Visual programming for next-generation sequencing data analytics.

PubMed

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

Extending Iris: The VAO SED Analysis Tool

NASA Astrophysics Data System (ADS)

Laurino, O.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2013-10-01

Iris is a tool developed by the Virtual Astronomical Observatory (VAO) for building and analyzing Spectral Energy Distributions (SEDs). Iris was designed to be extensible, so that new components and models can be developed by third parties and then included at runtime. Iris can be extended in different ways: new file readers allow users to integrate data in custom formats into Iris SEDs; new models can be fitted to the data, in the form of template libraries for template fitting, data tables, and arbitrary Python functions. The interoperability-centered design of Iris and the Virtual Observatory standards and protocols can enable new science functionalities involving SED data.

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

NASA Astrophysics Data System (ADS)

Kesseli, Aurora Y.; West, Andrew A.; Veyette, Mark; Harrison, Brandon; Feldman, Dan; Bochanski, John J.

2017-06-01

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

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

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

Kesseli, Aurora Y.; West, Andrew A.; Veyette, Mark

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

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

DOE PAGES

Jones, Susan; Thornton, Janet M.

2003-01-01

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. Inmore » this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.« less

Multi-Station Broad Regional Event Detection Using Waveform Correlation

NASA Astrophysics Data System (ADS)

Slinkard, M.; Stephen, H.; Young, C. J.; Eckert, R.; Schaff, D. P.; Richards, P. G.

2013-12-01

Previous waveform correlation studies have established the occurrence of repeating seismic events in various regions, and the utility of waveform-correlation event-detection on broad regional or even global scales to find events currently not included in traditionally-prepared bulletins. The computational burden, however, is high, limiting previous experiments to relatively modest template libraries and/or processing time periods. We have developed a distributed computing waveform correlation event detection utility that allows us to process years of continuous waveform data with template libraries numbering in the thousands. We have used this system to process several years of waveform data from IRIS stations in East Asia, using libraries of template events taken from global and regional bulletins. Detections at a given station are confirmed by 1) comparison with independent bulletins of seismicity, and 2) consistent detections at other stations. We find that many of the detected events are not in traditional catalogs, hence the multi-station comparison is essential. In addition to detecting the similar events, we also estimate magnitudes very precisely based on comparison with the template events (when magnitudes are available). We have investigated magnitude variation within detected families of similar events, false alarm rates, and the temporal and spatial reach of templates.

The Plotting Library http://astroplotlib.stsci.edu

NASA Astrophysics Data System (ADS)

Úbeda, L.

2014-05-01

astroplotlib is a multi-language astronomical library of plots. It is a collection of software templates that are useful to create paper-quality figures. All current templates are coded in IDL, some in Python and Mathematica. This free resource supported at Space Telescope Science Institute allows users to download any plot and customize it to their own needs. It is also intended as an educational tool.

Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil

PubMed Central

Nogales, Balbina; Moore, Edward R. B.; Llobet-Brossa, Enrique; Rossello-Mora, Ramon; Amann, Rudolf; Timmis, Kenneth N.

2001-01-01

The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia and Pseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of the Proteobacteria, and to the genus Burkholderia in particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study. PMID:11282645

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.

PubMed

Sanders, Ashley D; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Lansdorp, Peter M

2017-06-01

The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication. This protocol, which takes up to 4 d to complete, relies on the directionality of DNA, in which each single strand of a DNA molecule is distinguished based on its 5'-3' orientation. Culturing cells in a thymidine analog for one round of cell division labels nascent DNA strands, allowing for their selective removal during genomic library construction. To preserve directionality of template strands, genomic preamplification is bypassed and labeled nascent strands are nicked and not amplified during library preparation. Each single-cell library is multiplexed for pooling and sequencing, and the resulting sequence data are aligned, mapping to either the minus or plus strand of the reference genome, to assign template strand states for each chromosome in the cell. The major adaptations to conventional single-cell sequencing protocols include harvesting of daughter cells after a single round of BrdU incorporation, bypassing of whole-genome amplification, and removal of the BrdU + strand during Strand-seq library preparation. By sequencing just template strands, the structure and identity of each homolog are preserved.

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

A comparison of different functions for predicted protein model quality assessment.

PubMed

Li, Juan; Fang, Huisheng

2016-07-01

In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template library was developed and 138 target sequences were modeled. The target sequences were all distant from the proteins in the template library and were aligned with template library proteins on the basis of the transformation matrix. The quality of each model was first assessed with QMEAN and its six parameters, which are C_β interaction energy (C_beta), all-atom pairwise energy (PE), solvation energy (SE), torsion angle energy (TAE), secondary structure agreement (SSA), and solvent accessibility agreement (SAE). Finally, the alignment score (score) was also used to assess the quality of model. Hence, a total of eight parameters (i.e., QMEAN, C_beta, PE, SE, TAE, SSA, SAE, score) were independently used to assess the quality of each model. The results indicate that SSA is the best parameter to estimate the quality of the model.

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

SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.

PubMed

Litfin, Thomas; Zhou, Yaoqi; Yang, Yuedong

2017-04-15

The high cost of drug discovery motivates the development of accurate virtual screening tools. Binding-homology, which takes advantage of known protein-ligand binding pairs, has emerged as a powerful discrimination technique. In order to exploit all available binding data, modelled structures of ligand-binding sequences may be used to create an expanded structural binding template library. SPOT-Ligand 2 has demonstrated significantly improved screening performance over its previous version by expanding the template library 15 times over the previous one. It also performed better than or similar to other binding-homology approaches on the DUD and DUD-E benchmarks. The server is available online at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. 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

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Developing a Strategic Plan for Transitioning to Healthcare Knowledge Services Centers (HKSCs)

PubMed Central

Goldstein, H. Mark; Coletti, Margaret H.

2012-01-01

Facing a negative trend in the form of downsizing, layoffs, and closures, a small committee of hospital librarians in New England was formed in 2004 to provide library advocacy. Between 2008 and 2010, 23 hospital libraries closed in New England. In 2010, the committee shifted its focus from advocacy to a platform for change. This resulted in the creation of the Healthcare Knowledge Services Center (HKSC) Template. The Template is the basis for a 3-phased, 5-year strategic plan to establish several regional pilots, transitioning traditional hospital libraries to healthcare knowledge services centers. This article focuses on Phase One of the strategic plan, Development. PMID:23125551

Mapping monomeric threading to protein-protein structure prediction.

PubMed

Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2013-03-25

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD <2.5 Å by SPRING is 134% and 167% higher than these competing methods. SPRING is controlled with ZDOCK on 77 docking benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

PoLi: A Virtual Screening Pipeline Based On Template Pocket And Ligand Similarity

PubMed Central

Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

2015-01-01

Often in pharmaceutical research, the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand binding pockets in proteins is small. PoLi identifies similar ligand binding pockets in a holo-template protein library, selectively copies relevant parts of template ligands and uses them for VS. In practice, PoLi is a hybrid structure and ligand based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6 respectively, in the top 1% of the screened library. In contrast, traditional docking based VS using AutoDock Vina and homology-based VS using FINDSITEfilt have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods. PMID:26225536

Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

PubMed Central

Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T.; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic

2013-01-01

Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries. PMID:24205269

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

DOE PAGES

Bowers, Robert M.; Clum, Alicia; Tice, Hope; ...

2015-10-24

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

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

Bowers, Robert M.; Clum, Alicia; Tice, Hope

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

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.

Targeted RNA-Sequencing with Competitive Multiplex-PCR Amplicon Libraries

PubMed Central

Blomquist, Thomas M.; Crawford, Erin L.; Lovett, Jennie L.; Yeo, Jiyoun; Stanoszek, Lauren M.; Levin, Albert; Li, Jia; Lu, Mei; Shi, Leming; Muldrew, Kenneth; Willey, James C.

2013-01-01

Whole transcriptome RNA-sequencing is a powerful tool, but is costly and yields complex data sets that limit its utility in molecular diagnostic testing. A targeted quantitative RNA-sequencing method that is reproducible and reduces the number of sequencing reads required to measure transcripts over the full range of expression would be better suited to diagnostic testing. Toward this goal, we developed a competitive multiplex PCR-based amplicon sequencing library preparation method that a) targets only the sequences of interest and b) controls for inter-target variation in PCR amplification during library preparation by measuring each transcript native template relative to a known number of synthetic competitive template internal standard copies. To determine the utility of this method, we intentionally selected PCR conditions that would cause transcript amplification products (amplicons) to converge toward equimolar concentrations (normalization) during library preparation. We then tested whether this approach would enable accurate and reproducible quantification of each transcript across multiple library preparations, and at the same time reduce (through normalization) total sequencing reads required for quantification of transcript targets across a large range of expression. We demonstrate excellent reproducibility (R2 = 0.997) with 97% accuracy to detect 2-fold change using External RNA Controls Consortium (ERCC) reference materials; high inter-day, inter-site and inter-library concordance (R2 = 0.97–0.99) using FDA Sequencing Quality Control (SEQC) reference materials; and cross-platform concordance with both TaqMan qPCR (R2 = 0.96) and whole transcriptome RNA-sequencing following “traditional” library preparation using Illumina NGS kits (R2 = 0.94). Using this method, sequencing reads required to accurately quantify more than 100 targeted transcripts expressed over a 107-fold range was reduced more than 10,000-fold, from 2.3×109 to 1.4×105 sequencing reads. These studies demonstrate that the competitive multiplex-PCR amplicon library preparation method presented here provides the quality control, reproducibility, and reduced sequencing reads necessary for development and implementation of targeted quantitative RNA-sequencing biomarkers in molecular diagnostic testing. PMID:24236095

Green Power Partnership Resource Library: Solicitations

EPA Pesticide Factsheets

Green Power Partnership Resource Library includes documents meant to aid organizations and individuals in navigating the renewable energy procurement and renewable energy project development processes. It includes guidance documents, templates and actual e

A linear concatenation strategy to construct 5'-enriched amplified cDNA libraries using multiple displacement amplification.

PubMed

Gadkar, Vijay J; Filion, Martin

2013-06-01

In various experimental systems, limiting available amounts of RNA may prevent a researcher from performing large-scale analyses of gene transcripts. One way to circumvent this is to 'pre-amplify' the starting RNA/cDNA, so that sufficient amounts are available for any downstream analysis. In the present study, we report the development of a novel protocol for constructing amplified cDNA libraries using the Phi29 DNA polymerase based multiple displacement amplification (MDA) system. Using as little as 200 ng of total RNA, we developed a linear concatenation strategy to make the single-stranded cDNA template amenable for MDA. The concatenation, made possible by the template switching property of the reverse transcriptase enzyme, resulted in the amplified cDNA library with intact 5' ends. MDA generated micrograms of template, allowing large-scale polymerase chain reaction analyses or other large-scale downstream applications. As the amplified cDNA library contains intact 5' ends, it is also compatible with 5' RACE analyses of specific gene transcripts. Empirical validation of this protocol is demonstrated on a highly characterized (tomato) and an uncharacterized (corn gromwell) experimental system.

The Role of Standardized and Study-specific Human Brain Diffusion Tensor Templates in Inter-subject Spatial Normalization

PubMed Central

Zhang, Shengwei; Arfanakis, Konstantinos

2012-01-01

Purpose To investigate the effect of standardized and study-specific human brain diffusion tensor templates on the accuracy of spatial normalization, without ignoring the important roles of data quality and registration algorithm effectiveness. Materials and Methods Two groups of diffusion tensor imaging (DTI) datasets, with and without visible artifacts, were normalized to two standardized diffusion tensor templates (IIT2, ICBM81) as well as study-specific templates, using three registration approaches. The accuracy of inter-subject spatial normalization was compared across templates, using the most effective registration technique for each template and group of data. Results It was demonstrated that, for DTI data with visible artifacts, the study-specific template resulted in significantly higher spatial normalization accuracy than standardized templates. However, for data without visible artifacts, the study-specific template and the standardized template of higher quality (IIT2) resulted in similar normalization accuracy. Conclusion For DTI data with visible artifacts, a carefully constructed study-specific template may achieve higher normalization accuracy than that of standardized templates. However, as DTI data quality improves, a high-quality standardized template may be more advantageous than a study-specific template, since in addition to high normalization accuracy, it provides a standard reference across studies, as well as automated localization/segmentation when accompanied by anatomical labels. PMID:23034880

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

PubMed

Oyola, Samuel O; Otto, Thomas D; Gu, Yong; Maslen, Gareth; Manske, Magnus; Campino, Susana; Turner, Daniel J; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Swerdlow, Harold P; Quail, Michael A

2012-01-03

Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.

MLS data segmentation using Point Cloud Library procedures. (Polish Title: Segmentacja danych MLS z użyciem procedur Point Cloud Library)

NASA Astrophysics Data System (ADS)

Grochocka, M.

2013-12-01

Mobile laser scanning is dynamically developing measurement technology, which is becoming increasingly widespread in acquiring three-dimensional spatial information. Continuous technical progress based on the use of new tools, technology development, and thus the use of existing resources in a better way, reveals new horizons of extensive use of MLS technology. Mobile laser scanning system is usually used for mapping linear objects, and in particular the inventory of roads, railways, bridges, shorelines, shafts, tunnels, and even geometrically complex urban spaces. The measurement is done from the perspective of use of the object, however, does not interfere with the possibilities of movement and work. This paper presents the initial results of the segmentation data acquired by the MLS. The data used in this work was obtained as part of an inventory measurement infrastructure railway line. Measurement of point clouds was carried out using a profile scanners installed on the railway platform. To process the data, the tools of 'open source' Point Cloud Library was used. These tools allow to use templates of programming libraries. PCL is an open, independent project, operating on a large scale for processing 2D/3D image and point clouds. Software PCL is released under the terms of the BSD license (Berkeley Software Distribution License), which means it is a free for commercial and research use. The article presents a number of issues related to the use of this software and its capabilities. Segmentation data is based on applying the templates library pcl_ segmentation, which contains the segmentation algorithms to separate clusters. These algorithms are best suited to the processing point clouds, consisting of a number of spatially isolated regions. Template library performs the extraction of the cluster based on the fit of the model by the consensus method samples for various parametric models (planes, cylinders, spheres, lines, etc.). Most of the mathematical operation is carried out on the basis of Eigen library, a set of templates for linear algebra.

An In Vitro Translation, Selection, and Amplification System for Peptide Nucleic Acids

PubMed Central

Brudno, Yevgeny; Birnbaum, Michael E.; Kleiner, Ralph E.; Liu, David R.

2009-01-01

Methods to evolve synthetic, rather than biological, polymers could significantly expand the functional potential of polymers that emerge from in vitro evolution. Requirements for synthetic polymer evolution include: (i) sequence-specific polymerization of synthetic building blocks on an amplifiable template; (ii) display of the newly translated polymer strand in a manner that allows it to adopt folded structures; (iii) selection of synthetic polymer libraries for desired binding or catalytic properties; and (iv) amplification of template sequences surviving selection in a manner that allows subsequent translation. Here we report the development of such a system for peptide nucleic acids (PNAs) using a set of twelve PNA pentamer building blocks. We validated the system by performing six iterated cycles of translation, selection, and amplification on a library of 4.3 × 108 PNA-encoding DNA templates and observed >1,000,000-fold overall enrichment of a template encoding a biotinylated (streptavidin-binding) PNA. These results collectively provide an experimental foundation for PNA evolution in the laboratory. PMID:20081830

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures.

PubMed

Vallat, Brinda; Madrid-Aliste, Carlos; Fiser, Andras

2015-08-01

Predicting the three-dimensional structure of proteins from their amino acid sequences remains a challenging problem in molecular biology. While the current structural coverage of proteins is almost exclusively provided by template-based techniques, the modeling of the rest of the protein sequences increasingly require template-free methods. However, template-free modeling methods are much less reliable and are usually applicable for smaller proteins, leaving much space for improvement. We present here a novel computational method that uses a library of supersecondary structure fragments, known as Smotifs, to model protein structures. The library of Smotifs has saturated over time, providing a theoretical foundation for efficient modeling. The method relies on weak sequence signals from remotely related protein structures to create a library of Smotif fragments specific to the target protein sequence. This Smotif library is exploited in a fragment assembly protocol to sample decoys, which are assessed by a composite scoring function. Since the Smotif fragments are larger in size compared to the ones used in other fragment-based methods, the proposed modeling algorithm, SmotifTF, can employ an exhaustive sampling during decoy assembly. SmotifTF successfully predicts the overall fold of the target proteins in about 50% of the test cases and performs competitively when compared to other state of the art prediction methods, especially when sequence signal to remote homologs is diminishing. Smotif-based modeling is complementary to current prediction methods and provides a promising direction in addressing the structure prediction problem, especially when targeting larger proteins for modeling.

The protein structure prediction problem could be solved using the current PDB library

PubMed Central

Zhang, Yang; Skolnick, Jeffrey

2005-01-01

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Å with ≈82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Å (97% of them below 4 Å). On average, the RMSD of full-length models is 2.25 Å, with aligned regions improved from 2.5 Å to 1.88 Å, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. PMID:15653774

LOTUS 1-2-3 and Decision Support: Allocating the Monograph Budget.

ERIC Educational Resources Information Center

Perry-Holmes, Claudia

1985-01-01

Describes the use of electronic spreadsheet software for library decision support systems using personal computers. Discussion covers templates, formulas for allocating the materials budget, LOTUS 1-2-3 and budget allocations, choosing a formula, the spreadsheet itself, graphing capabilities, and advantages and disadvantages of templates. Six…

Design and Synthesis of Biaryl DNA-Encoded Libraries.

PubMed

Ding, Yun; Franklin, G Joseph; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Clark, Matthew A; Skinner, Steven R; Belyanskaya, Svetlana

2016-10-10

DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).

Template-based de novo design for type II kinase inhibitors and its extented application to acetylcholinesterase inhibitors.

PubMed

Su, Bo-Han; Huang, Yi-Syuan; Chang, Chia-Yun; Tu, Yi-Shu; Tseng, Yufeng J

2013-10-31

There is a compelling need to discover type II inhibitors targeting the unique DFG-out inactive kinase conformation since they are likely to possess greater potency and selectivity relative to traditional type I inhibitors. Using a known inhibitor, such as a currently available and approved drug or inhibitor, as a template to design new drugs via computational de novo design is helpful when working with known ligand-receptor interactions. This study proposes a new template-based de novo design protocol to discover new inhibitors that preserve and also optimize the binding interactions of the type II kinase template. First, sorafenib (Nexavar) and nilotinib (Tasigna), two type II inhibitors with different ligand-receptor interactions, were selected as the template compounds. The five-step protocol can reassemble each drug from a large fragment library. Our procedure demonstrates that the selected template compounds can be successfully reassembled while the key ligand-receptor interactions are preserved. Furthermore, to demonstrate that the algorithm is able to construct more potent compounds, we considered kinase inhibitors and other protein dataset, acetylcholinesterase (AChE) inhibitors. The de novo optimization was initiated using a template compound possessing a less than optimal activity from a series of aminoisoquinoline and TAK-285 inhibiting type II kinases, and E2020 derivatives inhibiting AChE respectively. Three compounds with greater potency than the template compound were discovered that were also included in the original congeneric series. This template-based lead optimization protocol with the fragment library can help to design compounds with preferred binding interactions of known inhibitors automatically and further optimize the compounds in the binding pockets.

DNA polymerase preference determines PCR priming efficiency.

PubMed

Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

2014-01-30

Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially available DNA polymerases. The results suggest that the interaction of the DNA polymerase with the primer:template junction during the initiation of DNA polymerization is very important in terms of overall amplification bias and has broader implications for both the primer design process and multiplex PCR.

Sequence-independent construction of ordered combinatorial libraries with predefined crossover points.

PubMed

Jézéquel, Laetitia; Loeper, Jacqueline; Pompon, Denis

2008-11-01

Combinatorial libraries coding for mosaic enzymes with predefined crossover points constitute useful tools to address and model structure-function relationships and for functional optimization of enzymes based on multivariate statistics. The presented method, called sequence-independent generation of a chimera-ordered library (SIGNAL), allows easy shuffling of any predefined amino acid segment between two or more proteins. This method is particularly well adapted to the exchange of protein structural modules. The procedure could also be well suited to generate ordered combinatorial libraries independent of sequence similarities in a robotized manner. Sequence segments to be recombined are first extracted by PCR from a single-stranded template coding for an enzyme of interest using a biotin-avidin-based method. This technique allows the reduction of parental template contamination in the final library. Specific PCR primers allow amplification of two complementary mosaic DNA fragments, overlapping in the region to be exchanged. Fragments are finally reassembled using a fusion PCR. The process is illustrated via the construction of a set of mosaic CYP2B enzymes using this highly modular approach.

VizieR Online Data Catalog: 05 through L3 empirical stellar spectra from SDSS (Kesseli+, 2017)

NASA Astrophysics Data System (ADS)

Kesseli, A. Y.; West, A. A.; Veyette, M.; Harrison, B.; Feldman, D.; Bochanski, J. J.

2017-08-01

We present a library of empirical stellar spectra created using spectra from the Sloan Digital Sky Survey's Baryon Oscillation Spectroscopic Survey. The templates cover spectral types O5 through L3, are binned by metallicity from -2.0dex through +1.0dex, and are separated into main-sequence (dwarf) stars and giant stars. With recently developed M dwarf metallicity indicators, we are able to extend the metallicity bins down through the spectral subtype M8, making this the first empirical library with this degree of temperature and metallicity coverage. The wavelength coverage for the templates is from 3650 to 10200Å at a resolution of better than R~2000. Using the templates, we identify trends in color space with metallicity and surface gravity, which will be useful for analyzing large data sets from upcoming missions like the Large Synoptic Survey Telescope. Along with the templates, we are releasing a code for automatically (and/or visually) identifying the spectral type and metallicity of a star. (3 data files).

Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries.

PubMed

Huang, Renhua; Fang, Pete; Kay, Brian K

2012-09-01

Site-directed mutagenesis is routinely performed in protein engineering experiments. One method, termed Kunkel mutagenesis, is frequently used for constructing libraries of peptide or protein variants in M13 bacteriophage, followed by affinity selection of phage particles. To make this method more efficient, the following two modifications were introduced: culture was incubated at 25°C for phage replication, which yielded two- to sevenfold more single-stranded DNA template compared to growth at 37°C, and restriction endonuclease recognition sites were used to remove non-recombinants. With both of the improvements, we could construct primary libraries of high complexity and that were 99-100% recombinant. Finally, with a third modification to the standard protocol of Kunkel mutagenesis, two secondary (mutagenic) libraries of a fibronectin type III (FN3) monobody were constructed with DNA segments that were amplified by error-prone and asymmetric PCR. Two advantages of this modification are that it bypasses the lengthy steps of restriction enzyme digestion and ligation, and that the pool of phage clones, recovered after affinity selection, can be used directly to generate a secondary library. Screening one of the two mutagenic libraries yielded variants that bound two- to fourfold tighter to human Pak1 kinase than the starting clone. The protocols described in this study should accelerate the discovery of phage-displayed recombinant affinity reagents. Copyright © 2012 Elsevier Inc. All rights reserved.

The Environment for Application Software Integration and Execution (EASIE), version 1.0. Volume 2: Program integration guide

NASA Technical Reports Server (NTRS)

Jones, Kennie H.; Randall, Donald P.; Stallcup, Scott S.; Rowell, Lawrence F.

1988-01-01

The Environment for Application Software Integration and Execution, EASIE, provides a methodology and a set of software utility programs to ease the task of coordinating engineering design and analysis codes. EASIE was designed to meet the needs of conceptual design engineers that face the task of integrating many stand-alone engineering analysis programs. Using EASIE, programs are integrated through a relational data base management system. In volume 2, the use of a SYSTEM LIBRARY PROCESSOR is used to construct a DATA DICTIONARY describing all relations defined in the data base, and a TEMPLATE LIBRARY. A TEMPLATE is a description of all subsets of relations (including conditional selection criteria and sorting specifications) to be accessed as input or output for a given application. Together, these form the SYSTEM LIBRARY which is used to automatically produce the data base schema, FORTRAN subroutines to retrieve/store data from/to the data base, and instructions to a generic REVIEWER program providing review/modification of data for a given template. Automation of these functions eliminates much of the tedious, error prone work required by the usual approach to data base integration.

A template-based approach for responsibility management in executable business processes

NASA Astrophysics Data System (ADS)

Cabanillas, Cristina; Resinas, Manuel; Ruiz-Cortés, Antonio

2018-05-01

Process-oriented organisations need to manage the different types of responsibilities their employees may have w.r.t. the activities involved in their business processes. Despite several approaches provide support for responsibility modelling, in current Business Process Management Systems (BPMS) the only responsibility considered at runtime is the one related to performing the work required for activity completion. Others like accountability or consultation must be implemented by manually adding activities in the executable process model, which is time-consuming and error-prone. In this paper, we address this limitation by enabling current BPMS to execute processes in which people with different responsibilities interact to complete the activities. We introduce a metamodel based on Responsibility Assignment Matrices (RAM) to model the responsibility assignment for each activity, and a flexible template-based mechanism that automatically transforms such information into BPMN elements, which can be interpreted and executed by a BPMS. Thus, our approach does not enforce any specific behaviour for the different responsibilities but new templates can be modelled to specify the interaction that best suits the activity requirements. Furthermore, libraries of templates can be created and reused in different processes. We provide a reference implementation and build a library of templates for a well-known set of responsibilities.

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Faunus: An object oriented framework for molecular simulation

PubMed Central

Lund, Mikael; Trulsson, Martin; Persson, Björn

2008-01-01

Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

Farm 2 Fly | National Agricultural Library

Science.gov Websites

identify gaps where further research, development or investment may be needed to facilitate readiness of a FSRL checklist and report template for performing a feedstock evaluation, as well as examples of a materials and residues, and a template for the report, as well as examples. Farm2fly Program csv xlsx 1 2 3

Encoded Library Synthesis Using Chemical Ligation and the Discovery of sEH Inhibitors from a 334-Million Member Library

NASA Astrophysics Data System (ADS)

Litovchick, Alexander; Dumelin, Christoph E.; Habeshian, Sevan; Gikunju, Diana; Guié, Marie-Aude; Centrella, Paolo; Zhang, Ying; Sigel, Eric A.; Cuozzo, John W.; Keefe, Anthony D.; Clark, Matthew A.

2015-06-01

A chemical ligation method for construction of DNA-encoded small-molecule libraries has been developed. Taking advantage of the ability of the Klenow fragment of DNA polymerase to accept templates with triazole linkages in place of phosphodiesters, we have designed a strategy for chemically ligating oligonucleotide tags using cycloaddition chemistry. We have utilized this strategy in the construction and selection of a small molecule library, and successfully identified inhibitors of the enzyme soluble epoxide hydrolase.

Incorporating the Internet into Traditional Library Instruction.

ERIC Educational Resources Information Center

Fonseca, Tony; King, Monica

2000-01-01

Presents a template for teaching traditional library research and one for incorporating the Web. Highlights include the differences between directories and search engines; devising search strategies; creating search terms; how to choose search engines; evaluating online resources; helpful Web sites; and how to read URLs to evaluate a Web site's…

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

SynapticDB, effective web-based management and sharing of data from serial section electron microscopy.

