose, Michael

2017-06-01

Double-wall panels are known for their superior sound insulation properties over single wall panels as a sound barrier. The sound transmission phenomenon through a double-wall structure is a complex process involving vibroacoustic interaction between structural panels, the air-cushion in between, and the secondary acoustic domain. It is in this context a versatile and a fully coupled technique based on the finite-element-boundary element model is developed that enables estimation of sound transfer through a double-wall panel into an adjacent enclosure while satisfying the displacement compatibility across the interface. The contribution of individual components in the transmitted energy is identified through numerical simulations.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang; , Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2013-03-12

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G [Champaign, IL; Rogers, John A [Champaign, IL; Menard, Etienne [Durham, NC; Lee, Keon Jae [Tokyo, JP; Khang, Dahl-Young [Urbana, IL; Sun, Yugang [Westmont, IL; Meitl, Matthew [Raleigh, NC; Zhu, Zhengtao [Rapid City, SD; Ko, Heung Cho [Urbana, IL; Mack, Shawn [Goleta, CA

2011-10-18

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang, Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2010-09-21

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Fingerprinting Communication and Computation on HPC Machines

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

Peisert, Sean

2010-06-02

How do we identify what is actually running on high-performance computing systems? Names of binaries, dynamic libraries loaded, or other elements in a submission to a batch queue can give clues, but binary names can be changed, and libraries provide limited insight and resolution on the code being run. In this paper, we present a method for"fingerprinting" code running on HPC machines using elements of communication and computation. We then discuss how that fingerprint can be used to determine if the code is consistent with certain other types of codes, what a user usually runs, or what the user requestedmore » an allocation to do. In some cases, our techniques enable us to fingerprint HPC codes using runtime MPI data with a high degree of accuracy.« less

New Features in the Computational Infrastructure for Nuclear Astrophysics

NASA Astrophysics Data System (ADS)

Smith, M. S.; Lingerfelt, E. J.; Scott, J. P.; Hix, W. R.; Nesaraja, C. D.; Koura, H.; Roberts, L. F.

2006-04-01

The Computational Infrastructure for Nuclear Astrophysics is a suite of computer codes online at nucastrodata.org that streamlines the incorporation of recent nuclear physics results into astrophysical simulations. The freely-available, cross- platform suite enables users to upload cross sections and s-factors, convert them into reaction rates, parameterize the rates, store the rates in customizable libraries, setup and run custom post-processing element synthesis calculations, and visualize the results. New features include the ability for users to comment on rates or libraries using an email-type interface, a nuclear mass model evaluator, enhanced techniques for rate parameterization, better treatment of rate inverses, and creation and exporting of custom animations of simulation results. We also have online animations of r- process, rp-process, and neutrino-p process element synthesis occurring in stellar explosions.

Atmospheric particulate analysis using angular light scattering

NASA Technical Reports Server (NTRS)

Hansen, M. Z.

1980-01-01

Using the light scattering matrix elements measured by a polar nephelometer, a procedure for estimating the characteristics of atmospheric particulates was developed. A theoretical library data set of scattering matrices derived from Mie theory was tabulated for a range of values of the size parameter and refractive index typical of atmospheric particles. Integration over the size parameter yielded the scattering matrix elements for a variety of hypothesized particulate size distributions. A least squares curve fitting technique was used to find a best fit from the library data for the experimental measurements. This was used as a first guess for a nonlinear iterative inversion of the size distributions. A real index of 1.50 and an imaginary index of -0.005 are representative of the smoothed inversion results for the near ground level atmospheric aerosol in Tucson.

A portable MPI-based parallel vector template library

NASA Technical Reports Server (NTRS)

Sheffler, Thomas J.

1995-01-01

This paper discusses the design and implementation of a polymorphic collection library for distributed address-space parallel computers. The library provides a data-parallel programming model for C++ by providing three main components: a single generic collection class, generic algorithms over collections, and generic algebraic combining functions. Collection elements are the fourth component of a program written using the library and may be either of the built-in types of C or of user-defined types. Many ideas are borrowed from the Standard Template Library (STL) of C++, although a restricted programming model is proposed because of the distributed address-space memory model assumed. Whereas the STL provides standard collections and implementations of algorithms for uniprocessors, this paper advocates standardizing interfaces that may be customized for different parallel computers. Just as the STL attempts to increase programmer productivity through code reuse, a similar standard for parallel computers could provide programmers with a standard set of algorithms portable across many different architectures. The efficacy of this approach is verified by examining performance data collected from an initial implementation of the library running on an IBM SP-2 and an Intel Paragon.

A Portable MPI-Based Parallel Vector Template Library

NASA Technical Reports Server (NTRS)

Sheffler, Thomas J.

1995-01-01

This paper discusses the design and implementation of a polymorphic collection library for distributed address-space parallel computers. The library provides a data-parallel programming model for C + + by providing three main components: a single generic collection class, generic algorithms over collections, and generic algebraic combining functions. Collection elements are the fourth component of a program written using the library and may be either of the built-in types of c or of user-defined types. Many ideas are borrowed from the Standard Template Library (STL) of C++, although a restricted programming model is proposed because of the distributed address-space memory model assumed. Whereas the STL provides standard collections and implementations of algorithms for uniprocessors, this paper advocates standardizing interfaces that may be customized for different parallel computers. Just as the STL attempts to increase programmer productivity through code reuse, a similar standard for parallel computers could provide programmers with a standard set of algorithms portable across many different architectures. The efficacy of this approach is verified by examining performance data collected from an initial implementation of the library running on an IBM SP-2 and an Intel Paragon.

Identification of genes differentially expressed in association with acquired cisplatin resistance

PubMed Central

Johnsson, A; Zeelenberg, I; Min, Y; Hilinski, J; Berry, C; Howell, S B; Los, G

2000-01-01

The goal of this study was to identify genes whose mRNA levels are differentially expressed in human cells with acquired cisplatin (cDDP) resistance. Using the parental UMSCC10b head and neck carcinoma cell line and the 5.9-fold cDDP-resistant subline, UMSCC10b/Pt-S15, two suppressive subtraction hybridization (SSH) cDNA libraries were prepared. One library represented mRNAs whose levels were increased in the cDDP resistant variant (the UP library), the other one represented mRNAs whose levels were decreased in the resistant cells (the DOWN library). Arrays constructed with inserts recovered from these libraries were hybridized with SSH products to identify truly differentially expressed elements. A total of 51 cDNA fragments present in the UP library and 16 in the DOWN library met the criteria established for differential expression. The sequences of 87% of these cDNA fragments were identified in Genbank. Among the mRNAs in the UP library that were frequently isolated and that showed high levels of differential expression were cytochrome oxidase I, ribosomal protein 28S, elongation factor 1α, α-enolase, stathmin, and HSP70. The approach taken in this study permitted identification of many genes never before linked to the cDDP-resistant phenotype. © 2000 Cancer Research Campaign PMID:10993653

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

PubMed Central

Rise, Matthew L.; von Schalburg, Kristian R.; Brown, Gordon D.; Mawer, Melanie A.; Devlin, Robert H.; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A. Ross; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A.; Nelson, Colleen; Jones, Simon R.M.; Smailus, Duane E.; Jones, Steven J.M.; Schein, Jacqueline E.; Marra, Marco A.; Butterfield, Yaron S.N.; Stott, Jeff M.; Ng, Siemon H.S.; Davidson, William S.; Koop, Ben F.

2004-01-01

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3′ sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids. PMID:14962987

Engineering Plasmonic Nanocrystal Coupling through Template-Assisted Self-Assembly

NASA Astrophysics Data System (ADS)

Greybush, Nicholas J.

The construction of materials from nanocrystal building blocks represents a powerful new paradigm for materials design. Just as nature's materials orchestrate intricate combinations of atoms from the library of the periodic table, nanocrystal "metamaterials" integrate individual nanocrystals into larger architectures with emergent collective properties. The individual nanocrystal "meta-atoms" that make up these materials are themselves each a nanoscale atomic system with tailorable size, shape, and elemental composition, enabling the creation of hierarchical materials with predesigned structure at multiple length scales. However, an improved fundamental understanding of the interactions among individual nanocrystals is needed in order to translate this structural control into enhanced functionality. The ability to form precise arrangements of nanocrystals and measure their collective properties is therefore essential for the continued development of nanocrystal metamaterials. In this dissertation, we utilize template-assisted self-assembly and spatially-resolved spectroscopy to form and characterize individual nanocrystal oligomers. At the intersection of "top-down" and "bottom-up" nanoscale patterning schemes, template-assisted self-assembly combines the design freedom of lithography with the chemical control of colloidal synthesis to achieve unique nanocrystal configurations. Here, we employ shape-selective templates to assemble new plasmonic structures, including heterodimers of Au nanorods and upconversion phosphors, a series of hexagonally-packed Au nanocrystal oligomers, and triangular formations of Au nanorods. Through experimental analysis and numerical simulation, we elucidate the means through which inter-nanocrystal coupling imparts collective optical properties to the plasmonic assemblies. Our self-assembly and measurement strategy offers a versatile platform for exploring optical interactions in a wide range of material systems and application areas.

Development of Finite Elements for Two-Dimensional Structural Analysis Using the Integrated Force Method

NASA Technical Reports Server (NTRS)

Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

1996-01-01

The Integrated Force Method has been developed in recent years for the analysis of structural mechanics problems. This method treats all independent internal forces as unknown variables that can be calculated by simultaneously imposing equations of equilibrium and compatibility conditions. In this paper a finite element library for analyzing two-dimensional problems by the Integrated Force Method is presented. Triangular- and quadrilateral-shaped elements capable of modeling arbitrary domain configurations are presented. The element equilibrium and flexibility matrices are derived by discretizing the expressions for potential and complementary energies, respectively. The displacement and stress fields within the finite elements are independently approximated. The displacement field is interpolated as it is in the standard displacement method, and the stress field is approximated by using complete polynomials of the correct order. A procedure that uses the definitions of stress components in terms of an Airy stress function is developed to derive the stress interpolation polynomials. Such derived stress fields identically satisfy the equations of equilibrium. Moreover, the resulting element matrices are insensitive to the orientation of local coordinate systems. A method is devised to calculate the number of rigid body modes, and the present elements are shown to be free of spurious zero-energy modes. A number of example problems are solved by using the present library, and the results are compared with corresponding analytical solutions and with results from the standard displacement finite element method. The Integrated Force Method not only gives results that agree well with analytical and displacement method results but also outperforms the displacement method in stress calculations.

Ion beam production and study of radioactive isotopes with the laser ion source at ISOLDE

NASA Astrophysics Data System (ADS)

Fedosseev, Valentin; Chrysalidis, Katerina; Day Goodacre, Thomas; Marsh, Bruce; Rothe, Sebastian; Seiffert, Christoph; Wendt, Klaus

2017-08-01

At ISOLDE the majority of radioactive ion beams are produced using the resonance ionization laser ion source (RILIS). This ion source is based on resonant excitation of atomic transitions by wavelength tunable laser radiation. Since its installation at the ISOLDE facility in 1994, the RILIS laser setup has been developed into a versatile remotely operated laser system comprising state-of-the-art solid state and dye lasers capable of generating multiple high quality laser beams at any wavelength in the range of 210-950 nm. A continuous programme of atomic ionization scheme development at CERN and at other laboratories has gradually increased the number of RILIS-ionized elements. At present, isotopes of 40 different elements have been selectively laser-ionized by the ISOLDE RILIS. Studies related to the optimization of the laser-atom interaction environment have yielded new laser ion source types: the laser ion source and trap and the versatile arc discharge and laser ion source. Depending on the specific experimental requirements for beam purity or versatility to switch between different ionization mechanisms, these may offer a favourable alternative to the standard hot metal cavity configuration. In addition to its main purpose of ion beam production, the RILIS is used for laser spectroscopy of radioisotopes. In an ongoing experimental campaign the isotope shifts and hyperfine structure of long isotopic chains have been measured by the extremely sensitive in-source laser spectroscopy method. The studies performed in the lead region were focused on nuclear deformation and shape coexistence effects around the closed proton shell Z = 82. The paper describes the functional principles of the RILIS, the current status of the laser system and demonstrated capabilities for the production of different ion beams including the high-resolution studies of short-lived isotopes and other applications of RILIS lasers for ISOLDE experiments. This article belongs to the Focus on Exotic Beams at ISOLDE: A Laboratory Portrait special issue.

Computational design of chimeric protein libraries for directed evolution.

PubMed

Silberg, Jonathan J; Nguyen, Peter Q; Stevenson, Taylor

2010-01-01

The best approach for creating libraries of functional proteins with large numbers of nondisruptive amino acid substitutions is protein recombination, in which structurally related polypeptides are swapped among homologous proteins. Unfortunately, as more distantly related proteins are recombined, the fraction of variants having a disrupted structure increases. One way to enrich the fraction of folded and potentially interesting chimeras in these libraries is to use computational algorithms to anticipate which structural elements can be swapped without disturbing the integrity of a protein's structure. Herein, we describe how the algorithm Schema uses the sequences and structures of the parent proteins recombined to predict the structural disruption of chimeras, and we outline how dynamic programming can be used to find libraries with a range of amino acid substitution levels that are enriched in variants with low Schema disruption.

Little by Little Does the Trick: Design and Construction of a Discrete Event Agent-Based Simulation Framework

DTIC Science & Technology

2007-12-01

model. Finally, we build a small agent-based model using the component architecture to demonstrate the library’s functionality. 15. NUMBER OF...and a Behavioral model. Finally, we build a small agent-based model using the component architecture to demonstrate the library’s functionality...prototypes an architectural design which is generalizable, reusable, and extensible. We have created an initial set of model elements that demonstrate

MPSalsa Version 1.5: A Finite Element Computer Program for Reacting Flow Problems: Part 1 - Theoretical Development

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

Devine, K.D.; Hennigan, G.L.; Hutchinson, S.A.

1999-01-01

The theoretical background for the finite element computer program, MPSalsa Version 1.5, is presented in detail. MPSalsa is designed to solve laminar or turbulent low Mach number, two- or three-dimensional incompressible and variable density reacting fluid flows on massively parallel computers, using a Petrov-Galerkin finite element formulation. The code has the capability to solve coupled fluid flow (with auxiliary turbulence equations), heat transport, multicomponent species transport, and finite-rate chemical reactions, and to solve coupled multiple Poisson or advection-diffusion-reaction equations. The program employs the CHEMKIN library to provide a rigorous treatment of multicomponent ideal gas kinetics and transport. Chemical reactions occurringmore » in the gas phase and on surfaces are treated by calls to CHEMKIN and SURFACE CHEMK3N, respectively. The code employs unstructured meshes, using the EXODUS II finite element database suite of programs for its input and output files. MPSalsa solves both transient and steady flows by using fully implicit time integration, an inexact Newton method and iterative solvers based on preconditioned Krylov methods as implemented in the Aztec. solver library.« less

36 CFR 72.45 - Fundable elements: Innovation grants.

Code of Federal Regulations, 2011 CFR

2011-07-01

...., schools, community centers, libraries; unique program expansions or increases in services; purchase of... must be open to the public, incorporate some activities for the general population, and address needs...

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing.

PubMed

Cooper, James; Ding, Yi; Song, Jiuzhou; Zhao, Keji

2017-11-01

Increased chromatin accessibility is a feature of cell-type-specific cis-regulatory elements; therefore, mapping of DNase I hypersensitive sites (DHSs) enables the detection of active regulatory elements of transcription, including promoters, enhancers, insulators and locus-control regions. Single-cell DNase sequencing (scDNase-seq) is a method of detecting genome-wide DHSs when starting with either single cells or <1,000 cells from primary cell sources. This technique enables genome-wide mapping of hypersensitive sites in a wide range of cell populations that cannot be analyzed using conventional DNase I sequencing because of the requirement for millions of starting cells. Fresh cells, formaldehyde-cross-linked cells or cells recovered from formalin-fixed paraffin-embedded (FFPE) tissue slides are suitable for scDNase-seq assays. To generate scDNase-seq libraries, cells are lysed and then digested with DNase I. Circular carrier plasmid DNA is included during subsequent DNA purification and library preparation steps to prevent loss of the small quantity of DHS DNA. Libraries are generated for high-throughput sequencing on the Illumina platform using standard methods. Preparation of scDNase-seq libraries requires only 2 d. The materials and molecular biology techniques described in this protocol should be accessible to any general molecular biology laboratory. Processing of high-throughput sequencing data requires basic bioinformatics skills and uses publicly available bioinformatics software.

Semi-Automatic Modelling of Building FAÇADES with Shape Grammars Using Historic Building Information Modelling

NASA Astrophysics Data System (ADS)

Dore, C.; Murphy, M.

2013-02-01

This paper outlines a new approach for generating digital heritage models from laser scan or photogrammetric data using Historic Building Information Modelling (HBIM). HBIM is a plug-in for Building Information Modelling (BIM) software that uses parametric library objects and procedural modelling techniques to automate the modelling stage. The HBIM process involves a reverse engineering solution whereby parametric interactive objects representing architectural elements are mapped onto laser scan or photogrammetric survey data. A library of parametric architectural objects has been designed from historic manuscripts and architectural pattern books. These parametric objects were built using an embedded programming language within the ArchiCAD BIM software called Geometric Description Language (GDL). Procedural modelling techniques have been implemented with the same language to create a parametric building façade which automatically combines library objects based on architectural rules and proportions. Different configurations of the façade are controlled by user parameter adjustment. The automatically positioned elements of the façade can be subsequently refined using graphical editing while overlaying the model with orthographic imagery. Along with this semi-automatic method for generating façade models, manual plotting of library objects can also be used to generate a BIM model from survey data. After the 3D model has been completed conservation documents such as plans, sections, elevations and 3D views can be automatically generated for conservation projects.

The MHOST finite element program: 3-D inelastic analysis methods for hot section components. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Nakazawa, Shohei

1989-01-01

The user options available for running the MHOST finite element analysis package is described. MHOST is a solid and structural analysis program based on the mixed finite element technology, and is specifically designed for 3-D inelastic analysis. A family of 2- and 3-D continuum elements along with beam and shell structural elements can be utilized, many options are available in the constitutive equation library, the solution algorithms and the analysis capabilities. The outline of solution algorithms is discussed along with the data input and output, analysis options including the user subroutines and the definition of the finite elements implemented in the program package.

Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.

PubMed

Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian

2008-04-24

Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.

Rapid development of medical imaging tools with open-source libraries.

PubMed

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Pass-transistor very large scale integration

NASA Technical Reports Server (NTRS)

Maki, Gary K. (Inventor); Bhatia, Prakash R. (Inventor)

2004-01-01

Logic elements are provided that permit reductions in layout size and avoidance of hazards. Such logic elements may be included in libraries of logic cells. A logical function to be implemented by the logic element is decomposed about logical variables to identify factors corresponding to combinations of the logical variables and their complements. A pass transistor network is provided for implementing the pass network function in accordance with this decomposition. The pass transistor network includes ordered arrangements of pass transistors that correspond to the combinations of variables and complements resulting from the logical decomposition. The logic elements may act as selection circuits and be integrated with memory and buffer elements.

Validation of Hansen-Roach library for highly enriched uranium metal systems

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

Wenz, T.R.; Busch, R.D.

The Hansen-Roach 16-group cross-section library has been validated for use in pure uranium metal systems by modeling the Godiva critical assembly using the neutronics transport theory code ONEDANT to perform effective multiplication factor (k{sub eff}) calculations. The cross-section library used contains data for 118 isotopes (34 unique elements), including the revised cross sections for {sup 235}U and {sup 238}U. The Godiva critical assembly is a 17.4-cm sphere composed of 93.7 wt% {sup 235}U, 1.0 wt% {sup 234}U, and 5.3 wt% {sup 238}U with an effective homogeneous density of 18.7 g/cm{sup 3}.

Documentation for the machine-readable version of A Library of Stellar Spectra (Jacoby, Hunter and Christian 1984)

NASA Technical Reports Server (NTRS)

Warren, W. H., Jr.