PubMed

Shi, Bitao; Bourne, Jennifer; Harris, Kristen M

2011-03-01

Serial section electron microscopy (ssEM) is rapidly expanding as a primary tool to investigate synaptic circuitry and plasticity. The ultrastructural images collected through ssEM are content rich and their comprehensive analysis is beyond the capacity of an individual laboratory. Hence, sharing ultrastructural data is becoming crucial to visualize, analyze, and discover the structural basis of synaptic circuitry and function in the brain. We devised a web-based management system called SynapticDB (http://synapses.clm.utexas.edu/synapticdb/) that catalogues, extracts, analyzes, and shares experimental data from ssEM. The management strategy involves a library with check-in, checkout and experimental tracking mechanisms. We developed a series of spreadsheet templates (MS Excel, Open Office spreadsheet, etc) that guide users in methods of data collection, structural identification, and quantitative analysis through ssEM. SynapticDB provides flexible access to complete templates, or to individual columns with instructional headers that can be selected to create user-defined templates. New templates can also be generated and uploaded. Research progress is tracked via experimental note management and dynamic PDF forms that allow new investigators to follow standard protocols and experienced researchers to expand the range of data collected and shared. The combined use of templates and tracking notes ensures that the supporting experimental information is populated into the database and associated with the appropriate ssEM images and analyses. We anticipate that SynapticDB will serve future meta-analyses towards new discoveries about the composition and circuitry of neurons and glia, and new understanding about structural plasticity during development, behavior, learning, memory, and neuropathology.

Expression Templates for Truncated Power Series

NASA Astrophysics Data System (ADS)

Cary, John R.; Shasharina, Svetlana G.

1997-05-01

Truncated power series are used extensively in accelerator transport modeling for rapid tracking and analysis of nonlinearity. Such mathematical objects are naturally represented computationally as objects in C++. This is more intuitive and produces more transparent code through operator overloading. However, C++ object use often comes with a computational speed loss due, e.g., to the creation of temporaries. We have developed a subset of truncated power series expression templates(http://monet.uwaterloo.ca/blitz/). Such expression templates use the powerful template processing facility of C++ to combine complicated expressions into series operations that exectute more rapidly. We compare computational speeds with existing truncated power series libraries.

One New Method to Generate 3-Dimensional Virtual Mannequin

NASA Astrophysics Data System (ADS)

Xiu-jin, Shi; Zhi-jun, Wang; Jia-jin, Le

The personal virtual mannequin is very important in electronic made to measure (eMTM) system. There is one new easy method to generate personal virtual mannequin. First, the characteristic information of customer's body is got from two photos. Secondly, some human body part templates corresponding with the customer are selected from the templates library. Thirdly, these templates are modified and assembled according to certain rules to generate a personalized 3-dimensional human, and then the virtual mannequin is realized. Experimental result shows that the method is easy and feasible.

Microbeads display of proteins using emulsion PCR and cell-free protein synthesis.

PubMed

Gan, Rui; Yamanaka, Yumiko; Kojima, Takaaki; Nakano, Hideo

2008-01-01

We developed a method for coupling protein to its coding DNA on magnetic microbeads using emulsion PCR and cell-free protein synthesis in emulsion. A PCR mixture containing streptavidin-coated microbeads was compartmentalized by water-in-oil (w/o) emulsion with estimated 0.5 template molecules per droplet. The template molecules were amplified and immobilized on beads via bead-linked reverse primers and biotinylated forward primers. After amplification, the templates were sequentially labeled with streptavidin and biotinylated anti-glutathione S-transferase (GST) antibody. The pool of beads was then subjected to cell-free protein synthesis compartmentalized in another w/o emulsion, in which templates were coupled to their coding proteins. We mixed two types of DNA templates of Histidine6 tag (His6)-fused and FLAG tag-fused GST in a ratio of 1:1,000 (His6: FLAG) for use as a model DNA library. After incubation with fluorescein isothiocyanate (FITC)-labeled anti-His6 (C-term) antibody, the beads with the His6 gene were enriched 917-fold in a single-round screening by using flow cytometry. A library with a theoretical diversity of 10(6) was constructed by randomizing the middle four residues of the His6 tag. After a two-round screening, the randomized sequences were substantially converged to peptide-encoding sequences recognized by the anti-His6 antibody.

Encoded Library Synthesis Using Chemical Ligation and the Discovery of sEH Inhibitors from a 334-Million Member Library

PubMed Central

Litovchick, Alexander; Dumelin, Christoph E.; Habeshian, Sevan; Gikunju, Diana; Guié, Marie-Aude; Centrella, Paolo; Zhang, Ying; Sigel, Eric A.; Cuozzo, John W.; Keefe, Anthony D.; Clark, Matthew A.

2015-01-01

A chemical ligation method for construction of DNA-encoded small-molecule libraries has been developed. Taking advantage of the ability of the Klenow fragment of DNA polymerase to accept templates with triazole linkages in place of phosphodiesters, we have designed a strategy for chemically ligating oligonucleotide tags using cycloaddition chemistry. We have utilized this strategy in the construction and selection of a small molecule library, and successfully identified inhibitors of the enzyme soluble epoxide hydrolase. PMID:26061191

Next generation sequencing technology: a powerful tool for the genome characterization of sugarcane mosaic virus from Sorghum almum

USDA-ARS?s Scientific Manuscript database

Next generation sequencing (NGS) technology was used to analyze the occurrence of viruses in Sorghum almum plants in Florida exhibiting mosaic symptoms. Total RNA was extracted from symptomatic leaves and used as a template for cDNA library preparation. The resulting library was sequenced on an Illu...

Target-induced formation of neuraminidase inhibitors from in vitro virtual combinatorial libraries

PubMed Central

Hochgürtel, Matthias; Kroth, Heiko; Piecha, Dorothea; Hofmann, Michael W.; Nicolau, Claude; Krause, Sonja; Schaaf, Otmar; Sonnenmoser, Gabriele; Eliseev, Alexey V.

2002-01-01

Neuraminidase, a key enzyme responsible for influenza virus propagation, has been used as a template for selective synthesis of small subsets of its own inhibitors from theoretically highly diverse dynamic combinatorial libraries. We show that the library building blocks, aldehydes and amines, form significant amounts of the library components resulting from their coupling by reductive amination only in the presence of the enzyme. The target amplifies the best hits at least 120-fold. The dynamic libraries synthesized and screened in such an in vitro virtual mode form the components that possess high inhibitory activity, as confirmed by enzyme assays with independently synthesized individual compounds. PMID:11891312

Template-DTW based on inertial signals: Preliminary results for step characterization.

PubMed

Mantilla, Juan; Oudre, Laurent; Barrois, Remi; Vienne, Alienor; Ricard, Damien

2017-07-01

In this paper, we present a method for the creation of a library of inertial signals based on Dynamic Time Warping (DTW) for step characterization, with preliminary results in control subjects and patients with neurological diseases. Subjects performed a protocol including a 10 m straight walking, then turn back and walking for additional 10 m. The library is constructed with inertial signals (acceleration and angular velocities recorded in three directions) aligned with the DTW. Templates in the library are obtained for a specific cohort and for the different walking phases of the protocol. They are compared to the signal of a single subject by calculating a Pearson correlation coefficient. The method has been tested on a database of 864 exercises, obtained from 71 healthy controls, 24 patients with Parkinson disease and 48 patients with Radiation Induced Leukoencephalopathy (RIL). Pearson correlation classification reports a precision of about 85% for step detection. For exercise characterization the sensitivity is about 57%, 56% and 82% for Parkinson, RIL and control subjects respectively.

The Design of SimpleITK.

PubMed

Lowekamp, Bradley C; Chen, David T; Ibáñez, Luis; Blezek, Daniel

2013-01-01

SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org.

The Appropriateness of Language Found in Research Consent Form Templates: A Computational Linguistic Analysis.

PubMed

Villafranca, Alexander; Kereliuk, Stephanie; Hamlin, Colin; Johnson, Andrea; Jacobsohn, Eric

2017-01-01

To facilitate informed consent, consent forms should use language below the grade eight level. Research Ethics Boards (REBs) provide consent form templates to facilitate this goal. Templates with inappropriate language could promote consent forms that participants find difficult to understand. However, a linguistic analysis of templates is lacking. We reviewed the websites of 124 REBs for their templates. These included English language medical school REBs in Australia/New Zealand (n = 23), Canada (n = 14), South Africa (n = 8), the United Kingdom (n = 34), and a geographically-stratified sample from the United States (n = 45). Template language was analyzed using Coh-Metrix linguistic software (v.3.0, Memphis, USA). We evaluated the proportion of REBs with five key linguistic outcomes at or below grade eight. Additionally, we compared quantitative readability to the REBs' own readability standards. To determine if the template's country of origin or the presence of a local REB readability standard influenced the linguistic variables, we used a MANOVA model. Of the REBs who provided templates, 0/94 (0%, 95% CI = 0-3.9%) provided templates with all linguistic variables at or below the grade eight level. Relaxing the standard to a grade 12 level did not increase this proportion. Further, only 2/22 (9.1%, 95% CI = 2.5-27.8) REBs met their own readability standard. The country of origin (DF = 20, 177.5, F = 1.97, p = 0.01), but not the presence of an REB-specific standard (DF = 5, 84, F = 0.73, p = 0.60), influenced the linguistic variables. Inappropriate language in templates is an international problem. Templates use words that are long, abstract, and unfamiliar. This could undermine the validity of participant informed consent. REBs should set a policy of screening templates with linguistic software.

Application of a novel design paradigm to generate general nonpeptide combinatorial templates mimicking beta-turns: synthesis of ligands for melanocortin receptors.

PubMed

Webb, Thomas R; Jiang, Luyong; Sviridov, Sergey; Venegas, Ruben E; Vlaskina, Anna V; McGrath, Douglas; Tucker, John; Wang, Jian; Deschenes, Alain; Li, Rongshi

2007-01-01

We report the further application of a novel approach to template and ligand design by the synthesis of agonists of the melanocortin receptor. This design method uses the conserved structural data from the three-dimensional conformations of beta-turn peptides to design rigid nonpeptide templates that mimic the orientation of the main chain C-alpha atoms in a peptide beta-turn. We report details on a new synthesis of derivatives of template 1 that are useful for the synthesis of exploratory libraries. The utility of this technique is further exemplified by several iterative rounds of high-throughput synthesis and screening, which result in new partially optimized nonpeptide agonists for several melanocortin receptors.

Exact diagonalization library for quantum electron models

NASA Astrophysics Data System (ADS)

Iskakov, Sergei; Danilov, Michael

2018-04-01

We present an exact diagonalization C++ template library (EDLib) for solving quantum electron models, including the single-band finite Hubbard cluster and the multi-orbital impurity Anderson model. The observables that can be computed using EDLib are single particle Green's functions and spin-spin correlation functions. This code provides three different types of Hamiltonian matrix storage that can be chosen based on the model.

Modular preoperative planning software for computer-aided oral implantology and the application of a novel stereolithographic template: a pilot study.

PubMed

Chen, Xiaojun; Yuan, Jianbing; Wang, Chengtao; Huang, Yuanliang; Kang, Lu

2010-09-01

In the field of oral implantology, there is a trend toward computer-aided implant surgery, especially the application of computerized tomography (CT)-derived surgical templates. However, because of relatively unsatisfactory match between the templates and receptor sites, conventional surgical templates may not be accurate enough for the severely resorbed edentulous cases during the procedure of transferring the preoperative plan to the actual surgery. The purpose of this study is to introduce a novel bone-tooth-combined-supported surgical guide, which is designed by utilizing a special modular software and fabricated via stereolithography technique using both laser scanning and CT imaging, thus improving the fit accuracy and reliability. A modular preoperative planning software was developed for computer-aided oral implantology. With the introduction of dynamic link libraries and some well-known free, open-source software libraries such as Visualization Toolkit (Kitware, Inc., New York, USA) and Insight Toolkit (Kitware, Inc.) a plug-in evolutive software architecture was established, allowing for expandability, accessibility, and maintainability in our system. To provide a link between the preoperative plan and the actual surgery, a novel bone-tooth-combined-supported surgical template was fabricated, utilizing laser scanning, image registration, and rapid prototyping. Clinical studies were conducted on four partially edentulous cases to make a comparison with the conventional bone-supported templates. The fixation was more stable than tooth-supported templates because laser scanning technology obtained detailed dentition information, which brought about the unique topography between the match surface of the templates and the adjacent teeth. The average distance deviations at the coronal and apical point of the implant were 0.66 mm (range: 0.3-1.2) and 0.86 mm (range: 0.4-1.2), and the average angle deviation was 1.84 degrees (range: 0.6-2.8 degrees ). This pilot study proves that the novel combined-supported templates are superior to the conventional ones. However, more clinical cases will be conducted to demonstrate their feasibility and reliability.

[Construction of dengue virus-specific full-length fully human antibody libraries by mammalian display technology].

PubMed

Wen, Yangming; Lan, Kaijian; Wang, Junjie; Yu, Jingyi; Qu, Yarong; Zhao, Wei; Zhang, Fuchun; Tan, Wanlong; Cao, Hong; Zhou, Chen

2013-06-01

To construct dengue virus-specific full-length fully human antibody libraries using mammalian cell surface display technique. Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) from convalescent patients with dengue fever. The reservoirs of the light chain and heavy chain variable regions (LCκ and VH) of the antibody genes were amplified by RT-PCR and inserted into the vector pDGB-HC-TM separately to construct the light chain and heavy chain libraries. The library DNAs were transfected into CHO cells and the expression of full-length fully human antibodies on the surface of CHO cells was analyzed by flow cytometry. Using 1.2 µg of the total RNA isolated from the PBMCs as the template, the LCκ and VH were amplified and the full-length fully human antibody mammalian display libraries were constructed. The kappa light chain gene library had a size of 1.45×10(4) and the heavy chain gene library had a size of 1.8×10(5). Sequence analysis showed that 8 out of the 10 light chain clones and 7 out of the 10 heavy chain clones randomly picked up from the constructed libraries contained correct open reading frames. FACS analysis demonstrated that all the 15 clones with correct open reading frames expressed full-length antibodies, which could be detected on CHO cell surfaces. After co-transfection of the heavy chain and light chain gene libraries into CHO cells, the expression of full-length antibodies on CHO cell surfaces could be detected by FACS analysis with an expressible diversity of the antibody library reaching 1.46×10(9) [(1.45×10(4)×80%)×(1.8×10(5)×70%)]. Using 1.2 µg of total RNA as template, the LCκ and VH full-length fully human antibody libraries against dengue virus have been successfully constructed with an expressible diversity of 10(9).

SnapDock—template-based docking by Geometric Hashing

PubMed Central

Estrin, Michael; Wolfson, Haim J.

2017-01-01

Abstract Motivation: A highly efficient template-based protein–protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein–protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well. Results: To evaluate the performance of the algorithm a blind re-modelling of 3547 PDB complexes, which have been uploaded after the PIFACE publication has been performed with success ratio of about 35%. Interestingly, a similar experiment with the template free PatchDock docking algorithm yielded a success rate of about 23% with roughly 1/3 of the solutions different from those of SnapDock. Consequently, the combination of the two methods gave a 42% success ratio. Availability and implementation: A web server of the application is under development. Contact: michaelestrin@gmail.com or wolfson@tau.ac.il PMID:28881968

Photometric redshifts for the next generation of deep radio continuum surveys - I. Template fitting

NASA Astrophysics Data System (ADS)

Duncan, Kenneth J.; Brown, Michael J. I.; Williams, Wendy L.; Best, Philip N.; Buat, Veronique; Burgarella, Denis; Jarvis, Matt J.; Małek, Katarzyna; Oliver, S. J.; Röttgering, Huub J. A.; Smith, Daniel J. B.

2018-01-01

We present a study of photometric redshift performance for galaxies and active galactic nuclei detected in deep radio continuum surveys. Using two multiwavelength data sets, over the NOAO Deep Wide Field Survey Boötes and COSMOS fields, we assess photometric redshift (photo-z) performance for a sample of ∼4500 radio continuum sources with spectroscopic redshifts relative to those of ∼63 000 non-radio-detected sources in the same fields. We investigate the performance of three photometric redshift template sets as a function of redshift, radio luminosity and infrared/X-ray properties. We find that no single template library is able to provide the best performance across all subsets of the radio-detected population, with variation in the optimum template set both between subsets and between fields. Through a hierarchical Bayesian combination of the photo-z estimates from all three template sets, we are able to produce a consensus photo-z estimate that equals or improves upon the performance of any individual template set.

Towards a high performance geometry library for particle-detector simulations

DOE PAGES

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.; ...

2015-05-22

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Towards a high performance geometry library for particle-detector simulations

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

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Archiving Spectral Libraries in the Planetary Data System

NASA Astrophysics Data System (ADS)

Slavney, S.; Guinness, E. A.; Scholes, D.; Zastrow, A.

2017-12-01

Spectral libraries are becoming popular candidates for archiving in PDS. With the increase in the number of individual investigators funded by programs such as NASA's PDART, the PDS Geosciences Node is receiving many requests for support from proposers wishing to archive various forms of laboratory spectra. To accommodate the need for a standardized approach to archiving spectra, the Geosciences Node has designed the PDS Spectral Library Data Dictionary, which contains PDS4 classes and attributes specifically for labeling spectral data, including a classification scheme for samples. The Reflectance Experiment Laboratory (RELAB) at Brown University, which has long been a provider of spectroscopy equipment and services to the science community, has provided expert input into the design of the dictionary. Together the Geosciences Node and RELAB are preparing the whole of the RELAB Spectral Library, consisting of many thousands of spectra collected over the years, to be archived in PDS. An online interface for searching, displaying, and downloading selected spectra is planned, using the Spectral Library metadata recorded in the PDS labels. The data dictionary and online interface will be extended to include spectral libraries submitted by other data providers. The Spectral Library Data Dictionary is now available from PDS at https://pds.nasa.gov/pds4/schema/released/. It can be used in PDS4 labels for reflectance spectra as well as for Raman, XRF, XRD, LIBS, and other types of spectra. Ancillary data such as images, chemistry, and abundance data are also supported. To help generate PDS4-compliant labels for spectra, the Geosciences Node provides a label generation program called MakeLabels (http://pds-geosciences.wustl.edu/tools/makelabels.html) which creates labels from a template, and which can be used for any kind of PDS4 label. For information, contact the Geosciences Node at geosci@wunder.wustl.edu.

Population differences in brain morphology: Need for population specific brain template.

PubMed

Rao, Naren P; Jeelani, Haris; Achalia, Rashmin; Achalia, Garima; Jacob, Arpitha; Bharath, Rose Dawn; Varambally, Shivarama; Venkatasubramanian, Ganesan; K Yalavarthy, Phaneendra

2017-07-30

Brain templates provide a standard anatomical platform for population based morphometric assessments. Typically, standard brain templates for such assessments are created using Caucasian brains, which may not be ideal to analyze brains from other ethnicities. To effectively demonstrate this, we compared brain morphometric differences between T1 weighted structural MRI images of 27 healthy Indian and Caucasian subjects of similar age and same sex ratio. Furthermore, a population specific brain template was created from MRI images of healthy Indian subjects and compared with standard Montreal Neurological Institute (MNI-152) template. We also examined the accuracy of registration of by acquiring a different T1 weighted MRI data set and registering them to newly created Indian template and MNI-152 template. The statistical analysis indicates significant difference in global brain measures and regional brain structures of Indian and Caucasian subjects. Specifically, the global brain measurements of the Indian brain template were smaller than that of the MNI template. Also, Indian brain images were better realigned to the newly created template than to the MNI-152 template. The notable variations in Indian and Caucasian brains convey the need to build a population specific Indian brain template and atlas. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Mapping the Association of College and Research Libraries information literacy framework and nursing professional standards onto an assessment rubric.

PubMed

Willson, Gloria; Angell, Katelyn

2017-04-01

The authors developed a rubric for assessing undergraduate nursing research papers for information literacy skills critical to their development as researchers and health professionals. We developed a rubric mapping six American Nurses Association professional standards onto six related concepts of the Association of College & Research Libraries (ACRL) Framework for Information Literacy for Higher Education. We used this rubric to evaluate fifty student research papers and assess inter-rater reliability. Students tended to score highest on the "Information Has Value" dimension and lowest on the "Scholarship as Conversation" dimension. However, we found a discrepancy between the grading patterns of the two investigators, with inter-rater reliability being "fair" or "poor" for all six rubric dimensions. The development of a rubric that dually assesses information literacy skills and maps relevant disciplinary competencies holds potential. This study offers a template for a rubric inspired by the ACRL Framework and outside professional standards. However, the overall low inter-rater reliability demands further calibration of the rubric. Following additional norming, this rubric can be used to help students identify the key information literacy competencies that they need in order to succeed as college students and future nurses. These skills include developing an authoritative voice, determining the scope of their information needs, and understanding the ramifications of their information choices.

Mapping the Association of College and Research Libraries information literacy framework and nursing professional standards onto an assessment rubric

PubMed Central

Willson, Gloria; Angell, Katelyn

2017-01-01

Objective The authors developed a rubric for assessing undergraduate nursing research papers for information literacy skills critical to their development as researchers and health professionals. Methods We developed a rubric mapping six American Nurses Association professional standards onto six related concepts of the Association of College & Research Libraries (ACRL) Framework for Information Literacy for Higher Education. We used this rubric to evaluate fifty student research papers and assess inter-rater reliability. Results Students tended to score highest on the “Information Has Value” dimension and lowest on the “Scholarship as Conversation” dimension. However, we found a discrepancy between the grading patterns of the two investigators, with inter-rater reliability being “fair” or “poor” for all six rubric dimensions. Conclusions The development of a rubric that dually assesses information literacy skills and maps relevant disciplinary competencies holds potential. This study offers a template for a rubric inspired by the ACRL Framework and outside professional standards. However, the overall low inter-rater reliability demands further calibration of the rubric. Following additional norming, this rubric can be used to help students identify the key information literacy competencies that they need in order to succeed as college students and future nurses. These skills include developing an authoritative voice, determining the scope of their information needs, and understanding the ramifications of their information choices. PMID:28377678

IDSP- INTERACTIVE DIGITAL SIGNAL PROCESSOR

NASA Technical Reports Server (NTRS)

Mish, W. H.

1994-01-01

The Interactive Digital Signal Processor, IDSP, consists of a set of time series analysis "operators" based on the various algorithms commonly used for digital signal analysis work. The processing of a digital time series to extract information is usually achieved by the application of a number of fairly standard operations. However, it is often desirable to "experiment" with various operations and combinations of operations to explore their effect on the results. IDSP is designed to provide an interactive and easy-to-use system for this type of digital time series analysis. The IDSP operators can be applied in any sensible order (even recursively), and can be applied to single time series or to simultaneous time series. IDSP is being used extensively to process data obtained from scientific instruments onboard spacecraft. It is also an excellent teaching tool for demonstrating the application of time series operators to artificially-generated signals. IDSP currently includes over 43 standard operators. Processing operators provide for Fourier transformation operations, design and application of digital filters, and Eigenvalue analysis. Additional support operators provide for data editing, display of information, graphical output, and batch operation. User-developed operators can be easily interfaced with the system to provide for expansion and experimentation. Each operator application generates one or more output files from an input file. The processing of a file can involve many operators in a complex application. IDSP maintains historical information as an integral part of each file so that the user can display the operator history of the file at any time during an interactive analysis. IDSP is written in VAX FORTRAN 77 for interactive or batch execution and has been implemented on a DEC VAX-11/780 operating under VMS. The IDSP system generates graphics output for a variety of graphics systems. The program requires the use of Versaplot and Template plotting routines and IMSL Math/Library routines. These software packages are not included in IDSP. The virtual memory requirement for the program is approximately 2.36 MB. The IDSP system was developed in 1982 and was last updated in 1986. Versaplot is a registered trademark of Versatec Inc. Template is a registered trademark of Template Graphics Software Inc. IMSL Math/Library is a registered trademark of IMSL Inc.

Synthesis of 4-(5-iodo-3-methylpyrazolyl) phenylsulfonamide and its elaboration to a COX II inhibitor library by solution-phase suzuki coupling using Pd/C as a solid-supported catalyst.

PubMed

Organ, Michael G; Mayer, Stanislas

2003-01-01

An effective synthesis of 4-(5-iodo-3-methylpyrazolyl) phenylsulfonamide has been developed. This aromatic iodide template served as an efficient oxidative addition partner for the preparation of a solution-phase library of Celecoxib analogues via Suzuki coupling using Pd/C, a readily filterable catalyst.

Matching organic libraries with protein-substructures

NASA Astrophysics Data System (ADS)

Preissner, R.; Goede, A.; Rother, K.; Osterkamp, F.; Koert, U.; Froemmel, C.

2001-09-01

We present a general approach which allows automatic identification of sub-structures in proteins that resemble given three-dimensional templates. This paper documents its success with non-peptide templates such as β-turn mimetics. We considered well-tested turn-mimetics such as the bicyclic turned dipeptide (BTD), spiro lactam (Spiro) and the 2,5-disubstituded tetrahydrofuran (THF), a new furan-derivative which was recently developed and characterized. The detected geometric similarity between the templates and the protein patches corresponds to r.m.s.-values of 0.3 Å for more than 80% of the constituting atoms, which is typical for active site comparisons of homologous proteins. This fast automatic procedure might be of biomedical value for finding special mimicking leads for particular protein sub-structures as well as for template-assembled synthetic protein (TASP) design.

Knowledge management for efficient quantitative analyses during regulatory reviews.

PubMed

Krudys, Kevin; Li, Fang; Florian, Jeffry; Tornoe, Christoffer; Chen, Ying; Bhattaram, Atul; Jadhav, Pravin; Neal, Lauren; Wang, Yaning; Gobburu, Joga; Lee, Peter I D

2011-11-01

Knowledge management comprises the strategies and methods employed to generate and leverage knowledge within an organization. This report outlines the activities within the Division of Pharmacometrics at the US FDA to effectively manage knowledge with the ultimate goal of improving drug development and advancing public health. The infrastructure required for pharmacometric knowledge management includes provisions for data standards, queryable databases, libraries of modeling tools, archiving of analysis results and reporting templates for effective communication. Two examples of knowledge management systems developed within the Division of Pharmacometrics are used to illustrate these principles. The benefits of sound knowledge management include increased productivity, allowing reviewers to focus on research questions spanning new drug applications, such as improved trial design and biomarker development. The future of knowledge management depends on the collaboration between the FDA and industry to implement data and model standards to enhance sharing and dissemination of knowledge.

The Design of SimpleITK

PubMed Central

Lowekamp, Bradley C.; Chen, David T.; Ibáñez, Luis; Blezek, Daniel

2013-01-01

SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org. PMID:24416015

NA-42 TI Shared Software Component Library FY2011 Final Report

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

Knudson, Christa K.; Rutz, Frederick C.; Dorow, Kevin E.