1984-01-01

The machine readable library as it is currently being distributed from the Astronomical Data Center is described. The library contains digital spectral for 161 stars of spectral classes O through M and luminosity classes 1, 3 and 5 in the wavelength range 3510 A to 7427 A. The resolution is approximately 4.5 A, while the typical photometric uncertainty of each resolution element is approximately 1 percent and broadband variations are 3 percent. The documentation includes a format description, a table of the indigenous characteristics of the magnetic tape file, and a sample listing of logical records exactly as they are recorded on the tape.

Modular Affective Reasoning-Based Versatile Introspective Architecture (MARVIN)

DTIC Science & Technology

2008-08-14

monolithic kernels found in most mass market OSs, where these kinds of system processes run within the kernel , and thus need to be highly optimized as well as...without modifying pre- existing process management elements, we expect the process of transitioning this component from MINIX to monolithic kernels to...necessary to incorporate them into a monolithic kernel . To demonstrate how the APMM would work in practice, we used it as the basis for building a simulated

Particle Tracking Model Transport Process Verification: Diffusion Algorithm

DTIC Science & Technology

2015-07-01

sediment densities in space and time along with final particle fates (Demirbilek et al. 2004; Davies et al. 2005; McDonald et al. 2006; Lackey and... McDonald 2007). Although a versatile model currently utilized in various coastal, estuarine, and riverine applications, PTM is specifically designed to...Algorithm 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7

MHOST version 4.2. Volume 1: Users' manual

NASA Technical Reports Server (NTRS)

Nakazawa, Shohei

1989-01-01

This manual describes the user options available for running the MHOST finite element analysis package. MHOST is a solid and structural analysis program based on mixed finite element technology, and is specifically designed for three-dimensional inelastic analysis. A family of two- and three-dimensional continuum elements along with beam and shell structural elements can be utilized. Many options are available in the constitutive equation library, the solution algorithms and the analysis capabilities. An overview of the algorithms, a general description of the input data formats, and a discussion of input data for selecting solution algorithms are given.

Development of CCSDS DCT to Support Spacecraft Dynamic Events

NASA Technical Reports Server (NTRS)

Sidhwa, Anahita F

2011-01-01

This report discusses the development of Consultative Committee for Space Data Systems (CCSDS) Design Control Table (DCT) to support spacecraft dynamic events. The Consultative Committee for Space Data Systems (CCSDS) Design Control Table (DCT) is a versatile link calculation tool to analyze different kinds of radio frequency links. It started out as an Excel-based program, and is now being evolved into a Mathematica-based link analysis tool. The Mathematica platform offers a rich set of advanced analysis capabilities, and can be easily extended to a web-based architecture. Last year the CCSDS DCT's for the uplink, downlink, two-way, and ranging models were developed as well as the corresponding input and output interfaces. Another significant accomplishment is the integration of the NAIF SPICE library into the Mathematica computation platform.

Machine learning for neuroimaging with scikit-learn.

PubMed

Abraham, Alexandre; Pedregosa, Fabian; Eickenberg, Michael; Gervais, Philippe; Mueller, Andreas; Kossaifi, Jean; Gramfort, Alexandre; Thirion, Bertrand; Varoquaux, Gaël

2014-01-01

Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain.

Machine learning for neuroimaging with scikit-learn

PubMed Central

Abraham, Alexandre; Pedregosa, Fabian; Eickenberg, Michael; Gervais, Philippe; Mueller, Andreas; Kossaifi, Jean; Gramfort, Alexandre; Thirion, Bertrand; Varoquaux, Gaël

2014-01-01

Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain. PMID:24600388

MUTILS - a set of efficient modeling tools for multi-core CPUs implemented in MEX

NASA Astrophysics Data System (ADS)

Krotkiewski, Marcin; Dabrowski, Marcin

2013-04-01

The need for computational performance is common in scientific applications, and in particular in numerical simulations, where high resolution models require efficient processing of large amounts of data. Especially in the context of geological problems the need to increase the model resolution to resolve physical and geometrical complexities seems to have no limits. Alas, the performance of new generations of CPUs does not improve any longer by simply increasing clock speeds. Current industrial trends are to increase the number of computational cores. As a result, parallel implementations are required in order to fully utilize the potential of new processors, and to study more complex models. We target simulations on small to medium scale shared memory computers: laptops and desktop PCs with ~8 CPU cores and up to tens of GB of memory to high-end servers with ~50 CPU cores and hundereds of GB of memory. In this setting MATLAB is often the environment of choice for scientists that want to implement their own models with little effort. It is a useful general purpose mathematical software package, but due to its versatility some of its functionality is not as efficient as it could be. In particular, the challanges of modern multi-core architectures are not fully addressed. We have developed MILAMIN 2 - an efficient FEM modeling environment written in native MATLAB. Amongst others, MILAMIN provides functions to define model geometry, generate and convert structured and unstructured meshes (also through interfaces to external mesh generators), compute element and system matrices, apply boundary conditions, solve the system of linear equations, address non-linear and transient problems, and perform post-processing. MILAMIN strives to combine the ease of code development and the computational efficiency. Where possible, the code is optimized and/or parallelized within the MATLAB framework. Native MATLAB is augmented with the MUTILS library - a set of MEX functions that implement the computationally intensive, performance critical parts of the code, which we have identified to be bottlenecks. Here, we discuss the functionality and performance of the MUTILS library. Currently, it includes: 1. time and memory efficient assembly of sparse matrices for FEM simulations 2. parallel sparse matrix - vector product with optimizations speficic to symmetric matrices and multiple degrees of freedom per node 3. parallel point in triangle location and point in tetrahedron location for unstructured, adaptive 2D and 3D meshes (useful for 'marker in cell' type of methods) 4. parallel FEM interpolation for 2D and 3D meshes of elements of different types and orders, and for different number of degrees of freedom per node 5. a stand-alone, MEX implementation of the Conjugate Gradients iterative solver 6. interface to METIS graph partitioning and a fast implementation of RCM reordering

Local phase method for designing and optimizing metasurface devices.

PubMed

Hsu, Liyi; Dupré, Matthieu; Ndao, Abdoulaye; Yellowhair, Julius; Kanté, Boubacar

2017-10-16

Metasurfaces have attracted significant attention due to their novel designs for flat optics. However, the approach usually used to engineer metasurface devices assumes that neighboring elements are identical, by extracting the phase information from simulations with periodic boundaries, or that near-field coupling between particles is negligible, by extracting the phase from single particle simulations. This is not the case most of the time and the approach thus prevents the optimization of devices that operate away from their optimum. Here, we propose a versatile numerical method to obtain the phase of each element within the metasurface (meta-atoms) while accounting for near-field coupling. Quantifying the phase error of each element of the metasurfaces with the proposed local phase method paves the way to the design of highly efficient metasurface devices including, but not limited to, deflectors, high numerical aperture metasurface concentrators, lenses, cloaks, and modulators.

An Autonomous BMP2 Regulatory Element in Mesenchymal Cells

PubMed Central

Kruithof, Boudewijn P.T.; Fritz, David T.; Liu, Yijun; Garsetti, Diane E.; Frank, David B.; Pregizer, Steven K.; Gaussin, Vinciane; Mortlock, Douglas P.; Rogers, Melissa B.

2014-01-01

BMP2 is a morphogen that controls mesenchymal cell differentiation and behavior. For example, BMP2 concentration controls the differentiation of mesenchymal precursors into myocytes, adipocytes, chondrocytes, and osteoblasts. Sequences within the 3′untranslated region (UTR) of the Bmp2 mRNA mediate a post-transcriptional block of protein synthesis. Interaction of cell and developmental stage-specific trans-regulatory factors with the 3′UTR is a nimble and versatile mechanism for modulating this potent morphogen in different cell types. We show here, that an ultra-conserved sequence in the 3′UTR functions independently of promoter, coding region, and 3′UTR context in primary and immortalized tissue culture cells and in transgenic mice. Our findings indicate that the ultra-conserved sequence is an autonomously functioning post-transcriptional element that may be used to modulate the level of BMP2 and other proteins while retaining tissue specific regulatory elements. PMID:21268088

Investigations of calcium spectral lines in laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Ching, Sim Yit; Tariq, Usman; Haider, Zuhaib; Tufail, Kashif; Sabri, Salwanie; Imran, Muhammad; Ali, Jalil

2017-03-01

Laser-induced breakdown spectroscopy (LIBS) is a direct and versatile analytical technique that performs the elemental composition analysis based on optical emission produced by laser induced-plasma, with a little or no sample preparation. The performance of the LIBS technique relies on the choice of experimental conditions which must be thoroughly explored and optimized for each application. The main parameters affecting the LIBS performance are the laser energy, laser wavelength, pulse duration, gate delay, geometrical set-up of the focusing and collecting optics. In LIBS quantitative analysis, the gate delay and laser energy are very important parameters that have pronounced impact on the accuracy of the elemental composition information of the materials. The determination of calcium elements in the pelletized samples was investigated and served for the purpose of optimizing the gate delay and laser energy by studying and analyzing the results from emission intensities collected and signal to background ratio (S/B) for the specified wavelengths.

Thermophysical Properties of Energetic Ionic Liquids/Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations

DTIC Science & Technology

2013-01-01

W L. Physical properties of concentrated nitric acid . UNT Digital Library. http://digital.library.unt.edu/ark:/67531/metadc56640/.) 23 M. Engelmann... Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations 5a. CONTRACT NUMBER FA9300-11-C-3012 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Rev. 8-98) Prescribed by ANSI Std. 239.18 1     Thermophysical  Properties  of  Energetic  Ionic  Liquids/ Nitric   Acid

Application of a Silicon Compiler to VLSI (Very Large Scale Integrated Circuits) Design of Digital Pipelined Multipliers.

DTIC Science & Technology

1984-06-01

programming environment and then dumped, as described in the Franz Lisp manual [Ref. 13]. A synopsis of the functional elements which make up this LISP...the average system usage rate. Lines i4 and 15 reflect a function of Franz Lisp wherein past used storage locations are reclaimed for the available... Franz Lisp Opus 38. Also included in this distribu- tion are two library files containing the bonding Fad a layouts in CIF, and a library file

Into the Curriculum. Reading/Language Arts: Three Little Kittens and the Lost Mittens; Reading/Language Arts: A Caldecott Archaeological Dig; Science: Discovering the Periodic Table of Elements; Science: The Red-Eyed Tree Frog Jumps into Nonfiction; Social Studies: Our Nation's Beginnings-Jamestown and Plymouth Settlements.

ERIC Educational Resources Information Center

Cherry, Carolyn; Louk, Cathy; Barwick, Martha; Kidd, Gentry E.

2001-01-01

Provides five fully developed school library media activities that are designed for use with specific curriculum units in reading/language arts, science, and social studies. Library media skills objectives, curriculum (subject area) objectives, grade levels, resources, instructional roles, activity and procedures for completion, evaluation, and…

EXODUS II: A finite element data model

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

Schoof, L.A.; Yarberry, V.R.

1994-09-01

EXODUS II is a model developed to store and retrieve data for finite element analyses. It is used for preprocessing (problem definition), postprocessing (results visualization), as well as code to code data transfer. An EXODUS II data file is a random access, machine independent, binary file that is written and read via C, C++, or Fortran library routines which comprise the Application Programming Interface (API).

Trace Elements: What They Do and Where to Get Them

MedlinePlus

... Daily Conferences Fellowships and Residencies School of Perfusion Technology Education Resources Library & Learning Resource Center CME Resources THI Journal THI Cardiac Society Save the Date: International Symposium on Cardiovascular Regenerative ...

Earthdata User Interface Patterns: Building Usable Web Interfaces Through a Shared UI Pattern Library

NASA Astrophysics Data System (ADS)

Siarto, J.

2014-12-01

As more Earth science software tools and services move to the web--the design and usability of those tools become ever more important. A good user interface is becoming expected and users are becoming increasingly intolerant of websites and web applications that work against them. The Earthdata UI Pattern Library attempts to give these scientists and developers the design tools they need to make usable, compelling user interfaces without the associated overhead of using a full design team. Patterns are tested and functional user interface elements targeted specifically at the Earth science community and will include web layouts, buttons, tables, typography, iconography, mapping and visualization/graphing widgets. These UI elements have emerged as the result of extensive user testing, research and software development within the NASA Earthdata team over the past year.

Evolution of Scientific and Technical Information Distribution

NASA Technical Reports Server (NTRS)

Esler, Sandra; Nelson, Michael L.

1998-01-01

World Wide Web (WWW) and related information technologies are transforming the distribution of scientific and technical information (STI). We examine 11 recent, functioning digital libraries focusing on the distribution of STI publications, including journal articles, conference papers, and technical reports. We introduce 4 main categories of digital library projects: based on the architecture (distributed vs. centralized) and the contributor (traditional publisher vs. authoring individual/organization). Many digital library prototypes merely automate existing publishing practices or focus solely on the digitization of the publishing cycle output, not sampling and capturing elements of the input. Still others do not consider for distribution the large body of "gray literature." We address these deficiencies in the current model of STI exchange by suggesting methods for expanding the scope and target of digital libraries by focusing on a greater source of technical publications and using "buckets," an object-oriented construct for grouping logically related information objects, to include holdings other than technical publications.

Predicting novel substrates for enzymes with minimal experimental effort with active learning

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

Pertusi, Dante A.; Moura, Matthew E.; Jeffryes, James G.

Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. To demonstrate this, we used existing studies and tested compounds for four different enzymes,more » developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of similar to 80% using similar to 33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. The application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways.« less

JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules

PubMed Central

Blurock, Edward; Warth, V.; Grandmougin, X.; Bounaceur, R.; Glaude, P.A.; Battin-Leclerc, F.

2013-01-01

JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML. PMID:23761949

Monolithic composite “pressure + acceleration + temperature + infrared” sensor using a versatile single-sided “SiN/Poly-Si/Al” process-module.

PubMed

Ni, Zao; Yang, Chen; Xu, Dehui; Zhou, Hong; Zhou, Wei; Li, Tie; Xiong, Bin; Li, Xinxin

2013-01-16

We report a newly developed design/fabrication module with low-cost single-sided "low-stress-silicon-nitride (LS-SiN)/polysilicon (poly-Si)/Al" process for monolithic integration of composite sensors for sensing-network-node applications. A front-side surface-/bulk-micromachining process on a conventional Si-substrate is developed, featuring a multifunctional SiN/poly-Si/Al layer design for diverse sensing functions. The first "pressure + acceleration + temperature + infrared" (PATIR) composite sensor with the chip size of 2.5 mm × 2.5 mm is demonstrated. Systematic theoretical design and analysis methods are developed. The diverse sensing components include a piezoresistive absolute-pressure sensor (up to 700 kPa, with a sensitivity of 49 mV/MPa under 3.3 V supplied voltage), a piezoresistive accelerometer (±10 g, with a sensitivity of 66 μV/g under 3.3 V and a -3 dB bandwidth of 780 Hz), a thermoelectric infrared detector (with a responsivity of 45 V/W and detectivity of 3.6 × 107 cm·Hz1/2/W) and a thermistor (-25-120 °C). This design/fabrication module concept enables a low-cost monolithically-integrated "multifunctional-library" technique. It can be utilized as a customizable tool for versatile application-specific requirements, which is very useful for small-size, low-cost, large-scale sensing-network node developments.

Predicting novel substrates for enzymes with minimal experimental effort with active learning.

PubMed

Pertusi, Dante A; Moura, Matthew E; Jeffryes, James G; Prabhu, Siddhant; Walters Biggs, Bradley; Tyo, Keith E J

2017-11-01

Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. To demonstrate this, we used existing studies and tested compounds for four different enzymes, developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of ~80% using ~33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. The application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing

PubMed Central

Budiman, Muhammad A.; Mao, Long; Wood, Todd C.; Wing, Rod A.

2000-01-01

Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed characterization of a 15.0 haploid genome equivalent BAC library for the cultivated tomato, Lycopersicon esculentum cv. Heinz 1706. The library contains 129,024 clones with an average insert size of 117.5 kb and a chloroplast content of 1.11%. BAC end sequences from 1490 ends were generated and analyzed as a preliminary evaluation for using this library to develop an STC framework to sequence the tomato genome. A total of 1205 BAC end sequences (80.9%) were obtained, with an average length of 360 high-quality bases, and were searched against the GenBank database. Using a cutoff expectation value of <10−6, and combining the results from BLASTN, BLASTX, and TBLASTX searches, 24.3% of the BAC end sequences were similar to known sequences, of which almost half (48.7%) share sequence similarities to retrotransposons and 7% to known genes. Some of the transposable element sequences were the first reported in tomato, such as sequences similar to maize transposon Activator (Ac) ORF and tobacco pararetrovirus-like sequences. Interestingly, there were no BAC end sequences similar to the highly repeated TGRI and TGRII elements. However, the majority (70.3%) of STCs did not share significant sequence similarities to any sequences in GenBank at either the DNA or predicted protein levels, indicating that a large portion of the tomato genome is still unknown. Our data demonstrate that this BAC library is suitable for developing an STC database to sequence the tomato genome. The advantages of developing an STC framework for whole-genome sequencing of tomato are discussed. [The BAC end sequences described in this paper have been deposited in the GenBank data library under accession nos. AQ367111–AQ368361.] PMID:10645957

CGNS Mid-Level Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Poirier, Diane; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: - The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media; - The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; - The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and - The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The CGNS Mid-level Library was designed to ease the implementation of CGNS by providing developers with a collection of handy I/O functions. Since knowledge of the ADF core is not required to use this library, it will greatly facilitate the task of interfacing with CGNS. There are currently 48 user callable functions that comprise the Mid-level library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Element sensitive reconstruction of nanostructured surfaces with finite elements and grazing incidence soft X-ray fluorescence.

PubMed

Soltwisch, Victor; Hönicke, Philipp; Kayser, Yves; Eilbracht, Janis; Probst, Jürgen; Scholze, Frank; Beckhoff, Burkhard

2018-03-29

The geometry of a Si3N4 lamellar grating was investigated experimentally with reference-free grazing-incidence X-ray fluorescence analysis. While simple layered systems are usually treated with the matrix formalism to determine the X-ray standing-wave field, this approach fails for laterally structured surfaces. Maxwell solvers based on finite elements are often used to model electrical field strengths for any 2D or 3D structures in the optical spectral range. We show that this approach can also be applied in the field of X-rays. The electrical field distribution obtained with the Maxwell solver can subsequently be used to calculate the fluorescence intensities in full analogy to the X-ray standing-wave field obtained by the matrix formalism. Only the effective 1D integration for the layer system has to be replaced by a 2D integration of the finite elements, taking into account the local excitation conditions. We will show that this approach is capable of reconstructing the geometric line shape of a structured surface with high elemental sensitivity. This combination of GIXRF and finite-element simulations paves the way for a versatile characterization of nanoscale-structured surfaces.

Atomistic Modeling of Nanostructures via the BFS Quantum Approximate Method

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Garces, Jorge E.; Noebe, Ronald D.; Farias, D.

2003-01-01

Ideally, computational modeling techniques for nanoscopic physics would be able to perform free of limitations on the type and number of elements, while providing comparable accuracy when dealing with bulk or surface problems. Computational efficiency is also desirable, if not mandatory, for properly dealing with the complexity of typical nano-strucured systems. A quantum approximate technique, the BFS method for alloys, which attempts to meet these demands, is introduced for the calculation of the energetics of nanostructures. The versatility of the technique is demonstrated through analysis of diverse systems, including multi-phase precipitation in a five element Ni-Al-Ti-Cr-Cu alloy and the formation of mixed composition Co-Cu islands on a metallic Cu(III) substrate.

An adaptive interferometer for optical testing .

NASA Astrophysics Data System (ADS)

Pariani, G.; Colella, L.; Bertarelli, C.; Aliverti, M.; Riva, M.; Bianco, A.

Interferometry is a well-established technique to test optical elements. However, its use is challenging in the case of free-form and aspheric elements, due to the lack of the reference optics. The proposed idea concerns the development of a versatile interferometer, where its reference arm is equipped with a reprogrammable Computer Generated Hologram. This principle takes advantage from our study on photochromic materials for optical applications, which shows a strong and reversible modulation of transparency in the visible region. The encoding of the desired hologram can be done off-line, or directly into the interferometer, and different patterns may be realized sequentially after the erasing of the previous hologram. We report on the present state of the research and on the future perspectives. skip=5pt

Nickel Base Superalloy Turbine Disk

NASA Technical Reports Server (NTRS)

Gabb, Timothy P. (Inventor); Gauda, John (Inventor); Telesman, Ignacy (Inventor); Kantzos, Pete T. (Inventor)

2005-01-01

A low solvus, high refractory alloy having unusually versatile processing mechanical property capabilities for advanced disks and rotors in gas turbine engines. The nickel base superalloy has a composition consisting essentially of, in weight percent, 3.0-4.0 N, 0.02-0.04 B, 0.02-0.05 C, 12.0-14.0 Cr, 19.0-22.0 Co, 2.0-3.5 Mo, greater than 1.0 to 2.1 Nb, 1.3 to 2.1 Ta,3.04.OTi,4.1 to 5.0 W, 0.03-0.06 Zr, and balance essentially Ni and incidental impurities. The superalloy combines ease of processing with high temperature capabilities to be suitable for use in various turbine engine disk, impeller, and shaft applications. The Co and Cr levels of the superalloy can provide low solvus temperature for high processing versatility. The W, Mo, Ta, and Nb refractory element levels of the superalloy can provide sustained strength, creep, and dwell crack growth resistance at high temperatures.

SAFSIM theory manual: A computer program for the engineering simulation of flow systems

NASA Astrophysics Data System (ADS)

Dobranich, Dean

1993-12-01

SAFSIM (System Analysis Flow SIMulator) is a FORTRAN computer program for simulating the integrated performance of complex flow systems. SAFSIM provides sufficient versatility to allow the engineering simulation of almost any system, from a backyard sprinkler system to a clustered nuclear reactor propulsion system. In addition to versatility, speed and robustness are primary SAFSIM development goals. SAFSIM contains three basic physics modules: (1) a fluid mechanics module with flow network capability; (2) a structure heat transfer module with multiple convection and radiation exchange surface capability; and (3) a point reactor dynamics module with reactivity feedback and decay heat capability. Any or all of the physics modules can be implemented, as the problem dictates. SAFSIM can be used for compressible and incompressible, single-phase, multicomponent flow systems. Both the fluid mechanics and structure heat transfer modules employ a one-dimensional finite element modeling approach. This document contains a description of the theory incorporated in SAFSIM, including the governing equations, the numerical methods, and the overall system solution strategies.

Conserved versatile master regulators in signalling pathways in response to stress in plants

PubMed Central

Balderas-Hernández, Victor E.; Alvarado-Rodríguez, Miguel; Fraire-Velázquez, Saúl

2013-01-01

From the first land plants to the complex gymnosperms and angiosperms of today, environmental conditions have forced plants to develop molecular strategies to surpass natural obstacles to growth and proliferation, and these genetic gains have been transmitted to the following generations. In this long natural process, novel and elaborate mechanisms have evolved to enable plants to cope with environmental limitations. Elements in many signalling cascades enable plants to sense different, multiple and simultaneous ambient cues. A group of versatile master regulators of gene expression control plant responses to stressing conditions. For crop breeding purposes, the task is to determine how to activate these key regulators to enable accurate and optimal reactions to common stresses. In this review, we discuss how plants sense biotic and abiotic stresses, how and which master regulators are implied in the responses to these stresses, their evolution in the life kingdoms, and the domains in these proteins that interact with other factors to lead to a proper and efficient plant response. PMID:24147216

A VERSATILE SHARP INTERFACE IMMERSED BOUNDARY METHOD FOR INCOMPRESSIBLE FLOWS WITH COMPLEX BOUNDARIES

PubMed Central

Mittal, R.; Dong, H.; Bozkurttas, M.; Najjar, F.M.; Vargas, A.; von Loebbecke, A.

2010-01-01

A sharp interface immersed boundary method for simulating incompressible viscous flow past three-dimensional immersed bodies is described. The method employs a multi-dimensional ghost-cell methodology to satisfy the boundary conditions on the immersed boundary and the method is designed to handle highly complex three-dimensional, stationary, moving and/or deforming bodies. The complex immersed surfaces are represented by grids consisting of unstructured triangular elements; while the flow is computed on non-uniform Cartesian grids. The paper describes the salient features of the methodology with special emphasis on the immersed boundary treatment for stationary and moving boundaries. Simulations of a number of canonical two- and three-dimensional flows are used to verify the accuracy and fidelity of the solver over a range of Reynolds numbers. Flow past suddenly accelerated bodies are used to validate the solver for moving boundary problems. Finally two cases inspired from biology with highly complex three-dimensional bodies are simulated in order to demonstrate the versatility of the method. PMID:20216919

Selenium as a versatile center in fluorescence probe for the redox cycle between HClO oxidative stress and H2S repair.

PubMed

Lou, Zhangrong; Li, Peng; Han, Keli

2015-01-01

Selenium is a biologically important trace element and acts as an active center of glutathione peroxidase (GPx). GPx is the important antioxidant enzyme to protect organisms from oxidative damage via catalyzing the reaction between ROS and glutathione (GSH). Mimicking the oxidation-reduction cycles of the versatile selenium core in GPx, we can develop fluorescence probes to detect oxidation and reduction events in living systems. The cellular redox balance between hypochloric acid (HClO) and hydrogen sulfide (H2S) has broad implications in human health and diseases, such as Alzheimer's disease (AD). Therefore, to further investigate the roles of this redox balance and understand the pathogenesis of neurodegenerative diseases, it is necessary to detect the redox state between HClO and H2S in real time. We have developed a reversible fluorescence probe MPhSe-BOD for imaging of the redox cycle between HClO and H2S based on oxidation and reduction of selenide in living cells.

A versatile electrostatic trap with open optical access

NASA Astrophysics Data System (ADS)

Li, Sheng-Qiang; Yin, Jian-Ping

2018-04-01

A versatile electrostatic trap with open optical access for cold polar molecules in weak-field-seeking state is proposed in this paper. The trap is composed of a pair of disk electrodes and a hexapole. With the help of a finite element software, the spatial distribution of the electrostatic field is calculated. The results indicate that a three-dimensional closed electrostatic trap is formed. Taking ND3 molecules as an example, the dynamic process of loading and trapping is simulated. The results show that when the velocity of the molecular beam is 10 m/s and the loading time is 0.9964 ms, the maximum loading efficiency reaches 94.25% and the temperature of the trapped molecules reaches about 30.3 mK. A single well can be split into two wells, which is of significant importance to the precision measurement and interference of matter waves. This scheme, in addition, can be further miniaturized to construct one-dimensional, two-dimensional, and three-dimensional spatial electrostatic lattices.

Structural Sizing Methodology for the Tendon-Actuated Lightweight In-Space MANipulator (TALISMAN) System

NASA Technical Reports Server (NTRS)

Jones, Thomas C.; Dorsey, John T.; Doggett, William R.

2015-01-01

The Tendon-Actuated Lightweight In-Space MANipulator (TALISMAN) is a versatile long-reach robotic manipulator that is currently being tested at NASA Langley Research Center. TALISMAN is designed to be highly mass-efficient and multi-mission capable, with applications including asteroid retrieval and manipulation, in-space servicing, and astronaut and payload positioning. The manipulator uses a modular, periodic, tension-compression design that lends itself well to analytical modeling. Given the versatility of application for TALISMAN, a structural sizing methodology was developed that could rapidly assess mass and configuration sensitivities for any specified operating work space, applied loads and mission requirements. This methodology allows the systematic sizing of the key structural members of TALISMAN, which include the truss arm links, the spreaders and the tension elements. This paper summarizes the detailed analytical derivations and methodology that support the structural sizing approach and provides results from some recent TALISMAN designs developed for current and proposed mission architectures.

General Synthetic Strategy for Libraries of Supported Multicomponent Metal Nanoparticles.

PubMed

Yang, Hui; Bradley, Siobhan J; Wu, Xin; Chan, Andrew; Waterhouse, Geoffrey I N; Nann, Thomas; Zhang, Jian; Kruger, Paul E; Ma, Shengqian; Telfer, Shane G

2018-04-18

Nanoparticles comprising three or more different metals are challenging to prepare. General methods that tackle this challenge are highly sought after as multicomponent metal nanoparticles display favorable properties in applications such as catalysis, biomedicine, and imaging. Herein, we report a practical and versatile approach for the synthesis of nanoparticles composed of up to four different metals. This method relies on the thermal decomposition of nanostructured composite materials assembled from platinum nanoparticles, a metal-organic framework (ZIF-8), and a tannic acid coordination polymer. The controlled integration of multiple metal cations (Ni, Co, Cu, Mn, Fe, and/or Tb) into the tannic acid shell of the precursor material dictates the composition of the final multicomponent metal nanoparticles. Upon thermolysis, the platinum nanoparticles seed the growth of the multicomponent metal nanoparticles via coalescence with the metallic constituents of the tannic acid coordination polymer. The nanoparticles are supported in the walls of hollow nitrogen-doped porous carbon capsules created by the decomposition of the organic components of the precursor. The capsules prevent sintering and detachment of the nanoparticles, and their porosity allows for efficient mass transport. To demonstrate the utility of producing a broad library of supported multicomponent metal nanoparticles, we tested their electrocatalytic performance toward the hydrogen evolution reaction and oxygen evolution reaction. We discovered functional relationships between the composition of the nanoparticles and their electrochemical activity and identified the PtNiCu and PtNiCuFe nanoparticles as particularly efficient catalysts. This highlights how to generate diverse libraries of multicomponent metal nanoparticles that can be synthesized and subsequently screened to identify high-performance materials for target applications.

The High Level Data Reduction Library

NASA Astrophysics Data System (ADS)

Ballester, P.; Gabasch, A.; Jung, Y.; Modigliani, A.; Taylor, J.; Coccato, L.; Freudling, W.; Neeser, M.; Marchetti, E.

2015-09-01

The European Southern Observatory (ESO) provides pipelines to reduce data for most of the instruments at its Very Large telescope (VLT). These pipelines are written as part of the development of VLT instruments, and are used both in the ESO's operational environment and by science users who receive VLT data. All the pipelines are highly specific geared toward instruments. However, experience showed that the independently developed pipelines include significant overlap, duplication and slight variations of similar algorithms. In order to reduce the cost of development, verification and maintenance of ESO pipelines, and at the same time improve the scientific quality of pipelines data products, ESO decided to develop a limited set of versatile high-level scientific functions that are to be used in all future pipelines. The routines are provided by the High-level Data Reduction Library (HDRL). To reach this goal, we first compare several candidate algorithms and verify them during a prototype phase using data sets from several instruments. Once the best algorithm and error model have been chosen, we start a design and implementation phase. The coding of HDRL is done in plain C and using the Common Pipeline Library (CPL) functionality. HDRL adopts consistent function naming conventions and a well defined API to minimise future maintenance costs, implements error propagation, uses pixel quality information, employs OpenMP to take advantage of multi-core processors, and is verified with extensive unit and regression tests. This poster describes the status of the project and the lesson learned during the development of reusable code implementing algorithms of high scientific quality.

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

PubMed Central

Stephens, P A; Campbell, J M

1995-01-01

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. PMID:8547910

Monograph support provided by the National Library of Medicine and its regional medical libraries in the medical behavioral sciences.

PubMed Central

Saye, J D; Griffith, B C

1988-01-01

The National Library of Medicine's (NLM) monographic resources in the medical behavioral sciences (MBS) were examined to assess NLM's ability to support the needs of researchers writing in this area. A sample of 239 representative monographs derived from citations in MBS-related articles published in 61 journals in 1981 were evaluated. These monographs were limited to works published between 1978 and 1981, inclusive. The subject distribution of the sample included fourteen of the twenty-one main classes in the LC classification, although BF (psychology), H (social sciences), and R (medicine) constituted 80.3% of the sample. The study revealed that NLM held 48.5% of the sample. The holdings of ten research medical libraries, including six of the seven regional medical libraries, were also evaluated in order to gauge NLM's ability to support that element of the medical library network. The holding rates of these libraries ranged widely (9.6% to 36%), although NLM was found to have far more extensive holdings overall, and when assessed against classes BF, H, and R. Overall, NLM could have supplied from 28.8% to 44.5% of the monographs not held by the medical libraries. In only a few cases were the ten medical libraries able to provide access to monographs not held by NLM. The findings of the study indicate that, regardless of NLM's indication of support to the MBS area, the holdings of more general research and academic libraries are essential to support the monograph needs of MBS researchers. PMID:3224221

Two-port active coupled microstrip antenna

NASA Astrophysics Data System (ADS)

Avitabile, G. F.; Maci, S.; Biffi Gentili, G.; Roselli, L.; Manes, G. F.

1992-12-01

A multilayer structure, based on a patch antenna coupled through a nonresonant slot to a pair of feeding microstrips is a versatile module which can be used as a radiating and resonating element in a number of different configurations. Direct connection to a low cost transistor in a feedback loop results in a very simple active antenna, as reported in the Letter. Different termination conditions at the four microstrip ports give rise to a number of alternative configurations for active generation/detection and multipatch arrays.

[Decentralization of psychiatric health service].

PubMed

Dabrowski, S

1996-01-01

The article discusses two stages of de-centralization of psychiatric hospitals: the first consists in further division into sub-districts, the second one includes successive establishment of psychiatric wards in general hospitals. With the growth of their number these wards are to take over more and more general psychiatric tasks from the specialized psychiatric hospitals. These wards will not substitute psychiatric hospitals completely. The hospitals, though decreasing in size and number, will be a necessary element of the de-centralized and versatile psychiatric care for a long time to come.

Liquid lens: advances in adaptive optics

NASA Astrophysics Data System (ADS)

Casey, Shawn Patrick

2010-12-01

'Liquid lens' technologies promise significant advancements in machine vision and optical communications systems. Adaptations for machine vision, human vision correction, and optical communications are used to exemplify the versatile nature of this technology. Utilization of liquid lens elements allows the cost effective implementation of optical velocity measurement. The project consists of a custom image processor, camera, and interface. The images are passed into customized pattern recognition and optical character recognition algorithms. A single camera would be used for both speed detection and object recognition.

Betty Petersen Memorial Library - NCWCP Publications - NWS

Science.gov Websites

. Polger P. Comparative Analysis of a New Integration Method With Certain Standard Methods (.PDF file) 52 file) 169 1978 Gerrity J. Elemental-Filter Design Considerations (.PDF file) 170 1978 Shuman F. G

Electron lithography STAR design guidelines. Part 2: The design of a STAR for space applications

NASA Technical Reports Server (NTRS)

Trotter, J. D.; Newman, W.

1982-01-01

The STAR design system developed by NASA enables any user with a logic diagram to design a semicustom digital MOS integrated circuit. The system is comprised of a library of standard logic cells and computr programs to place, route, and display designs implemented with cells from the library. Also described is the development of a radiation-hard array designed for the STAR system. The design is based on the CMOS silicon gate technology developed by SANDIA National Laboratories. The design rules used are given as well as the model parameters developed for the basic array element. Library cells of the CMOS metal gate and CMOS silicon gate technologies were simulated using SPICE, and the results are shown and compared.

“... And Gladly Teach”: The American Hospital Association's Experience in Conducting Institutes on Hospital Librarianship

PubMed Central

Yast, Helen

1964-01-01

As part of its overall educational program, the American Hospital Association has since 1959 conducted three institutes on hospital librarianship to meet the demand for more competent librarians in medical, nursing school, and patients' libraries. The purpose of such institutes is to teach the basic elements of library science to untrained personnel in hospital libraries. Discussed are steps in initiating an institute; factors determining length, date, and place; financing; publicity; choice and responsibility of local advisory committee; program content; qualifications of instructors; characteristics of registrants; materials for distribution; evaluations. Details of the most recent institute are outlined. A summary of problems still facing this type of educational program and suggestions for future improvements conclude the paper. PMID:14119309

Method and system for gathering a library of response patterns for sensor arrays

DOEpatents

Zaromb, Solomon

1992-01-01

A method of gathering a library of response patterns for one or more sensor arrays used in the detection and identification of chemical components in a fluid includes the steps of feeding samples of fluid with time-spaced separation of known components to the sensor arrays arranged in parallel or series configurations. Modifying elements such as heating filaments of differing materials operated at differing temperatures are included in the configurations to duplicate operational modes designed into the portable detection systems with which the calibrated sensor arrays are to be used. The response patterns from the known components are collected into a library held in the memory of a microprocessor for comparison with the response patterns of unknown components.

TAP 2: A finite element program for thermal analysis of convectively cooled structures

NASA Technical Reports Server (NTRS)

Thornton, E. A.

1980-01-01

A finite element computer program (TAP 2) for steady-state and transient thermal analyses of convectively cooled structures is presented. The program has a finite element library of six elements: two conduction/convection elements to model heat transfer in a solid, two convection elements to model heat transfer in a fluid, and two integrated conduction/convection elements to represent combined heat transfer in tubular and plate/fin fluid passages. Nonlinear thermal analysis due to temperature-dependent thermal parameters is performed using the Newton-Raphson iteration method. Transient analyses are performed using an implicit Crank-Nicolson time integration scheme with consistent or lumped capacitance matrices as an option. Program output includes nodal temperatures and element heat fluxes. Pressure drops in fluid passages may be computed as an option. User instructions and sample problems are presented in appendixes.

RADIOLOGICAL SEALED SOURCE LIBRARY: A NUCLEAR FORENSICS TOOL

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

Canaday, Jodi; Chamberlain, David; Finck, Martha

If a terrorist were to obtain and possibly detonate a device that contained radiological material, radiological forensic analysis of the material and source capsule could provide law enforcement with valuable clues about the origin of the radiological material; this information could then provide further leads on where the material and sealed source was obtained, and the loss of control point. This information could potentially be utilized for attribution and prosecution. Analyses of nuclear forensic signatures for radiological materials are generally understood to include isotopic ratios, trace element concentrations, the time since irradiation or purification, and morphology. Radiological forensic signatures formore » sealed sources provide additional information that leverages information on the physical design and chemical composition of the source capsule and containers, physical markings indicative of an owner or manufacturer. Argonne National Laboratory (Argonne), in collaboration with Idaho National Laboratory (INL), has been working since 2003 to understand signatures that could be used to identify specific source manufacturers. These signatures include the materials from which the capsule is constructed, dimensions, weld details, elemental composition, and isotopic abundances of the radioactive material. These signatures have been compiled in a library known as the Argonne/INL Radiological Sealed Source Library. Data collected for the library has included open-source information from vendor catalogs and web pages; discussions with source manufacturers and touring of production facilities (both protected through non-disclosure agreements); technical publications; and government registries such as the U.S. Nuclear Regulatory Commission’s Sealed Source and Device Registry.« less

Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate

PubMed Central

Curson, Andrew R. J.; Burns, Oliver J.; Voget, Sonja; Daniel, Rolf; Todd, Jonathan D.; McInnis, Kathryn; Wexler, Margaret; Johnston, Andrew W. B.

2014-01-01

Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again, through the removal of the toxic product acrylyl-CoA. PMID:24848004

A novel library-independent approach based on high-throughput cultivation in Bioscreen and fingerprinting by FTIR spectroscopy for microbial source tracking in food industry.