The NA-42 TI program initiated an effort in FY2010 to standardize its software development efforts with the long term goal of migrating toward a software management approach that will allow for the sharing and reuse of code developed within the TI program, improve integration, ensure a level of software documentation, and reduce development costs. The Pacific Northwest National Laboratory (PNNL) has been tasked with two activities that support this mission. PNNL has been tasked with the identification, selection, and implementation of a Shared Software Component Library. The intent of the library is to provide a common repository that is accessiblemore » by all authorized NA-42 software development teams. The repository facilitates software reuse through a searchable and easy to use web based interface. As software is submitted to the repository, the component registration process captures meta-data and provides version control for compiled libraries, documentation, and source code. This meta-data is then available for retrieval and review as part of library search results. In FY2010, PNNL and staff from the Remote Sensing Laboratory (RSL) teamed up to develop a software application with the goal of replacing the aging Aerial Measuring System (AMS). The application under development includes an Advanced Visualization and Integration of Data (AVID) framework and associated AMS modules. Throughout development, PNNL and RSL have utilized a common AMS code repository for collaborative code development. The AMS repository is hosted by PNNL, is restricted to the project development team, is accessed via two different geographic locations and continues to be used. The knowledge gained from the collaboration and hosting of this repository in conjunction with PNNL software development and systems engineering capabilities were used in the selection of a package to be used in the implementation of the software component library on behalf of NA-42 TI. The second task managed by PNNL is the development and continued maintenance of the NA-42 TI Software Development Questionnaire. This questionnaire is intended to help software development teams working under NA-42 TI in documenting their development activities. When sufficiently completed, the questionnaire illustrates that the software development activities recorded incorporate significant aspects of the software engineering lifecycle. The questionnaire template is updated as comments are received from NA-42 and/or its development teams and revised versions distributed to those using the questionnaire. PNNL also maintains a list of questionnaire recipients. The blank questionnaire template, the AVID and AMS software being developed, and the completed AVID AMS specific questionnaire are being used as the initial content to be established in the TI Component Library. This report summarizes the approach taken to identify requirements, search for and evaluate technologies, and the approach taken for installation of the software needed to host the component library. Additionally, it defines the process by which users request access for the contribution and retrieval of library content.« less

Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline

NASA Astrophysics Data System (ADS)

Rardin, Matthew J.

2018-04-01

Proper sample preparation in proteomic workflows is essential to the success of modern mass spectrometry experiments. Complex workflows often require reagents which are incompatible with MS analysis (e.g., detergents) necessitating a variety of sample cleanup procedures. Efforts to understand and mitigate sample contamination are a continual source of disruption with respect to both time and resources. To improve the ability to rapidly assess sample contamination from a diverse array of sources, I developed a molecular library in Skyline for rapid extraction of contaminant precursor signals using MS1 filtering. This contaminant template library is easily managed and can be modified for a diverse array of mass spectrometry sample preparation workflows. Utilization of this template allows rapid assessment of sample integrity and indicates potential sources of contamination. [Figure not available: see fulltext.

The spectral energy distribution of galaxies at z > 2.5: Implication from the Herschel/SPIRE color-color diagram

NASA Astrophysics Data System (ADS)

Yuan, Fangting; Buat, Veronique; Burgarella, Denis; Ciesla, Laure; Heinis, Sebastien; Shen, Shiyin; Shao, Zhengyi; Hou, Jinliang

2015-08-01

We use the Herschel SPIRE color-color diagram to study the spectral energy distribution (SED) and the redshift estimation of high-z galaxies. We collect a sample of 57 galaxies with spectroscopically confirmed redshifts and reliable flux measurements at redshift z=2.5-6.4, and compare their average SPIRE colors with SED templates from local and high-z libraries. We find that local SEDs are inconsistent with high-z observations. For the libraries of Chary & Elbaz (2001) and Dale & Helou (2002), the local calibrations of the parameters LIR and alpha need to be adjusted to around 1011Lsun and 1.5 to describe the average colors given by the observations. For high-z libraries, the templates of Magdis et al. (2012) can well describe the average colors of the observations at high redshift, justifying their assumption of an evolution of SED from z=0 to 3. Using the templates of Magdis et al. (2012), we defined color cuts to divide the SPIRE color-color diagram into different regions with different mean redshifts. We tested this method and two other color cut methods 500 micron risers and the method of Amblard et al. (2010) using a large sample of 786 Herschel-selected galaxies, and find that these color cut methods can separate the sample into populations with different mean redshifts, although the dispersion of redshifts in each population is quite large.

Content analysis of physical examination templates in electronic health records using SNOMED CT.

PubMed

Gøeg, Kirstine Rosenbeck; Chen, Rong; Højen, Anne Randorff; Elberg, Pia

2014-10-01

Most electronic health record (EHR) systems are built on proprietary information models and terminology, which makes achieving semantic interoperability a challenge. Solving interoperability problems requires well-defined standards. In contrast, the need to support clinical work practice requires a local customization of EHR systems. Consequently, contrasting goals may be evident in EHR template design because customization means that local EHR organizations can define their own templates, whereas standardization implies consensus at some level. To explore the complexity of balancing these two goals, this study analyzes the differences and similarities between templates in use today. A similarity analysis was developed on the basis of SNOMED CT. The analysis was performed on four physical examination templates from Denmark and Sweden. The semantic relationships in SNOMED CT were used to quantify similarities and differences. Moreover, the analysis used these identified similarities to investigate the common content of a physical examination template. The analysis showed that there were both similarities and differences in physical examination templates, and the size of the templates varied from 18 to 49 fields. In the SNOMED CT analysis, exact matches and terminology similarities were represented in all template pairs. The number of exact matches ranged from 7 to 24. Moreover, the number of unrelated fields differed a lot from 1/18 to 22/35. Cross-country comparisons tended to have more unrelated content than within-country comparisons. On the basis of identified similarities, it was possible to define the common content of a physical examination. Nevertheless, a complete view on the physical examination required the inclusion of both exact matches and terminology similarities. This study revealed that a core set of items representing the physical examination templates can be generated when the analysis takes into account not only exact matches but also terminology similarities. This core set of items could be a starting point for standardization and semantic interoperability. However, both unmatched terms and terminology matched terms pose a challenge for standardization. Future work will include using local templates as a point of departure in standardization to see if local requirements can be maintained in a standardized framework. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Enhancement and Analysis of Human Antiaflatoxin B1 (AFB1) scFv Antibody-Ligand Interaction Using Chain Shuffling.

PubMed

Rangnoi, Kuntalee; Choowongkomon, Kiattawee; O'Kennedy, Richard; Rüker, Florian; Yamabhai, Montarop

2018-06-06

A human antiaflatoxin B1 (AFB1) scFv antibody (yAFB1-c3), selected from a naı̈ve human phage-displayed scFv library, was used as a template for improving and analysis of antibody-ligand interactions using the chain-shuffling technique. The variable-heavy and variable-light (VH/VL)-shuffled library was constructed from the VH of 25 preselected clones recombined with the VL of yAFB1-c3 and vice versa. Affinity selection from these libraries demonstrated that the VH domain played an important role in the binding of scFv to free AFB1. Therefore, in the next step, VH-shuffled scFv library was constructed from variable-heavy (VH) chain repertoires, amplified from the naı̈ve library, recombined with the variable-light (VL) chain of the clone yAFB1-c3. This library was then used to select a specific scFv antibody against soluble AFB1 by a standard biopanning method. Three clones that showed improved binding properties were isolated. Amino acid sequence analysis indicated that the improved clones have amino acid mutations in framework 1 (FR1) and the complementarity determining region (CDR1) of the VH chain. One clone, designated sAFH-3e3, showed 7.5-fold improvement in sensitivity over the original scFv clone and was selected for molecular binding studies with AFB1. Homology modeling and molecular docking were used to compare the binding of this and the original clones. The results confirmed that VH is more important than VL for AFB1 binding.

Implementationof a modular software system for multiphysical processes in porous media

NASA Astrophysics Data System (ADS)

Naumov, Dmitri; Watanabe, Norihiro; Bilke, Lars; Fischer, Thomas; Lehmann, Christoph; Rink, Karsten; Walther, Marc; Wang, Wenqing; Kolditz, Olaf

2016-04-01

Subsurface georeservoirs are a candidate technology for large scale energy storage required as part of the transition to renewable energy sources. The increased use of the subsurface results in competing interests and possible impacts on protected entities. To optimize and plan the use of the subsurface in large scale scenario analyses,powerful numerical frameworks are required that aid process understanding and can capture the coupled thermal (T), hydraulic (H), mechanical (M), and chemical (C) processes with high computational efficiency. Due to having a multitude of different couplings between basic T, H, M, or C processes and the necessity to implement new numerical schemes the development focus has moved to software's modularity. The decreased coupling between the components results in two major advantages: easier addition of specialized processes and improvement of the code's testability and therefore its quality. The idea of modularization is implemented on several levels, in addition to library based separation of the previous code version, by using generalized algorithms available in the Standard Template Library and the Boost library, relying on efficient implementations of liner algebra solvers, using concepts when designing new types, and localization of frequently accessed data structures. This procedure shows certain benefits for a flexible high-performance framework applied to the analysis of multipurpose georeservoirs.

Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction.

PubMed

Lazinski, David W; Camilli, Andrew

2013-01-01

The amplification of DNA fragments, cloned between user-defined 5' and 3' end sequences, is a prerequisite step in the use of many current applications including massively parallel sequencing (MPS). Here we describe an improved method, called homopolymer tail-mediated ligation PCR (HTML-PCR), that requires very little starting template, minimal hands-on effort, is cost-effective, and is suited for use in high-throughput and robotic methodologies. HTML-PCR starts with the addition of homopolymer tails of controlled lengths to the 3' termini of a double-stranded genomic template. The homopolymer tails enable the annealing-assisted ligation of a hybrid oligonucleotide to the template's recessed 5' ends. The hybrid oligonucleotide has a user-defined sequence at its 5' end. This primer, together with a second primer composed of a longer region complementary to the homopolymer tail and fused to a second 5' user-defined sequence, are used in a PCR reaction to generate the final product. The user-defined sequences can be varied to enable compatibility with a wide variety of downstream applications. We demonstrate our new method by constructing MPS libraries starting from nanogram and sub-nanogram quantities of Vibrio cholerae and Streptococcus pneumoniae genomic DNA.

Component, Context and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2013-03-01

Penn State team were stored in a relational database for easy access, storage and maintainability. The relational database consisted of a PostGres ...file into a format that can be imported into the PostGres database. This same custom application was used to generate Microsoft Excel templates...Press Break Forming Equipment 4.14 Manufacturing Model Library Database Structure The data storage mechanism for the ARL PSU MML was a PostGres database

VizieR Online Data Catalog: Low-resolution near-infrared stellar spectra from CIBER (Kim+, 2017)

NASA Astrophysics Data System (ADS)

Kim, M. G.; Lee, H. M.; Arai, T.; Bock, J.; Cooray, A.; Jeong, W.-S.; Kim, S. J.; Korngut, P.; Lanz, A.; Lee, D. H.; Lee, M. G.; Matsumoto, T.; Matsuura, S.; Nam, U. W.; Onishi, Y.; Shirahata, M.; Smidt, J.; Tsumura, K.; Yamamura, I.; Zemcov, M.

2017-06-01

We present flux-calibrated near-infrared spectra of 105 stars from 0.8{<=}λ{<=}1.8μm with spectral resolution 15{<=}λ/Δλ{<=}30 over the range. The Low-Resolution Spectrometer (LRS) is one of the four optical instruments of the Cosmic Infrared Background Experiment (CIBER) payload; the others are a narrowband spectrometer and two wide-field imagers. The LRS is a prism-dispersed spectrometer with five rectangular 5.35°*2.8' slits imaging a 5.8°*5.8° field of view. The detector has 256*256 pixels at a pixel scale of 1.36'*1.36'. CIBER has flown four times (2009 February, 2010 July, 2012 March, and 2013 June) with apogees and total exposure times of over 325km and ~240s, respectively, in the first three flights and of 550km and 335s in the final, non-recovered flight. Due to spurious signal contamination from thermal emission from the shock-heated rocket skin, we do not use the first flight data in this work. The star spectral types are determined by fitting known spectral templates to the measured LRS spectra. We use the Infrared Telescope Facility (IRTF) and Pickles 1998 (Cat. J/PASP/110/863) templates for the SED fitting. The SpeX instrument installed on the IRTF observed stars using a medium-resolution spectrograph (R=2000). The template library contains spectra for 210 cool stars (F to M type) with wavelength coverage from 0.8 to 2.5μm (Cushing 2005ApJ...623.1115C; Rayner 2009ApJS..185..289R). The Pickles library is a synthetic spectral library that combines spectral data from various observations to achieve wavelength coverage from the UV (0.115μm) to the near-infrared (2.5μm). It contains 131 spectral templates for all star types (i.e., O to M type) with a uniform sampling interval of 5Å. (6 data files).

How to synthesize macrocycles efficiently by using virtual combinatorial libraries.

PubMed

Storm, Ole; Lüning, Ulrich

2002-02-15

The selection of different diimines 4 a-c by alkaline earth ions from a virtual combinatorial library (VCL) is described. The products were stabilized by reduction to the diamines 6 a-c; this allowed easy analysis. The library can be directed toward different target molecules 6 a-c upon addition of alkaline earth ions with different radii. Competition experiments show the possibility of synthesizing the macrocycles 6 a, 6 b, and 6 c simultaneously when using Mg(2+), Ca(2+), and Ba(2+) as template ions. The scope of this thermodynamically controlled, reversible approach for macrocycle syntheses is illustrated.

CLIPS++: Embedding CLIPS into C++

NASA Technical Reports Server (NTRS)

Obermeyer, Lance; Miranker, Daniel P.

1994-01-01

This paper describes a set of C++ extensions to the CLIPS language and their embodiment in CLIPS++. These extensions and the implementation approach of CLIPS++ provide a new level of embeddability with C and C++. These extensions are a C++ include statement and a defcontainer construct; (include (c++-header-file.h)) and (defcontainer (c++-type)). The include construct allows C++ functions to be embedded in both the LHS and RHS of CLIPS rules. The header file in an include construct is the same header file the programmer uses for his/her own C++ code, independent of CLIPS. The defcontainer construct allows the inference engine to treat C++ class instances as CLIPS deftemplate facts. Consequently existing C++ class libraries may be transparently imported into CLIPS. These C++ types may use advanced features like inheritance, virtual functions, and templates. The implementation has been tested with several class libraries, including Rogue Wave Software's Tools.h++, GNU's libg++, and USL's C++ Standard Components. The execution speed of CLIPS++ has been determined to be 5 to 700 times the execution speed of CLIPS 6.0 (10 to 20X typical).

Inhibitor profiling of the Pseudomonas aeruginosa virulence factor LasB using N-alpha mercaptoamide template-based inhibitors.

PubMed

Cathcart, George R; Gilmore, Brendan F; Greer, Brett; Harriott, Pat; Walker, Brian

2009-11-01

We report on the synthesis and biological evaluation of a focussed library of N-alpha mercaptoamide containing dipeptides as inhibitors of the zinc metallopeptidase Pseudomonas aeruginosa elastase (LasB, EC 3.4.24.26). The aim of the study was to derive an inhibitor profile for LasB with regard to mapping the S'1 binding site of the enzyme. Consequently, a focussed library of 160 members has been synthesised, using standard Fmoc-solid phase methods (on a Rink-amide resin), in which a subset of amino acids including examples of those with basic (Lys, Arg), aromatic (Phe, Trp), large aliphatic (Val, Leu) and acidic (Asp, Glu) side-chains populated the P'2 position of the inhibitor sequence and all 20 natural amino acids were incorporated, in turn, at the P'1 position. The study has revealed a preference for aromatic and/or large aliphatic amino acids at P'1 and a distinct bias against acidic residues at P'2. Ten inhibitor sequences were discovered that exhibited sub to low micromolar Ki values.

Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues.

PubMed

Mei, Hui; Liao, Jen-Yu; Jimenez, Randi M; Wang, Yajun; Bala, Saikat; McCloskey, Cailen; Switzer, Christopher; Chaput, John C

2018-05-02

In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.

A catalog of M-type star candidates in the LAMOST data release 1

NASA Astrophysics Data System (ADS)

Zhong, Jing; Lépine, Sébastien; Li, Jing; Chen, Li; Hou, Jinliang

2016-08-01

In this work, we present a set of M-type star candidates selected from the LAMOST DR1. A discrimination method with the spectral index diagram is used to separate M giants and M dwarfs. Then, we have successfully assembled a set of M giants templates from M0 to M6, using the spectra identified from the LAMOST spectral database. After combining the M dwarf templates in Zhong et al. (2015a) and the new created M giant templates, we use the M-type spectral library to perform the template-fit method to classify and identify M-type stars in the LAMOST DR1. A catalog of M-type star candidates including 8639 M giants and 101690 M dwarfs/subdwarfs is provided. As an additional results, we also present other fundamental parameters like proper motion, photometry, radial velocity and spectroscopic distance.

Iris: Constructing and Analyzing Spectral Energy Distributions with the Virtual Observatory

NASA Astrophysics Data System (ADS)

Laurino, O.; Budynkiewicz, J.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2014-05-01

We present Iris 2.0, the latest release of the Virtual Astronomical Observatory application for building and analyzing Spectral Energy Distributions (SEDs). With Iris, users may read in and display SEDs inspect and edit any selection of SED data, fit models to SEDs in arbitrary spectral ranges, and calculate confidence limits on best-fit parameters. SED data may be loaded into the application from VOTable and FITS files compliant with the International Virtual Observatoy Alliance interoperable data models, or retrieved directly from NED or the Italian Space Agency Science Data Center; data in non-standard formats may also be converted within the application. Users may seamlessy exchange data between Iris and other Virtual Observatoy tools using the Simple Application Messaging Protocol. Iris 2.0 also provides a tool for redshifting, interpolating, and measuring integratd fluxes, and allows simple aperture corrections for individual points and SED segments. Custom Python functions, template models and template libraries may be imported into Iris for fitting SEDs. Iris may be extended through Java plugins; users can install third-party packages, or develop their own plugin using Iris' Software Development Kit. Iris 2.0 is available for Linux and Mac OS X systems.

Template for success: using a resident-designed sign-out template in the handover of patient care.

PubMed

Clark, Clancy J; Sindell, Sarah L; Koehler, Richard P

2011-01-01

Report our implementation of a standardized handover process in a general surgery residency program. The standardized handover process, sign-out template, method of implementation, and continuous quality improvement process were designed by general surgery residents with support of faculty and senior hospital administration using standard work principles and business models of the Virginia Mason Production System and the Toyota Production System. Nonprofit, tertiary referral teaching hospital. General surgery residents, residency faculty, patient care providers, and hospital administration. After instruction in quality improvement initiatives, a team of general surgery residents designed a sign-out process using an electronic template and standard procedures. The initial implementation phase resulted in 73% compliance. Using resident-driven continuous quality improvement processes, real-time feedback enabled residents to modify and improve this process, eventually attaining 100% compliance and acceptance by residents. The creation of a standardized template and protocol for patient handovers might eliminate communication failures. Encouraging residents to participate in this process can establish the groundwork for successful implementation of a standardized handover process. Integrating a continuous quality-improvement process into such an initiative can promote active participation of busy general surgery residents and lead to successful implementation of standard procedures. Copyright © 2011 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

ERESE: An online forum for research-based earth science inquiry

NASA Astrophysics Data System (ADS)

Symons, C. M.; Koppers, A.; Helly, M.; Staudigel, H.; Miller, S. P.

2007-12-01

The Enduring Resources for Earth Science Education (ERESE) Project bridges the gap between earth science research and science education by providing a forum for electronic collaboration between practicing scientists and classroom teachers. By combining the resources of Scripps Institution of Oceanography (SIO) and the expertise of educators, ERESE leverages a wide variety of assets to provide state-of-the-art, online digital resources through two National Science Digital Library collections: Earthref.org (http://www.Earthref.org/ERESE) and SIOExplorer (http://SIOExplorer.ucsd.edu). Earthref.org provides a wealth of plate tectonic-related content appropriate for designing and enacting inquiry lessons. The SIOExplorer Digital Library houses marine geophysical data from over 800 research cruises each containing a variety of data types from meteorological, to oceanographic, geophysical and navigational data. Built on successful collaboration between scientists and middle and high school teachers from across the country beginning in 2004, ERESE has expanded into a multifaceted repository for thought-provoking earth science data and images, virtual field trips and inquiry lessons designed by our partner teachers. More than static interfaces, both Earthref.org and SIOExplorer introduce users to current topics in science, seeking to answer outstanding questions about the earth, its processes, formation, and future. To provide a starting point for new users to design and contribute lessons to Earthref.org we have created a basic inquiry lesson plan template that models the process of investigating a real scientific problem. The template is designed on the basis of our five-stage model of inquiry adapted to the National Science Education Standards. As with all inquiry lessons, our model focuses on the shift of power from the teacher at the outset of the lesson to the students upon completion of the lesson.

POLARIS: Helping Managers Get Answers Fast!

NASA Technical Reports Server (NTRS)

Corcoran, Patricia M.; Webster, Jeffery

2007-01-01

This viewgraph presentation reviews the Project Online Library and Resource Information System (POLARIS) system. It is NASA-wide, web-based system, providing access to information related to Program and Project Management. It will provide a one-stop shop for access to: a searchable, sortable database of all requirements for all product lines, project life cycle diagrams with reviews, project life cycle diagrams with reviews, project review definitions with products review information from NPR 7123.1, NASA Systems Engineering Processes and Requirements, templates and examples of products, project standard WBSs with dictionaries, and requirements for implementation and approval, information from NASA s Metadata Manager (MdM): Attributes of Missions, Themes, Programs & Projects, NPR7120.5 waiver form and instructions and much more. The presentation reviews the plans and timelines for future revisions and modifications.

Cell-free unnatural amino acid incorporation with alternative energy systems and linear expression templates.

PubMed

Shrestha, Prashanta; Smith, Mark Thomas; Bundy, Bradley Charles

2014-01-25

Site-specific incorporation of unnatural amino acids (uAAs) during protein synthesis expands the proteomic code through the addition of unique residue chemistry. This field provides a unique tool to improve pharmacokinetics, cancer treatments, vaccine development, proteomics and protein engineering. The limited ability to predict the characteristics of proteins with uAA-incorporation creates a need for a low-cost system with the potential for rapid screening. Escherichia coli-based cell-free protein synthesis is a compelling platform for uAA incorporation due to the open and accessible nature of the reaction environment. However, typical cell-free systems can be expensive due to the high cost of energizing reagents. By employing alternative energy sources, we reduce the cost of uAA-incorporation in CFPS by 55%. While alternative energy systems reduce cost, the time investment to develop gene libraries can remain cumbersome. Cell-free systems allow the direct use of PCR products known as linear expression templates, thus alleviating tedious plasmid library preparations steps. We report the specific costs of CFPS with uAA incorporation, demonstrate that LETs are suitable expression templates with uAA-incorporation, and consider the substantial reduction in labor intensity using LET-based expression for CFPS uAA incorporation. Copyright © 2013 Elsevier B.V. All rights reserved.

Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction

PubMed Central

Lazinski, David W.; Camilli, Andrew

2013-01-01

The amplification of DNA fragments, cloned between user-defined 5′ and 3′ end sequences, is a prerequisite step in the use of many current applications including massively parallel sequencing (MPS). Here we describe an improved method, called homopolymer tail-mediated ligation PCR (HTML-PCR), that requires very little starting template, minimal hands-on effort, is cost-effective, and is suited for use in high-throughput and robotic methodologies. HTML-PCR starts with the addition of homopolymer tails of controlled lengths to the 3′ termini of a double-stranded genomic template. The homopolymer tails enable the annealing-assisted ligation of a hybrid oligonucleotide to the template's recessed 5′ ends. The hybrid oligonucleotide has a user-defined sequence at its 5′ end. This primer, together with a second primer composed of a longer region complementary to the homopolymer tail and fused to a second 5′ user-defined sequence, are used in a PCR reaction to generate the final product. The user-defined sequences can be varied to enable compatibility with a wide variety of downstream applications. We demonstrate our new method by constructing MPS libraries starting from nanogram and sub-nanogram quantities of Vibrio cholerae and Streptococcus pneumoniae genomic DNA. PMID:23311318

IAOseq: inferring abundance of overlapping genes using RNA-seq data.

PubMed

Sun, Hong; Yang, Shuang; Tun, Liangliang; Li, Yixue

2015-01-01

Overlapping transcription constitutes a common mechanism for regulating gene expression. A major limitation of the overlapping transcription assays is the lack of high throughput expression data. We developed a new tool (IAOseq) that is based on reads distributions along the transcribed regions to identify the expression levels of overlapping genes from standard RNA-seq data. Compared with five commonly used quantification methods, IAOseq showed better performance in the estimation accuracy of overlapping transcription levels. For the same strand overlapping transcription, currently existing high-throughput methods are rarely available to distinguish which strand was present in the original mRNA template. The IAOseq results showed that the commonly used methods gave an average of 1.6 fold overestimation of the expression levels of same strand overlapping genes. This work provides a useful tool for mining overlapping transcription levels from standard RNA-seq libraries. IAOseq could be used to help us understand the complex regulatory mechanism mediated by overlapping transcripts. IAOseq is freely available at http://lifecenter.sgst.cn/main/en/IAO_seq.jsp.

Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

PubMed

Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

2012-01-01

Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of functionally important mutations. Through these examples, the principles of the technique are illustrated and the suitability of automating various aspects of the procedure for given applications are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

SU-F-T-47: MRI T2 Exclusive Based Planning Using the Endocavitary/interstitial Gynecological Benidorm Applicator: A Proposed TPS Library and Preplan Efficient Methodology

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

Richart, J; Otal, A; Rodriguez, S

Purpose: ABS and GEC-ESTRO have recommended MRI T2 for image guided brachytherapy. Recently, a new applicator (Benidorm Template, TB) has been developed in our Department (Rodriguez et al 2015). TB is fully MRI compatible because the Titanium needles and it allows the use of intrauterine tandem. Currently, TPS applicators library are not currently available for non-rigid applicators in case of interstitial component as the TB.The purpose of this work is to present the development of a library for the TB, together with its use on a pre-planning technique. Both new goals allow a very efficient and exclusive T2 MRI basedmore » planning clinical TB implementation. Methods: The developed library has been implemented in Oncentra Brachytherapy TPS, version 4.3.0 (Elekta) and now is being implemented on Sagiplan v 2.0 TPS (Eckert&Ziegler BEBIG). To model the TB, free and open software named FreeCAD and MeshLab have been used. The reconstruction process is based on three inserted A-vitamin pellets together with the data provided by the free length. The implemented preplanning procedure is as follow: 1) A MRI T2 acquisition is performed with the template in place just with the vaginal cylinder (no uterine tube nor needles). 2) The CTV is drawn and the required needles are selected using a developed Java based application and 3) A post-implant MRI T2 is performed. Results: This library procedure has been successfully applied by now in 25 patients. In this work the use of the developed library will be illustrated with clinical examples. The preplanning procedure has been applied by now in 6 patients, having significant advantages: needle depth estimation, needle positions and number are optimized a priori, time saving, etc Conclusion: TB library and pre-plan techniques are feasible and very efficient and their use will be illustrated in this work.« less

An electrooculogram-based binary saccade sequence classification (BSSC) technique for augmentative communication and control.