PubMed

Shapaval, V; Møretrø, T; Wold Åsli, A; Suso, H P; Schmitt, J; Lillehaug, D; Kohler, A

2017-05-01

Microbiological source tracking (MST) for food industry is a rapid growing area of research and technology development. In this paper, a new library-independent approach for MST is presented. It is based on a high-throughput liquid microcultivation and FTIR spectroscopy. In this approach, FTIR spectra obtained from micro-organisms isolated along the production line and a product are compared to each other. We tested and evaluated the new source tracking approach by simulating a source tracking situation. In this simulation study, a selection of 20 spoilage mould strains from a total of six genera (Alternaria, Aspergillus, Mucor, Paecilomyces, Peyronellaea and Phoma) was used. The simulation of the source tracking situation showed that 80-100% of the sources could be correctly identified with respect to genus/species level. When performing source tracking simulations, the FTIR identification diverged for Phoma glomerata strain in the reference collection. When reidentifying the strain by sequencing, it turned out that the strain was a Peyronellaea arachidicola. The obtained results demonstrated that the proposed approach is a versatile tool for identifying sources of microbial contamination. Thus, it has a high potential for routine control in the food industry due to low costs and analysis time. The source tracking of fungal contamination in the food industry is an important aspect of food safety. Currently, all available methods are time consuming and require the use of a reference library that may limit the accuracy of the identification. In this study, we report for the first time, a library-independent FTIR spectroscopic approach for MST of fungal contamination along the food production line. It combines high-throughput microcultivation and FTIR spectroscopy and is specific on the genus and species level. Therefore, such an approach possesses great importance for food safety control in food industry. © 2016 The Society for Applied Microbiology.

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink(Registered TradeMark) (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

The NITON{reg_sign} XL-800 Series Multi-Element Spectrum Analyzer (Alloy Analyzer). Innovative Technology Summary Report

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

None

2000-04-01

The NITON{reg_sign} 800 series analyzer is a hand-held, battery operated unit that measures 8-in x 3-in x 2-in and weighs 2.5 pounds. The analyzer uses x-ray fluorescence spectrum analysis to identify and quantify elements in metal and then compares the readings to a built-in library to determine a metal's alloy. The library contains 300 elements and alloys, and can be customized to identify other elements and alloys (depending on the sources in the instrument). The basic unit utilizes a Cadmium-109 source, but each analyzer unit can hold up to two sources. These sources include Iron-55 and Americium-241. Pushing a safetymore » button located on the side of the unit and placing it against a surface opens the shutter window. Within seconds the unit beeps, and displays the results. The analyzer stores up to 1,000 data sets, including sample identification codes using a barcode reader. The data is easily downloaded to a conventional computer when sampling has been completed. Batteries are good for 8-hrs and charge in less than 2 hours and it can be carried, shipped, or transported without exterior labeling, conforming to 49 CFR 143.421.« less

Selection of peptides interfering with protein-protein interaction.

PubMed

Gaida, Annette; Hagemann, Urs B; Mattay, Dinah; Räuber, Christina; Müller, Kristian M; Arndt, Katja M

2009-01-01

Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.

Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

NASA Astrophysics Data System (ADS)

Zhan, Aibin; Bao, Zhenmin; Hu, Xiaoli; Lu, Wei; Hu, Jingjie

2009-06-01

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop ( Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

NIFTY - Numerical Information Field Theory. A versatile PYTHON library for signal inference

NASA Astrophysics Data System (ADS)

Selig, M.; Bell, M. R.; Junklewitz, H.; Oppermann, N.; Reinecke, M.; Greiner, M.; Pachajoa, C.; Enßlin, T. A.

2013-06-01

NIFTy (Numerical Information Field Theory) is a software package designed to enable the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTy offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically without concerning the user. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and then apply the developed code in higher-dimensional settings of real world problems. The set of spaces on which NIFTy operates comprises point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those. The functionality and diversity of the package is demonstrated by a Wiener filter code example that successfully runs without modification regardless of the space on which the inference problem is defined. NIFTy homepage http://www.mpa-garching.mpg.de/ift/nifty/; Excerpts of this paper are part of the NIFTy source code and documentation.

A Versatile Microfluidic Device for Automating Synthetic Biology.

PubMed

Shih, Steve C C; Goyal, Garima; Kim, Peter W; Koutsoubelis, Nicolas; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Singh, Anup K

2015-10-16

New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

Bitshuffle: Filter for improving compression of typed binary data

NASA Astrophysics Data System (ADS)

Masui, Kiyoshi

2017-12-01

Bitshuffle rearranges typed, binary data for improving compression; the algorithm is implemented in a python/C package within the Numpy framework. The library can be used alongside HDF5 to compress and decompress datasets and is integrated through the dynamically loaded filters framework. Algorithmically, Bitshuffle is closely related to HDF5's Shuffle filter except it operates at the bit level instead of the byte level. Arranging a typed data array in to a matrix with the elements as the rows and the bits within the elements as the columns, Bitshuffle "transposes" the matrix, such that all the least-significant-bits are in a row, etc. This transposition is performed within blocks of data roughly 8kB long; this does not in itself compress data, but rearranges it for more efficient compression. A compression library is necessary to perform the actual compression. This scheme has been used for compression of radio data in high performance computing.

Into the Curriculum. Art: Elements of Art: Vincent Van Gogh [and] Health/Reading/Language Arts: What Makes Goosebumps [and] Reading/Language Arts: African Folktales: An Interdisciplinary Project [and] Science: What's in our Skulls? [and] Science: Hidden Animals in a World of Camouflage [and] Social Studies: Early Primates and Prehistoric Man [and] Social Studies: Native Americans.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1996

1996-01-01

Provides seven library media activities that are designed for use with specific curriculum units in art, health, reading and language arts, science, and social studies. Library media skills, objectives, grade levels, instructional roles, procedures, evaluations, and follow-up are described for each activity. (LRW)

zorder-lib: Library API for Z-Order Memory Layout

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

Nowell, Lucy; Edward W. Bethel

2015-04-01

This document describes the motivation for, elements of, and use of the zorder-lib, a library API that implements organization of and access to data in memory using either a-order (also known as "row-major" order) or z-order memory layouts. The primary motivation for this work is to improve the performance of many types of data- intensive codes by increasing both spatial and temporal locality of memory accesses. The basic idea is that the cost associated with accessing a datum is less when it is nearby in either space or time.

Versatile telluracycle synthesis via the sequential electrophilic telluration of C(sp2)–Zn and C(sp2)–H bonds† †Electronic supplementary information (ESI) available. CCDC 1523262–1523264. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01162h Click here for additional data file. Click here for additional data file.

PubMed Central

Wu, Bin; Melvina; Wu, Xiangyang; Lee Yeow, Edwin Kok

2017-01-01

We report herein a new approach for the synthesis of tellurium-bridged aromatic compounds based on the sequential electrophilic telluration of C(sp2)–Zn and C(sp2)–H bonds with tellurium(iv) chlorides. A combination of transition metal-catalyzed (migratory) arylmetalation of alkynes and sequential telluration allows for the expedient construction of a library of functionalized benzo[b]tellurophenes. Furthermore, a variety of heteroarene-fused benzotellurophenes and other novel tellurium-embedded polycyclic aromatics can be readily synthesized from the corresponding 2-iodoheterobiaryls. PMID:28970880

Libraries of 2β-(N-substituted piperazino)-5α-androstane-3α, 17β-diols: chemical synthesis and cytotoxic effects on human leukemia HL-60 cells and on normal lymphocytes.

PubMed

Roy, Jenny; Maltais, René; Jegham, Hajer; Poirier, Donald

2011-05-01

Libraries of steroid derivatives with two levels of molecular diversity were prepared to optimize the antiproliferative activity on leukemia HL-60 cells by first varying the amino acid (AA) at R(1) (libraries A, B, C, and D: with 45, 45, 20, and 20 members, respectively) and, subsequently, the capping group at R(2) (library E: 168 members). The screening of these aminosteroids revealed interesting structure-activity relationships. In library A, the compounds bearing a tetrahydroisoquinolone residue as the first element of diversity showed potent cytotoxicity, principally when isovaleric or cyclohexyl acetic acid was used as a capping group (>40% of cell growth inhibition at 1 μM). In library B, the phenylalanine (Phe) derivatives bearing a cyano group induced a higher growth inhibition than the other Phe derivatives. The screening of library C indicated the increase of hydrophobicity of proline (Pro) seems to preserve the cytotoxic effect achieved by the lead compound. However, the synthesis of structural Pro variants (library D) clearly shows weaker activities when compared to L-Pro building blocks. Finally, by incorporating some of the most active AA of libraries A-D in library E, we observed that the amide coupling functionality gave stronger cytotoxic activity compared to the corresponding sulfonamides or benzylamines. Six of the most active amide derivatives (E-37P, E-41P, E-42P, E-46P, E-48F, and E-12T) were selected and IC(50) determined on HL-60 cells as well as on normal human lymphocytes. Among this series of new anticancer agents, good to high selectivity indices (SI = IC(50) (lymphocytes)/IC(50) (HL-60 cells) = 5 - 55) were obtained.

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae.

PubMed

Gross, Roy; Guzman, Carlos A; Sebaihia, Mohammed; dos Santos, Vítor A P Martins; Pieper, Dietmar H; Koebnik, Ralf; Lechner, Melanie; Bartels, Daniela; Buhrmester, Jens; Choudhuri, Jomuna V; Ebensen, Thomas; Gaigalat, Lars; Herrmann, Stefanie; Khachane, Amit N; Larisch, Christof; Link, Stefanie; Linke, Burkhard; Meyer, Folker; Mormann, Sascha; Nakunst, Diana; Rückert, Christian; Schneiker-Bekel, Susanne; Schulze, Kai; Vorhölter, Frank-Jörg; Yevsa, Tetyana; Engle, Jacquelyn T; Goldman, William E; Pühler, Alfred; Göbel, Ulf B; Goesmann, Alexander; Blöcker, Helmut; Kaiser, Olaf; Martinez-Arias, Rosa

2008-09-30

Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

PubMed Central

Gross, Roy; Guzman, Carlos A; Sebaihia, Mohammed; Martins dos Santos, Vítor AP; Pieper, Dietmar H; Koebnik, Ralf; Lechner, Melanie; Bartels, Daniela; Buhrmester, Jens; Choudhuri, Jomuna V; Ebensen, Thomas; Gaigalat, Lars; Herrmann, Stefanie; Khachane, Amit N; Larisch, Christof; Link, Stefanie; Linke, Burkhard; Meyer, Folker; Mormann, Sascha; Nakunst, Diana; Rückert, Christian; Schneiker-Bekel, Susanne; Schulze, Kai; Vorhölter, Frank-Jörg; Yevsa, Tetyana; Engle, Jacquelyn T; Goldman, William E; Pühler, Alfred; Göbel, Ulf B; Goesmann, Alexander; Blöcker, Helmut; Kaiser, Olaf; Martinez-Arias, Rosa

2008-01-01

Background Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. Results In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. Conclusion The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches. PMID:18826580

Development and testing of the VITAMIN-B7/BUGLE-B7 coupled neutron-gamma multigroup cross-section libraries

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

Risner, J.M.; Wiarda, D.; Miller, T.M.

2011-07-01

The U.S. Nuclear Regulatory Commission's Regulatory Guide 1.190 states that calculational methods used to estimate reactor pressure vessel (RPV) fluence should use the latest version of the evaluated nuclear data file (ENDF). The VITAMIN-B6 fine-group library and BUGLE-96 broad-group library, which are widely used for RPV fluence calculations, were generated using ENDF/B-VI.3 data, which was the most current data when Regulatory Guide 1.190 was issued. We have developed new fine-group (VITAMIN-B7) and broad-group (BUGLE-B7) libraries based on ENDF/B-VII.0. These new libraries, which were processed using the AMPX code system, maintain the same group structures as the VITAMIN-B6 and BUGLE-96 libraries.more » Verification and validation of the new libraries were accomplished using diagnostic checks in AMPX, 'unit tests' for each element in VITAMIN-B7, and a diverse set of benchmark experiments including critical evaluations for fast and thermal systems, a set of experimental benchmarks that are used for SCALE regression tests, and three RPV fluence benchmarks. The benchmark evaluation results demonstrate that VITAMIN-B7 and BUGLE-B7 are appropriate for use in RPV fluence calculations and meet the calculational uncertainty criterion in Regulatory Guide 1.190. (authors)« less

Development and Testing of the VITAMIN-B7/BUGLE-B7 Coupled Neutron-Gamma Multigroup Cross-Section Libraries

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

Risner, Joel M; Wiarda, Dorothea; Miller, Thomas Martin

2011-01-01

The U.S. Nuclear Regulatory Commission s Regulatory Guide 1.190 states that calculational methods used to estimate reactor pressure vessel (RPV) fluence should use the latest version of the Evaluated Nuclear Data File (ENDF). The VITAMIN-B6 fine-group library and BUGLE-96 broad-group library, which are widely used for RPV fluence calculations, were generated using ENDF/B-VI data, which was the most current data when Regulatory Guide 1.190 was issued. We have developed new fine-group (VITAMIN-B7) and broad-group (BUGLE-B7) libraries based on ENDF/B-VII. These new libraries, which were processed using the AMPX code system, maintain the same group structures as the VITAMIN-B6 and BUGLE-96more » libraries. Verification and validation of the new libraries was accomplished using diagnostic checks in AMPX, unit tests for each element in VITAMIN-B7, and a diverse set of benchmark experiments including critical evaluations for fast and thermal systems, a set of experimental benchmarks that are used for SCALE regression tests, and three RPV fluence benchmarks. The benchmark evaluation results demonstrate that VITAMIN-B7 and BUGLE-B7 are appropriate for use in LWR shielding applications, and meet the calculational uncertainty criterion in Regulatory Guide 1.190.« less

Micromechanics Analysis Code With Generalized Method of Cells (MAC/GMC): User Guide. Version 3

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Bednarcyk, B. A.; Wilt, T. E.; Trowbridge, D.

1999-01-01

The ability to accurately predict the thermomechanical deformation response of advanced composite materials continues to play an important role in the development of these strategic materials. Analytical models that predict the effective behavior of composites are used not only by engineers performing structural analysis of large-scale composite components but also by material scientists in developing new material systems. For an analytical model to fulfill these two distinct functions it must be based on a micromechanics approach which utilizes physically based deformation and life constitutive models and allows one to generate the average (macro) response of a composite material given the properties of the individual constituents and their geometric arrangement. Here the user guide for the recently developed, computationally efficient and comprehensive micromechanics analysis code, MAC, who's predictive capability rests entirely upon the fully analytical generalized method of cells, GMC, micromechanics model is described. MAC/ GMC is a versatile form of research software that "drives" the double or triply periodic micromechanics constitutive models based upon GMC. MAC/GMC enhances the basic capabilities of GMC by providing a modular framework wherein 1) various thermal, mechanical (stress or strain control) and thermomechanical load histories can be imposed, 2) different integration algorithms may be selected, 3) a variety of material constitutive models (both deformation and life) may be utilized and/or implemented, and 4) a variety of fiber architectures (both unidirectional, laminate and woven) may be easily accessed through their corresponding representative volume elements contained within the supplied library of RVEs or input directly by the user, and 5) graphical post processing of the macro and/or micro field quantities is made available.

Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient

PubMed Central

Kouprina, Natalay; Noskov, Vladimir N.; Waterfall, Joshua J.; Walker, Robert L.; Meltzer, Paul S.; Topol, Eric J.; Larionov, Vladimir

2018-01-01

Tandem segmental duplications (SDs) greater than 10 kb are widespread in complex genomes. They provide material for gene divergence and evolutionary adaptation, while formation of specific de novo SDs is a hallmark of cancer and some human diseases. Most SDs map to distinct genomic regions termed ‘duplication blocks’. SDs organization within these blocks is often poorly characterized as they are mosaics of ancestral duplicons juxtaposed with younger duplicons arising from more recent duplication events. Structural and functional analysis of SDs is further hampered as long repetitive DNA structures are underrepresented in existing BAC and YAC libraries. We applied Transformation-Associated Recombination (TAR) cloning, a versatile technique for large DNA manipulation, to selectively isolate the coronary artery disease (CAD) interval sequence within the 9p21.3 chromosome locus from a patient with coronary artery disease and normal individuals. Four tandem head-to-tail duplicons, each ∼50 kb long, were recovered in the patient but not in normal individuals. Sequence analysis revealed that the repeats varied by 10-15 SNPs between each other and by 82 SNPs between the human genome sequence (version hg19). SNPs polymorphism within the junctions between repeats allowed two junction types to be distinguished, Type 1 and Type 2, which were found at a 2:1 ratio. The junction sequences contained an Alu element, a sequence previously shown to play a role in duplication. Knowledge of structural variation in the CAD interval from more patients could help link this locus to cardiovascular diseases susceptibility, and maybe relevant to other cases of regional amplification, including cancer. PMID:29632643

Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool.

PubMed

Ammann, Adrian A

2007-04-01

Inductively coupled plasma (ICP) mass spectrometry (MS) is routinely used in many diverse research fields such as earth, environmental, life and forensic sciences and in food, material, chemical, semiconductor and nuclear industries. The high ion density and the high temperature in a plasma provide an ideal atomizer and element ionizer for all types of samples and matrices introduced by a variety of specialized devices. Outstanding properties such as high sensitivity (ppt-ppq), relative salt tolerance, compound-independent element response and highest quantitation accuracy lead to the unchallenged performance of ICP MS in efficiently detecting, identifying and reliably quantifying trace elements. The increasing availability of relevant reference compounds and high separation selectivity extend the molecular identification capability of ICP MS hyphenated to species-specific separation techniques. While molecular ion source MS is specialized in determining the structure of unknown molecules, ICP MS is an efficient and highly sensitive tool for target-element orientated discoveries of relevant and unknown compounds. This special-feature, tutorial article presents the principle and advantages of ICP MS, highlighting these using examples from recently published investigations. Copyright 2007 John Wiley & Sons, Ltd.

Benchmarking and Performance Measurement.

ERIC Educational Resources Information Center

Town, J. Stephen

This paper defines benchmarking and its relationship to quality management, describes a project which applied the technique in a library context, and explores the relationship between performance measurement and benchmarking. Numerous benchmarking methods contain similar elements: deciding what to benchmark; identifying partners; gathering…

Procurement Without Problems: Preparing the RFP.

ERIC Educational Resources Information Center

Epstein, Susan Baerg

1983-01-01

Discussion of factors contributing to successful procurement of automated library system focuses on preparation of Request for Proposal (RFP) and elements included in the RFP--administrative requirements, functional requirements, performance requirements, reliability requirements, testing procedures, standardized response language, location table,…

Automating Acquisitions: The Planning Process.

ERIC Educational Resources Information Center

Bryant, Bonita

1984-01-01

Account of process followed at large academic library in preparing for automation of acquisition and fund accounting functions highlights planning criteria, local goals, planning process elements (selecting participants, assigning tasks, devising timetable, providing foundations, evaluating systems, determining costs, formulating recommendations).…

A HLA class I cis-regulatory element whose activity can be modulated by hormones.

PubMed

Sim, B C; Hui, K M

1994-12-01

To elucidate the basis of the down-regulation in major histocompatibility complex (MHC) class I gene expression and to identify possible DNA-binding regulatory elements that have the potential to interact with class I MHC genes, we have studied the transcriptional regulation of class I HLA genes in human breast carcinoma cells. A 9 base pair (bp) negative cis-regulatory element (NRE) has been identified using band-shift assays employing DNA sequences derived from the 5'-flanking region of HLA class I genes. This 9-bp element, GTCATGGCG, located within exon I of the HLA class I gene, can potently inhibit the expression of a heterologous thymidine kinase (TK) gene promoter and the HLA enhancer element. Furthermore, this regulatory element can exert its suppressive function in either the sense or anti-sense orientation. More interestingly, NRE can suppress dexamethasone-mediated gene activation in the context of the reported glucocorticoid-responsive element (GRE) in MCF-7 cells but has no influence on the estrogen-mediated transcriptional activation of MCF-7 cells in the context of the reported estrogen-responsive element (ERE). Furthermore, the presence of such a regulatory element within the HLA class I gene whose activity can be modulated by hormones correlates well with our observation that the level of HLA class I gene expression can be down-regulated by hormones in human breast carcinoma cells. Such interactions between negative regulatory elements and specific hormone trans-activators are novel and suggest a versatile form of transcriptional control.