PubMed

Keegan, Johnalan; Burke, Edward; Condron, James

2009-01-01

In the field of assistive technology, the electrooculogram (EOG) can be used as a channel of communication and the basis of a man-machine interface. For many people with severe motor disabilities, simple actions such as changing the TV channel require assistance. This paper describes a method of detecting saccadic eye movements and the use of a saccade sequence classification algorithm to facilitate communication and control. Saccades are fast eye movements that occurs when a person's gaze jumps from one fixation point to another. The classification is based on pre-defined sequences of saccades, guided by a static visual template (e.g. a page or poster). The template, consisting of a table of symbols each having a clearly identifiable fixation point, is situated within view of the user. To execute a particular command, the user moves his or her gaze through a pre-defined path of eye movements. This results in a well-formed sequence of saccades which are translated into a command if a match is found in a library of predefined sequences. A coordinate transformation algorithm is applied to each candidate sequence of recorded saccades to mitigate the effect of changes in the user's position and orientation relative to the visual template. Upon recognition of a saccade sequence from the library, its associated command is executed. A preliminary experiment in which two subjects were instructed to perform a series of command sequences consisting of 8 different commands are presented in the final sections. The system is also shown to be extensible to facilitate convenient text entry via an alphabetic visual template.

ASRM standard embryo transfer protocol template: a committee opinion.

PubMed

Penzias, Alan; Bendikson, Kristin; Butts, Samantha; Coutifaris, Christos; Falcone, Tommaso; Fossum, Gregory; Gitlin, Susan; Gracia, Clarisa; Hansen, Karl; Mersereau, Jennifer; Odem, Randall; Rebar, Robert; Reindollar, Richard; Rosen, Mitchell; Sandlow, Jay; Vernon, Michael

2017-04-01

Standardization improves performance and safety. A template for standardizing the embryo transfer procedure is presented here with 12 basic steps supported by published scientific literature and a survey of common practice of SART programs; it can be used by ART practices to model their own standard protocol. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Standard Evaluation Procedures (SEPs) and Data Entry Spreadsheet Templates (DESTs) for Endocrine Disruptor Screening Program (EDSP) Tier 1 Assays

EPA Pesticide Factsheets

This page provides information and access to Standard Evaluation Procedures (SEPs) and Data Entry Spreadsheet Templates (DESTs) developed by EPA's Office of Chemical Safety and Pollution Prevention (OCSPP).

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

Multi-template polymerase chain reaction.

PubMed

Kalle, Elena; Kubista, Mikael; Rensing, Christopher

2014-12-01

PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

Hydroxyapatite-binding peptides for bone growth and inhibition

DOEpatents

Bertozzi, Carolyn R [Berkeley, CA; Song, Jie [Shrewsbury, MA; Lee, Seung-Wuk [Walnut Creek, CA

2011-09-20

Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

Nanowire and microwire fabrication technique and product

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

Sumant, Anirudha V.; Zach, Michael; Marten, Alan David

A continuous or semi-continuous process for fabricating nanowires or microwires makes use of the substantially planar template that may be moved through electrochemical solution to grow nanowires or microwires on exposed conductive edges on the surface of that template. The planar template allows fabrication of the template using standard equipment and techniques. Adhesive transfer may be used to remove the wires from the template and in one embodiment to draw a continuous wire from the template to be wound around the drum.

Synthetic Molecular Evolution of Membrane-Active Peptides

NASA Astrophysics Data System (ADS)

Wimley, William

The physical chemistry of membrane partitioning largely determines the function of membrane active peptides. Membrane-active peptides have potential utility in many areas, including in the cellular delivery of polar compounds, cancer therapy, biosensor design, and in antibacterial, antiviral and antifungal therapies. Yet, despite decades of research on thousands of known examples, useful sequence-structure-function relationships are essentially unknown. Because peptide-membrane interactions within the highly fluid bilayer are dynamic and heterogeneous, accounts of mechanism are necessarily vague and descriptive, and have little predictive power. This creates a significant roadblock to advances in the field. We are bypassing that roadblock with synthetic molecular evolution: iterative peptide library design and orthogonal high-throughput screening. We start with template sequences that have at least some useful activity, and create small, focused libraries using structural and biophysical principles to design the sequence space around the template. Orthogonal high-throughput screening is used to identify gain-of-function peptides by simultaneously selecting for several different properties (e.g. solubility, activity and toxicity). Multiple generations of iterative library design and screening have enabled the identification of membrane-active sequences with heretofore unknown properties, including clinically relevant, broad-spectrum activity against drug-resistant bacteria and enveloped viruses as well as pH-triggered macromolecular poration.

Primer Extension Mutagenesis Powered by Selective Rolling Circle Amplification

PubMed Central

Huovinen, Tuomas; Brockmann, Eeva-Christine; Akter, Sultana; Perez-Gamarra, Susan; Ylä-Pelto, Jani; Liu, Yuan; Lamminmäki, Urpo

2012-01-01

Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material. PMID:22355397

Sirepo for Synchrotron Radiation Workshop

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

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

Implications of a wavelength-dependent PSF for weak lensing measurements

NASA Astrophysics Data System (ADS)

Eriksen, Martin; Hoekstra, Henk

2018-07-01

The convolution of galaxy images by the point spread function (PSF) is the dominant source of bias for weak gravitational lensing studies, and an accurate estimate of the PSF is required to obtain unbiased shape measurements. The PSF estimate for a galaxy depends on its spectral energy distribution (SED), because the instrumental PSF is generally a function of the wavelength. In this paper we explore various approaches to determine the resulting `effective' PSF using broad-band data. Considering the Euclid mission as a reference, we find that standard SED template fitting methods result in biases that depend on source redshift, although this may be remedied if the algorithms can be optimized for this purpose. Using a machine learning algorithm we show that, at least in principle, the required accuracy can be achieved with the current survey parameters. It is also possible to account for the correlations between photometric redshift and PSF estimates that arise from the use of the same photometry. We explore the impact of errors in photometric calibration, errors in the assumed wavelength dependence of the PSF model, and limitations of the adopted template libraries. Our results indicate that the required accuracy for Euclid can be achieved using the data that are planned to determine photometric redshifts.

Implications of a wavelength dependent PSF for weak lensing measurements.

NASA Astrophysics Data System (ADS)

Eriksen, Martin; Hoekstra, Henk

2018-05-01

The convolution of galaxy images by the point-spread function (PSF) is the dominant source of bias for weak gravitational lensing studies, and an accurate estimate of the PSF is required to obtain unbiased shape measurements. The PSF estimate for a galaxy depends on its spectral energy distribution (SED), because the instrumental PSF is generally a function of the wavelength. In this paper we explore various approaches to determine the resulting `effective' PSF using broad-band data. Considering the Euclid mission as a reference, we find that standard SED template fitting methods result in biases that depend on source redshift, although this may be remedied if the algorithms can be optimised for this purpose. Using a machine-learning algorithm we show that, at least in principle, the required accuracy can be achieved with the current survey parameters. It is also possible to account for the correlations between photometric redshift and PSF estimates that arise from the use of the same photometry. We explore the impact of errors in photometric calibration, errors in the assumed wavelength dependence of the PSF model and limitations of the adopted template libraries. Our results indicate that the required accuracy for Euclid can be achieved using the data that are planned to determine photometric redshifts.

An Ensemble Approach to Building Mercer Kernels with Prior Information

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2005-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly dimensional feature space. we describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using pre-defined kernels. These data adaptive kernels can encode prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. Specifically, we demonstrate the use of the algorithm in situations with extremely small samples of data. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS) and demonstrate the method's superior performance against standard methods. The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains templates for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic-algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code.

Surgical pathology report in the era of desktop publishing.

PubMed

Pillarisetti, S G

1993-01-01

Since it is believed that "a picture is worth a thousand words," incorporation of computer-generated line art was used as a adjunct to gross description in surgical pathology reporting in selected cases. The lack of an integrated software program was overcome by using commercially available graphic and word processing software. A library of drawings was developed over the last few years. Most time-consuming is the development of templates and the graphic library. With some effort it is possible to integrate graphics of high quality into surgical pathology reports.

Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences†

PubMed Central

Speksnijder, Arjen G. C. L.; Kowalchuk, George A.; De Jong, Sander; Kline, Elizabeth; Stephen, John R.; Laanbroek, Hendrikus J.

2001-01-01

A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a mutational hot spot, and cloning of heteroduplexes and chimeras. These data may partially explain the high degree of microheterogeneity typical of sequence clusters detected in environmental clone libraries. PMID:11133483

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

PubMed Central

Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

2015-01-01

Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer’s, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how analysis can be repeated from saved sequencing images using the Long Template Protocol to increase accuracy. PMID:25860802

Problem-Solving Test: Expression Cloning of the Erythropoietin Receptor

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2008-01-01

Terms to be familiar with before you start to solve the test: cytokines, cytokine receptors, cDNA library, cDNA synthesis, poly(A)[superscript +] RNA, primer, template, reverse transcriptase, restriction endonucleases, cohesive ends, expression vector, promoter, Shine-Dalgarno sequence, poly(A) signal, DNA helicase, DNA ligase, topoisomerases,…

Passenger or Crew? Who Do You Want in Charge?

ERIC Educational Resources Information Center

Kowalski, Sue

2009-01-01

School library professionals are, by nature, the nurturing sort. They thrive on systems and strategies to scaffold student success. They create templates, lists, and signage to make life easier for their patrons. They model quality research strategies; they demonstrate technology applications; and they provide exemplars of final products. Since…

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

PubMed

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

2003-11-01

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

Rational design and synthesis of water-compatible molecularly imprinted polymers for selective solid phase extraction of amiodarone.

PubMed

Muhammad, Turghun; Cui, Liu; Jide, Wang; Piletska, Elena V; Guerreiro, Antonio R; Piletsky, Sergey A

2012-01-04

Novel water-compatible molecularly imprinted polymers (MIPs) selective for amiodarone (AD) were designed via a new methodology which relies on screening library of non-imprinted polymers (NIPs). The NIP library consisted of eighteen cross-linked co-polymers synthesized from monomers commonly used in molecular imprinting. The binding capacity of each polymer in the library was analyzed in two different solvents. Binding in water was used to assess non-specific (hydrophobic) interactions and binding in an appropriate organic solvent was used to assess specific interactions. A good correlation was found between the screening tests and modeling of monomer-template interactions performed using computational approach. Additionally, analysis of template-monomer interactions was performed using UV-vis spectroscopy. As the result, 4-vinylpyridine (4-VP) was selected as the best monomer for developing MIP for AD. The 4-VP-based polymers demonstrated imprinting factor equal 3.9. The polymers performance in SPE was evaluated using AD and its structural analogues. The recovery of AD was as high as 96% when extracted from spiked phosphate buffer (pH 4.5) solution and 82.1% from spiked serum samples. The developed MIP shown as a material with specific binding to AD, comparing to its structural analogues, 1-(2-diethylaminoethoxy)-2,6-diiodo-4-nitrobenzene and lidocaine, which shown 9.9% and 25.4% of recovery from the buffer solution, correspondingly. We believe that the screening of NIP library could be proposed as an alternative to commonly used computational and combinatorial approaches. Copyright © 2011 Elsevier B.V. All rights reserved.

Standards for the academic veterinary medical library

PubMed Central

Murphy, Sarah Anne; Bedard, Martha A.; Crawley-Low, Jill; Fagen, Diane; Jette, Jean-Paul

2005-01-01

The Standards Committee of the Veterinary Medical Libraries Section was appointed in May 2000 and charged to create standards for the ideal academic veterinary medical library, written from the perspective of veterinary medical librarians. The resulting Standards for the Academic Veterinary Medical Library were approved by members of the Veterinary Medical Libraries Section during MLA '03 in San Diego, California. The standards were approved by Section Council in April 2005 and received final approval from the Board of Directors of the Medical Library Association during MLA '04 in Washington, DC. PMID:15685288

Effective communication of molecular genetic test results to primary care providers.

PubMed

Scheuner, Maren T; Edelen, Maria Orlando; Hilborne, Lee H; Lubin, Ira M

2013-06-01

We evaluated a template for molecular genetic test reports that was developed as a strategy to reduce communication errors between the laboratory and ordering clinician. We surveyed 1,600 primary care physicians to assess satisfaction, ease of use, and effectiveness of genetic test reports developed using our template and reports developed by clinical laboratories. Mean score differences of responses between the reports were compared using t-tests. Two-way analysis of variance evaluated the effect of template versus standard reports and the influence of physician characteristics. There were 396 (24%) respondents. Template reports had higher scores than the standard reports for each survey item. The gender and specialty of the physician did not influence scores; however, younger physicians gave higher scores regardless of report type. There was significant interaction between report type and whether physicians ordered or reviewed any genetic tests (none versus at least one) in the past year, P = 0.005. For each survey item assessing satisfaction, ease of use, and effectiveness, physicians gave higher ratings to genetic test reports developed with the template than standard reports used by clinical laboratories. Physicians least familiar with genetic test reports, and possibly having the greatest need for better communication, were best served by the template reports.

78 FR 23289 - Public Review of Draft National Shoreline Data Content Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-18

...The Federal Geographic Data Committee (FGDC) is conducting a public review of the draft National Shoreline Data Content Standard. The FGDC has developed a draft National Shoreline Data Content Standard that provides a framework for shoreline data development, sharing of data, and shoreline data transformation and fusion. The FGDC Coastal and Marine Spatial Data Subcommittee, chaired by the National Oceanic and Atmospheric Administration (NOAA), sponsored development of the draft standard. The FGDC Coordination Group, comprised of representatives of Federal agencies, has approved releasing this draft standard for public review and comment. The draft National Shoreline Data Content Standard defines attributes or elements that are common for shoreline data development and provides suggested domains for the elements. The functional scope includes definition of data models, schemas, entities, relationships, definitions, and crosswalks to related standards. The draft National Shoreline Data Content Standard is intended to enhance the shoreline framework by providing technical guidance on shoreline semantics, data structures and their relationships to builders and users of shoreline data. The geographical scope of the draft standard comprises all shorelines of navigable waters within the United States and its territories. The primary intended users of the National Shoreline Data Content Standard are the mapping, shoreline engineering, coastal zone management, flood insurance, and natural resource management communities. The FGDC invites all stakeholders to comment on this draft standard to ensure that it meets their needs. The draft National Shoreline Data Content Standard may be downloaded from https://www.fgdc.gov/standards/projects/FGDC-standards- projects/shoreline-data-content/ revisedDraftNationalShorelineDataContentStandard. Comments shall be submitted using the content template at http://www.fgdc.gov/standards/ process/standards-directives/template.doc. Instructions for completing the comment template are found in FGDC Standards Directive 2d, Standards Working Group Review Guidelines: Review Comment Template, http://www.fgdc.gov/standards/process/standards-directives/directive- 2d-standards-working-group-review-guidelines-review-comment-template. Comments that concern specific issues/changes/additions may result in revisions to the National Shoreline Data Content Standard. Reviewers may obtain information about how comments were addressed upon request. After formal endorsement of the standard by the FGDC, the National Shoreline Data Content Standard and a summary analysis of the changes will be made available to the public on the FGDC Web site, www.fgdc.gov.

BgCut: automatic ship detection from UAV images.

PubMed

Xu, Chao; Zhang, Dongping; Zhang, Zhengning; Feng, Zhiyong

2014-01-01

Ship detection in static UAV aerial images is a fundamental challenge in sea target detection and precise positioning. In this paper, an improved universal background model based on Grabcut algorithm is proposed to segment foreground objects from sea automatically. First, a sea template library including images in different natural conditions is built to provide an initial template to the model. Then the background trimap is obtained by combing some templates matching with region growing algorithm. The output trimap initializes Grabcut background instead of manual intervention and the process of segmentation without iteration. The effectiveness of our proposed model is demonstrated by extensive experiments on a certain area of real UAV aerial images by an airborne Canon 5D Mark. The proposed algorithm is not only adaptive but also with good segmentation. Furthermore, the model in this paper can be well applied in the automated processing of industrial images for related researches.

BgCut: Automatic Ship Detection from UAV Images

PubMed Central

Zhang, Zhengning; Feng, Zhiyong

2014-01-01

Ship detection in static UAV aerial images is a fundamental challenge in sea target detection and precise positioning. In this paper, an improved universal background model based on Grabcut algorithm is proposed to segment foreground objects from sea automatically. First, a sea template library including images in different natural conditions is built to provide an initial template to the model. Then the background trimap is obtained by combing some templates matching with region growing algorithm. The output trimap initializes Grabcut background instead of manual intervention and the process of segmentation without iteration. The effectiveness of our proposed model is demonstrated by extensive experiments on a certain area of real UAV aerial images by an airborne Canon 5D Mark. The proposed algorithm is not only adaptive but also with good segmentation. Furthermore, the model in this paper can be well applied in the automated processing of industrial images for related researches. PMID:24977182

Template Interfaces for Agile Parallel Data-Intensive Science

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

Ramakrishnan, Lavanya; Gunter, Daniel; Pastorello, Gilerto Z.

Tigres provides a programming library to compose and execute large-scale data-intensive scientific workflows from desktops to supercomputers. DOE User Facilities and large science collaborations are increasingly generating large enough data sets that it is no longer practical to download them to a desktop to operate on them. They are instead stored at centralized compute and storage resources such as high performance computing (HPC) centers. Analysis of this data requires an ability to run on these facilities, but with current technologies, scaling an analysis to an HPC center and to a large data set is difficult even for experts. Tigres ismore » addressing the challenge of enabling collaborative analysis of DOE Science data through a new concept of reusable "templates" that enable scientists to easily compose, run and manage collaborative computational tasks. These templates define common computation patterns used in analyzing a data set.« less

Molecular replication

NASA Technical Reports Server (NTRS)

Orgel, L. E.

1986-01-01

The object of our research program is to understand how polynucleotide replication originated on the primitive Earth. This is a central issue in studies of the origins of life, since a process similar to modern DNA and RNA synthesis is likely to have formed the basis for the most primitive system of genetic information transfer. The major conclusion of studies so far is that a preformed polynucleotide template under many different experimental conditions will facilitate the synthesis of a new oligonucleotide with a sequence complementary to that of the template. It has been shown, for example, that poly(C) facilitates the synthesis of long oligo(G)s and that the short template CCGCC facilities the synthesis of its complement GGCGG. Very recently we have shown that template-directed synthesis is not limited to the standard oligonucleotide substrates. Nucleic acid-like molecules with a pyrophosphate group replacing the phosphate of the standard nucleic acid backbone are readily synthesized from deoxynucleotide 3'-5'-diphosphates on appropriate templates.

Exemplary design of a DICOM structured report template for CBIR integration into radiological routine

NASA Astrophysics Data System (ADS)

Welter, Petra; Deserno, Thomas M.; Gülpers, Ralph; Wein, Berthold B.; Grouls, Christoph; Günther, Rolf W.

2010-03-01

The large and continuously growing amount of medical image data demands access methods with regards to content rather than simple text-based queries. The potential benefits of content-based image retrieval (CBIR) systems for computer-aided diagnosis (CAD) are evident and have been approved. Still, CBIR is not a well-established part of daily routine of radiologists. We have already presented a concept of CBIR integration for the radiology workflow in accordance with the Integrating the Healthcare Enterprise (IHE) framework. The retrieval result is composed as a Digital Imaging and Communication in Medicine (DICOM) Structured Reporting (SR) document. The use of DICOM SR provides interchange with PACS archive and image viewer. It offers the possibility of further data mining and automatic interpretation of CBIR results. However, existing standard templates do not address the domain of CBIR. We present a design of a SR template customized for CBIR. Our approach is based on the DICOM standard templates and makes use of the mammography and chest CAD SR templates. Reuse of approved SR sub-trees promises a reliable design which is further adopted to the CBIR domain. We analyze the special CBIR requirements and integrate the new concept of similar images into our template. Our approach also includes the new concept of a set of selected images for defining the processed images for CBIR. A commonly accepted pre-defined template for the presentation and exchange of results in a standardized format promotes the widespread application of CBIR in radiological routine.

cDNA encoding a polypeptide including a hevein sequence

DOEpatents

Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

1993-02-16

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

DICE/ColDICE: 6D collisionless phase space hydrodynamics using a lagrangian tesselation

NASA Astrophysics Data System (ADS)

Sousbie, Thierry

2018-01-01

DICE is a C++ template library designed to solve collisionless fluid dynamics in 6D phase space using massively parallel supercomputers via an hybrid OpenMP/MPI parallelization. ColDICE, based on DICE, implements a cosmological and physical VLASOV-POISSON solver for cold systems such as dark matter (CDM) dynamics.

A 3D Kinematic Measurement of Knee Prosthesis Using X-ray Projection Images

NASA Astrophysics Data System (ADS)

Hirokawa, Shunji; Ariyoshi, Shogo; Hossain, Mohammad Abrar

We have developed a technique for estimating 3D motion of knee prosthesis from its 2D perspective projections. As Fourier descriptors were used for compact representation of library templates and contours extracted from the prosthetic X-ray images, the entire silhouette contour of each prosthetic component was required. This caused such a problem as our algorithm did not function when the silhouettes of tibio and femoral components overlapped with each other. Here we planned a novel method to overcome it; which was processed in two steps. First, the missing part of silhouette contour due to overlap was interpolated using a free-formed curvature such as Bezier. Then the first step position/orientation estimation was performed. In the next step, a clipping window was set in the projective coordinate so as to separate the overlapped silhouette drawn using the first step estimates. After that the localized library whose templates were clipped in shape was prepared and the second step estimation was performed. Computer model simulation demonstrated sufficient accuracies of position/orientation estimation even for overlapped silhouettes; equivalent to those without overlap.

Automated main-chain model building by template matching and iterative fragment extension.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm for the automated macromolecular model building of polypeptide backbones is described. The procedure is hierarchical. In the initial stages, many overlapping polypeptide fragments are built. In subsequent stages, the fragments are extended and then connected. Identification of the locations of helical and beta-strand regions is carried out by FFT-based template matching. Fragment libraries of helices and beta-strands from refined protein structures are then positioned at the potential locations of helices and strands and the longest segments that fit the electron-density map are chosen. The helices and strands are then extended using fragment libraries consisting of sequences three amino acids long derived from refined protein structures. The resulting segments of polypeptide chain are then connected by choosing those which overlap at two or more C(alpha) positions. The fully automated procedure has been implemented in RESOLVE and is capable of model building at resolutions as low as 3.5 A. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition.

Compound Libraries: Recent Advances and Their Applications in Drug Discovery.

PubMed

Gong, Zhen; Hu, Guoping; Li, Qiang; Liu, Zhiguo; Wang, Fei; Zhang, Xuejin; Xiong, Jian; Li, Peng; Xu, Yan; Ma, Rujian; Chen, Shuhui; Li, Jian

2017-01-01

Hit identification is the starting point of small-molecule drug discovery and is therefore very important to the pharmaceutical industry. One of the most important approaches to identify a new hit is to screen a compound library using an in vitro assay. High-throughput screening has made great contributions to drug discovery since the 1990s but requires expensive equipment and facilities, and its success depends on the size of the compound library. Recent progress in the development of compound libraries has provided more efficient ways to identify new hits for novel drug targets, thereby helping to promote the development of the pharmaceutical industry, especially for firstin- class drugs. A multistage and systematic research of articles published between 1986 and 2017 has been performed, which was organized into 5 sections and discussed in detail. In this review, the sources and classification of compound libraries are summarized. The progress made in combinatorial libraries and DNA-encoded libraries is reviewed. Library design methods, especially for focused libraries, are introduced in detail. In the final part, the status of the compound libraries at WuXi is reported. The progress related to compound libraries, especially drug template libraries, DELs, and focused libraries, will help to identify better hits for novel drug targets and promote the development of the pharmaceutical industry. Moreover, these libraries can facilitate hit identification, which benefits most research organizations, including academics and small companies. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

PubMed

de Muinck, Eric J; Trosvik, Pål; Gilfillan, Gregor D; Hov, Johannes R; Sundaram, Arvind Y M

2017-07-06

Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.

Development of a template for the classification of traditional medical knowledge in Korea.

PubMed

Kim, Sungha; Kim, Boyoung; Mun, Sujeong; Park, Jeong Hwan; Kim, Min-Kyeoung; Choi, Sunmi; Lee, Sanghun

2016-02-03

Traditional Medical Knowledge (TMK) is a form of Traditional Knowledge associated with medicine that is handed down orally or by written material. There are efforts to document TMK, and make database to conserve Traditional Medicine and facilitate future research to validate traditional use. Despite of these efforts, there is no widely accepted template in data file format that is specific for TMK and, at the same time, helpful for understanding and organizing TMK. We aimed to develop a template to classify TMK. First, we reviewed books, articles, and health-related classification systems, and used focus group discussion to establish the definition, scope, and constituents of TMK. Second, we developed an initial version of the template to classify TMK, and applied it to TMK data. Third, we revised the template, based on the results of the initial template and input from experts, and applied it to the data. We developed the template for classification of TMK. The constituents of the template were summary, properties, tools/ingredients, indication/preparation/application, and international standard classification. We applied International Patent Classification, International Classification of Diseases (Korea version), and Classification of Korean Traditional Knowledge Resources to provide legal protection of TMK and facilitate academic research. The template provides standard terms for ingredients, preparation, administration route, and procedure method to assess safety and efficacy. This is the first template that is specialized for TMK for arranging and classifying TMK. The template would have important roles in preserving TMK, and protecting intellectual property. TMK data classified with the template could be used as the preliminary data to screen potential candidates for new pharmaceuticals. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Evaluating Public Libraries Using Standard Scores: The Library Quotient.

ERIC Educational Resources Information Center

O'Connor, Daniel O.

1982-01-01

Describes a method for assessing the performance of public libraries using a standardized scoring system and provides an analysis of public library data from New Jersey as an example. Library standards and the derivation of measurement ratios are also discussed. A 33-item bibliography and three data tables are included. (JL)

25 CFR 36.40 - Standard XIII-Library/media program.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 25 Indians 1 2012-04-01 2011-04-01 true Standard XIII-Library/media program. 36.40 Section 36.40... § 36.40 Standard XIII—Library/media program. (a) Each school shall provide a library/media program... developed by a library committee in collaboration with the librarian and be approved by the school board...

Standards Collection Development and Management in an Academic Library: A Case Study at the University of Western Ontario Libraries

ERIC Educational Resources Information Center

Dunn, Linda K.; Xie, Shiyi

2017-01-01

How can academic libraries ensure their standards collections meet the teaching and research needs of science and engineering faculties? Nowadays, most academic libraries face financial constraints that greatly impact collection development. This article documents an academic library's experience with standards collections and the investigation…

25 CFR 36.40 - Standard XIII-Library/media program.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 1 2014-04-01 2014-04-01 false Standard XIII-Library/media program. 36.40 Section 36.40... § 36.40 Standard XIII—Library/media program. (a) Each school shall provide a library/media program... developed by a library committee in collaboration with the librarian and be approved by the school board...

25 CFR 36.40 - Standard XIII-Library/media program.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 1 2013-04-01 2013-04-01 false Standard XIII-Library/media program. 36.40 Section 36.40... § 36.40 Standard XIII—Library/media program. (a) Each school shall provide a library/media program... developed by a library committee in collaboration with the librarian and be approved by the school board...

Library Standards: Evidence of Library Effectiveness and Accreditation.

ERIC Educational Resources Information Center

Ebbinghouse, Carol

1999-01-01

Discusses accreditation standards for libraries based on experiences in an academic law library. Highlights include the accreditation process; the impact of distance education and remote technologies on accreditation; and a list of Internet sources of standards and information. (LRW)

MagAl: A new tool to analyse galaxies photometric data

NASA Astrophysics Data System (ADS)

Schoenell, W.; Benítez, N.; Cid Fernandes, R.

2014-10-01

On galaxy spectra, one can find mainly two features: emission lines, which tell us about the ionised gas content, and the continuum plus absorption lines, which tell us about the stellar content. They thus allow us to derive gas-phase abundances, the main radiation sources, chemical enrichment and star formation histories. Braad-band photometry, on the other hand, is much more limited and hinders our ability to recover a galaxy's physical properties to such a degree of detail. However, with the recent development of redshift surveys using the technology of ultra-narrow filters (≍ 100 Å), such as ALHAMBRA, J-PAS and DES, it will be invaluable to be able to retrieve information on physical properties of galaxies from photometric data. Motivated by this data avalanche (which goes up to the petabyte scale), we decided to build our own SED-fitting code: Magnitudes Analyser (MagAl), which has three modules. 1) A template library generation module: generates empirical and theoretical template libraries. 2) Bayesian fitting module: calculates probability distribution functions (PDFs) for given observed and library template data. This is similar to the method to measure photometric redshifts by Benitez (2000). 3) A result-analyser module: streamlines data analysis from the large output PDFs files. A fourth module to manage 3D data is being developed and a few preliminary tests are also shown. To investigate the reliability of results obtained by MagAl, we have created a mock galaxy sample for the ALHAMBRA survey filter system (http://alhambrasurvey.com) and tried to recover their physical properties. We show that for our sample of simulated galaxies we can measure stellar ages, metallicities and extinctions with a precision of less than 0.3 dex. Also, we apply the code to the ALHAMBRA survey catalog and show that we can measure stellar masses with an accuracy of 0.2 dex when comparing to previous results like COSMOS masses measured by Bundy et al. (2006).

Virtual imprinting as a tool to design efficient MIPs for photosynthesis-inhibiting herbicides.

PubMed

Breton, Florent; Rouillon, Regis; Piletska, Elena V; Karim, Kal; Guerreiro, Antonio; Chianella, Iva; Piletsky, Sergey A

2007-04-15

Molecular modelling and computational screening were used to identify functional monomers capable of interacting with several different photosynthesis-inhibiting herbicides. The process involved the design of a virtual library of molecular models of functional monomers containing polymerizable residues and residues able to interact with the template through electrostatic, hydrophobic, Van der Waals forces and dipole-dipole interactions. Each of the entries in the virtual library was probed for its possible interactions with molecular models of the template molecules. It was anticipated that the monomers giving the highest binding score would represent good candidates for the preparation of affinity polymers. Strong interactions were computationally determined between acidic functional monomers like methacrylic acid (MAA) or itaconic acid (IA) with triazines, and between vinylimidazole with bentazone and bromoxynil. Nevertheless, weaker interactions were seen with phenylureas. The corresponding blank polymers were prepared using the selected monomers and tested in the solid phase extraction (SPE) of herbicides from chloroform solutions. A good correlation was found between the binding score of the monomers and the affinities of the corresponding polymers. The use of computationally designed blanks can potentially eliminate the need for molecular imprinting, (adding a template to the monomer mixture to create specific binding sites). Data also showed that some monomers have a natural selectivity for some herbicides, which can be further enhanced by imprinting. Thus, in regard to retention on the blank polymer, we can estimate if the resulting imprinted polymer will be effective or not.

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

PubMed

Waugh, Caryll; Cromer, Deborah; Grimm, Andrew; Chopra, Abha; Mallal, Simon; Davenport, Miles; Mak, Johnson

2015-04-09

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles. Using HIV as a model we have characterised the major sources of error during the conversion of viral RNA to cDNA, namely excess RNA template and the RNaseH activity of the polymerase enzyme, reverse transcriptase. In addition we have analysed the effect of PCR cycle on detection of recombinants and assessed the contribution of transfection of highly similar plasmid DNA to the formation of recombinant species during the production of our control viruses. We have identified RNA template concentrations, RNaseH activity of reverse transcriptase, and PCR conditions as key parameters that must be carefully optimised to minimise chimeric artefacts. Using our optimised RT-PCR conditions, in combination with our modified PCR amplification procedure, we have developed a reliable technique for accurate determination of RNA species using NGS technology.

The Gap in Standards for Special Libraries.

ERIC Educational Resources Information Center

Dodd, James Beaupre

1982-01-01

The issue of standards for special libraries is discussed, highlighting surveys conducted concerning the diversity of special libraries and salaries of members of the Special Libraries Association (SLA). Efforts of SLA's Standards and Statistics Committee are noted. Twenty references are listed. (EJS)

A hospital-specific template for benchmarking its cost and quality.

PubMed

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-10-01

Develop an improved method for auditing hospital cost and quality tailored to a specific hospital's patient population. Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, New York, and Texas between 2004 and 2006. A template of 300 representative patients from a single index hospital was constructed and used to match 300 patients at 43 hospitals that had a minimum of 500 patients over a 3-year study period. From each of 43 hospitals we chose 300 patients most resembling the template using multivariate matching. We found close matches on procedures and patient characteristics, far more balanced than would be expected in a randomized trial. There were little to no differences between the index hospital's template and the 43 hospitals on most patient characteristics yet large and significant differences in mortality, failure-to-rescue, and cost. Matching can produce fair, directly standardized audits. From the perspective of the index hospital, "hospital-specific" template matching provides the fairness of direct standardization with the specific institutional relevance of indirect standardization. Using this approach, hospitals will be better able to examine their performance, and better determine why they are achieving the results they observe. © Health Research and Educational Trust.

Milestone Completion Report WBS 1.3.5.05 ECP/VTK-m FY17Q2 [MS-17/01] Better Dynamic Types Design SDA05-1

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

Moreland, Kenneth D.

The FY17Q2 milestone of the ECP/VTK-m project, which is the first milestone, includes the completion of design documents for the introduction of virtual methods into the VTK-m framework. Specifically, the ability from within the code of a device (e.g. GPU or Xeon Phi) to jump to a virtual method specified at run time. This change will enable us to drastically reduce the compile time and the executable code size for the VTK-m library. Our first design introduced the idea of adding virtual functions to classes that are used during algorithm execution. (Virtual methods were previously banned from the so calledmore » execution environment.) The design was straightforward. VTK-m already has the generic concepts of an “array handle” that provides a uniform interface to memory of different structures and an “array portal” that provides generic access to said memory. These array handles and portals use C++ templating to adjust them to different memory structures. This composition provides a powerful ability to adapt to data sources, but requires knowing static types. The proposed design creates a template specialization of an array portal that decorates another array handle while hiding its type. In this way we can wrap any type of static array handle and then feed it to a single compiled instance of a function. The second design focused on the mechanics of implementing virtual methods on parallel devices with a focus on CUDA. Our initial experiments on CUDA showed a very large overhead for using virtual C++ classes with virtual methods, the standard approach. Instead, we are using an alternate method provided by C that uses function pointers. With the completion of this milestone, we are able to move to the implementation of objects with virtual (like) methods. The upshot will be much faster compile times and much smaller library/executable sizes.« less

Post-Fragmentation Whole Genome Amplification-Based Method

NASA Technical Reports Server (NTRS)

Benardini, James; LaDuc, Myron T.; Langmore, John

2011-01-01

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Readability of patient discharge instructions with and without the use of electronically available disease-specific templates.

PubMed

Mueller, Stephanie K; Giannelli, Kyla; Boxer, Robert; Schnipper, Jeffrey L

2015-07-01

Low health literacy is common, leading to patient vulnerability during hospital discharge, when patients rely on written health instructions. We aimed to examine the impact of the use of electronic, patient-friendly, templated discharge instructions on the readability of discharge instructions provided to patients at discharge. We performed a retrospective cohort study of 233 patients discharged from a large tertiary care hospital to their homes following the implementation of a web-based "discharge module," which included the optional use of diagnosis-specific templated discharge instructions. We compared the readability of discharge instructions, as measured by the Flesch Reading Ease Level test (FREL, on a 0-100 scale, with higher scores indicating greater readability) and the Flesch-Kincaid Grade Level test (FKGL, measured in grade levels), between discharges that used templated instructions (with or without modification) versus discharges that used clinician-generated instructions (with or without available templated instructions for the specific discharge diagnosis). Templated discharge instructions were provided to patients in 45% of discharges. Of the 55% of patients that received clinician-generated discharge instructions, the majority (78.1%) had no available templated instruction for the specific discharge diagnosis. Templated discharge instructions had higher FREL scores (71 vs. 57, P < .001) and lower FKGL scores (5.6 vs. 7.6, P < .001), compared to clinician-generated discharge instructions. The use of electronically available templated discharge instructions was associated with better readability (a higher FREL score and a lower FKGL score) than the use of clinician-generated discharge instructions. The main reason for clinicians to create discharge instructions was the lack of available templates for the patient's specific discharge diagnosis. Use of electronically available templated discharge instructions may be a viable option to improve the readability of written material provided to patients at discharge, although the library of available templates requires expansion. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

A study of the standard brain in Japanese children: morphological comparison with the MNI template.

PubMed

Uchiyama, Hitoshi T; Seki, Ayumi; Tanaka, Daisuke; Koeda, Tatsuya; Jcs Group

2013-03-01

Functional magnetic resonance imaging (MRI) studies involve normalization so that the brains of different subjects can be described using the same coordinate system. However, standard brain templates, including the Montreal Neurological Institute (MNI) template that is most frequently used at present, were created based on the brains of Western adults. Because morphological characteristics of the brain differ by race and ethnicity and between adults and children, errors are likely to occur when data from the brains of non-Western individuals are processed using these templates. Therefore, this study was conducted to collect basic data for the creation of a Japanese pediatric standard brain. Participants in this study were 45 healthy children (contributing 65 brain images) between the ages of 6 and 9 years, who had nothing notable in their perinatal and other histories and neurological findings, had normal physical findings and cognitive function, exhibited no behavioral abnormalities, and provided analyzable MR images. 3D-T1-weighted images were obtained using a 1.5-T MRI device, and images from each child were adjusted to the reference image by affine transformation using SPM8. The lengths were measured and compared with those of the MNI template. The Western adult standard brain and the Japanese pediatric standard brain obtained in this study differed greatly in size, particularly along the anteroposterior diameter and in height, suggesting that the correction rates are high, and that errors are likely to occur in the normalization of pediatric brain images. We propose that the use of the Japanese pediatric standard brain created in this study will improve the accuracy of identification of brain regions in functional brain imaging studies involving children. Copyright © 2012 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

SU-F-BRD-10: Lung IMRT Planning Using Standardized Beam Bouquet Templates

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

Yuan, L; Wu, Q J.; Yin, F

2014-06-15

Purpose: We investigate the feasibility of choosing from a small set of standardized templates of beam bouquets (i.e., entire beam configuration settings) for lung IMRT planning to improve planning efficiency and quality consistency, and also to facilitate automated planning. Methods: A set of beam bouquet templates is determined by learning from the beam angle settings in 60 clinical lung IMRT plans. A k-medoids cluster analysis method is used to classify the beam angle configuration into clusters. The value of the average silhouette width is used to determine the ideal number of clusters. The beam arrangements in each medoid of themore » resulting clusters are taken as the standardized beam bouquet for the cluster, with the corresponding case taken as the reference case. The resulting set of beam bouquet templates was used to re-plan 20 cases randomly selected from the database and the dosimetric quality of the plans was evaluated against the corresponding clinical plans by a paired t-test. The template for each test case was manually selected by a planner based on the match between the test and reference cases. Results: The dosimetric parameters (mean±S.D. in percentage of prescription dose) of the plans using 6 beam bouquet templates and those of the clinical plans, respectively, and the p-values (in parenthesis) are: lung Dmean: 18.8±7.0, 19.2±7.0 (0.28), esophagus Dmean: 32.0±16.3, 34.4±17.9 (0.01), heart Dmean: 19.2±16.5, 19.4±16.6 (0.74), spinal cord D2%: 47.7±18.8, 52.0±20.3 (0.01), PTV dose homogeneity (D2%-D99%): 17.1±15.4, 20.7±12.2 (0.03).The esophagus Dmean, cord D02 and PTV dose homogeneity are statistically better in the plans using the standardized templates, but the improvements (<5%) may not be clinically significant. The other dosimetric parameters are not statistically different. Conclusion: It's feasible to use a small number of standardized beam bouquet templates (e.g. 6) to generate plans with quality comparable to that of clinical plans. Partially supported by NIH/NCI under grant #R21CA161389 and a master research grant by Varian Medical System.« less

Sub-threshold standard cell library design for ultra-low power biomedical applications.

PubMed

Li, Ming-Zhong; Ieong, Chio-In; Law, Man-Kay; Mak, Pui-In; Vai, Mang-I; Martins, Rui P

2013-01-01

Portable/Implantable biomedical applications usually exhibit stringent power budgets for prolonging battery life time, but loose operating frequency requirements due to small bio-signal bandwidths, typically below a few kHz. The use of sub-threshold digital circuits is ideal in such scenario to achieve optimized power/speed tradeoffs. This paper discusses the design of a sub-threshold standard cell library using a standard 0.18-µm CMOS technology. A complete library of 56 standard cells is designed and the methodology is ensured through schematic design, transistor width scaling and layout design, as well as timing, power and functionality characterization. Performance comparison between our sub-threshold standard cell library and a commercial standard cell library using a 5-stage ring oscillator and an ECG designated FIR filter is performed. Simulation results show that our library achieves a total power saving of 95.62% and a leakage power reduction of 97.54% when compared with the same design implemented by the commercial standard cell library (SCL).

SU-F-J-100: Standardized Biodistribution Template for Nuclear Medicine Dosimetry Collection and Reporting

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

Kesner, A; Poli, G; Beykan, S

Purpose: As the field of Nuclear Medicine moves forward with efforts to integrate radiation dosimetry into clinical practice we can identify the challenge posed by the lack of standardized dose calculation methods and protocols. All personalized internal dosimetry is derived by projecting biodistribution measurements into dosimetry calculations. In an effort to standardize organization of data and its reporting, we have developed, as a sequel to the EANM recommendation of “Good Dosimetry Reporting”, a freely available biodistribution template, which can be used to create a common point of reference for dosimetry data. It can be disseminated, interpreted, and used for methodmore » development widely across the field. Methods: A generalized biodistribution template was built in a comma delineated format (.csv) to be completed by users performing biodistribution measurements. The template is available for free download. The download site includes instructions and other usage details on the template. Results: This is a new resource developed for the community. It is our hope that users will consider integrating it into their dosimetry operations. Having biodistribution data available and easily accessible for all patients processed is a strategy for organizing large amounts of information. It may enable users to create their own databases that can be analyzed for multiple aspects of dosimetry operations. Furthermore, it enables population data to easily be reprocessed using different dosimetry methodologies. With respect to dosimetry-related research and publications, the biodistribution template can be included as supplementary material, and will allow others in the community to better compare calculations and results achieved. Conclusion: As dosimetry in nuclear medicine become more routinely applied in clinical applications, we, as a field, need to develop the infrastructure for handling large amounts of data. Our organ level biodistribution template can be used as a standard format for data collection, organization, as well as for dosimetry research and software development.« less

Standards for hospital libraries 2002

PubMed Central

Gluck, Jeannine Cyr; Hassig, Robin Ackley; Balogh, Leeni; Bandy, Margaret; Doyle, Jacqueline Donaldson; Kronenfeld, Michael R.; Lindner, Katherine Lois; Murray, Kathleen; Petersen, JoAn; Rand, Debra C.

2002-01-01

The Medical Library Association's “Standards for Hospital Libraries 2002” have been developed as a guide for hospital administrators, librarians, and accrediting bodies to ensure that hospitals have the resources and services to effectively meet their needs for knowledge-based information. Specific requirements for knowledge-based information include that the library be a separate department with its own budget. Knowledge-based information in the library should be directed by a qualified librarian who functions as a department head and is a member of the Academy of Health Information Professionals. The standards define the role of the medical librarian and the links between knowledge-based information and other functions such as patient care, patient education, performance improvement, and education. In addition, the standards address the development and implementation of the knowledge-based information needs assessment and plans, the promotion and publicity of the knowledge-based information services, and the physical space and staffing requirements. The role, qualifications, and functions of a hospital library consultant are outlined. The health sciences library is positioned to play a key role in the hospital. The increasing use of the Internet and new information technologies by medical, nursing, and allied health staffs; patients; and the community require new strategies, strategic planning, allocation of adequate resources, and selection and evaluation of appropriate information resources and technologies. The Hospital Library Standards Committee has developed this document as a guideline to be used in facing these challenges. Editor's Note: The “Standards for Hospital Libraries 2002” were approved by the members of the Hospital Library Section during MLA '02 in Dallas, Texas. They were subsequently approved by Section Council and received final approval from the MLA Board of Directors in June 2002. They succeed the Standards for Hospital Libraries published in 1994 and the Minimum Standards for Health Sciences Libraries in Hospitals from 1983. A Frequently Asked Questions document discussing the development of the new standards can be found on the Hospital Library Section Website at http://www.hls.mlanet.org. PMID:12398254

36 CFR 1281.4 - What are the architectural and design standards for Presidential libraries?

Code of Federal Regulations, 2012 CFR

2012-07-01

... and design standards for Presidential libraries? 1281.4 Section 1281.4 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.4 What are the architectural and design standards for Presidential libraries? The Archivist is...

36 CFR 1281.4 - What are the architectural and design standards for Presidential libraries?

Code of Federal Regulations, 2014 CFR

2014-07-01

... and design standards for Presidential libraries? 1281.4 Section 1281.4 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.4 What are the architectural and design standards for Presidential libraries? The Archivist is...

36 CFR 1281.4 - What are the architectural and design standards for Presidential libraries?

Code of Federal Regulations, 2011 CFR

2011-07-01

... and design standards for Presidential libraries? 1281.4 Section 1281.4 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.4 What are the architectural and design standards for Presidential libraries? The Archivist is...

36 CFR 1281.4 - What are the architectural and design standards for Presidential libraries?

Code of Federal Regulations, 2010 CFR

2010-07-01

... and design standards for Presidential libraries? 1281.4 Section 1281.4 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.4 What are the architectural and design standards for Presidential libraries? The Archivist is...

Standards for Health Sciences Libraries.

ERIC Educational Resources Information Center

Stinson, E. Ray

1982-01-01

Discusses service standards (level of excellence or adequacy in performance of library service) and their incorporation in the accreditation process for hospital library service and academic health sciences libraries. The certification program developed for health sciences librarians by the Medical Library Association is reviewed. Fifty-nine…

Hospital library service and the changes in national standards.

PubMed Central

Glitz, B; Flack, V; Lovas, I M; Newell, P

1998-01-01

Two important sets of standards affecting hospital libraries were significantly revised in 1994, those of the Medical Library Association (MLA) and the Joint Commission on Accreditation of Healthcare Organizations (JCAHO). As part of its continuing efforts to monitor library services within its region, the University of California, Los Angeles Biomedical Library, Regional Medical Library for the Pacific Southwest Region of the National Network of Libraries of Medicine (NN/LM) conducted a survey in late 1994, in part to determine the effects of these revised standards on regional hospital libraries. Data from the survey were also used to provide a view of hospital libraries in the Pacific Southwest region, and to make comparisons with similar data collected in 1989. Results showed that while libraries remained stable in overall number, size, and staffing, services, especially those associated with end-user searching and interlibrary loan, increased enormously. With respect to the MLA standards, results show a high compliance level. Interesting differences were seen between the perceptions of library staff concerning their rate of compliance with the JCAHO standards and their actual compliance as measured by the MLA criteria. While some libraries appear to measure up better than their own perceptions would indicate, others may be fully aware of their actual compliance level. PMID:9549016

An integrated runtime and compile-time approach for parallelizing structured and block structured applications

NASA Technical Reports Server (NTRS)

Agrawal, Gagan; Sussman, Alan; Saltz, Joel

1993-01-01

Scientific and engineering applications often involve structured meshes. These meshes may be nested (for multigrid codes) and/or irregularly coupled (called multiblock or irregularly coupled regular mesh problems). A combined runtime and compile-time approach for parallelizing these applications on distributed memory parallel machines in an efficient and machine-independent fashion was described. A runtime library which can be used to port these applications on distributed memory machines was designed and implemented. The library is currently implemented on several different systems. To further ease the task of application programmers, methods were developed for integrating this runtime library with compilers for HPK-like parallel programming languages. How this runtime library was integrated with the Fortran 90D compiler being developed at Syracuse University is discussed. Experimental results to demonstrate the efficacy of our approach are presented. A multiblock Navier-Stokes solver template and a multigrid code were experimented with. Our experimental results show that our primitives have low runtime communication overheads. Further, the compiler parallelized codes perform within 20 percent of the code parallelized by manually inserting calls to the runtime library.

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

PubMed

Neria-González, Isabel; Wang, En Tao; Ramírez, Florina; Romero, Juan M; Hernández-Rodríguez, César

2006-06-01

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

North Dakota Standards and Benchmarks--Content Standards: Library/Technology Literacy

ERIC Educational Resources Information Center

North Dakota Department of Public Instruction, 2003

2003-01-01

The Library/Technology Literacy Standards for the State of North Dakota were developed during 2000-2002 by a team of library and technology specialists, assisted by representatives from the Department of Public Instruction. The initial task was to decide whether technology and library curricula overlapped enough to create a shared set of…

Texas School Libraries: Standards, Resources, Services, and Students' Performance.

ERIC Educational Resources Information Center

Smith, Ester G.

This study of Texas school libraries had three objectives: examine school library resources, services, and use, on the basis of the School Library Programs: Standards and Guidelines for Texas and determine the need for updating these standards and guidelines so that they better serve communities across the state; determine the impact that school…

25 CFR 36.40 - Standard XIII-Library/media program.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Standard XIII-Library/media program. 36.40 Section 36.40... § 36.40 Standard XIII—Library/media program. (a) Each school shall provide a library/media program... objectives have been met. (2) A written policy for the selection of materials and equipment shall be...

36 CFR § 1281.4 - What are the architectural and design standards for Presidential libraries?

Code of Federal Regulations, 2013 CFR

2013-07-01

... design standards for Presidential libraries? § 1281.4 Section § 1281.4 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.4 What are the architectural and design standards for Presidential libraries? The Archivist is...

Framing an Urban School Library with the "National School Library Standards"

ERIC Educational Resources Information Center

Keeling, Mary

2018-01-01

What is the future of urban school libraries? The American Association of School Librarians (AASL) "National School Library Standards" offer a framework for school librarians to reflect on how they can tailor their professional practice to serve their specific school communities. Through the lens of the standards, school librarians can…

The Revised National Board Library Media Standards and You

ERIC Educational Resources Information Center

Garry, Candi Pierce

2010-01-01

The National Board for Professional Teaching Standards (NBPTS) offers a voluntary certification program as a means to recognize accomplished teaching in sixteen subject areas, including Library Media. The original standards for Library Media K-12 were published in 2000. In 2009, NBPTS selected a committee of library professionals from across the…

A Hospital-Specific Template for Benchmarking its Cost and Quality

PubMed Central

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-01-01

Objective Develop an improved method for auditing hospital cost and quality tailored to a specific hospital’s patient population. Data Sources/Setting Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, New York, and Texas between 2004 and 2006. Study Design A template of 300 representative patients from a single index hospital was constructed and used to match 300 patients at 43 hospitals that had a minimum of 500 patients over a 3-year study period. Data Collection/Extraction Methods From each of 43 hospitals we chose 300 patients most resembling the template using multivariate matching. Principal Findings We found close matches on procedures and patient characteristics, far more balanced than would be expected in a randomized trial. There were little to no differences between the index hospital’s template and the 43 hospitals on most patient characteristics yet large and significant differences in mortality, failure-to-rescue, and cost. Conclusion Matching can produce fair, directly standardized audits. From the perspective of the index hospital, “hospital-specific” template matching provides the fairness of direct standardization with the specific institutional relevance of indirect standardization. Using this approach, hospitals will be better able to examine their performance, and better determine why they are achieving the results they observe. PMID:25201167

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards.

PubMed

Jiang, Guoqian; Evans, Julie; Endle, Cory M; Solbrig, Harold R; Chute, Christopher G

2016-01-01

The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message development in the standards developing organizations (SDOs). The increasing sophistication and complexity of the BRIDG model requires new approaches to the management and utilization of the underlying semantics to harmonize domain-specific standards. The objective of this study is to develop and evaluate a Semantic Web-based approach that integrates the BRIDG model with ISO 21090 data types to generate domain-specific templates to support clinical study metadata standards development. We developed a template generation and visualization system based on an open source Resource Description Framework (RDF) store backend, a SmartGWT-based web user interface, and a "mind map" based tool for the visualization of generated domain-specific templates. We also developed a RESTful Web Service informed by the Clinical Information Modeling Initiative (CIMI) reference model for access to the generated domain-specific templates. A preliminary usability study is performed and all reviewers (n = 3) had very positive responses for the evaluation questions in terms of the usability and the capability of meeting the system requirements (with the average score of 4.6). Semantic Web technologies provide a scalable infrastructure and have great potential to enable computable semantic interoperability of models in the intersection of health care and clinical research.

Standards for vision science libraries: 2014 revision.

PubMed

Motte, Kristin; Caldwell, C Brooke; Lamson, Karen S; Ferimer, Suzanne; Nims, J Chris

2014-10-01

This Association of Vision Science Librarians revision of the "Standards for Vision Science Libraries" aspires to provide benchmarks to address the needs for the services and resources of modern vision science libraries (academic, medical or hospital, pharmaceutical, and so on), which share a core mission, are varied by type, and are located throughout the world. Through multiple meeting discussions, member surveys, and a collaborative revision process, the standards have been updated for the first time in over a decade. While the range of types of libraries supporting vision science services, education, and research is wide, all libraries, regardless of type, share core attributes, which the standards address. The current standards can and should be used to help develop new vision science libraries or to expand the growth of existing libraries, as well as to support vision science librarians in their work to better provide services and resources to their respective users.