Trace elemental analysis of Indian natural moonstone gems by PIXE and XRD techniques.

PubMed

Venkateswara Rao, R; Venkateswarulu, P; Kasipathi, C; Sivajyothi, S

2013-12-01

A selected number of Indian Eastern Ghats natural moonstone gems were studied with a powerful nuclear analytical and non-destructive Proton Induced X-ray Emission (PIXE) technique. Thirteen elements, including V, Co, Ni, Zn, Ga, Ba and Pb, were identified in these moonstones and may be useful in interpreting the various geochemical conditions and the probable cause of their inceptions in the moonstone gemstone matrix. Furthermore, preliminary XRD studies of different moonstone patterns were performed. The PIXE technique is a powerful method for quickly determining the elemental concentration of a substance. A 3MeV proton beam was employed to excite the samples. The chemical constituents of moonstones from parts of the Eastern Ghats geological formations of Andhra Pradesh, India were determined, and gemological studies were performed on those gems. The crystal structure and the lattice parameters of the moonstones were estimated using X-Ray Diffraction studies, trace and minor elements were determined using the PIXE technique, and major compositional elements were confirmed by XRD. In the present work, the usefulness and versatility of the PIXE technique for research in geo-scientific methodology is established. © 2013 Elsevier Ltd. All rights reserved.

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion.

PubMed

Vaschetto, Luis María

2018-04-01

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.

A programmable nonlinear acoustic metamaterial

NASA Astrophysics Data System (ADS)

Yang, Tianzhi; Song, Zhi-Guang; Clerkin, Eoin; Zhang, Ye-Wei; Sun, Jia-He; Su, Yi-Shu; Chen, Li-Qun; Hagedorn, Peter

2017-09-01

Acoustic metamaterials with specifically designed lattices can manipulate acoustic/elastic waves in unprecedented ways. Whereas there are many studies that focus on passive linear lattice, with non-reconfigurable structures. In this letter, we present the design, theory and experimental demonstration of an active nonlinear acoustic metamaterial, the dynamic properties of which can be modified instantaneously with reversibility. By incorporating active and nonlinear elements in a single unit cell, a real-time tunability and switchability of the band gap is achieved. In addition, we demonstrate a dynamic "editing" capability for shaping transmission spectra, which can be used to create the desired band gap and resonance. This feature is impossible to achieve in passive metamaterials. These advantages demonstrate the versatility of the proposed device, paving the way toward smart acoustic devices, such as logic elements, diode and transistor.

Control and gating of kinesin-microtubule motility on electrically heated thermo-chips.

PubMed

Ramsey, Laurence; Schroeder, Viktor; van Zalinge, Harm; Berndt, Michael; Korten, Till; Diez, Stefan; Nicolau, Dan V

2014-06-01

First lab-on-chip devices based on active transport by biomolecular motors have been demonstrated for basic detection and sorting applications. However, to fully employ the advantages of such hybrid nanotechnology, versatile spatial and temporal control mechanisms are required. Using a thermo-responsive polymer, we demonstrated a temperature controlled gate that either allows or disallows the passing of microtubules through a topographically defined channel. The gate is addressed by a narrow gold wire, which acts as a local heating element. It is shown that the electrical current flowing through a narrow gold channel can control the local temperature and as a result the conformation of the polymer. This is the first demonstration of a spatially addressable gate for microtubule motility which is a key element of nanodevices based on biomolecular motors.

Laser Induced Breakdown Spectroscopy for Elemental Analysis in Environmental, Cultural Heritage and Space Applications: A Review of Methods and Results

PubMed Central

Gaudiuso, Rosalba; Dell’Aglio, Marcella; De Pascale, Olga; Senesi, Giorgio S.; De Giacomo, Alessandro

2010-01-01

Analytical applications of Laser Induced Breakdown Spectroscopy (LIBS), namely optical emission spectroscopy of laser-induced plasmas, have been constantly growing thanks to its intrinsic conceptual simplicity and versatility. Qualitative and quantitative analysis can be performed by LIBS both by drawing calibration lines and by using calibration-free methods and some of its features, so as fast multi-elemental response, micro-destructiveness, instrumentation portability, have rendered it particularly suitable for analytical applications in the field of environmental science, space exploration and cultural heritage. This review reports and discusses LIBS achievements in these areas and results obtained for soils and aqueous samples, meteorites and terrestrial samples simulating extraterrestrial planets, and cultural heritage samples, including buildings and objects of various kinds. PMID:22163611

Use of Laser-Induced Breakdown Spectroscopy for the Detection of Glycemic Elements in Indian Medicinal Plants

PubMed Central

Rai, Prashant Kumar; Srivastava, Amrita Kumari; Sharma, Bechan; Dhar, Preeti; Mishra, Ajay Kumar; Watal, Geeta

2013-01-01

The demand for interdisciplinary research is increasing in the new millennium to help us understand complex problems and find solutions by integrating the knowledge from different disciplines. The present review is an excellent example of this and shows how unique combination of physics, chemistry, and biological techniques can be used for the evaluation of Indian medicinal herbs used for treating diabetes mellitus. Laser-induced breakdown spectroscopy (LIBS) is a sensitive optical technique that is widely used for its simplicity and versatility. This review presents the most recent application of LIBS for detection of glycemic elements in medicinal plants. The characteristics of matrices, object analysis, use of laser system, and analytical performances with respect to Indian herbs are discussed. PMID:24228060

Elemental and isotopic imaging of biological samples using NanoSIMS.

PubMed

Kilburn, Matt R; Clode, Peta L

2014-01-01

With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

Laser induced breakdown spectroscopy for elemental analysis in environmental, cultural heritage and space applications: a review of methods and results.

PubMed

Gaudiuso, Rosalba; Dell'Aglio, Marcella; De Pascale, Olga; Senesi, Giorgio S; De Giacomo, Alessandro

2010-01-01

Analytical applications of Laser Induced Breakdown Spectroscopy (LIBS), namely optical emission spectroscopy of laser-induced plasmas, have been constantly growing thanks to its intrinsic conceptual simplicity and versatility. Qualitative and quantitative analysis can be performed by LIBS both by drawing calibration lines and by using calibration-free methods and some of its features, so as fast multi-elemental response, micro-destructiveness, instrumentation portability, have rendered it particularly suitable for analytical applications in the field of environmental science, space exploration and cultural heritage. This review reports and discusses LIBS achievements in these areas and results obtained for soils and aqueous samples, meteorites and terrestrial samples simulating extraterrestrial planets, and cultural heritage samples, including buildings and objects of various kinds.

Evaluation of the DRAGON code for VHTR design analysis.

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

Taiwo, T. A.; Kim, T. K.; Nuclear Engineering Division

2006-01-12

This letter report summarizes three activities that were undertaken in FY 2005 to gather information on the DRAGON code and to perform limited evaluations of the code performance when used in the analysis of the Very High Temperature Reactor (VHTR) designs. These activities include: (1) Use of the code to model the fuel elements of the helium-cooled and liquid-salt-cooled VHTR designs. Results were compared to those from another deterministic lattice code (WIMS8) and a Monte Carlo code (MCNP). (2) The preliminary assessment of the nuclear data library currently used with the code and libraries that have been provided by themore » IAEA WIMS-D4 Library Update Project (WLUP). (3) DRAGON workshop held to discuss the code capabilities for modeling the VHTR.« less

The role of the University of the West Indies Mona libraries in HIV/AIDS information access and dissemination.

PubMed

Harris, S

2013-01-01

The recommendations for controlling HIV/AIDS, whether prescriptive or descriptive, underscore the value of information: its translation into knowledge, and knowledge into behaviour. Thus, accessing, evaluating, disseminating and applying authoritative, credible and scholarly information on HIV/AIDS are critical elements in the control of this pandemic in the Web 2.0 era. The University of the West Indies (UWI) Mona libraries have embraced this information role. This article provides insights into three of the information initiatives implemented by the UWI Mona libraries in this important capacity. In this regard, it also provides ideas for other West Indian information units and enhances communication on access to information products and services, albeit incrementally, in an important area of health services for the West Indies.

Convergence Toward Common Standards in Machine-Readable Cataloging *

PubMed Central

Gull, C. D.

1969-01-01

The adoption of the MARC II format for the communication of bibliographic information by the three National Libraries of the U.S.A. makes it possible for those libraries to converge on the remaining necessary common standards for machine-readable cataloging. Three levels of standards are identified: fundamental, the character set; intermediate, MARC II; and detailed, the codes for identifying data elements. The convergence on these standards implies that the National Libraries can create and operate a Joint Bibliographic Data Bank requiring standard book numbers and universal serial numbers for identifying monographs and serials and that the system will thoroughly process contributed catalog entries before adding them to the Data Bank. There is reason to hope that the use of the MARC II format will facilitate catalogers' decision processes. PMID:5782261

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements. PMID:26865697

Social network analysis: Presenting an underused method for nursing research.

PubMed

Parnell, James Michael; Robinson, Jennifer C

2018-06-01

This paper introduces social network analysis as a versatile method with many applications in nursing research. Social networks have been studied for years in many social science fields. The methods continue to advance but remain unknown to most nursing scholars. Discussion paper. English language and interpreted literature was searched from Ovid Healthstar, CINAHL, PubMed Central, Scopus and hard copy texts from 1965 - 2017. Social network analysis first emerged in nursing literature in 1995 and appears minimally through present day. To convey the versatility and applicability of social network analysis in nursing, hypothetical scenarios are presented. The scenarios are illustrative of three approaches to social network analysis and include key elements of social network research design. The methods of social network analysis are underused in nursing research, primarily because they are unknown to most scholars. However, there is methodological flexibility and epistemological versatility capable of supporting quantitative and qualitative research. The analytic techniques of social network analysis can add new insight into many areas of nursing inquiry, especially those influenced by cultural norms. Furthermore, visualization techniques associated with social network analysis can be used to generate new hypotheses. Social network analysis can potentially uncover findings not accessible through methods commonly used in nursing research. Social networks can be analysed based on individual-level attributes, whole networks and subgroups within networks. Computations derived from social network analysis may stand alone to answer a research question or incorporated as variables into robust statistical models. © 2018 John Wiley & Sons Ltd.

Applications of synchrotron μ-XRF to study the distribution of biologically important elements in different environmental matrices: a review.

PubMed

Majumdar, Sanghamitra; Peralta-Videa, Jose R; Castillo-Michel, Hiram; Hong, Jie; Rico, Cyren M; Gardea-Torresdey, Jorge L

2012-11-28

Environmental matrices including soils, sediments, and living organisms are reservoirs of several essential as well as non-essential elements. Accurate qualitative and quantitative information on the distribution and interaction of biologically significant elements is vital to understand the role of these elements in environmental and biological samples. Synchrotron micro-X-ray fluorescence (μ-SXRF) allows in situ mapping of biologically important elements at nanometer to sub-micrometer scale with high sensitivity, negligible sample damage and enable tuning of the incident energy as desired. Beamlines in the synchrotron facilities are rapidly increasing their analytical versatility in terms of focusing optics, detector technologies, incident energy, and sample environment. Although extremely competitive, it is now feasible to find stations offering complimentary techniques like micro-X-ray diffraction (μ-XRD) and micro-X-ray absorption spectroscopy (μ-XAS) that will allow a more complete characterization of complex matrices. This review includes the most recent literature on the emerging applications and challenges of μ-SXRF in studying the distribution of biologically important elements and manufactured nanoparticles in soils, sediments, plants, and microbes. The advantages of using μ-SXRF and complimentary techniques in contrast to conventional techniques used for the respective studies are discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Right-Brain/Left-Brain Integrated Associative Processor Employing Convertible Multiple-Instruction-Stream Multiple-Data-Stream Elements

NASA Astrophysics Data System (ADS)

Hayakawa, Hitoshi; Ogawa, Makoto; Shibata, Tadashi

2005-04-01

A very large scale integrated circuit (VLSI) architecture for a multiple-instruction-stream multiple-data-stream (MIMD) associative processor has been proposed. The processor employs an architecture that enables seamless switching from associative operations to arithmetic operations. The MIMD element is convertible to a regular central processing unit (CPU) while maintaining its high performance as an associative processor. Therefore, the MIMD associative processor can perform not only on-chip perception, i.e., searching for the vector most similar to an input vector throughout the on-chip cache memory, but also arithmetic and logic operations similar to those in ordinary CPUs, both simultaneously in parallel processing. Three key technologies have been developed to generate the MIMD element: associative-operation-and-arithmetic-operation switchable calculation units, a versatile register control scheme within the MIMD element for flexible operations, and a short instruction set for minimizing the memory size for program storage. Key circuit blocks were designed and fabricated using 0.18 μm complementary metal-oxide-semiconductor (CMOS) technology. As a result, the full-featured MIMD element is estimated to be 3 mm2, showing the feasibility of an 8-parallel-MIMD-element associative processor in a single chip of 5 mm× 5 mm.

Tailoring gas sensor arrays via the design of short peptides sequences as binding elements.

PubMed

Mascini, Marcello; Pizzoni, Daniel; Perez, German; Chiarappa, Emilio; Di Natale, Corrado; Pittia, Paola; Compagnone, Dario

2017-07-15

A semi-combinatorial virtual approach was used to prepare peptide-based gas sensors with binding properties towards five different chemical classes (alcohols, aldehydes, esters, hydrocarbons and ketones). Molecular docking simulations were conducted for a complete tripeptide library (8000 elements) versus 58 volatile compounds belonging to those five chemical classes. By maximizing the differences between chemical classes, a subset of 120 tripeptides was extracted and used as scaffolds for generating a combinatorial library of 7912 tetrapeptides. This library was processed in an analogous way to the former. Five tetrapeptides (IHRI, KSDS, LGFD, TGKF and WHVS) were chosen depending on their virtual affinity and cross-reactivity for the experimental step. The five peptides were covalently bound to gold nanoparticles by adding a terminal cysteine to each tetrapeptide and deposited onto 20MHz quartz crystal microbalances to construct the gas sensors. The behavior of peptides after this chemical modification was simulated at the pH range used in the immobilization step. ΔF signals analyzed by principal component analysis matched the virtually screened data. The array was able to clearly discriminate the 13 volatile compounds tested based on their hydrophobicity and hydrophilicity molecules as well as the molecular weight. Copyright © 2016 Elsevier B.V. All rights reserved.

Rubble-pile Simulations Using The Open Dynamics Engine

NASA Astrophysics Data System (ADS)

Korycansky, Donald; Asphaug, E.

2008-09-01

We describe a series of calculations of low-speed collisions of km-scale rubble piles (i.e. asteroids or planetesimals), similar to previous work (Korycansky and Asphaug 2006). The rubble piles are aggregates of polyhedra held together by gravity and friction. Collision velocities are typically of order 1 to 100 m/sec.In this work we make use of a so-called "physics engine" to solve the equations of rigid-body motion and collisions of the polyhedra. Such code libraries have been primarily developed for computer simulations and games. The chief advantage of these libraries is the inclusion of sophisticated algorithms for collision detection, which we have found to be the main computational bottleneck in our calculations. The package we have used is the Open Dynamics Engine, a freely available open-source library (www.ode.org). It solves the equations of motion to first-order accuracy in time and utilizes a fast algorithm for collision detection. We have found a factor of approximately 30 speed-up for our calculations, allowing the exploration of a much larger range of parameter space and the running of multiple calculations in order to sample the stochasticity of the results. For the calculations we report on here, the basic model is the collision of an impactor in the range 0.1--1 km in diameter with a target of 1 km diameter.argets are modeled with 1000 polyhedral elements and impactors modeled with 1 to 1000 elements depending on mass. Collisions of objects with both equal-mass elements, and elements chosen from a power-law distribution, are studied. We concentrate on determining the energy required for catastrophic disruption (Q*D) as a function of impactor/target mass atio and impactor parameter for off-center collisions. This work has been supported by NASA Planetary Geology and Geophysics Program grant NNX07AQ04G.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

Safe Haven.

ERIC Educational Resources Information Center

Bush, Gail

2003-01-01

Discusses school libraries as safe havens for teenagers and considers elements that foster that atmosphere, including the physical environment, lack of judgments, familiarity, leisure, and a welcoming nature. Focuses on the importance of relationships, and taking the time to listen to teens and encourage them. (LRW)

Management Information in Tertiary Institutions.

ERIC Educational Resources Information Center

Findlay, A. W.

1981-01-01

A college or university's management information system corresponds roughly to the institution's structure, with these elements in descending order in the hierarchy: policy and planning, a planning system, control and coordination, and typical operating systems (payroll, exams, scheduling, library, facilities assignments, and accounting…

Proteus: Mythology to modern times.

PubMed

Sellaturay, Senthy V; Nair, Raj; Dickinson, Ian K; Sriprasad, Seshadri

2012-10-01

It is common knowledge that proteus bacteria are associated with urinary tract infections and urinary stones. Far more interesting however, is the derivation of the word proteus. This study examines the origin of the word proteus, its mythological, historical and literary connections and evolution to present-day usage. A detailed search for primary and secondary sources was undertaken using the library and internet. Greek mythology describes Proteus as an early sea-god, noted for being versatile and capable of assuming many different forms. In the 8(th) century BC, the ancient Greek poet, Homer, famous for his epic poems the Iliad and Odyssey, describes Proteus as a prophetic old sea-god, and herdsman of the seals of Poseidon, God of the Sea. Shakespeare re-introduced Proteus into English literature, in the 15(th) century AD, in the comedy The Two Gentleman of Verona, as one of his main characters who is inconstant with his affections. The 'elephant man' was afflicted by a severely disfiguring disease, described as 'Proteus syndrome'. It is particularly difficult to distinguish from neurofibromatosis, due to its various forms in different individuals. The Oxford English Dictionary defines the word 'protean' as to mean changeable, variable, and existing in multiple forms. Proteus bacteria directly derive their name from the Sea God, due to their rapid swarming growth and motility on agar plates. They demonstrate versatility by secreting enzymes, which allow them to evade the host's defense systems. Thus proteus, true to its name, has had a myriad of connotations over the centuries.

In situ 3D nanoprinting of free-form coupling elements for hybrid photonic integration

NASA Astrophysics Data System (ADS)

Dietrich, P.-I.; Blaicher, M.; Reuter, I.; Billah, M.; Hoose, T.; Hofmann, A.; Caer, C.; Dangel, R.; Offrein, B.; Troppenz, U.; Moehrle, M.; Freude, W.; Koos, C.

2018-04-01

Hybrid photonic integration combines complementary advantages of different material platforms, offering superior performance and flexibility compared with monolithic approaches. This applies in particular to multi-chip concepts, where components can be individually optimized and tested. The assembly of such systems, however, requires expensive high-precision alignment and adaptation of optical mode profiles. We show that these challenges can be overcome by in situ printing of facet-attached beam-shaping elements. Our approach allows precise adaptation of vastly dissimilar mode profiles and permits alignment tolerances compatible with cost-efficient passive assembly techniques. We demonstrate a selection of beam-shaping elements at chip and fibre facets, achieving coupling efficiencies of up to 88% between edge-emitting lasers and single-mode fibres. We also realize printed free-form mirrors that simultaneously adapt beam shape and propagation direction, and we explore multi-lens systems for beam expansion. The concept paves the way to automated assembly of photonic multi-chip systems with unprecedented performance and versatility.

Structural determinants of arrestin functions.

PubMed

Gurevich, Vsevolod V; Gurevich, Eugenia V

2013-01-01

Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. Copyright © 2013 Elsevier Inc. All rights reserved.

Structural Determinants of Arrestin Functions

PubMed Central

Gurevich, Vsevolod V.; Gurevich, Eugenia V.

2015-01-01

Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. PMID:23764050

A versatile detector system to measure the change states, mass compositions and energy spectra of interplanetary and magnetosphere ions

NASA Technical Reports Server (NTRS)

Gloeckler, G.

1977-01-01

An instrument is described for measuring the mass and charge state composition as well as the energy spectra and angular distributions of 0.5 to 350 kev/charge ions in interplanetary space and in magnetospheres of planets such as Jupiter and earth. Electrostatic deflection combined with a time-of-flight and energy measurement allows three-parameter analysis of output signals from which the mass, charge states, and energy are determined. Post-acceleration by 30 kV extends the energy range of the detector system into the solar wind and magnetosphere plasma regime. Isotopes of H and He are easily resolved as are individual elements up to Ne and the dominant elements up to and including Fe. This instrument has an extremely large dynamic range in intensity and is sensitive to rare elements even in the presence of high intensity radiation, and is adapted for interplanetary, deep-space, and out-of-the-ecliptic missions, as well as for flights on spacecraft orbiting Jupiter and earth.

FENDL: International reference nuclear data library for fusion applications

NASA Astrophysics Data System (ADS)

Pashchenko, A. B.; Wienke, H.; Ganesan, S.

1996-10-01

The IAEA Nuclear Data Section, in co-operation with several national nuclear data centres and research groups, has created the first version of an internationally available Fusion Evaluated Nuclear Data Library (FENDL-1). The FENDL library has been selected to serve as a comprehensive source of processed and tested nuclear data tailored to the requirements of the engineering design activity (EDA) of the ITER project and other fusion-related development projects. The present version of FENDL consists of the following sublibraries covering the necessary nuclear input for all physics and engineering aspects of the material development, design, operation and safety of the ITER project in its current EDA phase: FENDL/A-1.1: neutron activation cross-sections, selected from different available sources, for 636 nuclides, FENDL/D-1.0: nuclear decay data for 2900 nuclides in ENDF-6 format, FENDL/DS-1.0: neutron activation data for dosimetry by foil activation, FENDL/C-1.0: data for the fusion reactions D(d,n), D(d,p), T(d,n), T(t,2n), He-3(d,p) extracted from ENDF/B-6 and processed, FENDL/E-1.0:data for coupled neutron—photon transport calculations, including a data library for neutron interaction and photon production for 63 elements or isotopes, selected from ENDF/B-6, JENDL-3, or BROND-2, and a photon—atom interaction data library for 34 elements. The benchmark validation of FENDL-1 as required by the customer, i.e. the ITER team, is considered to be a task of high priority in the coming months. The well tested and validated nuclear data libraries in processed form of the FENDL-2 are expected to be ready by mid 1996 for use by the ITER team in the final phase of ITER EDA after extensive benchmarking and integral validation studies in the 1995-1996 period. The FENDL data files can be electronically transferred to users from the IAEA nuclear data section online system through INTERNET. A grand total of 54 (sub)directories with 845 files with total size of about 2 million blocks or about 1 Gigabyte (1 block = 512 bytes) of numerical data is currently available on-line.

Experiences with the use of axisymmetric elements in cosmic NASTRAN for static analysis

NASA Technical Reports Server (NTRS)

Cooper, Michael J.; Walton, William C.

1991-01-01

Discussed here are some recent finite element modeling experiences using the axisymmetric elements CONEAX, TRAPAX, and TRIAAX, from the COSMIC NASTRAN element library. These experiences were gained in the practical application of these elements to the static analysis of helicopter rotor force measuring systems for two design projects for the NASA Ames Research Center. These design projects were the Rotor Test Apparatus and the Large Rotor Test Apparatus, which are dedicated to basic helicopter research. Here, a genetic axisymmetric model is generated for illustrative purposes. Modeling considerations are discussed, and the advantages and disadvantages of using axisymmetric elements are presented. Asymmetric mechanical and thermal loads are applied to the structure, and single and multi-point constraints are addressed. An example that couples the axisymmetric model to a non-axisymmtric model is demonstrated, complete with DMAP alters. Recommendations for improving the elements and making them easier to use are offered.

STS-98 Destiny in Atlantis's payload bay

NASA Technical Reports Server (NTRS)

2001-01-01

KENNEDY SPACE CENTER, Fla. -- At Launch Pad 39A, the U.S. Laboratory Destiny waits in Atlantis'''s payload bay for closure of the payload bay doors. Destiny, a key element in the construction of the International Space Station, is 28 feet long and weighs 16 tons. This research and command-and-control center is the most sophisticated and versatile space laboratory ever built. It will ultimately house a total of 23 experiment racks for crew support and scientific research. Destiny will be launched Feb. 7 on STS-98, the seventh construction flight to the ISS.

Mineral of the month: aluminum

USGS Publications Warehouse

Plunkert, Patricia A.

2005-01-01

Aluminum is the second most abundant metallic element in Earth’s crust after silicon. Even so, it is a comparatively new industrial metal that has been produced in commercial quantities for little more than 100 years. Aluminum is lightweight, ductile, malleable and corrosion resistant, and is a good conductor of heat and electricity. Weighing about one-third as much as steel or copper per unit of volume, aluminum is used more than any other metal except iron. Aluminum can be fabricated into desired forms and shapes by every major metalworking technique to add to its versatility.

Infrastructure Retrofit Design via Composite Mechanics

NASA Technical Reports Server (NTRS)

Chamis, Christos, C.; Gotsis,Pascal K.

1998-01-01

Select applications are described to illustrate the concept for retrofitting reinforced concrete infrastructure with fiber reinforced plastic laminates. The concept is first illustrated by using an axially loaded reinforced concrete column. A reinforced concrete arch and a dome are then used to illustrate the versatility of the concept. Advanced methods such as finite element structural analysis and progressive structural fracture are then used to evaluate the retrofitting laminate adequacy. Results obtains show that retrofits can be designed to double and even triple the as-designed load of the select reinforced concrete infrastructures.

Conversion of zirconacyclopentadienes into metalloles: Fagan-Nugent reaction and beyond.

PubMed

Yan, Xiaoyu; Xi, Chanjuan

2015-04-21

Metalloles are derivatives of cyclopentadiene in which the methylene unit is replaced by a heteroatom, such as S, Se, Te, N, P, As, Sb, Bi, Si, Ge, Sn, B, Al, Ga, and so on. Many metallole derivatives have been widely used as photovoltaic cells, organic light emitting diodes (OLEDs), chemical sensors, electrochromic devices, microelectronic actuators, and organic field effect transistors (OFETs). In the meantime, many of them showed promising biological actives. Due to the similarity to cyclopentadiene, the anionic forms of metalloles were also widely explored in coordination chemistry. As a result, development of a general method for the formation of metalloles from available starting materials is highly desired. In this Account, we outline formation of various p-block element metalloles from zirconacyclopentadienes. The zirconacyclopentadienes can be easily prepared from two molecules of alkynes and a low-valent zirconocene species "Cp2Zr(II)" (Cp = cyclopentadienyl). Fagan and Nugent first reported the formation of main group metalloles from zirconacyclopentadiene, which provided a versatile approach for the construction of metalloles, especially for the formation of metalloles in heavier p-block elements. To further expand the substrate scope, a number of stepwise conversions were developed, which involve 1,4-dimetallo- or dihalo-1,3-butadiene as intermediates from zirconacyclopentadienes. Here, four processes are classified based on direct and indirect conversion of zirconacyclopentadienes into metalloles. Direct reaction of zirconacyclopentadienes with element halides afforded heterocycles of main group elements, which provided a versatile method for the synthesis of metalloles. Nonetheless, the reaction scope was restricted to heavier p-block elements such as S, Se, P, As, Sb, Bi, Ge, Sn, Ga, and In. And these reactions usually suffered low yields and long reaction time. Transmetalation of zirconacyclopentadiene with copper chloride greatly enriched the zirconacyclopentadiene chemistry. The synthesis of stannoles and pyrroles from zirconacyclopentadienes has been developed in the presence of CuCl. The direct reaction of the zirconacyclopentadienes with SiCl4 or R2SiCl2 does not give the desired silacyclopendadiene derivatives, even in the presence of CuCl. It can be circumvented by using dilithiated dienes from diiododienes, which are easily prepared by the iodination of zirconacyclopentadienes using CuCl as an additive. Finally, an umpolung strategy, reaction of electrophilic 1,4-diiodo-1,3-butadiene with nucleophilic amine or sulfide reagents, was successfully used in the formation of pyrroles and thiophenes.

Delivering customized apps, multimedia and NASA data to libraries and their patrons

NASA Astrophysics Data System (ADS)

Harold, J. B.; Dusenbery, P.; Holland, A.; LaConte, K.; Johnson, A.; Randall, C.; Fitzhugh, G.

2017-12-01

With funding through NASA's Science Mission Directorate, the NASA @ My Library project has been working with the public library community to enhance the STEM literacy of library patrons throughout the nation. One element of the project is to disseminate a variety of materials to 75 partner libraries in order to support their implementation of hands-on, NASA related STEM activities for their patrons. These materials range from very low tech (UV beads) to high tech (a 4.5" Orion Dobsonian telescope), and include an 8" tablet. This tablet provides us with a wide range of possibilities for delivering NASA content. Besides NASA multimedia and real-time spacecraft data, the tablets can be used for interactive activities, including public apps as well as apps specifically designed for this program, such as a green screen app that incorporates NASA imagery as part of a larger storytelling activity. The tablets also include a full sensor suite (magnetometer, light sensor, accelerometer, etc.), allowing us to develop library activities that use the tablet as a measuring device - detecting magnetism in a "Meteorite or Wrong" activity, or using the light sensor as a transit device. The tablet is centrally managed and includes a "kiosk mode", allowing the libraries to use it in either a locked down or conventional mode. The management system also allows us to create a curated collection of apps and multimedia, push out updated software, and collect analytics data on how the tablet is being used. In this presentation we will discuss the library pre-survey that guided our tablet development process, as well as our lessons learned to date, including the practicality and effectiveness of deploying tablets at this scale, their ability to support NASA specific STEM efforts, and what we have learned about library usage.

MEMS resonant load cells for micro-mechanical test frames: feasibility study and optimal design

NASA Astrophysics Data System (ADS)

Torrents, A.; Azgin, K.; Godfrey, S. W.; Topalli, E. S.; Akin, T.; Valdevit, L.

2010-12-01

This paper presents the design, optimization and manufacturing of a novel micro-fabricated load cell based on a double-ended tuning fork. The device geometry and operating voltages are optimized for maximum force resolution and range, subject to a number of manufacturing and electromechanical constraints. All optimizations are enabled by analytical modeling (verified by selected finite elements analyses) coupled with an efficient C++ code based on the particle swarm optimization algorithm. This assessment indicates that force resolutions of ~0.5-10 nN are feasible in vacuum (~1-50 mTorr), with force ranges as large as 1 N. Importantly, the optimal design for vacuum operation is independent of the desired range, ensuring versatility. Experimental verifications on a sub-optimal device fabricated using silicon-on-glass technology demonstrate a resolution of ~23 nN at a vacuum level of ~50 mTorr. The device demonstrated in this article will be integrated in a hybrid micro-mechanical test frame for unprecedented combinations of force resolution and range, displacement resolution and range, optical (or SEM) access to the sample, versatility and cost.

Digital Alchemy for Materials Design: Colloids and Beyond

NASA Astrophysics Data System (ADS)

van Anders, Greg; Klotsa, Daphne; Karas, Andrew; Dodd, Paul; Glotzer, Sharon

Starting with the early alchemists, a holy grail of science has been to make desired materials by manipulating basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that connecting building-block attributes to bulk structure is both necessary for rationally engineering materials and difficult because building block attributes can be altered in many ways. We show how to exploit the malleability of colloidal nanoparticle ``elements'' to quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term ``digital alchemy''. We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through a set of novel thermodynamic response functions. We thereby establish direct links between the attributes of colloidal building blocks and the bulk structures they form. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature and can be applied to other types of matter.

pTcGW plasmid vectors 1.1 version: a versatile tool for Trypanosoma cruzi gene characterisation

PubMed Central

Kugeratski, Fernanda G; Batista, Michel; Inoue, Alexandre Haruo; Ramos, Bruno Dias; Krieger, Marco Aurelio; Marchini/, Fabricio K

2015-01-01

The functional characterisation of thousands of Trypanosoma cruzi genes remains a challenge. Reverse genetics approaches compatible with high-throughput cloning strategies can provide the tool needed to tackle this challenge. We previously published the pTcGW platform, composed by plasmid vectors carrying different options of N-terminal fusion tags based on Gateway® technology. Here, we present an improved 1.1 version of pTcGW vectors, which is characterised by a fully flexible structure allowing an easy customisation of each element of the vectors in a single cloning step. Additionally, both N and C-terminal fusions are available with new tag options for protein complexes purification. Three of the newly created vectors were successfully used to determine the cellular localisation of four T. cruzi proteins. The 1.1 version of pTcGW platform can be used in a variety of assays, such as protein overexpression, identification of protein-protein interaction and protein localisation. This powerful and versatile tool allows adding valuable functional information to T. cruzi genes and is freely available for scientific community. PMID:26200713

A versatile single molecular precursor for the synthesis of layered oxide cathode materials for Li-ion batteries.

PubMed

Li, Maofan; Liu, Jiajie; Liu, Tongchao; Zhang, Mingjian; Pan, Feng

2018-02-01

A carbonyl-bridged single molecular precursor LiTM(acac) 3 [transition metal (TM) = cobalt/manganese/nickel (Co/Mn/Ni), acac = acetylacetone], featuring a one-dimensional chain structure, was designed and applied to achieve the layered oxide cathode materials: LiTMO 2 (TM = Ni/Mn/Co, NMC). As examples, layered oxides, primary LiCoO 2 , binary LiNi 0.8 Co 0.2 O 2 and ternary LiNi 0.5 Mn 0.3 Co 0.2 O 2 were successfully prepared to be used as cathode materials. When they are applied to lithium-ion batteries (LIBs), all exhibit good electrochemical performance because of their unique morphology and great uniformity of element distribution. This versatile precursor is predicted to accommodate many other metal cations, such as aluminum (Al 3+ ), iron (Fe 2+ ), and sodium (Na + ), because of the flexibility of organic ligand, which not only facilitates the doping-modification of the NMC system, but also enables synthesis of Na-ion layered oxides. This opens a new direction of research for the synthesis of high-performance layered oxide cathode materials for LIBs.

Development of high efficiency Versatile Arc Discharge Ion Source at CERN ISOLDE.

PubMed

Penescu, L; Catherall, R; Lettry, J; Stora, T

2010-02-01

We report here recent developments of Forced Electron Beam Induced Arc Discharge (FEBIAD) ion sources at the ISOLDE radioactive ion beam facility, hosted at the European Organization for Nuclear Research (CERN). As a result of the propositions to improve the ionization efficiency, two FEBIAD prototypes have been produced and successfully tested in 2008. Off-line studies showed that the 1+ ionization efficiencies for noble gases are 5-20 times larger than with the standard ISOLDE FEBIAD ion sources and reach 60% for radon, which allowed the identification at ISOLDE of (229)Rn, an isotope that had never previously been observed in the laboratory. A factor of 3 increase is also expected for the ionization efficiency of the other elements. The experimental and theoretical methodology is presented. The theoretical model, which gives precise insights on the processes affecting the ionization, is used to design optimal sources (grouped under the name of VADIS--Versatile Arc Discharge Ion Source) for the different chemical classes of the produced isotopes, as already demonstrated for the noble gases.

Suppression of grp78 core promoter element-mediated stress induction by the dbpA and dbpB (YB-1) cold shock domain proteins.

PubMed Central

Li, W W; Hsiung, Y; Wong, V; Galvin, K; Zhou, Y; Shi, Y; Lee, A S

1997-01-01

The highly conserved grp78 core promoter element plays an important role in the induction of grp78 under diverse stress signals. Previous studies have established a functional region in the 3' half of the core (stress-inducible change region [SICR]) which exhibits stress-inducible changes in stressed nuclei. The human transcription factor YY1 is shown to bind the SICR and transactivate the core element under stress conditions. Here we report that expression library screening with the core element has identified two new core binding proteins, YB-1 and dbpA. Both proteins belong to the Y-box family of proteins characterized by an evolutionarily conserved DNA binding motif, the cold shock domain (CSD). In contrast to YY1, which binds only double-stranded SICR, the Y-box/CSD proteins much prefer the lower strand of the SICR. The Y-box proteins can repress the inducibility of the grp78 core element mediated by treatment of cells with A23187, thapsigargin, and tunicamycin. In gel shift assays, YY1 binding to the core element is inhibited by either YB-1 or dbpA. A yeast interaction trap screen using LexA-YY1 as a bait and a HeLa cell cDNA-acid patch fusion library identified YB-1 as a YY1-interacting protein. In cotransfection experiments, the Y-box proteins antagonize the YY1-mediated enhancement of transcription directed by the grp78 core in stressed cells. Thus, the CSD proteins may be part of the stress signal transduction mechanism in the mammalian system. PMID:8972186

Program planning for the community teaching hospital medical library.

PubMed Central

McCorkel, J; Cook, V

1985-01-01

To respond to the increasing demand for information from medical educators and clinicians and to persuade administrators to purchase the newly available microcomputer library systems, medical librarians in community teaching hospitals may find it useful to engage in intermediate term (for example, five-year) program planning. To increase the probability that the plan which emerges will be implemented, the planning process should fit the organizational nexus. Planning involves needs assessment, prioritized program elements, a written plan, and facilities planning (if applicable), which lead to program implementation. Components of a model program plan are presented. PMID:4027443

CESAR5.3: Isotopic depletion for Research and Testing Reactor decommissioning

NASA Astrophysics Data System (ADS)

Ritter, Guillaume; Eschbach, Romain; Girieud, Richard; Soulard, Maxime

2018-05-01

CESAR stands in French for "simplified depletion applied to reprocessing". The current version is now number 5.3 as it started 30 years ago from a long lasting cooperation with ORANO, co-owner of the code with CEA. This computer code can characterize several types of nuclear fuel assemblies, from the most regular PWR power plants to the most unexpected gas cooled and graphite moderated old timer research facility. Each type of fuel can also include numerous ranges of compositions like UOX, MOX, LEU or HEU. Such versatility comes from a broad catalog of cross section libraries, each corresponding to a specific reactor and fuel matrix design. CESAR goes beyond fuel characterization and can also provide an evaluation of structural materials activation. The cross-sections libraries are generated using the most refined assembly or core level transport code calculation schemes (CEA APOLLO2 or ERANOS), based on the European JEFF3.1.1 nuclear data base. Each new CESAR self shielded cross section library benefits all most recent CEA recommendations as for deterministic physics options. Resulting cross sections are organized as a function of burn up and initial fuel enrichment which allows to condensate this costly process into a series of Legendre polynomials. The final outcome is a fast, accurate and compact CESAR cross section library. Each library is fully validated, against a stochastic transport code (CEA TRIPOLI 4) if needed and against a reference depletion code (CEA DARWIN). Using CESAR does not require any of the neutron physics expertise implemented into cross section libraries generation. It is based on top quality nuclear data (JEFF3.1.1 for ˜400 isotopes) and includes up to date Bateman equation solving algorithms. However, defining a CESAR computation case can be very straightforward. Most results are only 3 steps away from any beginner's ambition: Initial composition, in core depletion and pool decay scenario. On top of a simple utilization architecture, CESAR includes a portable Graphical User Interface which can be broadly deployed in R&D or industrial facilities. Aging facilities currently face decommissioning and dismantling issues. This way to the end of the nuclear fuel cycle requires a careful assessment of source terms in the fuel, core structures and all parts of a facility that must be disposed of with "industrial nuclear" constraints. In that perspective, several CESAR cross section libraries were constructed for early CEA Research and Testing Reactors (RTR's). The aim of this paper is to describe how CESAR operates and how it can be used to help these facilities care for waste disposal, nuclear materials transport or basic safety cases. The test case will be based on the PHEBUS Facility located at CEA - Cadarache.

Understanding physicians' professional knowledge and practice in research on skilled migration.