An optical to IR sky brightness model for the LSST

NASA Astrophysics Data System (ADS)

Yoachim, Peter; Coughlin, Michael; Angeli, George Z.; Claver, Charles F.; Connolly, Andrew J.; Cook, Kem; Daniel, Scott; Ivezić, Željko; Jones, R. Lynne; Petry, Catherine; Reuter, Michael; Stubbs, Christopher; Xin, Bo

2016-07-01

To optimize the observing strategy of a large survey such as the LSST, one needs an accurate model of the night sky emission spectrum across a range of atmospheric conditions and from the near-UV to the near-IR. We have used the ESO SkyCalc Sky Model Calculator1, 2 to construct a library of template spectra for the Chilean night sky. The ESO model includes emission from the upper and lower atmosphere, scattered starlight, scattered moonlight, and zodiacal light. We have then extended the ESO templates with an empirical fit to the twilight sky emission as measured by a Canon all-sky camera installed at the LSST site. With the ESO templates and our twilight model we can quickly interpolate to any arbitrary sky position and date and return the full sky spectrum or surface brightness magnitudes in the LSST filter system. Comparing our model to all-sky observations, we find typical residual RMS values of +/-0.2-0.3 magnitudes per square arcsecond.

Pythran: enabling static optimization of scientific Python programs

NASA Astrophysics Data System (ADS)

Guelton, Serge; Brunet, Pierrick; Amini, Mehdi; Merlini, Adrien; Corbillon, Xavier; Raynaud, Alan

2015-01-01

Pythran is an open source static compiler that turns modules written in a subset of Python language into native ones. Assuming that scientific modules do not rely much on the dynamic features of the language, it trades them for powerful, possibly inter-procedural, optimizations. These optimizations include detection of pure functions, temporary allocation removal, constant folding, Numpy ufunc fusion and parallelization, explicit thread-level parallelism through OpenMP annotations, false variable polymorphism pruning, and automatic vector instruction generation such as AVX or SSE. In addition to these compilation steps, Pythran provides a C++ runtime library that leverages the C++ STL to provide generic containers, and the Numeric Template Toolbox for Numpy support. It takes advantage of modern C++11 features such as variadic templates, type inference, move semantics and perfect forwarding, as well as classical idioms such as expression templates. Unlike the Cython approach, Pythran input code remains compatible with the Python interpreter. Output code is generally as efficient as the annotated Cython equivalent, if not more, but without the backward compatibility loss.

An introduction to the COLIN optimization interface.

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

Hart, William Eugene

2003-03-01

We describe COLIN, a Common Optimization Library INterface for C++. COLIN provides C++ template classes that define a generic interface for both optimization problems and optimization solvers. COLIN is specifically designed to facilitate the development of hybrid optimizers, for which one optimizer calls another to solve an optimization subproblem. We illustrate the capabilities of COLIN with an example of a memetic genetic programming solver.

State Indoor Radon Grants Resources

EPA Pesticide Factsheets

This guidance explains the standardized state template for SIRG measures,as required by the OMB and answers questions about the template. The Program guidance is intended to reconcile all legal, policy and programmatic changes that affected SIRG.

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE PAGES

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi; ...

2016-07-21

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

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

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Sharing Site-Based Research Data: Standardizing and Packaging for Reuse

NASA Astrophysics Data System (ADS)

Gordon, S.; DiLauro, T.; Jett, J. G.; Thomer, A.

2014-12-01

One of the key aims of the Institute of Museum and Library Services-funded Site-Based Data Curation (SBDC) Project[1] is to increase the reuse of data gathered or generated through research at sites like Yellowstone National Park (YNP) by improving its usefulness, discoverability, and accessibility. Toward this goal, SBDC worked closely with a geobiologist conducting fieldwork at YNP to explore existing data practices and held a two-day stakeholders workshop at the park with some of the scientists who study it and the National Park Service (NPS) staff who support research activities there. The resulting workshop report[2] recommends, among other things, improvements to the level of detail and consistency of documentation of data and of its sampling and analysis methods. A set of core metadata elements and domain-specific extension elements is proposed (Appendix 9) to provide a more coherent view into the data. Armed with these findings, we are pursuing approaches that will reduce the effort, complexity, and risk tied to adoption of these recommendations. During our investigation, we discovered the EarthChem templates[3], into which we began mapping the geobiologist's data. We find the Vent Fluids template particularly appropriate and adaptable, as many of the high-interest features at YNP are shallow water vents. We are currently building an EarthChem-compatible template that will capture the environmental context of microbes, tracing their identities from water sample through to GenBank entry. Given the variety of potential targets (e.g., site, institutional, and domain repositories; visualization and presentation tools), we decided to record the data in a structured package, which we can transform for a given target. We are using the Data Conservancy's Packaging Tool[4], which provides an intuitive file system view, stores file checksums, and serializes a graph of relationships. This permits a researcher to conveniently group desired data products into a single self-documenting TAR or Zip file. Initial target repositories are NPS's IRMA, Data Conservancy, and SEAD/Medici. [1]http://cirssweb.lis.illinois.edu/SBDC [2] https://www.ideals.illinois.edu/handle/2142/47070 [3] http://www.earthchem.org/data/templates [4] http://dataconservancy.org/dcs-packaging-specification/

Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues

NASA Technical Reports Server (NTRS)

Kozlov, I. A.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction. The substitution of D for A, on the contrary, leads to increased incorporation of U into the products. We found no evidence for the template-directed facilitation of oligomerization of A or I through A-I base pairing. The significance of these results for prebiotic chemistry is discussed.

Standards for Libraries Within Regional Library Systems in Saskatchewan.

ERIC Educational Resources Information Center

Saskatchewan Library Association, Regina.

These quantitative standards for the delivery of library services to a dispersed population, which were developed by the Saskatchewan Library Association, are based on the decentralized delivery of library services backed up by the centralized provision of technical services, resource people, and special collections in Saskatchewan. The roles of…

State Indoor Radon Grants Guidance and Tools

EPA Pesticide Factsheets

This guidance explains the standardized state template for SIRG measures,as required by the OMB and answers questions about the template. The Program guidance is intended to reconcile all legal, policy and programmatic changes that affected SIRG.

Template based protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Juyong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native-like structural aspects present in multiple templates. The LEE protocol is identical to the nns one except that CASP11-released server models are used as templates. The success of LEE in utilizing CASP11 server models indicates that proper template screening and template clustering assisted by appropriate cluster ranking promises a new direction to enhance protein 3D modeling. Proteins 2016; 84(Suppl 1):221-232. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

School Librarian as Inquisitor of Practice: Reimagine, Reflect, and React with the New Standards

ERIC Educational Resources Information Center

Burns, Elizabeth

2018-01-01

The modern school library is a complex social setting "grounded in standards and best practice" (AASL 2018). The new "National School Library Standards" have refreshed the student learning standards and aligned new Shared Foundations to the school library. Additionally, the competencies for learners are now complemented by…

Building a portable data and information interoperability infrastructure-framework for a standard Taiwan Electronic Medical Record Template.

PubMed

Jian, Wen-Shan; Hsu, Chien-Yeh; Hao, Te-Hui; Wen, Hsyien-Chia; Hsu, Min-Huei; Lee, Yen-Liang; Li, Yu-Chuan; Chang, Polun

2007-11-01

Traditional electronic health record (EHR) data are produced from various hospital information systems. They could not have existed independently without an information system until the incarnation of XML technology. The interoperability of a healthcare system can be divided into two dimensions: functional interoperability and semantic interoperability. Currently, no single EHR standard exists that provides complete EHR interoperability. In order to establish a national EHR standard, we developed a set of local EHR templates. The Taiwan Electronic Medical Record Template (TMT) is a standard that aims to achieve semantic interoperability in EHR exchanges nationally. The TMT architecture is basically composed of forms, components, sections, and elements. Data stored in the elements which can be referenced by the code set, data type, and narrative block. The TMT was established with the following requirements in mind: (1) transformable to international standards; (2) having a minimal impact on the existing healthcare system; (3) easy to implement and deploy, and (4) compliant with Taiwan's current laws and regulations. The TMT provides a basis for building a portable, interoperable information infrastructure for EHR exchange in Taiwan.

Construction of population-specific Indian MRI brain template: Morphometric comparison with Chinese and Caucasian templates.

PubMed

Bhalerao, Gaurav Vivek; Parlikar, Rujuta; Agrawal, Rimjhim; Shivakumar, Venkataram; Kalmady, Sunil V; Rao, Naren P; Agarwal, Sri Mahavir; Narayanaswamy, Janardhanan C; Reddy, Y C Janardhan; Venkatasubramanian, Ganesan

2018-06-01

Spatial normalization of brain MR images is highly dependent on the choice of target brain template. Morphological differences caused by factors like genetic and environmental exposures, generates a necessity to construct population specific brain templates. Brain image analysis performed using brain templates from Caucasian population may not be appropriate for non-Caucasian population. In this study, our objective was to construct an Indian brain template from a large population (N = 157 subjects) and compare the morphometric parameters of this template with that of Chinese-56 and MNI-152 templates. In addition, using an independent MRI data of 15 Indian subjects, we also evaluated the potential registration accuracy differences using these three templates. Indian brain template was constructed using iterative routines as per established procedures. We compared our Indian template with standard MNI-152 template and Chinese template by measuring global brain features. We also examined accuracy of registration by aligning 15 new Indian brains to Indian, Chinese and MNI templates. Furthermore, we supported our measurement protocol with inter-rater and intra-rater reliability analysis. Our results showed that there were significant differences in global brain features of Indian template in comparison with Chinese and MNI brain templates. The results of registration accuracy analysis revealed that fewer deformations are required when Indian brains are registered to Indian template as compared to Chinese and MNI templates. This study concludes that population specific Indian template is likely to be more appropriate for structural and functional image analysis of Indian population. Copyright © 2018 Elsevier B.V. All rights reserved.

Texas Library Systems Act and Rules for Administering the Library Systems Act.

ERIC Educational Resources Information Center

Texas State Library, Austin. Dept. of Library Development.

This guide to the administration of the Library Systems Act for the State of Texas begins by presenting the text of the Library Systems Act. The relevant regulations from the Texas Administrative Code are then provided, covering such topics as standards for accreditation of a major resource system of libraries, minimum standards for accreditation…

SALT spectroscopic classification of SN 2017erp as a type-Ia supernova well before maximum light

NASA Astrophysics Data System (ADS)

Jha, S. W.; Camacho, Y.; Dettman, K.; Pan, Y.-C.; Foley, R. J.; Rest, A.; Scolnic, D.; Skelton, R.

2017-06-01

We obtained SALT (+RSS) spectroscopy of SN 2017erp (discovered by K. Itagaki) on 2017 Jun 13.9 UT, covering the wavelength range 350-940 nm. Cross-correlation of the supernova spectrum with a template library using SNID (Blondin & Tonry 2007, ApJ, 666, 1024) shows SN 2017erp is a type-Ia supernova before maximum light.

Standards for vision science libraries: 2014 revision

PubMed Central

Motte, Kristin; Caldwell, C. Brooke; Lamson, Karen S.; Ferimer, Suzanne; Nims, J. Chris

2014-01-01

Objective: This Association of Vision Science Librarians revision of the “Standards for Vision Science Libraries” aspires to provide benchmarks to address the needs for the services and resources of modern vision science libraries (academic, medical or hospital, pharmaceutical, and so on), which share a core mission, are varied by type, and are located throughout the world. Methods: Through multiple meeting discussions, member surveys, and a collaborative revision process, the standards have been updated for the first time in over a decade. Results: While the range of types of libraries supporting vision science services, education, and research is wide, all libraries, regardless of type, share core attributes, which the standards address. Conclusions: The current standards can and should be used to help develop new vision science libraries or to expand the growth of existing libraries, as well as to support vision science librarians in their work to better provide services and resources to their respective users. PMID:25349547

Standards for Community College Library Facilities.

ERIC Educational Resources Information Center

California State Postsecondary Education Commission, Sacramento.

This report contains proposed standards for community college library facilities developed by the California Postsecondary Education Commission. Formulae for calculating stack space, staff space, reader station space, and total space are included in the report. Three alternative models for revising the present library standards were considered:…

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.

DNA-Encoded Dynamic Combinatorial Chemical Libraries.

PubMed

Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

2015-06-26

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

larvalign: Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.

PubMed

Muenzing, Sascha E A; Strauch, Martin; Truman, James W; Bühler, Katja; Thum, Andreas S; Merhof, Dorit

2018-01-01

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

Statistical density modification using local pattern matching

DOEpatents

Terwilliger, Thomas C.

2007-01-23

A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

Examining New Technologies, Legislation, Standards and Budgets [and] Libraries: Global Reach, Local Touch [and] Achieving Professional Standards [and] Putting Knowledge To Work [and] View from the Head of the Table [and] Copyright is My Life [and] Leadership in Library and Information Services [and] PIALA in Micronesia [and] Te Rau Herenga.

ERIC Educational Resources Information Center

Voogt, Leo; Ford, Barbara J.; Hendry, J.; Bender, David; Field, Judy; Whitney, Paul; Adams, Karen; Crotts, Joanne Tarpley; Cooper, Sue

1997-01-01

Representatives from seven international library associations give a global view of the library and information sector by outlining goals of the international library association and discussing information literacy, repositioning libraries at the center of the information society, "virtual associations," reassessing library roles and…

Standards for University Libraries = Normes pour les bibliotheques universitaires = Richtwerte fur Universitatsbibliotheken = Normas de bibliotecas universitarias. IFLA Professional Reports No. 10.

ERIC Educational Resources Information Center

Lynch, Beverly P., Ed.

This statement prepared by the International Federation of Library Associations' Section of University Libraries and Other General Research Libraries presents standards of general principles designed to accomplish the following: (1) provide a means by which the quality of the library serving a university can be assessed; (2) offer guidance for…

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

Identifying Needed Technical Standards: The LITA TESLA Committee at Work.

ERIC Educational Resources Information Center

Carter, Ruth C.

1984-01-01

Efforts of the Technical Standards for Library Automation Committee (TESLA), a division-wide committee of the Library Information and Technology Association (LITA) of the American Library Association, are described. The current status of suggested technical standards and recommended action are detailed. Five sources are given. (Author/EJS)

The LBI Standard for Library Binding: The Glossary.

ERIC Educational Resources Information Center

Parisi, Paul A.; Terrill-Oldham, Jan

1986-01-01

Contains a glossary of 33 terms for book preservation intended for use with the text of the eighth edition of "Library Binding Institute Standard for Library Binding." It defines words not easily understood by laypersons that actually appear in the standards and should be used along with the illustrations. (EM)

Used Nuclear Fuel-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS)

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

Banerjee, Kaushik; Clarity, Justin B; Cumberland, Riley M

This will be licensed via RSICC. A new, integrated data and analysis system has been designed to simplify and automate the performance of accurate and efficient evaluations for characterizing the input to the overall nuclear waste management system -UNF-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS). A relational database within UNF-ST&DARDS provides a standard means by which UNF-ST&DARDS can succinctly store and retrieve modeling and simulation (M&S) parameters for specific spent nuclear fuel analysis. A library of various analysis model templates provides the ability to communicate the various set of M&S parameters to the most appropriate M&S application.more » Interactive visualization capabilities facilitate data analysis and results interpretation. UNF-ST&DARDS current analysis capabilities include (1) assembly-specific depletion and decay, (2) and spent nuclear fuel cask-specific criticality and shielding. Currently, UNF-ST&DARDS uses SCALE nuclear analysis code system for performing nuclear analysis.« less

EnergyPlus Graphical User Interface

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

2011-01-04

LBNL, Infosys Technologies and Digital Alchemy are developing a free, comprehensive graphical user interface (GUI) that will enable EnergyPlus to be used more easily and effectively by building designers and other professionals, facilitating its widespread adoption. User requirements have been defined through a series of practitioner workshops. A new schematic editor for HVAC systems will be combined with different building envelope geometry generation tools and IFC-based BIM import and export. LBNL and Digital Alchemy have generated a detailed function requirements specification, which is being implemented in software by Infosys, LBNL and and Digital Alchemy. LBNL and practitioner subcontractors will developmore » a comprehensive set of templates and libraries and will perform extensive testing of the GUI before it is released in Q3 2011. It is planned to use an Open Platfom approach, in which a comprehensive set of well documented Application Programming Interfaces (API's) would be provided to facilitate both the development of third party contributions to the official, standard GUI and the development of derivative works.« less

Standardized Protocol for Virtual Surgical Plan and 3-Dimensional Surgical Template-Assisted Single-Stage Mandible Contour Surgery.

PubMed

Fu, Xi; Qiao, Jia; Girod, Sabine; Niu, Feng; Liu, Jian Feng; Lee, Gordon K; Gui, Lai

2017-09-01

Mandible contour surgery, including reduction gonioplasty and genioplasty, has become increasingly popular in East Asia. However, it is technically challenging and, hence, leads to a long learning curve and high complication rates and often needs secondary revisions. The increasing use of 3-dimensional (3D) technology makes accurate single-stage mandible contour surgery with minimum complication rates possible with a virtual surgical plan (VSP) and 3-D surgical templates. This study is to establish a standardized protocol for VSP and 3-D surgical templates-assisted mandible contour surgery and evaluate the accuracy of the protocol. In this study, we enrolled 20 patients for mandible contour surgery. Our protocol is to perform VSP based on 3-D computed tomography data. Then, design and 3-D print surgical templates based on preoperative VSP. The accuracy of the method was analyzed by 3-D comparison of VSP and postoperative results using detailed computer analysis. All patients had symmetric, natural osteotomy lines and satisfactory facial ratios in a single-stage operation. The average relative error of VSP and postoperative result on the entire skull was 0.41 ± 0.13 mm. The average new left gonial error was 0.43 ± 0.77 mm. The average new right gonial error was 0.45 ± 0.69 mm. The average pognion error was 0.79 ± 1.21 mm. Patients were very satisfied with the aesthetic results. Surgeons were very satisfied with the performance of surgical templates to facilitate the operation. Our standardized protocol of VSP and 3-D printed surgical templates-assisted single-stage mandible contour surgery results in accurate, safe, and predictable outcome in a single stage.

Improving care transitions from hospital to home: standardized orders for home health nursing with remote telemonitoring.

PubMed

Heeke, Sheila; Wood, Felecia; Schuck, Jennifer

2014-01-01

A task force at a multihospital health care system partnered with home health agencies to improve gaps during the discharge transition process. A standardized order template for home health nursing and remote telemonitoring was developed to decrease discrepancies in communication between hospital health care providers and home health nurses caring for patients with heart failure. Pilot results showed significantly improved communication with no readmissions, using the order template.

The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery.

PubMed

O'Reilly, Rachel K; Turberfield, Andrew J; Wilks, Thomas R

2017-10-17

Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures. The largest libraries made by conventional synthesis are currently of the order of 10 8 distinct molecules. To put this in context, there are 10 13 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO 2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous "DNA robots" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.

The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery

PubMed Central

2017-01-01

Conspectus Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify “successful” structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure—a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery—imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous “DNA robots” have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution. PMID:28915003

A population MRI brain template and analysis tools for the macaque.

PubMed

Seidlitz, Jakob; Sponheim, Caleb; Glen, Daniel; Ye, Frank Q; Saleem, Kadharbatcha S; Leopold, David A; Ungerleider, Leslie; Messinger, Adam

2018-04-15

The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the "National Institute of Mental Health Macaque Template", or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies. Copyright © 2017 ElsevierCompany. All rights reserved.

Development and Implementation of Clinical Trial Protocol Templates at the National Institute of Allergy and Infectious Diseases

PubMed Central

Bridge, Heather; Smolskis, Mary; Bianchine, Peter; Dixon, Dennis O.; Kelly, Grace; Herpin, Betsey; Tavel, Jorge

2009-01-01

Background: A clinical research protocol document must reflect both sound scientific rationale as well as local, national and, when applicable, international regulatory and human subject protections requirements. These requirements originate from a variety of sources, undergo frequent revision and are subject to interpretation. Tools to assist clinical investigators in the production of clinical protocols could facilitate navigating these requirements and ultimately increase the efficiency of clinical research. Purpose: The National Institute of Allergy and Infectious Diseases (NIAID) developed templates for investigators to serve as the foundation for protocol development. These protocol templates are designed as tools to support investigators in developing clinical protocols. Methods: NIAID established a series of working groups to determine how to improve its capacity to conduct clinical research more efficiently and effectively. The Protocol Template Working Group was convened to determine what protocol templates currently existed within NIAID and whether standard NIAID protocol templates should be produced. After review and assessment of existing protocol documents and requirements, the group reached consensus about required and optional content, determined the format and identified methods for distribution as well as education of investigators in the use of these templates. Results: The templates were approved by the NIAID Executive Committee in 2006 and posted as part of the NIAID Clinical Research Toolkit[1]website for broad access. These documents require scheduled revisions to stay current with regulatory and policy changes. Limitations: The structure of any clinical protocol template, whether comprehensive or specific to a particular study phase, setting or design, affects how it is used by investigators. Each structure presents its own set of advantages and disadvantages. While useful, protocol templates are not stand-alone tools for creating an optimal protocol document but must be complemented by institutional resources and support. Education and guidance of investigators in the appropriate use of templates is necessary to ensure a complete yet concise protocol document. Due to changing regulatory requirements, clinical protocol templates cannot become static but require frequent revisions. Conclusions: Standard protocol templates that meet applicable regulations can be important tools to assist investigators in the effective conduct of clinical research, but they require dedicated resources and ongoing input from key stakeholders. PMID:19625326

JCAH accreditation and the hospital library: a guide for librarians.

PubMed Central

Topper, J M; Bradley, J; Dudden, R F; Epstein, B A; Lambremont, J A; Putney, T R

1980-01-01

The continuing effort to develop standards for libraries in health care institutions has resulted in the creation of two broad groups of standards: (1) quantitative and specific, and (2) qualitative and flexible. The library standards of the Joint Commission on Accreditation of Hospitals (JCAH), a major example of the second type, were revised and expanded considerably in 1978, bringing them into line with standards for other hospital departments. Possible areas of unclarity or difficulty for the librarian in complying with the revised JCAH standards are discussed, including those relating to staffing, consultants, library technicians, analysis of resources, assessment of needs, documentation, policies and procedures manuals, and the library committee. The JCAH site visit, including preparation of the Hospital Survey Profile, gathering information for the surveyor, and the summary conference, offers opportunities to librarians to participate in an institution-wide effort, to upgrade management practices, and to demonstrate the need for, and effectiveness of, library services in their hospitals. PMID:6928793

Assessment of Electronic Government Information Products

DTIC Science & Technology

1999-03-30

Center for Environmental Info. & Statistics CM Consumer Handbook for Reducing Solid Waste CM Envirofacts Warehouse CM EPA Online Library System (OLS) CP...Hazardous Waste Site Query (CERCLIS Data) CM Surf Your Watershed CM Test Methods for Evaluating Solid Waste : Physical/Chemical Methods (SW-846) CM...SGML because they consider it "intelligent data" that can automatically generate other formats (e.g., web, BBS, Fax on Demand) through templates and

Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.

Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

AGN Populations in Large-volume X-Ray Surveys: Photometric Redshifts and Population Types Found in the Stripe 82X Survey

NASA Astrophysics Data System (ADS)

Ananna, Tonima Tasnin; Salvato, Mara; LaMassa, Stephanie; Urry, C. Megan; Cappelluti, Nico; Cardamone, Carolin; Civano, Francesca; Farrah, Duncan; Gilfanov, Marat; Glikman, Eilat; Hamilton, Mark; Kirkpatrick, Allison; Lanzuisi, Giorgio; Marchesi, Stefano; Merloni, Andrea; Nandra, Kirpal; Natarajan, Priyamvada; Richards, Gordon T.; Timlin, John

2017-11-01

Multiwavelength surveys covering large sky volumes are necessary to obtain an accurate census of rare objects such as high-luminosity and/or high-redshift active galactic nuclei (AGNs). Stripe 82X is a 31.3 X-ray survey with Chandra and XMM-Newton observations overlapping the legacy Sloan Digital Sky Survey Stripe 82 field, which has a rich investment of multiwavelength coverage from the ultraviolet to the radio. The wide-area nature of this survey presents new challenges for photometric redshifts for AGNs compared to previous work on narrow-deep fields because it probes different populations of objects that need to be identified and represented in the library of templates. Here we present an updated X-ray plus multiwavelength matched catalog, including Spitzer counterparts, and estimated photometric redshifts for 5961 (96% of a total of 6181) X-ray sources that have a normalized median absolute deviation, σnmad=0.06, and an outlier fraction, η = 13.7%. The populations found in this survey and the template libraries used for photometric redshifts provide important guiding principles for upcoming large-area surveys such as eROSITA and 3XMM (in X-ray) and the Large Synoptic Survey Telescope (optical).

Pelvic lymphadenectomy during robot-assisted radical prostatectomy: Assessing nodal yield, perioperative outcomes, and complications.

PubMed

Zorn, Kevin C; Katz, Mark H; Bernstein, Andrew; Shikanov, Sergey A; Brendler, Charles B; Zagaja, Gregory P; Shalhav, Arieh L

2009-08-01

To describe our pelvic lymphadenectomy (PLND) technique during robot-assisted radical prostatectomy and to evaluate the nodal yield and perioperative outcomes. PLND is commonly performed with radical prostatectomy for localized prostate cancer. Because of the limitations of the robotic arm pitch in accessing the pelvic sidewall and undersurface of the iliac bifurcation, uro-oncologists have questioned the adequacy of robotic PLND. PLND was routinely performed on men with higher risk preoperative prostate cancer parameters (ie, prostrate-specific antigen >10 ng/mL, primary Gleason score > or =4, or clinical Stage T2b or greater). The outcomes of robot-assisted radical prostatectomy with bilateral, standard template PLND (group 1; n = 296 [26%]) were compared with those of a cohort of 859 robot-assisted radical prostatectomy patients (74%) without PLND (group 2). We also compared these data with those from a single-surgeon experience of open, standard-template PLND for retropubic radical prostatectomy. The mean number of lymph nodes removed was 12.5 (interquartile range 7-16). The mean operative time (224 vs 216 minutes; P = .09), estimated blood loss (206 vs 229 mL; P = .14), and hospital stay (1.32 vs 1.24 days; P = .46) were comparable between the 2 groups. The rate of intraoperative complications (1% vs 1.5%; P = .2), overall postoperative complications (9% vs 7%; P = .8), and lymphocele formation (2% vs 0%; P = .9) were not significantly different. The review of our open series and the historically published open standard-template PLND series revealed a mean yield of 15 and a range of 6.7-15 lymph nodes removed, respectively. Our data support the feasibility and low complication rate of robotic standard-template PLND with lymph node yields comparable to those with open PLND. Considering the low morbidity of PLND in experienced hands, coupled with the potential of preoperative undergrading and understaging and the therapeutic benefit to patients with micrometastatic disease, an increase in overall standard-template PLND use should be considered.

Tips and Tricks of Incorporating Industry Standards into a Library Collection

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

Abbott, Jennifer; Sandberg, Tami

Professional literature on the incorporation of industry standards into a library collection is somewhat limited. The objective of this presentation is to discuss the intricate details of acquiring, managing, and delivering electronic industry standards to library patrons in a seamless manner. Lessons learned regarding vendor selection and license agreements will also be discussed. Results from a survey administer at the National Renewable Energy Laboratory will be used to analyze how collection policies can properly be developed to incorporate industry standards into a library setting. The key points of acquisition decisions, avoidance of liability issues, and cost will be addressed.

Automated PET-only quantification of amyloid deposition with adaptive template and empirically pre-defined ROI

NASA Astrophysics Data System (ADS)

Akamatsu, G.; Ikari, Y.; Ohnishi, A.; Nishida, H.; Aita, K.; Sasaki, M.; Yamamoto, Y.; Sasaki, M.; Senda, M.

2016-08-01

Amyloid PET is useful for early and/or differential diagnosis of Alzheimer’s disease (AD). Quantification of amyloid deposition using PET has been employed to improve diagnosis and to monitor AD therapy, particularly in research. Although MRI is often used for segmentation of gray matter and for spatial normalization into standard Montreal Neurological Institute (MNI) space where region-of-interest (ROI) template is defined, 3D MRI is not always available in clinical practice. The purpose of this study was to examine the feasibility of PET-only amyloid quantification with an adaptive template and a pre-defined standard ROI template that has been empirically generated from typical cases. A total of 68 subjects who underwent brain 11C-PiB PET were examined. The 11C-PiB images were non-linearly spatially normalized to the standard MNI T1 atlas using the same transformation parameters of MRI-based normalization. The automatic-anatomical-labeling-ROI (AAL-ROI) template was applied to the PET images. All voxel values were normalized by the mean value of cerebellar cortex to generate the SUVR-scaled images. Eleven typical positive images and eight typical negative images were normalized and averaged, respectively, and were used as the positive and negative template. Positive and negative masks which consist of voxels with SUVR  ⩾1.7 were extracted from both templates. Empirical PiB-prone ROI (EPP-ROI) was generated by subtracting the negative mask from the positive mask. The 11C-PiB image of each subject was non-rigidly normalized to the positive and negative template, respectively, and the one with higher cross-correlation was adopted. The EPP-ROI was then inversely transformed to individual PET images. We evaluated differences of SUVR between standard MRI-based method and PET-only method. We additionally evaluated whether the PET-only method would correctly categorize 11C-PiB scans as positive or negative. Significant correlation was observed between the SUVRs obtained with AAL-ROI and those with EPP-ROI when MRI-based normalization was used, the latter providing higher SUVR. When EPP-ROI was used, MRI-based method and PET-only method provided almost identical SUVR. All 11C-PiB scans were correctly categorized into positive and negative using a cutoff value of 1.7 as compared to visual interpretation. The 11C-PiB SUVR were 2.30  ±  0.24 and 1.25  ±  0.11 for the positive and negative images. PET-only amyloid quantification method with adaptive templates and EPP-ROI can provide accurate, robust and simple amyloid quantification without MRI.

Digital templating for THA: a simple computer-assisted application for complex hip arthritis cases.

PubMed

Hafez, Mahmoud A; Ragheb, Gad; Hamed, Adel; Ali, Amr; Karim, Said

2016-10-01

Total hip arthroplasty (THA) is the standard procedure for end-stage arthritis of the hip. Its technical success relies on preoperative planning of the surgical procedure and virtual setup of the operative performance. Digital hip templating is one methodology of preoperative planning for THA which requires a digital preoperative radiograph and a computer with special software. This is a prospective study involving 23 patients (25 hips) who were candidates for complex THA surgery (unilateral or bilateral). Digital templating is done by radiographic assessment using radiographic magnification correction, leg length discrepancy and correction measurements, acetabular component and femoral component templating as well as neck resection measurement. The overall accuracy for templating the stem implant's exact size is 81%. This percentage increased to 94% when considering sizing within 1 size. Digital templating has proven effective, reliable and essential technique for preoperative planning and accurate prediction of THA sizing and alignment.

Commandant Instruction 5216. 17A: Correspondence Standards

DOT National Transportation Integrated Search

1997-01-14

Emphasizes the requirement that users of both Standard Workstation II and III : use the approved pre-formatted macros on CG Standard Workstation II (CGSWII) and : templates on Standard Workstation III (WSIII) respectively. It also expands the : range...

Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions

NASA Astrophysics Data System (ADS)

Chaudhari, Rajan; Heim, Andrew J.; Li, Zhijun

2015-05-01

Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy of "modeling first, refinement next". In the present work, we developed an alternative modeling approach through the novel application of available multiple templates. First, conserved inter-residue interactions are derived from each additional template through conservation analysis of each template-target pairwise alignment. Then, these interactions are converted into distance restraints and incorporated in the homology modeling process. This approach was applied to modeling of the human β2 adrenergic receptor using the bovin rhodopsin and the human protease-activated receptor 1 as templates and improved model quality was demonstrated compared to the homology model generated by standard single-template and multiple-template methods. This method of "refined restraints first, modeling next", provides a fast and complementary way to the current modeling approaches. It allows rational identification and implementation of additional conserved distance restraints extracted from multiple templates and/or experimental data, and has the potential to be applicable to modeling of all helical transmembrane proteins.

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

NASA Technical Reports Server (NTRS)

Kozlov, I. A.; Politis, P. K.; Van Aerschot, A.; Busson, R.; Herdewijn, P.; Orgel, L. E.; Bada, J. L. (Principal Investigator); Dolan, M. (Principal Investigator)

1999-01-01

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

National Library Service for the Blind and Physically Handicapped. Working Paper.

ERIC Educational Resources Information Center

Battelle Memorial Inst., Columbus, OH. Columbus Labs.

Based on observations made at the National Library Service for the Blind and Physically Handicapped (NLS) on September 8, 9, and 10, 1982 and on documents supplied by NLS, this report compares standards published in the 1979 document entitled "Standards of Service for the Library of Congress Network of Libraries for the Blind and Physically…

\\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.

Low track height standard cell design in iN7 using scaling boosters

NASA Astrophysics Data System (ADS)

Sherazi, S. M. Y.; Jha, C.; Rodopoulos, D.; Debacker, P.; Chava, B.; Matti, L.; Bardon, M. G.; Schuddinck, P.; Raghavan, P.; Gerousis, V.; Spessot, A.; Verkest, D.; Mocuta, A.; Kim, R. H.; Ryckaert, J.

2017-04-01

In this paper, standard cell design for iN7 CMOS platform technology targeting the tightest contacted poly pitch (CPP) of 42 nm and a metal pitch of 32 nm in the FinFET technology is presented. Three standard cell architectures for iN7, a 7.5-Track library, 6.5-Track library, and 6-Track library have been designed. Scaling boosters are introduced for the libraries progressively: first an extra MOL layer to enable an efficient layout of the three libraries starting with 7.5-Track library; second, fully self aligned gate contact is introduced for 6.5 and 6-Track library and third, 6-Track cell design includes a buried rail track for supply. The 6-Track cells are on average 5% and 45% smaller than the 6.5 and 7.5-Track cells, respectively.

Incorporating intelligence into structured radiology reports

NASA Astrophysics Data System (ADS)

Kahn, Charles E.

2014-03-01

The new standard for radiology reporting templates being developed through the Integrating the Healthcare Enterprise (IHE) and DICOM organizations defines the storage and exchange of reporting templates as Hypertext Markup Language version 5 (HTML5) documents. The use of HTML5 enables the incorporation of "dynamic HTML," in which documents can be altered in response to their content. HTML5 documents can employ JavaScript, the HTML Document Object Model (DOM), and external web services to create intelligent reporting templates. Several reporting templates were created to demonstrate the use of scripts to perform in-template calculations and decision support. For example, a template for adrenal CT was created to compute contrast washout percentage from input values of precontrast, dynamic postcontrast, and delayed adrenal nodule attenuation values; the washout value can used to classify an adrenal nodule as a benign cortical adenoma. Dynamic templates were developed to compute volumes and apply diagnostic criteria, such as those for determination of internal carotid artery stenosis. Although reporting systems need not use a web browser to render the templates or their contents, the use of JavaScript creates innumerable opportunities to construct highly sophisticated HTML5 reporting templates. This report demonstrates the ability to incorporate dynamic content to enhance the use of radiology reporting templates.

A Study of the National Library Standards Showing the Increased Emphasis on Audiovisuals and the Effect on Library Science Education and State Certification Requirements.

ERIC Educational Resources Information Center

Franklin, Ann York

The purpose of this paper is to study the effect of the national library standards, beginning with a synopsis of the 1945 version up to the latest revision of 1969, and to show how the addition of audiovisuals, or non-print materials, has affected the connotation of the library or librarian. The definition or explanation of the library becomes…

"Cloud" functions and templates of engineering calculations for nuclear power plants

NASA Astrophysics Data System (ADS)

Ochkov, V. F.; Orlov, K. A.; Ko, Chzho Ko

2014-10-01

The article deals with an important problem of setting up computer-aided design calculations of various circuit configurations and power equipment carried out using the templates and standard computer programs available in the Internet. Information about the developed Internet-based technology for carrying out such calculations using the templates accessible in the Mathcad Prime software package is given. The technology is considered taking as an example the solution of two problems relating to the field of nuclear power engineering.

Cheating the Business Template: Filling in the Blanks

ERIC Educational Resources Information Center

Mechenbier, Mahli Xuan

2011-01-01

Business professionals often use standard templates when composing documents, and teachers of business writing direct students to textbook examples to use as sample formats. Good instructors do want to provide their students with informative examples of what is expected, especially in an online course environment where students cannot raise their…

SIOExplorer: Managing Data Flow into a Digital Library

NASA Astrophysics Data System (ADS)

Clark, D.; Miller, S. P.; Peckman, U.; Chase, A.; Helly, J.

2002-12-01

The diversity of the data held by the Geological Data Center at SIO is a tribute to the evolution of oceanography, from echo sounding rolls and hand-drawn charts to modern multibeam bathymetry. However, the changes in sensor technology and organizational approaches since 1903 present real challenges to the archivist, as we struggle to migrate the holdings into a web-accessible digital library for use by the public and scientific community (www.nsdl.org). Automation of the dataflow is an absolute necessity, with millions of files and a terabyte of data, although the biggest challenges come from complexity rather than bulk volume. The problems stem from our diverse archive collection, with its evolving data content, processing practices, naming conventions, and clutter from intermediate or obsolete files. This is not the only or the last data system to suffer from these problems, and an approach has been designed that can be applied to other projects. Instead of writing code to process each individual type of cruise, which varies from vessel to vessel over the fifty years and 795 cruises, we created a single Canonical Cruise Data Structure (CCDS). After some experimentation, the CCDS now consists of 9 basic categories and a reasonable number of sub-categories (directories) that can hold all the essential information. The key to flexibility and scalability comes from a template-driven rules approach that allows a processing script to harvest data from complex original data structures, and store them in the simple CCDS. The template mimics the structure of the CCDS. As the processing script traverses the template it finds rules for each category, instructing it on where to look for likely sources, and how to prioritize the results when multiple sources are detected. Over time as new situations are encountered, changes are simply made to the template, rather than the code. After the first tests, it became apparent that a visual method was needed to monitor the success of the harvesting, to make sure that every category is filled with the correct content. We can run simulated tests on our data staging area and report the results immediately in graphical form on our website. The web report shows data found (blue) and not found (red). A mouse-over operation shows the search string used as a rule for selection, and the list of files actually found. We are also employing visualization as a quality control technique to screen data prior to storage in the digital library. We are outputting a grid per multibeam file that can be viewed with public domain GMT tools, the Fledermaus visualization package, or ESRI Arcgis software, as a rapid check on sound velocity artifacts, noise levels, and editing status.

International Federation of Library Associations Annual Conference. Papers of the Management and Technology Division: Conservation Section (47th, Leipzig, East Germany, August 17-22, 1981).

ERIC Educational Resources Information Center

Sylvestre, J. G.; And Others

Five papers in this collection are concerned with the preservation of library materials; the remaining paper addresses library building standards, emphasizing their value and identifying other reports on library standards. The conservation papers cover: (1) training for conservation in Canada, identifying institutions and associations offering…

Non-native three-dimensional block copolymer morphologies

DOE PAGES

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory; ...

2016-12-22

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

SNSEDextend: SuperNova Spectral Energy Distributions extrapolation toolkit

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Non-native three-dimensional block copolymer morphologies

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

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

Template-Directed Ligation of Peptides to Oligonucleotides

NASA Technical Reports Server (NTRS)

Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

1996-01-01

Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

Easy preparation of a large-size random gene mutagenesis library in Escherichia coli.

PubMed

You, Chun; Percival Zhang, Y-H

2012-09-01

A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE-PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE-PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 10(7) protein mutants per 50 μl of the POE-PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day. Copyright © 2012 Elsevier Inc. All rights reserved.

VizieR Online Data Catalog: Intrinsic far-IR SED of luminous AGNs (Lyu+, 2017)

NASA Astrophysics Data System (ADS)

Lyu, J.; Rieke, G. H.

2018-01-01

The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR properties of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at ~20μm and can be matched by an Elvis+ (1994, J/ApJS/95/1)-like template with a minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at λ~20-100μm, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR. (3 data files).

Rational design of molecularly imprinted polymer: the choice of cross-linker.

PubMed

Muhammad, Turghun; Nur, Zohre; Piletska, Elena V; Yimit, Osmanjan; Piletsky, Sergey A

2012-06-07

The paper describes a rational approach for the selection of cross-linkers during the development of molecularly imprinted polymers (MIPs). As a model system for this research MIPs specific for the drug zidovudine (AZT) were designed and tested. Three cross-linkers trimethylolpropane trimethacrylate (TRIM), ethylene glycol dimethacrylate (EGDMA) and divinylbenzene (DVB) were studied. The analogue of zidovudine (AZT) ester (AZT-ES) was used as a dummy template. The imprinting factors for all of the polymers in the static adsorption experiments were calculated. The data on the AZT adsorption by control polymers (CP), which were prepared with different cross-linkers without a functional monomer, was also analyzed. DVB was found to be more inert towards zidovudine than EGDMA and TRIM, which was confirmed by both molecular modelling and adsorption experiments. It was demonstrated that DVB-based polymers had a higher imprinting factor (I = 1.85) compared with other tested cross-linked polymers. It was suggested that the selection of the cross-linker should be based on the strength of the interaction with the template: the cross-linker which displays lower binding of the template should be preferential because it generates MIPs with lower non-specific binding and a higher imprinting factor, and therefore specificity. Which cross-linker to use for the preparation of any particular MIP can be determined by analysis of the interactions between the cross-linker and template. This could be done either virtually using computational modelling or by template adsorption using a small library of polymers prepared using different cross-linkers.

The Intrinsic Far-infrared Continua of Type-1 Quasars

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

Lyu, Jianwei; Rieke, George H., E-mail: jianwei@email.arizona.edu

2017-06-01

The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR propertiesmore » of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at ∼20 μ m and can be matched by an Elvis et al.-like template with a minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at λ ∼ 20–100 μ m, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR.« less

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

PubMed

Meier, Armin; Söding, Johannes

2015-10-01

Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite.

Guidelines Regarding §16 of the German Transplantation Act - Initial Experiences with Structured Reporting.

PubMed

Pinto Dos Santos, Daniel; Arnhold, Gordon; Mildenberger, Peter; Düber, Christoph; Kloeckner, Roman

2017-12-01

Purpose  To transfer the report sheet from the guidelines regarding the German Transplantation Act to a standards-compliant report template and to evaluate it in the clinical routine. Materials and Methods  The template was developed using the freely available software brackets.io. It was implemented in the clinical routine using a reporting platform developed in-house. Interfaces to the department RIS and PACS allowed for integration into the usual reporting workflow. The evaluation period was 70 days. Results  Developing the template for implementation of the guidelines was possible without any difficulties. The content of the report sheet provided in the guidelines was transferred one to one. Additionally, a text field was included to allow for further remarks. In the period under review, 7 radiologists performed 44 evaluations in line with § 16 of the German Transplantation Act. Users of the template, referring physicians and the employees of the transplantation office reported a high degree of satisfaction. Conclusion  Implementing report sheets that are required by law (e. g. in the guidelines regarding § 16 of the German Transplantation Act) in the clinical routine electronically is easy and achieves a high degree of acceptance. The standard supported by the German Radiological Society (IHE - "Management of radiology report templates") allows for a quick response to the growing demand for structured and standardized reporting. Key Points   · Report sheets as required by law can easily be incorporated electronically into the clinical routine.. · Templates for structured reporting as supported by the German Radiological Society allow for a quick response to the growing demand for standardized reporting.. · Radiologists as well as referring physicians report a high degree of satisfaction with the electronic version of the report sheet.. Citation Format · Pinto dos Santos D, Arnhold G, Mildenberger P et al. Guidelines Regarding §16 of the German Transplantation Act - Initial Experiences with Structured Reporting. Fortschr Röntgenstr 2017; 189: 1145 - 1151. © Georg Thieme Verlag KG Stuttgart · New York.

Pattern of node metastases in patients treated with radical cystectomy and extended or superextended pelvic lymph node dissection due to bladder cancer.

PubMed

Moschini, Marco; Arbelaez, Emilio; Cornelius, Julian; Mattei, Agostino; Shariat, Shahrokh F; Dell Oglio, Paolo; Zaffuto, Emanuele; Salonia, Andrea; Montorsi, Francesco; Briganti, Alberto; Colombo, Renzo; Gallina, Andrea

2018-06-01

Pelvic lymph node dissection (PLND) has a diagnostic and therapeutic role during radical cystectomy in bladder cancer patients. However, at the time, no prospective data supports the value of extended PLND in improving survival expectances. We sought to describe incidence and location of node metastases in patients treated with extended and superextended PLND. We evaluated 653 contemporary patients with clinically nonmetastatic high risk nonmuscle invasive or muscle-invasive bladder cancer treated with radical cystectomy and extended or superextended PLND without neoadjuvant chemotherapy at a single tertiary referral center between 1990 and 2013. Limited PLND is defined as the removal of obturator and internal iliac nodes. Standard included also the external iliac nodes. Extended includes also common and presacral nodes. Finally, superextended PLND includes all the nodes removed along the inferior mesenteric artery. We evaluated incidence of pathologically node metastases. Logistic regression analyses evaluate preoperative and pathologic characteristics to the risk of harboring node metastases in the extended and superextended template. Overall, 191 (29.3%) patients were found with pathologically node confirmed metastases. Of these, 56 (29.3%) patients were found with a single node metastasis, while 135 (70.7%) had multiple node metastases. The vast majority of patients were found with node metastases standard template (n = 172, 26.3%), on the other hand 30 (4.6%) and 21 (3.2%) patients had node metastases in extended and superextended templates, respectively. However, of these only 2 patients were found without concomitant lymph node metastases in the limited or standard templates. On multivariable analyses, cN+ status (odds ratio = 4.40, P<0.001) and cT3-4 vs. cT1-2 (odds ratio = 2.25, P<0.001) were associated with an increased risk of harboring node metastases in the extended or superextended template. We found that the majority of patients harbored node disease in the limited or standard node dissection pattern. On the other hand, only a minority of patient were found with a disease in extended or superextended template without harboring a concomitant node disease in the limited pattern. Copyright © 2018 Elsevier Inc. All rights reserved.

Embracing Change: Adapting and Evolving Your Distance Learning Library Services to Meet the New ACRL Distance Learning Library Services Standards

ERIC Educational Resources Information Center

Marcum, Brad

2016-01-01

This article examines the update and revision of the current Association of College and Research Libraries (ACRL) Distance Learning Standards that has been proposed and submitted to the ACRL Standards Committee. An in-depth analysis of the update is included, along with some comparisons between the old and new. Practical advice detailing…

The Role of the Library Media Specialist in Standards-Based Learning.

ERIC Educational Resources Information Center

Corey, Linda

2002-01-01

Discusses the role of the school library media specialist in standards-based learning. Topics include standards-based assessment; information literacy standards; collaboration with classroom teachers; benchmarks and indicators for student performance; leadership in a standards-based climate; and the use of technology to support curriculum and…

Measuring Performance with Library Automated Systems.

ERIC Educational Resources Information Center

OFarrell, John P.

2000-01-01

Investigates the capability of three library automated systems to generate some of the datasets necessary to form the ISO (International Standards Organization) standard on performance measurement within libraries, based on research in Liverpool John Moores University (United Kingdom). Concludes that the systems are weak in generating the…

A C++11 implementation of arbitrary-rank tensors for high-performance computing

NASA Astrophysics Data System (ADS)

Aragón, Alejandro M.

2014-06-01

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU.

A C++11 implementation of arbitrary-rank tensors for high-performance computing

NASA Astrophysics Data System (ADS)

Aragón, Alejandro M.

2014-11-01

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU.

Mapping of a standard documentation template to the ICF core sets for arthritis and low back pain.

PubMed

Escorpizo, Reuben; Davis, Kandace; Stumbo, Teri

2010-12-01

To identify the contents of a documentation template in The Guide to Physical Therapist Practice using the International Classification of Functioning, Disability, and Health (ICF) Core Sets for rheumatoid arthritis, osteoarthritis, and low back pain (LBP) as reference. Concepts were identified from items of an outpatient documentation template and mapped to the ICF using established linking rules. The ICF categories that were linked were compared with existing arthritis and LBP Core Sets. Based on the ICF, the template had the highest number (29%) of linked categories under Activities and participation while Body structures had the least (17%). ICF categories in the arthritis and LBP Core Sets had a 37-55% match with the ICF categories found in the template. We found 164 concepts that were not classified or not defined and 37 as personal factors. The arthritis and LBP Core Sets were reflected in the contents of the template. ICF categories in the Core Sets were reflected in the template (demonstrating up to 55% match). Potential integration of ICF in documentation templates could be explored and examined in the future to enhance clinical encounters and multidisciplinary communication. Copyright © 2010 John Wiley & Sons, Ltd.

A method to incorporate interstitial components into the TPS gynecologic rigid applicator library.

PubMed

Otal, Antonio; Richart, Jose; Rodriguez, Silvia; Santos, Manuel; Perez-Calatayud, Jose

2017-02-01

T2 magnetic resonance imaging (MRI) is recommended as the imaging modality for image-guided brachytherapy. In locally advanced cervical carcinoma, combined endocavitary and interstitial applicators are appropriate (Vienna or Utrecht). To cover extensive disease, Template Benidorm (TB) was developed. Treatment planning system applicator libraries are currently unavailable for the Utrecht applicator or the TB. The purpose of this work is to develop an applicator library for both applicators. The library developed in this work has been used in the Oncentra Brachytherapy TPS, version 4.3.0, which has a brachytherapy module that includes a library of rigid applicators. To add the needles of the Utrecht applicator and to model the TB, we used FreeCAD and MeshLab. The reconstruction process was based on the points that the rigid section and the interstitial part have in common. This, together with the free length, allowed us to ascertain the position of the tip. In case of the Utrecht applicator, one of the sources of uncertainty in the reconstruction was determining the distance of the tip of needle from the ovoid. In case of the TB, the large number of needles involved made their identification time consuming. The developed library resolved both issues. The developed library for the Utrecht and TB is feasible and efficient improving accuracy. It allows all the required treatment planning to proceed using just a T2 MRI sequence. The additional use of specific free available software applications makes it possible to add this information to the already existing library of the Oncentra Brachytherapy TPS. Specific details not included on this manuscript will be available under request. This library is also currently being implemented also into the Sagiplan v 2.0 TPS.

Electroencephalography leads placed by nontechnologists using a template system produce signals equal in quality to technologist-applied, collodion disk leads.

PubMed

Kolls, Brad J; Olson, Daiwai M; Gallentine, William B; Skeen, Mark B; Skidmore, Christopher T; Sinha, Saurabh R

2012-02-01

The purpose of this study was to compare the quality of the electroencephalographic (EEG) data obtained with a BraiNet template in a practical use setting, to that obtained with standard 10/20 spaced, technologist-applied, collodion-based disk leads. Pairs of 8-hour blocks of EEG data were prospectively collected from 32 patients with a Glasgow coma score of ≤9 and clinical concern for underlying nonconvulsive status epilepticus over a 6-month period in the Neurocritical Care Unit at the Duke University Medical Center. The studies were initiated with the BraiNet template system applied by critical care nurse practitioners or physicians, followed by standard, collodion leads applied by registered technologists using the 10/20 system of placement. Impedances were measured at the beginning and end of each block recorded and variance in impedance, mean impedance, and the largest differences in impedances found within a given lead set were compared. Physicians experienced in reading EEG performed a masked review of the EEG segments obtained to assess the subjective quality of the recordings obtained with the templates. We found no clinically significant differences in the impedance measures. There was a 3-hour reduction in the time required to initiate EEG recording using the templates (P < 0.001). There was no difference in the overall subjective quality distributions for template-applied versus technologist-applied EEG leads. The templates were also found to be well accepted by the primary users in the intensive care unit. The findings suggest that the EEG data obtained with this approach are comparable with that obtained by registered technologist-applied leads and represents a possible solution to the growing clinical need for continuous EEG recording availability in the critical care setting.

The medico-legal prerequisite for initiating quarantine and isolation practices in public health emergency management in hospitals in Ghana.

PubMed

Norman, I D; Aikins, M; Binka, F N

2011-12-01

Hospitals and other health facilities in Ghana do not appear to have standardized practices for quarantine and isolation in public health emergency management. This paper reviews the legislative framework governing the medico-legal prerequisites for initiating quarantine and isolation procedures as articulated in the Infectious Disease Act (Cap 78) 1908 amended, 1935, the Quarantine Act (Cap 77) 1915 amended, 1938, the Emergency Powers Act of 1994, (Act 472), and the National Disaster Management Act, 1996, (Act 517) in consonance with the 1992 Constitution of Ghana. The findings provide that (1) The legislative framework outlines systematic standards and protocols to be followed in the committal of person or persons in quarantine and isolation during public health emergencies. (2) These standards and protocols consider as imperative, the creation of standardized national templates for the initiation of quarantine and isolation measures. (3) The non-compliance of the standards and protocols renders vulnerable medical facilities and hospitals with their personnel to the threat of medical malpractice suits and breach of professional ethics. This paper provides suggestions to hospital administrators and medical personnel of how to develop administrative templates in compliance with the law in managing public health emergencies. It also provides examples of such templates for possible adoption by hospitals and other health administrators.

Accuracy of templating the acetabular cup size in Total Hip Replacement using conventional acetate templates on digital radiographs.