PubMed

Weiß, Anja

2016-08-01

Research on the integration of migrant professionals into high-skilled labor markets either focuses on differences between nation states which may be exacerbated by national closure or it celebrates the global versatility of professional knowledge, especially in the natural and health sciences. Building on a pragmatist approach to professional knowledge, the article argues that professional knowledge should not be seen as either universal or local, but both the institutionalized and the incorporated aspects of cultural capital are characterized by 'local universality'. Professionals recreate professional knowledge in specific 'local' situations by relating to universal standards and to internalized 'libraries' of situated expert experience. While the more common notion of knowledge as a socially contested resource continues to be relevant for research on skilled migration, professional knowledge should also be seen as emerging in situations in response to socio-material problems. These problems can be structured by the nation-state, but they can also be transnational in nature.

Novel polyhydroxyalkanoate copolymers produced in Pseudomonas putida by metagenomic polyhydroxyalkanoate synthases.

PubMed

Cheng, Jiujun; Charles, Trevor C

2016-09-01

Bacterially produced biodegradable polyhydroxyalkanoates (PHAs) with versatile properties can be achieved using different PHA synthases (PhaCs). This work aims to expand the diversity of known PhaCs via functional metagenomics and demonstrates the use of these novel enzymes in PHA production. Complementation of a PHA synthesis-deficient Pseudomonas putida strain with a soil metagenomic cosmid library retrieved 27 clones expressing either class I, class II, or unclassified PHA synthases, and many did not have close sequence matches to known PhaCs. The composition of PHA produced by these clones was dependent on both the supplied growth substrates and the nature of the PHA synthase, with various combinations of short-chain-length (SCL) and medium-chain-length (MCL) PHA. These data demonstrate the ability to isolate diverse genes for PHA synthesis by functional metagenomics and their use for the production of a variety of PHA polymer and copolymer mixtures.

Performance of the Fully Digital FPGA-Based Front-End Electronics for the GALILEO Array

NASA Astrophysics Data System (ADS)

Barrientos, D.; Bellato, M.; Bazzacco, D.; Bortolato, D.; Cocconi, P.; Gadea, A.; González, V.; Gulmini, M.; Isocrate, R.; Mengoni, D.; Pullia, A.; Recchia, F.; Rosso, D.; Sanchis, E.; Toniolo, N.; Ur, C. A.; Valiente-Dobón, J. J.

2015-12-01

In this work we present the architecture and results of a fully digital Front End Electronics (FEE) read out system developed for the GALILEO array. The FEE system, developed in collaboration with the Advanced Gamma Tracking Array (AGATA) collaboration, is composed of three main blocks: preamplifiers, digitizers and preprocessing electronics. The slow control system contains a custom Linux driver, a dynamic library and a server implementing network services. This work presents the first results of the digital FEE system coupled with a GALILEO germanium detector, which has demonstrated the capability to achieve an energy resolution of 1.530/00 at an energy of 1.33 MeV, similar to the one obtained with a conventional analog system. While keeping a good performance in terms of energy resolution, digital electronics will allow to instrument the full GALILEO array with a versatile system with high integration and low power consumption and costs.

A MATLAB based 3D modeling and inversion code for MT data

NASA Astrophysics Data System (ADS)

Singh, Arun; Dehiya, Rahul; Gupta, Pravin K.; Israil, M.

2017-07-01

The development of a MATLAB based computer code, AP3DMT, for modeling and inversion of 3D Magnetotelluric (MT) data is presented. The code comprises two independent components: grid generator code and modeling/inversion code. The grid generator code performs model discretization and acts as an interface by generating various I/O files. The inversion code performs core computations in modular form - forward modeling, data functionals, sensitivity computations and regularization. These modules can be readily extended to other similar inverse problems like Controlled-Source EM (CSEM). The modular structure of the code provides a framework useful for implementation of new applications and inversion algorithms. The use of MATLAB and its libraries makes it more compact and user friendly. The code has been validated on several published models. To demonstrate its versatility and capabilities the results of inversion for two complex models are presented.

The NIFTy way of Bayesian signal inference

NASA Astrophysics Data System (ADS)

Selig, Marco

2014-12-01

We introduce NIFTy, "Numerical Information Field Theory", a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTy can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTy as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D3PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

Versatile gas-phase reactions for surface to bulk esterification of cellulose microfibrils aerogels.

PubMed

Fumagalli, Matthieu; Ouhab, Djamila; Boisseau, Sonia Molina; Heux, Laurent

2013-09-09

Aqueous suspensions of microfibrillated cellulose obtained by a high pressure homogenization process were freeze-dried after solvent exchange into tert-butanol. The resulting aerogels, which displayed a remarkable open morphology with a surface area reaching 100 m(2)/g, were subjected to a gas-phase esterification with palmitoyl chloride. Under these conditions, variations of the reaction temperature from 100 to 200 °C, of the reaction time from 0.5 to 2 h, and of the initial quantity of reagent, led to the preparation of a library of cellulose palmitates with DS varying from zero to 2.36. These products were characterized by gravimetry, FTIR, and (13)C solid-state NMR spectroscopy. Of special interest were the cellulose palmitate samples of low DS in the range of 0.1-0.4, which corresponded to hydrophobic cellulose microfibrils exclusively esterified at their surface while keeping intact their inner structure.

HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere

NASA Technical Reports Server (NTRS)

Gorski, K. M.; Hivon, Eric; Banday, A. J.; Wandelt, Benjamin D.; Hansen, Frode K.; Reinecke, Mstvos; Bartelmann, Matthia

2005-01-01

HEALPix the Hierarchical Equal Area isoLatitude Pixelization is a versatile structure for the pixelization of data on the sphere. An associated library of computational algorithms and visualization software supports fast scientific applications executable directly on discretized spherical maps generated from very large volumes of astronomical data. Originally developed to address the data processing and analysis needs of the present generation of cosmic microwave background experiments (e.g., BOOMERANG, WMAP), HEALPix can be expanded to meet many of the profound challenges that will arise in confrontation with the observational output of future missions and experiments, including, e.g., Planck, Herschel, SAFIR, and the Beyond Einstein inflation probe. In this paper we consider the requirements and implementation constraints on a framework that simultaneously enables an efficient discretization with associated hierarchical indexation and fast analysis/synthesis of functions defined on the sphere. We demonstrate how these are explicitly satisfied by HEALPix.

Computers and the design of ion beam optical systems

NASA Astrophysics Data System (ADS)

White, Nicholas R.

Advances in microcomputers have made it possible to maintain a library of advanced ion optical programs which can be used on inexpensive computer hardware, which are suitable for the design of a variety of ion beam systems including ion implanters, giving excellent results. This paper describes in outline the steps typically involved in designing a complete ion beam system for materials modification applications. Two computer programs are described which, although based largely on algorithms which have been in use for many years, make possible detailed beam optical calculations using microcomputers, specifically the IBM PC. OPTICIAN is an interactive first-order program for tracing beam envelopes through complex optical systems. SORCERY is a versatile program for solving Laplace's and Poisson's equations by finite difference methods using successive over-relaxation. Ion and electron trajectories can be traced through these potential fields, and plots of beam emittance obtained.

Genetic therapy for the nervous system.

PubMed

Bowers, William J; Breakefield, Xandra O; Sena-Esteves, Miguel

2011-04-15

Genetic therapy is undergoing a renaissance with expansion of viral and synthetic vectors, use of oligonucleotides (RNA and DNA) and sequence-targeted regulatory molecules, as well as genetically modified cells, including induced pluripotent stem cells from the patients themselves. Several clinical trials for neurologic syndromes appear quite promising. This review covers genetic strategies to ameliorate neurologic syndromes of different etiologies, including lysosomal storage diseases, Alzheimer's disease and other amyloidopathies, Parkinson's disease, spinal muscular atrophy, amyotrophic lateral sclerosis and brain tumors. This field has been propelled by genetic technologies, including identifying disease genes and disruptive mutations, design of genomic interacting elements to regulate transcription and splicing of specific precursor mRNAs and use of novel non-coding regulatory RNAs. These versatile new tools for manipulation of genetic elements provide the ability to tailor the mode of genetic intervention to specific aspects of a disease state.

Modeling of heterogeneous elastic materials by the multiscale hp-adaptive finite element method

NASA Astrophysics Data System (ADS)

Klimczak, Marek; Cecot, Witold

2018-01-01

We present an enhancement of the multiscale finite element method (MsFEM) by combining it with the hp-adaptive FEM. Such a discretization-based homogenization technique is a versatile tool for modeling heterogeneous materials with fast oscillating elasticity coefficients. No assumption on periodicity of the domain is required. In order to avoid direct, so-called overkill mesh computations, a coarse mesh with effective stiffness matrices is used and special shape functions are constructed to account for the local heterogeneities at the micro resolution. The automatic adaptivity (hp-type at the macro resolution and h-type at the micro resolution) increases efficiency of computation. In this paper details of the modified MsFEM are presented and a numerical test performed on a Fichera corner domain is presented in order to validate the proposed approach.

Design sensitivity analysis using EAL. Part 1: Conventional design parameters

NASA Technical Reports Server (NTRS)

Dopker, B.; Choi, Kyung K.; Lee, J.

1986-01-01

A numerical implementation of design sensitivity analysis of builtup structures is presented, using the versatility and convenience of an existing finite element structural analysis code and its database management system. The finite element code used in the implemenatation presented is the Engineering Analysis Language (EAL), which is based on a hybrid method of analysis. It was shown that design sensitivity computations can be carried out using the database management system of EAL, without writing a separate program and a separate database. Conventional (sizing) design parameters such as cross-sectional area of beams or thickness of plates and plane elastic solid components are considered. Compliance, displacement, and stress functionals are considered as performance criteria. The method presented is being extended to implement shape design sensitivity analysis using a domain method and a design component method.

Hybrid finite element/waveguide mode analysis of passive RF devices

NASA Astrophysics Data System (ADS)

McGrath, Daniel T.

1993-07-01

A numerical solution for time-harmonic electromagnetic fields in two-port passive radio frequency (RF) devices has been developed, implemented in a computer code, and validated. Vector finite elements are used to represent the fields in the device interior, and field continuity across waveguide apertures is enforced by matching the interior solution to a sum of waveguide modes. Consequently, the mesh may end at the aperture instead of extending into the waveguide. The report discusses the variational formulation and its reduction to a linear system using Galerkin's method. It describes the computer code, including its interface to commercial CAD software used for geometry generation. It presents validation results for waveguide discontinuities, coaxial transitions, and microstrip circuits. They demonstrate that the method is an effective and versatile tool for predicting the performance of passive RF devices.

OpenGl Visualization Tool and Library Version: 1.0

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

2010-06-22

GLVis is an OpenGL tool for visualization of finite element meshes and functions. When started without any options, GLVis starts a server, which waits for a socket connections and visualizes any recieved data. This way the results of simulations on a remote (parallel) machine can be visualized on the lical user desktop. GLVis can also be used to visualize a mesh with or without a finite element function (solution). It can run a batch sequence of commands (GLVis scripts), or display previously saved socket streams.

Fully-Implicit Navier-Stokes (FIN-S)

NASA Technical Reports Server (NTRS)

Kirk, Benjamin S.

2010-01-01

FIN-S is a SUPG finite element code for flow problems under active development at NASA Lyndon B. Johnson Space Center and within PECOS: a) The code is built on top of the libMesh parallel, adaptive finite element library. b) The initial implementation of the code targeted supersonic/hypersonic laminar calorically perfect gas flows & conjugate heat transfer. c) Initial extension to thermochemical nonequilibrium about 9 months ago. d) The technologies in FIN-S have been enhanced through a strongly collaborative research effort with Sandia National Labs.

Marketing Reference Services.

ERIC Educational Resources Information Center

Norman, O. Gene

1995-01-01

Relates the marketing concept to library reference services. Highlights include a review of the literature and an overview of marketing, including research, the marketing mix, strategic plan, marketing plan, and marketing audit. Marketing principles are applied to reference services through the marketing mix elements of product, price, place, and…

Machine Readable Bibliographic Records: Criteria and Creation.

ERIC Educational Resources Information Center

Bregzis, Ritvars

The centrality of bibliographic records in library automation, objectives of the bibliographic record file and elemental factors involved in bibliographic record creation are discussed. The practical work of creating bibliographic records involves: (1) data base environment, (2) technical aspects, (3) cost and (4) operational methodology. The…

Metadata: Pure and Simple, or Is It?

ERIC Educational Resources Information Center

Chalmers, Marilyn

2002-01-01

Discusses issues concerning metadata in Web pages based on experiences in a vocational education center library in Queensland (Australia). Highlights include Dublin Core elements; search engines; controlled vocabulary; performance measurement to assess usage patterns and provide quality control over the vocabulary; and considerations given the…

Professional Development for School Library Media Professionals: Elements for Success

ERIC Educational Resources Information Center

Brown, Carol A.; Dotson, Lana Kaye; Yontz, Elaine

2011-01-01

The American Association for School Librarians suggests an important mission for school librarians is to ensure personal growth through ongoing exposure to conferences, journal articles, webinars, presentations, and membership in professional organizations. As professional educators, School Librarians should exemplify the vision for being…

Disaster: Planning, Preparation, Prevention.

ERIC Educational Resources Information Center

Rutherford, Christine

1990-01-01

Discusses causes of library disasters and provides several examples of disasters. Emphasis is on the importance of awareness, insurance protection, a written disaster plan, cooperation with the fire marshall and insurance agent in planning, and staff training. Several elements of the written plan are listed. (22 references) (MES)

Creating a Community of Inquiry in Online Library Instruction

ERIC Educational Resources Information Center

Rapchak, Marcia E.

2017-01-01

According to the Community of Inquiry (CoI) model (Garrison, Anderson, & Archer, 2000), an enriching educational experience online in a collaborative learning environment requires three interdependent elements: social presence, teaching presence, and cognitive presence. Social presence provides interaction in the online environment that allows…

Into the Curriculum.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1992

1992-01-01

Provides six fully developed library media activities that are designed to be used with specific curriculum units. Highlights include elementary student activities for art (winter holiday crafts); reading/language arts (fantasy in stories, elements of folk stories from India, writing sequels to fairy tales); science (animal symbiosis); and social…

Confused about Fusion? Weed Your Science Collection with a Pro.

ERIC Educational Resources Information Center

O'Dell, Charli

1998-01-01

Provides guidelines on weeding science collections in junior high/high school libraries. Highlights include checking copyright dates, online sources, 13 science subject areas that deserve special consideration (plate tectonics, fission, fusion, radioactive dating, weather/climate, astronomy/space science, elements, integrated science,…

Parallel Electrochemical Treatment System and Application for Identifying Acid-Stable Oxygen Evolution Electrocatalysts

DOE PAGES

Jones, Ryan J. R.; Shinde, Aniketa; Guevarra, Dan; ...

2015-01-05

There are many energy technologies require electrochemical stability or preactivation of functional materials. Due to the long experiment duration required for either electrochemical preactivation or evaluation of operational stability, parallel screening is required to enable high throughput experimentation. We found that imposing operational electrochemical conditions to a library of materials in parallel creates several opportunities for experimental artifacts. We discuss the electrochemical engineering principles and operational parameters that mitigate artifacts int he parallel electrochemical treatment system. We also demonstrate the effects of resistive losses within the planar working electrode through a combination of finite element modeling and illustrative experiments. Operationmore » of the parallel-plate, membrane-separated electrochemical treatment system is demonstrated by exposing a composition library of mixed metal oxides to oxygen evolution conditions in 1M sulfuric acid for 2h. This application is particularly important because the electrolysis and photoelectrolysis of water are promising future energy technologies inhibited by the lack of highly active, acid-stable catalysts containing only earth abundant elements.« less

Albany v. 3.0

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

Salinger, Andrew; Phipps, Eric; Ostien, Jakob

2016-01-13

The Albany code is a general-purpose finite element code for solving partial differential equations (PDEs). Albany is a research code that demonstrates how a PDE code can be built by interfacing many of the open-source software libraries that are released under Sandia's Trilinos project. Part of the mission of Albany is to be a testbed for new Trilinos libraries, to refine their methods, usability, and interfaces. Albany includes hooks to optimization and uncertainty quantification algorithms, including those in Trilinos as well as those in the Dakota toolkit. Because of this, Albany is a desirable starting point for new code developmentmore » efforts that wish to make heavy use of Trilinos. Albany is both a framework and the host for specific finite element applications. These applications have project names, and can be controlled by configuration option when the code is compiled, but are all developed and released as part of the single Albany code base, These include LCM, QCAD, FELIX, Aeras, and ATO applications.« less

An advanced environment for hybrid modeling of biological systems based on modelica.

PubMed

Pross, Sabrina; Bachmann, Bernhard

2011-01-20

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Genome-wide mapping of autonomous promoter activity in human cells

PubMed Central

van Arensbergen, Joris; FitzPatrick, Vincent D.; de Haas, Marcel; Pagie, Ludo; Sluimer, Jasper; Bussemaker, Harmen J.; van Steensel, Bas

2017-01-01

Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of sequences that could be tested. Here we present Survey of Regulatory Elements (SuRE), a method to assay more than 108 DNA fragments, each 0.2–2kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library is constructed of random genomic fragments upstream of a 20bp barcode and decoded by paired-end sequencing. This library is then transfected into cells and transcribed barcodes are quantified in the RNA by high throughput sequencing. When applied to the human genome, we achieved a 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide. By computational modeling we delineated subregions within promoters that are relevant for their activity. For instance, we show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites. PMID:28024146

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR library

PubMed Central

Zhu, Shiyou; Li, Wei; Liu, Jingze; Chen, Chen-Hao; Liao, Qi; Xu, Ping; Xu, Han; Xiao, Tengfei; Cao, Zhongzheng; Peng, Jingyu; Yuan, Pengfei; Brown, Myles; Liu, Xiaole Shirley; Wei, Wensheng

2017-01-01

CRISPR/Cas9 screens have been widely adopted to analyse coding gene functions, but high throughput screening of non-coding elements using this method is more challenging, because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. Herein, we report a high throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We individually validated 9 lncRNAs using CRISPR/Cas9-mediated genomic deletion and functional rescue, CRISPR activation or inhibition, and gene expression profiling. Our high-throughput pgRNA genome deletion method should enable rapid identification of functional mammalian non-coding elements. PMID:27798563

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

PubMed

Canver, Matthew C; Lessard, Samuel; Pinello, Luca; Wu, Yuxuan; Ilboudo, Yann; Stern, Emily N; Needleman, Austen J; Galactéros, Frédéric; Brugnara, Carlo; Kutlar, Abdullah; McKenzie, Colin; Reid, Marvin; Chen, Diane D; Das, Partha Pratim; A Cole, Mitchel; Zeng, Jing; Kurita, Ryo; Nakamura, Yukio; Yuan, Guo-Cheng; Lettre, Guillaume; Bauer, Daniel E; Orkin, Stuart H

2017-04-01

Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.

PubMed

Silva, Cynthia C; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; Kruger, Ricardo H; Rodrigues, Marili Vn; Costa, Gustavo Gl; Vidal, Ramon O; Sousa, Maíra P; Torres, Ana Paula R; Santiago, Vânia Mj; Oliveira, Valéria M

2012-03-27

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

Enabling Efficient and Confident Annotation of LC−MS Metabolomics Data through MS1 Spectrum and Time Prediction

DOE PAGES

Broeckling, Corey D.; Ganna, Andrea; Layer, Mark; ...

2016-09-08

Liquid chromatography coupled to electrospray ionization-mass spectrometry (LC–ESI-MS) is a versatile and robust platform for metabolomic analysis. However, while ESI is a soft ionization technique, in-source phenomena including multimerization, nonproton cation adduction, and in-source fragmentation complicate interpretation of MS data. Here, we report chromatographic and mass spectrometric behavior of 904 authentic standards collected under conditions identical to a typical nontargeted profiling experiment. The data illustrate that the often high level of complexity in MS spectra is likely to result in misinterpretation during the annotation phase of the experiment and a large overestimation of the number of compounds detected. However, ourmore » analysis of this MS spectral library data indicates that in-source phenomena are not random but depend at least in part on chemical structure. These nonrandom patterns enabled predictions to be made as to which in-source signals are likely to be observed for a given compound. Using the authentic standard spectra as a training set, we modeled the in-source phenomena for all compounds in the Human Metabolome Database to generate a theoretical in-source spectrum and retention time library. A novel spectral similarity matching platform was developed to facilitate efficient spectral searching for nontargeted profiling applications. Taken together, this collection of experimental spectral data, predictive modeling, and informatic tools enables more efficient, reliable, and transparent metabolite annotation.« less

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

PubMed Central

Gagic, Dragana; Ciric, Milica; Wen, Wesley X.; Ng, Filomena; Rakonjac, Jasna

2016-01-01

Microbial surface and secreted proteins (the secretome) contain a large number of proteins that interact with other microbes, host and/or environment. These proteins are exported by the coordinated activities of the protein secretion machinery present in the cell. A group of bacteriophage, called filamentous phage, have the ability to hijack bacterial protein secretion machinery in order to amplify and assemble via a secretion-like process. This ability has been harnessed in the use of filamentous phage of Escherichia coli in biotechnology applications, including screening large libraries of variants for binding to “bait” of interest, from tissues in vivo to pure proteins or even inorganic substrates. In this review we discuss the roles of secretome proteins in pathogenic and non-pathogenic bacteria and corresponding secretion pathways. We describe the basics of phage display technology and its variants applied to discovery of bacterial proteins that are implicated in colonization of host tissues and pathogenesis, as well as vaccine candidates through filamentous phage display library screening. Secretome selection aided by next-generation sequence analysis was successfully applied for selective display of the secretome at a microbial community scale, the latter revealing the richness of secretome functions of interest and surprising versatility in filamentous phage display of secretome proteins from large number of Gram-negative as well as Gram-positive bacteria and archaea. PMID:27092113

Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction

DOE PAGES

Broeckling, Corey D.; Ganna, Andrea; Layer, Mark; ...

2016-08-25

Liquid chromatography coupled to electrospray ionization-mass spectrometry (LC–ESI-MS) is a versatile and robust platform for metabolomic analysis. However, while ESI is a soft ionization technique, in-source phenomena including multimerization, nonproton cation adduction, and in-source fragmentation complicate interpretation of MS data. Here, we report chromatographic and mass spectrometric behavior of 904 authentic standards collected under conditions identical to a typical nontargeted profiling experiment. The data illustrate that the often high level of complexity in MS spectra is likely to result in misinterpretation during the annotation phase of the experiment and a large overestimation of the number of compounds detected. However, ourmore » analysis of this MS spectral library data indicates that in-source phenomena are not random but depend at least in part on chemical structure. These nonrandom patterns enabled predictions to be made as to which in-source signals are likely to be observed for a given compound. Using the authentic standard spectra as a training set, we modeled the in-source phenomena for all compounds in the Human Metabolome Database to generate a theoretical in-source spectrum and retention time library. A novel spectral similarity matching platform was developed to facilitate efficient spectral searching for nontargeted profiling applications. Taken together, this collection of experimental spectral data, predictive modeling, and informatic tools enables more efficient, reliable, and transparent metabolite annotation.« less

Flowable Resin Composites: A Systematic Review and Clinical Considerations

PubMed Central

Rodrigues, Jean C.

2015-01-01

Background Little is known about flowable composite materials. Most literature mentions conventional composite materials at large, giving minimal emphasis to flowables in particular. This paper briefly gives an in depth insight to the multiple facets of this versatile material. Aim To exclusively review the most salient features of flowable composite materials in comparison to conventional composites and to give clinicians a detailed understanding of the advantages, drawbacks, indications and contraindications based on composition and physical/mechanical properties. Methodology Data Sources: A thorough literature search from the year 1996 up to January 2015 was done on PubMed Central, The Cochrane Library, Science Direct, Wiley Online Library, and Google Scholar. Grey literature (pending patents, technical reports etc.) was also screened. The search terms used were “dental flowable resin composites”. Search Strategy After omitting the duplicates/repetitions, a total of 491 full text articles were assessed. As including all articles were out of the scope of this paper. Only relevant articles that fulfilled the reviewer’s objectives {mentioning indications, contraindications, applications, assessment of physical/mechanical/biological properties (in vitro/ in vivo /ex vivo)} were considered. A total of 92 full text articles were selected. Conclusion Flowable composites exhibit a variable composition and consequently variable mechanical/ physical properties. Clinicians must be aware of this aspect to make a proper material selection based on specific properties and indications of each material relevant to a particular clinical situation. PMID:26266238

The randomised controlled trial design: unrecognized opportunities for health sciences librarianship.

PubMed

Eldredge, Jonathan D

2003-06-01

to describe the essential components of the Randomised Controlled Trial (RCT) and its major variations; to describe less conventional applications of the RCT design found in the health sciences literature with potential relevance to health sciences librarianship; to discuss the limited number of RCTs within health sciences librarianship. narrative review supported to a limited extent with PubMed and Library Literature database searches consistent with specific search parameters. In addition, more systematic methods, including handsearching of specific journals, to identify health sciences librarianship RCTs. While many RCTs within the health sciences follow more conventional patterns, some RCTs assume certain unique features. Selected examples illustrate the adaptations of this experimental design to answering questions of possible relevance to health sciences librarians. The author offers several strategies for controlling bias in library and informatics applications of the RCT and acknowledges the potential of the electronic era in providing many opportunities to utilize the blinding aspects of RCTs. RCTs within health sciences librarianship inhabit a limited number of subject domains such as education. This limited scope offers both advantages and disadvantages for making Evidence-Based Librarianship (EBL) a reality. The RCT design offers the potential to answer far more EBL questions than have been addressed by the design to date. Librarians need only extend their horizons through use of the versatile RCT design into new subject domains to facilitate making EBL a reality.

Next-generation AAV vectors for clinical use: an ever-accelerating race.

PubMed

Weinmann, Jonas; Grimm, Dirk

2017-10-01

During the past five decades, it has become evident that Adeno-associated virus (AAV) represents one of the most potent, most versatile, and thus most auspicious platforms available for gene delivery into cells, animals and, ultimately, humans. Particularly attractive is the ease with which the viral capsid-the major determinant of virus-host interaction including cell specificity and antibody recognition-can be modified and optimized at will. This has motivated countless researchers to develop high-throughput technologies in which genetically engineered AAV capsid libraries are subjected to a vastly hastened emulation of natural evolution, with the aim to enrich novel synthetic AAV capsids displaying superior features for clinical application. While the power and potential of these forward genetics approaches is undisputed, they are also inherently challenging as success depends on a combination of library quality, fidelity, and complexity. Here, we will describe and discuss two original, very exciting strategies that have emerged over the last three years and that promise to alleviate at least some of these concerns, namely, (i) a reverse genetics approach termed "ancestral AAV sequence reconstruction," and (ii) AAV genome barcoding as a technology that can advance both, forward and reverse genetics stratagems. Notably, despite the conceptual differences of these two technologies, they pursue the same goal which is tailored acceleration of AAV evolution and thus winning the race for the next-generation AAV vectors for clinical use.

Plasmonic Library Based on Substrate-Supported Gradiential Plasmonic Arrays

PubMed Central

2014-01-01

We present a versatile approach to produce macroscopic, substrate-supported arrays of plasmonic nanoparticles with well-defined interparticle spacing and a continuous particle size gradient. The arrays thus present a “plasmonic library” of locally noncoupling plasmonic particles of different sizes, which can serve as a platform for future combinatorial screening of size effects. The structures were prepared by substrate assembly of gold-core/poly(N-isopropylacrylamide)-shell particles and subsequent post-modification. Coupling of the localized surface plasmon resonance (LSPR) could be avoided since the polymer shell separates the encapsulated gold cores. To produce a particle array with a broad range of well-defined but laterally distinguishable particle sizes, the substrate was dip-coated in a growth solution, which resulted in an overgrowth of the gold cores controlled by the local exposure time. The kinetics was quantitatively analyzed and found to be diffusion rate controlled, allowing for precise tuning of particle size by adjusting the withdrawal speed. We determined the kinetics of the overgrowth process, investigated the LSPRs along the gradient by UV–vis extinction spectroscopy, and compared the spectroscopic results to the predictions from Mie theory, indicating the absence of local interparticle coupling. We finally discuss potential applications of these substrate-supported plasmonic particle libraries and perspectives toward extending the concept from size to composition variation and screening of plasmonic coupling effects. PMID:25137554

Zaba: a novel miniature transposable element present in genomes of legume plants.

PubMed

Macas, J; Neumann, P; Pozárková, D

2003-08-01

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141-190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.

SVGenes: a library for rendering genomic features in scalable vector graphic format.

PubMed

Etherington, Graham J; MacLean, Daniel

2013-08-01

Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements. SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion. The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License. dan.maclean@tsl.ac.uk.

Analysis of heterogeneous gallstones using laser-induced breakdown spectroscopy (LIBS) and wavelength dispersive X-ray fluorescence (WD-XRF).

PubMed

Jaswal, Brij Bir S; Kumar, Vinay; Sharma, Jitendra; Rai, Pradeep K; Gondal, Mohammed A; Gondal, Bilal; Singh, Vivek K

2016-04-01

Laser-induced breakdown spectroscopy (LIBS) is an emerging analytical technique with numerous advantages such as rapidity, multi-elemental analysis, no specific sample preparation requirements, non-destructiveness, and versatility. It has been proven to be a robust elemental analysis tool attracting interest because of being applied to a wide range of materials including biomaterials. In this paper, we have performed spectroscopic studies on gallstones which are heterogeneous in nature using LIBS and wavelength dispersive X-ray fluorescence (WD-XRF) techniques. It has been observed that the presence and relative concentrations of trace elements in different kind of gallstones (cholesterol and pigment gallstones) can easily be determined using LIBS technique. From the experiments carried out on gallstones for trace elemental mapping and detection, it was found that LIBS is a robust tool for such biomedical applications. The stone samples studied in the present paper were classified using the Fourier transform infrared (FTIR) spectroscopy. WD-XRF spectroscopy has been applied for the qualitative and quantitative analysis of major and trace elements present in the gallstone which was compared with the LIBS data. The results obtained in the present paper show interesting prospects for LIBS and WD-XRF to study cholelithiasis better.

Extrachromosomal genetic elements in Micrococcus.

PubMed

Dib, Julián Rafael; Liebl, Wolfgang; Wagenknecht, Martin; Farías, María Eugenia; Meinhardt, Friedhelm

2013-01-01

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

The GPRIME approach to finite element modeling

NASA Technical Reports Server (NTRS)

Wallace, D. R.; Mckee, J. H.; Hurwitz, M. M.

1983-01-01

GPRIME, an interactive modeling system, runs on the CDC 6000 computers and the DEC VAX 11/780 minicomputer. This system includes three components: (1) GPRIME, a user friendly geometric language and a processor to translate that language into geometric entities, (2) GGEN, an interactive data generator for 2-D models; and (3) SOLIDGEN, a 3-D solid modeling program. Each component has a computer user interface of an extensive command set. All of these programs make use of a comprehensive B-spline mathematics subroutine library, which can be used for a wide variety of interpolation problems and other geometric calculations. Many other user aids, such as automatic saving of the geometric and finite element data bases and hidden line removal, are available. This interactive finite element modeling capability can produce a complete finite element model, producing an output file of grid and element data.

Advancing MEMS Technology Usage through the MUMPS (Multi-User MEMS Processes) Program

NASA Technical Reports Server (NTRS)

Koester, D. A.; Markus, K. W.; Dhuler, V.; Mahadevan, R.; Cowen, A.

1995-01-01

In order to help provide access to advanced micro-electro-mechanical systems (MEMS) technologies and lower the barriers for both industry and academia, the Microelectronic Center of North Carolina (MCNC) and ARPA have developed a program which provides users with access to both MEMS processes and advanced electronic integration techniques. The four distinct aspects of this program, the multi-user MEMS processes (MUMP's), the consolidated micro-mechanical element library, smart MEMS, and the MEMS technology network are described in this paper. MUMP's is an ARPA-supported program created to provide inexpensive access to MEMS technology in a multi-user environment. It is both a proof-of-concept and educational tool that aids in the development of MEMS in the domestic community. MUMP's technologies currently include a 3-layer poly-silicon surface micromachining process and LIGA (lithography, electroforming, and injection molding) processes that provide reasonable design flexibility within set guidelines. The consolidated micromechanical element library (CaMEL) is a library of active and passive MEMS structures that can be downloaded by the MEMS community via the internet. Smart MEMS is the development of advanced electronics integration techniques for MEMS through the application of flip chip technology. The MEMS technology network (TechNet) is a menu of standard substrates and MEMS fabrication processes that can be purchased and combined to create unique process flows. TechNet provides the MEMS community greater flexibility and enhanced technology accessibility.

Role versatility among men who have sex with men in urban Peru.

PubMed

Goodreau, Steven M; Peinado, Jesus; Goicochea, Pedro; Vergara, Jorge; Ojeda, Nora; Casapia, Martin; Ortiz, Abner; Zamalloa, Victoria; Galvan, Rosa; Sanchez, Jorge R

2007-08-01

Role versatility refers to the practice in which individual men who have sex with men (MSM) play both insertive and receptive sexual roles over time. Versatility has been thought to be relatively uncommon among Latin American MSM but possibly rising. Versatility has also been shown to be a potentially large population-level risk factor for HIV infection. In this study we examine the correlates of versatile behavior and identity among 2,655 MSM in six Peruvian cities. Versatile behavior with recent male partners was found in 9% of men and versatile ("moderno") identity was reported by 16%. Significant predictors included high education, white-collar occupation, sex work, and residence in Lima. Age was not significant in any analysis. Since sex work is negatively correlated with other predictors, versatile men appear to comprise two distinct sub-populations. Insertive-only men appear to play a strong role in bridging the HIV epidemic between MSM and women.

Scaffold Library for Tissue Engineering: A Geometric Evaluation

PubMed Central

Chantarapanich, Nattapon; Puttawibul, Puttisak; Sucharitpwatskul, Sedthawatt; Jeamwatthanachai, Pongnarin; Inglam, Samroeng; Sitthiseripratip, Kriskrai

2012-01-01

Tissue engineering scaffold is a biological substitute that aims to restore, to maintain, or to improve tissue functions. Currently available manufacturing technology, that is, additive manufacturing is essentially applied to fabricate the scaffold according to the predefined computer aided design (CAD) model. To develop scaffold CAD libraries, the polyhedrons could be used in the scaffold libraries development. In this present study, one hundred and nineteen polyhedron models were evaluated according to the established criteria. The proposed criteria included considerations on geometry, manufacturing feasibility, and mechanical strength of these polyhedrons. CAD and finite element (FE) method were employed as tools in evaluation. The result of evaluation revealed that the close-cellular scaffold included truncated octahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. In addition, the suitable polyhedrons for using as open-cellular scaffold libraries included hexahedron, truncated octahedron, truncated hexahedron, cuboctahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. However, not all pore size to beam thickness ratios (PO : BT) were good for making the open-cellular scaffold. The PO : BT ratio of each library, generating the enclosed pore inside the scaffold, was excluded to avoid the impossibility of material removal after the fabrication. The close-cellular libraries presented the constant porosity which is irrespective to the different pore sizes. The relationship between PO : BT ratio and porosity of open-cellular scaffold libraries was displayed in the form of Logistic Power function. The possibility of merging two different types of libraries to produce the composite structure was geometrically evaluated in terms of the intersection index and was mechanically evaluated by means of FE analysis to observe the stress level. The couples of polyhedrons presenting low intersection index and high stress level were excluded. Good couples for producing the reinforced scaffold were hexahedron-truncated hexahedron and cuboctahedron-rhombitruncated cuboctahedron. PMID:23056147

Combinatorial synthesis and hydrogenation of Mg/Al libraries prepared by electron beam physical vapor deposition.

PubMed

Garcia, Gemma; Doménech-Ferrer, Roger; Pi, Francesc; Santiso, Josep; Rodríguez-Viejo, Javier

2007-01-01

We have grown thin film libraries of the Mg-Al system using a high-throughput synthesis methodology that combines the sequential deposition of pure elements (Mg and Al) by an electron-beam (e-beam) evaporation technique and the use of a special set of moving shadow masks. This novel mask has been designed to simultaneously prepare four identical arrays of different compositions that will permit the characterization of the same library after several treatments. Wavelength dispersive spectroscopy (WDS) and micro-X-ray diffraction have been used as high-throughput screening techniques for the determination of the composition and structure of every member of the library in the as-deposited state and after hydrogenation at 1 atm of H2 during 24 h at three different temperatures: 60, 80, and 110 degrees C. We have analyzed the influence of the Mg-Al ratio on the hydrogenation of magnesium, as well as on the appearance of complex hydride phases. We have also found that aluminum can act as a catalyzer for the hydrogenation reaction of magnesium.

INTRIGOSS: A new Library of High Resolution Synthetic Spectra

NASA Astrophysics Data System (ADS)

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.

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Optical mapping reveals a large genetic inversion between two methicillin-resistant Staphylococcus aureus strains.

PubMed

Shukla, Sanjay K; Kislow, Jennifer; Briska, Adam; Henkhaus, John; Dykes, Colin

2009-09-01

Staphylococcus aureus is a highly versatile and evolving bacterium of great clinical importance. S. aureus can evolve by acquiring single nucleotide polymorphisms and mobile genetic elements and by recombination events. Identification and location of novel genomic elements in a bacterial genome are not straightforward, unless the whole genome is sequenced. Optical mapping is a new tool that creates a high-resolution, in situ ordered restriction map of a bacterial genome. These maps can be used to determine genomic organization and perform comparative genomics to identify genomic rearrangements, such as insertions, deletions, duplications, and inversions, compared to an in silico (virtual) restriction map of a known genome sequence. Using this technology, we report here the identification, approximate location, and characterization of a genetic inversion of approximately 500 kb of a DNA element between the NRS387 (USA800) and FPR3757 (USA300) strains. The presence of the inversion and location of its junction sites were confirmed by site-specific PCR and sequencing. At both the left and right junction sites in NRS387, an IS1181 element and a 73-bp sequence were identified as inverted repeats, which could explain the possible mechanism of the inversion event.

Nanostructured mesophase electrode materials: modulating charge-storage behavior by thermal treatment.

PubMed

Kong, Hye Jeong; Kim, Saerona; Le, Thanh-Hai; Kim, Yukyung; Park, Geunsu; Park, Chul Soon; Kwon, Oh Seok; Yoon, Hyeonseok

2017-11-16

3D nanostructured carbonaceous electrode materials with tunable capacitive phases were successfully developed using graphene/particulate polypyrrole (PPy) nanohybrid (GPNH) precursors without a separate process for incorporating heterogeneous species. The electrode material, namely carbonized GPNHs (CGPNHs) featured a mesophase capacitance consisting of both electric double-layer (EDL) capacitive and pseudocapacitive elements at the molecular level. The ratio of EDL capacitive element to pseudocapacitive element (E-to-P) in the mesophase electrode materials was controlled by varying the PPy-to-graphite weight (P w /G w ) ratio and by heat treatment (T H ), which was demonstrated by characterizing the CGPNHs with elemental analysis, cyclic voltammetry, and a charge/discharge test. The concept of the E-to-P ratio (EPR) index was first proposed to easily identify the capacitive characteristics of the mesophase electrode using a numerical algorithm, which was reasonably consistent with the experimental findings. Finally, the CGPNHs were integrated into symmetric two-electrode capacitor cells, which rendered excellent energy and power densities in both aqueous and ionic liquid electrolytes. It is anticipated that our approach could be widely extended to fabricating versatile hybrid electrode materials with estimation of their capacitive characteristics.