PubMed

Krishnamoorthy, Vignesh P; Perumal, Rajamani; Daniel, Alfred J; Poonnoose, Pradeep M

2015-12-01

Templating of the acetabular cup size in Total Hip Replacement (THR) is normally done using conventional radiographs. As these are being replaced by digital radiographs, it has become essential to create a technique of templating using digital films. We describe a technique that involves templating the digital films using the universally available acetate templates for THR without the use of special software. Preoperative digital radiographs of the pelvis were taken with a 30 mm diameter spherical metal ball strapped over the greater trochanter. Using standard acetate templates provided by the implant company on magnified digital radiographs, the size of the metal ball (X mm) and acetabular cup (Y mm) were determined. The size of the acetabular cup to be implanted was estimated using the formula 30*Y/X. The estimated size was compared with the actual size of the cup used at surgery. Using this technique, it was possible to accurately predict the acetabular cup size in 28/40 (70%) of the hips. When the accuracy to within one size was considered, templating was correct in 90% (36/40). When assessed by two independent observers, there was good intra-observer and inter-observer reliability with intra-class correlation coefficient values greater than 0.8. It was possible to accurately and reliably predict the size of the acetabular cup, using acetate templates on digital films, without any digital templates.

A Spectrum of Interoperability: The Site for Science Prototype for the NSDL; Re-Inventing the Wheel? Standards, Interoperability and Digital Cultural Content; Preservation Risk Management for Web Resources: Virtual Remote Control in Cornell's Project Prism; Safekeeping: A Cooperative Approach to Building a Digital Preservation Resource; Object Persistence and Availability in Digital Libraries; Illinois Digital Cultural Heritage Community-Collaborative Interactions among Libraries, Museums and Elementary Schools.

ERIC Educational Resources Information Center

Arms, William Y.; Hillmann, Diane; Lagoze, Carl; Krafft, Dean; Marisa, Richard; Saylor, John; Terizzi, Carol; Van de Sompel, Herbert; Gill, Tony; Miller, Paul; Kenney, Anne R.; McGovern, Nancy Y.; Botticelli, Peter; Entlich, Richard; Payette, Sandra; Berthon, Hilary; Thomas, Susan; Webb, Colin; Nelson, Michael L.; Allen, B. Danette; Bennett, Nuala A.; Sandore, Beth; Pianfetti, Evangeline S.

2002-01-01

Discusses digital libraries, including interoperability, metadata, and international standards; Web resource preservation efforts at Cornell University; digital preservation at the National Library of Australia; object persistence and availability; collaboration among libraries, museums and elementary schools; Asian digital libraries; and a Web…

Development of a methodology for structured reporting of information in echocardiography.

PubMed

Homorodean, Călin; Olinic, Maria; Olinic, Dan

2012-03-01

In order to conduct research relying on ultrasound images, it is necessary to access a large number of relevant cases represented by images and their interpretation. DICOM standard defines the structured reporting information object. Templates are tree-like structures which offer structural guidance in report construction. Laying the foundations of a structured reporting methodology in echocardiography, through the generation of a consistent set of DICOM templates. We developed an information system with the ability of managing echocardiographic images and structured reports. In order to perform a complete description of the cardiac structures, we used 1900 coded concepts organized into 344 contexts by their semantic meaning in a variety of cardiac diseases. We developed 30 templates, with up to 10 nesting levels. The list of templates has a pyramid-like architecture. Two templates are used for reporting every measurement and description: "EchoMeasurement" and "EchoDescription". Intermediate level templates specify how to report the features of echoDoppler findings: "Spectral Curve", "Color Jet", "Intracardiac mass". Templates for every cardiovascular structure include the previous ones. "Echocardiography Procedure Report" includes all other templates. The templates were tested in reporting echo features of 100 patients by analyzing 500 DICOM images. The benefits of these templates has been proven during the testing process, through the quality of the echocardiography report, the ability to argue and to link every diagnostic feature to a defining image and by opening up opportunities for education, research. In the future, our template-based reporting methodology might be extended to other imaging modalities.

Documentation of Gender Identity in an Adolescent and Young Adult Clinic.

PubMed

Vance, Stanley R; Mesheriakova, Veronika V

2017-03-01

To determine if changing electronic health record (EHR) note templates can increase documentation of gender identity in an adolescent and young adult clinic. A two-step gender question was added to EHR note templates for physicals in February 2016. A retrospective chart review was performed 3 months before and after this addition. The primary measure was whether answers to the two-step question were documented. Gender identity/birth-assigned sex discordance, age, and use of the appropriate note template post-template change were also measured. One hundred twenty-five pretemplate change and 106 post-template change physicals were reviewed with an inter-rater reliability of 97%. Documentation of answers to the two-step gender identity question increased from 11% to 84% (p < .001). This study suggests that incorporating a standardized question into EHR note templates is effective at improving the documentation of gender identity in youth presenting for annual physicals. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Region based feature extraction from non-cooperative iris images using triplet half-band filter bank

NASA Astrophysics Data System (ADS)

Barpanda, Soubhagya Sankar; Majhi, Banshidhar; Sa, Pankaj Kumar

2015-09-01

In this paper, we have proposed energy based features using a multi-resolution analysis (MRA) on iris template. The MRA is based on our suggested triplet half-band filter bank (THFB). The THFB derivation process is discussed in detail. The iris template is divided into six equispaced sub-templates and two level decomposition has been made to each sub-template using THFB except second one. The reason for discarding the second template is due to the fact that it mostly contains the noise due to eyelids, eyelashes, and occlusion due to segmentation failure. Subsequently, energy features are derived from the decomposed coefficients of each sub-template. The proposed feature has been experimented on standard databases like CASIAv3, UBIRISv1, and IITD and mostly on iris images which encounter a segmentation failure. Comparative analysis has been done with existing features based on Gabor transform, Fourier transform, and CDF 9/7 filter bank. The proposed scheme shows superior performance with respect to FAR, GAR and AUC.

A robust and non-invertible fingerprint template for fingerprint matching system.

PubMed

Trivedi, Amit Kumar; Thounaojam, Dalton Meitei; Pal, Shyamosree

2018-05-20

Fingerprint Recognition System is widely deployed in variety of application domain, ranging from forensic to mobile phones. Its widespread deployment in various applications were person authentication are required, has caused concern that a leaked fingerprint template may be used to reconstruct the original fingerprint and the reconstructed fingerprint can be used to circumvent all the applications the person is enrolled. In this paper, a non-invertible fingerprint template that stores only the relative geometric information about the minutiae points is proposed. The spatial location of the minutiae points in original fingerprint and its orientations are not available in the proposed template which makes it impossible to estimate the orientation of fingerprint from the template. The proposed template is invariant to rotation, translation and distortion and immune to reconstruction algorithm. The proposed system is experimented using standard FVC2000 database and yields better results in terms of EER and FMR as compared with latest techniques. Copyright © 2018 Elsevier B.V. All rights reserved.

Standards of Practice for West African Libraries; Proceedings of a Seminar Held at the Institute of Librarianship, University of Ibadan, 15-16 April 1967.

ERIC Educational Resources Information Center

Dean, John, Ed.

A seminar on standards for libraries in West Africa was held in April 1967. This proceedings volume presents the papers given by each of the participants. Discussed are the standards for collections, facilities, staff, technical processes and services for public, school, university and special libraries. The purpose was to focus upon the nature,…

Standards for Medical Library Technicians, Medical Library Association.

ERIC Educational Resources Information Center

Medical Library Association, Chicago, IL.

A medical library technician is a semiprofessional library employee whose duties require knowledge and skill based on a minimum of two years' general college education that includes library instruction beyond the clerical level. The medical library technician must have a practical knowledge of library functions and services, an understanding of…

A Model Privacy Statement for Ohio Library Web Sites.

ERIC Educational Resources Information Center

Monaco, Michael J.

The purpose of this research was to develop a model privacy policy statement for library World Wide Web sites. First, standards of privacy protection were identified. These standards were culled from the privacy and confidentiality policies of the American Library Association, the Federal Trade Commission's online privacy reports, the guidelines…

Iranian Special Library Standards.

ERIC Educational Resources Information Center

Harvey, John F.

The purposes of these standards are: (1) to suggest the steps necessary for the establishment of special libraries; (2) for those recently established, to suggest the steps necessary to achieve satisfactory performance levels in all areas, and finally, (3) for well established libraries, to suggest the steps necessary to achieve excellence. These…

Utilizing the Cross-Reactivity of MIPs.

PubMed

Yilmaz, Ecevit; Billing, Johan; Nilsson, Carina; Boyd, Brian; Kecili, Rüstem; Nivhede, David; Axelsson, Sara; Rees, Anthony

2015-01-01

The crossreactivity of molecularly imprinted polymers (MIPs) and its practical implications are discussed. Screening of MIP libraries is presented as a fasttrack route to discovery of resins selective towards new targets, exploiting the fact that MIPs imprinted with one type of template molecule also show recognition to related and sometimes also to apparently unrelated molecules. Several examples from our own and others' studies are presented that illustrate this crossreactivity and the pattern of recognition is discussed for selected examples.

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

PubMed

Schneider, G; Lee, M L; Stahl, M; Schneider, P

2000-07-01

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.

Standards for Library Services to Disabled Students.

ERIC Educational Resources Information Center

Trezza, Alphonse F.

The paper addresses the quality and extent of services provided by academic libraries to students with disabilities. The issue of establishing standards for such services is considered, and while the author notes the formidable difficulties involved in establishing such standards, he asserts that standards must be developed and implemented. He…

Sandia National Laboratories: Working with Sandia: Contract Audit

Science.gov Websites

Government Auditing Standards. Electronic Cost Claims Electronic Cost Claim (ECC) An Electronic Cost Claim is ) ECC-Cost Reimbursable Template and Instructions (MS Excel) ECC-University Template (MS Excel) ECC -Indirect Rates (Indirect Rate Cost Claim) (MS Excel) Electronic Cost Proposals Electronic Cost Proposal

Tensorial dynamic time warping with articulation index representation for efficient audio-template learning.

PubMed

Le, Long N; Jones, Douglas L

2018-03-01

Audio classification techniques often depend on the availability of a large labeled training dataset for successful performance. However, in many application domains of audio classification (e.g., wildlife monitoring), obtaining labeled data is still a costly and laborious process. Motivated by this observation, a technique is proposed to efficiently learn a clean template from a few labeled, but likely corrupted (by noise and interferences), data samples. This learning can be done efficiently via tensorial dynamic time warping on the articulation index-based time-frequency representations of audio data. The learned template can then be used in audio classification following the standard template-based approach. Experimental results show that the proposed approach outperforms both (1) the recurrent neural network approach and (2) the state-of-the-art in the template-based approach on a wildlife detection application with few training samples.

Enserch Garden Banks 388 field development template tie-back of existing subsea satellite wells

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

Hellums, J.W.; Granhaug, O.

1995-12-31

The Flowline Jumper System (FJS) will be used by Enserch Exploration, Inc. to tie in three existing wells to the 24 well production template installed in Garden Banks Block 388. The FJS allows these existing satellite wells to be connected to the production template via standard wellbays, eliminating the need for dedicated receiver structures, or tie-in porches. Wellbays used for satellite well tie-ins are available for use as template wells following the removal of the jumper. This paper describes the considerations that led to the selection and influenced the design of the FJS. The advantages of vertical jumper systems aremore » fully discussed with respect to the GB-388 Project. A description of the major components and how they interface with the template is included to provide a better understanding of the FJS. Also included is an outline of the System Integration Testing (SIT) of the FJS.« less

Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities

PubMed Central

Cramer, Richard D.

2015-01-01

The possible applicability of the new template CoMFA methodology to the prediction of unknown biological affinities was explored. For twelve selected targets, all ChEMBL binding affinities were used as training and/or prediction sets, making these 3D-QSAR models the most structurally diverse and among the largest ever. For six of the targets, X-ray crystallographic structures provided the aligned templates required as input (BACE, cdk1, chk2, carbonic anhydrase-II, factor Xa, PTP1B). For all targets including the other six (hERG, cyp3A4 binding, endocrine receptor, COX2, D2, and GABAa), six modeling protocols applied to only three familiar ligands provided six alternate sets of aligned templates. The statistical qualities of the six or seven models thus resulting for each individual target were remarkably similar. Also, perhaps unexpectedly, the standard deviations of the errors of cross-validation predictions accompanying model derivations were indistinguishable from the standard deviations of the errors of truly prospective predictions. These standard deviations of prediction ranged from 0.70 to 1.14 log units and averaged 0.89 (8x in concentration units) over the twelve targets, representing an average reduction of almost 50% in uncertainty, compared to the null hypothesis of “predicting” an unknown affinity to be the average of known affinities. These errors of prediction are similar to those from Tanimoto coefficients of fragment occurrence frequencies, the predominant approach to side effect prediction, which template CoMFA can augment by identifying additional active structural classes, by improving Tanimoto-only predictions, by yielding quantitative predictions of potency, and by providing interpretable guidance for avoiding or enhancing any specific target response. PMID:26065424

Standardized ultrasound templates for diagnosing appendicitis reduce annual imaging costs.

PubMed

Nordin, Andrew B; Sales, Stephen; Nielsen, Jason W; Adler, Brent; Bates, David Gregory; Kenney, Brian

2018-01-01

Ultrasound is preferred over computed tomography (CT) for diagnosing appendicitis in children to avoid undue radiation exposure. We previously reported our experience in instituting a standardized appendicitis ultrasound template, which decreased CT rates by 67.3%. In this analysis, we demonstrate the ongoing cost savings associated with using this template. Retrospective chart review for the time period preceding template implementation (June 2012-September 2012) was combined with prospective review through December 2015 for all patients in the emergency department receiving diagnostic imaging for appendicitis. The type of imaging was recorded, and imaging rates and ultrasound test statistics were calculated. Estimated annual imaging costs based on pretemplate ultrasound and CT utilization rates were compared with post-template annual costs to calculate annual and cumulative savings. In the pretemplate period, ultrasound and CT rates were 80.2% and 44.3%, respectively, resulting in a combined annual cost of $300,527.70. Similar calculations were performed for each succeeding year, accounting for changes in patient volume. Using pretemplate rates, our projected 2015 imaging cost was $371,402.86; however, our ultrasound rate had increased to 98.3%, whereas the CT rate declined to 9.6%, yielding an annual estimated cost of $224,853.00 and a savings of $146,549.86. Since implementation, annual savings have steadily increased for a cumulative cost savings of $336,683.83. Standardizing ultrasound reports for appendicitis not only reduces the use of CT scans and the associated radiation exposure but also decreases annual imaging costs despite increased numbers of imaging studies. Continued cost reduction may be possible by using diagnostic algorithms. Copyright © 2017 Elsevier Inc. All rights reserved.

Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor.

PubMed

Weiss, Dahlia R; Ahn, SeungKirl; Sassano, Maria F; Kleist, Andrew; Zhu, Xiao; Strachan, Ryan; Roth, Bryan L; Lefkowitz, Robert J; Shoichet, Brian K

2013-05-17

A prospective, large library virtual screen against an activated β2-adrenergic receptor (β2AR) structure returned potent agonists to the exclusion of inverse-agonists, providing the first complement to the previous virtual screening campaigns against inverse-agonist-bound G protein coupled receptor (GPCR) structures, which predicted only inverse-agonists. In addition, two hits recapitulated the signaling profile of the co-crystal ligand with respect to the G protein and arrestin mediated signaling. This functional fidelity has important implications in drug design, as the ability to predict ligands with predefined signaling properties is highly desirable. However, the agonist-bound state provides an uncertain template for modeling the activated conformation of other GPCRs, as a dopamine D2 receptor (DRD2) activated model templated on the activated β2AR structure returned few hits of only marginal potency.

High-throughput sequencing: a failure mode analysis.

PubMed

Yang, George S; Stott, Jeffery M; Smailus, Duane; Barber, Sarah A; Balasundaram, Miruna; Marra, Marco A; Holt, Robert A

2005-01-04

Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported. Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. Two categories of failures are described; process-related failures (failures due to equipment or sample handling) and template-related failures (failures that are revealed by close inspection of electropherograms and are likely due to properties of the template DNA sequence itself). Preventative action based on a detailed understanding of failure modes is likely to improve the performance of other production sequencing pipelines.

The Erosion of Library Education.

ERIC Educational Resources Information Center

Eshelman, William R.

1983-01-01

Discussion of the work of the American Library Association's Committee on Accreditation includes committee membership, the proliferation of library programs, application of accreditation standards, the status of library schools, library school enrollments, the marketplace, curriculum, librarian certification, and practitioner problems. (EJS)

[Problems Inherent in Attempting Standardization of Libraries.

ERIC Educational Resources Information Center

Port, Idelle

In setting standards for a large and geographically dispersed library system, one must reconcile the many varying practices that affect what is being measured or discussed. The California State University and Colleges (CSUC) consists of 19 very distinct campuses. The problems and solutions of one type of CSUC library are not likely to be those of…

Stochastic sampling effects in STR typing: Implications for analysis and interpretation.

PubMed

Timken, Mark D; Klein, Sonja B; Buoncristiani, Martin R

2014-07-01

The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Design reflowable digital book template

NASA Astrophysics Data System (ADS)

Prasetya, Didik Dwi; Widiyaningtyas, Triyanna; Arifin, M. Zainal; Wahyu Sakti G., I.

2017-09-01

Electronic books (e-books or digital books) increasingly in demand and continue to grow in the form of future books. One of the standard format electronic books that potential is EPUB (electronic publication) published by the International Digital Publishing Forum (IDPF). This digital book has major advantages are able to provide interactive and reflowable content, which are not found in another book format, such as PDF. Reflowable content allows the book can be accessed through a variety of reader device, like desktop and mobile with a fit and comfort view. However, because the generating process of an EPUB digital book is not as easy a PDF, so this format is less popular. Therefore, in order to help overcome the existing problems, this paper develops digital reflowable text book templates to support electronic learning, especially in Indonesia. This template can be used by anyone to produce a standard digital book quickly and easily without requiring additional specialized knowledge.

Comparing a volume based template approach and ultrasound guided freehand approach in multicatheter interstitial accelerated partial breast irradiation.

PubMed

Koh, Vicky Y; Buhari, Shaik A; Tan, Poh Wee; Tan, Yun Inn; Leong, Yuh Fun; Earnest, Arul; Tang, Johann I

2014-06-01

Currently, there are two described methods of catheter insertion for women undergoing multicatheter interstitial accelerated partial breast irradiation (APBI). These are a volume based template approach (template) and a non-template ultrasound guidance freehand approach (non-template). We aim to compare dosimetric endpoints between the template and non-template approach. Twenty patients, who received adjuvant multicatheter interstitial APBI between August 2008 to March 2010 formed the study cohort. Dosimetric planning was based on the RTOG 04-13 protocol. For standardization, the planning target volume evaluation (PTV-Eval) and organs at risk were contoured with the assistance of the attending surgeon. Dosimetric endpoints include D90 of the PTV-Eval, Dose Homogeneity Index (DHI), V200, maximum skin dose (MSD), and maximum chest wall dose (MCD). A median of 18 catheters was used per patient. The dose prescribed was 34 Gy in 10 fractions BID over 5 days. The average breast volume was 846 cm(3) (526-1384) for the entire cohort and there was no difference between the two groups (p = 0.6). Insertion time was significantly longer for the non-template approach (mean 150 minutes) compared to the template approach (mean: 90 minutes) (p = 0.02). The planning time was also significantly longer for the non-template approach (mean: 240 minutes) compared to the template approach (mean: 150 minutes) (p < 0.01). The template approach yielded a higher D90 (mean: 95%) compared to the non-template approach (mean: 92%) (p < 0.01). There were no differences in DHI (p = 0.14), V200 (p = 0.21), MSD (p = 0.7), and MCD (p = 0.8). Compared to the non-template approach, the template approach offered significant shorter insertion and planning times with significantly improved dosimetric PTV-Eval coverage without significantly compromising organs at risk dosimetrically.

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

PubMed

Chiba, Hirokazu; Uchiyama, Ikuo

2017-02-08

Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data. SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

Three-dimensional liver motion tracking using real-time two-dimensional MRI

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

Brix, Lau, E-mail: lau.brix@stab.rm.dk; Ringgaard, Steffen; Sørensen, Thomas Sangild

2014-04-15

Purpose: Combined magnetic resonance imaging (MRI) systems and linear accelerators for radiotherapy (MR-Linacs) are currently under development. MRI is noninvasive and nonionizing and can produce images with high soft tissue contrast. However, new tracking methods are required to obtain fast real-time spatial target localization. This study develops and evaluates a method for tracking three-dimensional (3D) respiratory liver motion in two-dimensional (2D) real-time MRI image series with high temporal and spatial resolution. Methods: The proposed method for 3D tracking in 2D real-time MRI series has three steps: (1) Recording of a 3D MRI scan and selection of a blood vessel (ormore » tumor) structure to be tracked in subsequent 2D MRI series. (2) Generation of a library of 2D image templates oriented parallel to the 2D MRI image series by reslicing and resampling the 3D MRI scan. (3) 3D tracking of the selected structure in each real-time 2D image by finding the template and template position that yield the highest normalized cross correlation coefficient with the image. Since the tracked structure has a known 3D position relative to each template, the selection and 2D localization of a specific template translates into quantification of both the through-plane and in-plane position of the structure. As a proof of principle, 3D tracking of liver blood vessel structures was performed in five healthy volunteers in two 5.4 Hz axial, sagittal, and coronal real-time 2D MRI series of 30 s duration. In each 2D MRI series, the 3D localization was carried out twice, using nonoverlapping template libraries, which resulted in a total of 12 estimated 3D trajectories per volunteer. Validation tests carried out to support the tracking algorithm included quantification of the breathing induced 3D liver motion and liver motion directionality for the volunteers, and comparison of 2D MRI estimated positions of a structure in a watermelon with the actual positions. Results: Axial, sagittal, and coronal 2D MRI series yielded 3D respiratory motion curves for all volunteers. The motion directionality and amplitude were very similar when measured directly as in-plane motion or estimated indirectly as through-plane motion. The mean peak-to-peak breathing amplitude was 1.6 mm (left-right), 11.0 mm (craniocaudal), and 2.5 mm (anterior-posterior). The position of the watermelon structure was estimated in 2D MRI images with a root-mean-square error of 0.52 mm (in-plane) and 0.87 mm (through-plane). Conclusions: A method for 3D tracking in 2D MRI series was developed and demonstrated for liver tracking in volunteers. The method would allow real-time 3D localization with integrated MR-Linac systems.« less

[Primary culture of cat intestinal epithelial cell and construction of its cDNA library].

PubMed

Ye, L; Gui-Hua, Z; Kun, Y; Hong-Fa, W; Ting, X; Gong-Zhen, L; Wei-Xia, Z; Yong, C

2017-04-12

Objective To establish the primary cat intestinal epithelial cells (IECs) culture methods and construct the cDNA library for the following yeast two-hybrid experiment, so as to screen the virulence interaction factors among the final host. Methods The primary cat IECs were cultured by the tissue cultivation and combined digestion with collagenase XI and dispase I separately. Then the cat IECs cultured was identified with the morphological observation and cyto-keratin detection, by using goat anti-cyto-keratin monoclonal antibodies. The mRNA of cat IECs was isolated and used as the template to synthesize the first strand cDNA by SMART™ technology, and then the double-strand cDNAs were acquired by LD-PCR, which were subsequently cloned into the plasmid PGADT7-Rec to construct yeast two-hybrid cDNA library in the yeast strain Y187 by homologous recombination. Matchmaker™ Insert Check PCR was used to detect the size distribution of cDNA fragments after the capacity calculation of the cDNA library. Results The comparison of the two cultivation methods indicated that the combined digestion of collagenase XI and dispase I was more effective than the tissue cultivation. The cat IECs system of continuous culture was established and the cat IECs with high purity were harvested for constructing the yeast two-hybrid cDNA library. The library contained 1.1×10 6 independent clones. The titer was 2.8×10 9 cfu/ml. The size of inserted fragments was among 0.5-2.0 kb. Conclusion The yeast two-hybrid cDNA library of cat IECs meets the requirements of further screen research, and this study lays the foundation of screening the Toxoplasma gondii virulence interaction factors among the cDNA libraries of its final hosts.

Towards a library of synthetic galaxy spectra and preliminary results of classification and parametrization of unresolved galaxies for Gaia. II

NASA Astrophysics Data System (ADS)

Tsalmantza, P.; Kontizas, M.; Rocca-Volmerange, B.; Bailer-Jones, C. A. L.; Kontizas, E.; Bellas-Velidis, I.; Livanou, E.; Korakitis, R.; Dapergolas, A.; Vallenari, A.; Fioc, M.

2009-09-01

Aims: This paper is the second in a series, implementing a classification system for Gaia observations of unresolved galaxies. Our goals are to determine spectral classes and estimate intrinsic astrophysical parameters via synthetic templates. Here we describe (1) a new extended library of synthetic galaxy spectra; (2) its comparison with various observations; and (3) first results of classification and parametrization experiments using simulated Gaia spectrophotometry of this library. Methods: Using the PÉGASE.2 code, based on galaxy evolution models that take account of metallicity evolution, extinction correction, and emission lines (with stellar spectra based on the BaSeL library), we improved our first library and extended it to cover the domain of most of the SDSS catalogue. Our classification and regression models were support vector machines (SVMs). Results: We produce an extended library of 28 885 synthetic galaxy spectra at zero redshift covering four general Hubble types of galaxies, over the wavelength range between 250 and 1050 nm at a sampling of 1 nm or less. The library is also produced for 4 random values of redshift in the range of 0-0.2. It is computed on a random grid of four key astrophysical parameters (infall timescale and 3 parameters defining the SFR) and, depending on the galaxy type, on two values of the age of the galaxy. The synthetic library was compared and found to be in good agreement with various observations. The first results from the SVM classifiers and parametrizers are promising, indicating that Hubble types can be reliably predicted and several parameters estimated with low bias and variance.

"Hey, Did You See This?"

ERIC Educational Resources Information Center

Nelson, Cathy Jo

2011-01-01

The LMS and library media program standards were written to reflect the 21st century learner. The most current documents, "Standards for the 21st-Century Learner" and "Standards for the 21st-Century Learner in Action", have embraced the 21st century learner jargon, despite how vaguely the terms are defined. The library standards, although written…

Marketing Information Literacy

ERIC Educational Resources Information Center

Seale, Maura

2013-01-01

In 2012, more than a decade after the original Association of College and Research Libraries (ACRL) Information Literacy Competency Standards for Higher Education (hereafter the Standards) were institutionalized as the goal of academic library instruction, the Information Literacy Competency Standards Review Task Force convened by ACRL recommended…

The Contextualization of Archetypes: Clinical Template Governance.

PubMed

Pedersen, Rune; Ulriksen, Gro-Hilde; Ellingsen, Gunnar

2015-01-01

This paper is a status report from a large-scale openEHR-based EPR project from the North Norway Regional Health Authority. It concerns the standardization of a regional ICT portfolio and the ongoing development of a new process oriented EPR systems encouraged by the unfolding of a national repository for openEHR archetypes. Subject of interest; the contextualization of clinical templates is governed over multiple national boundaries which is complex due to the dependency of clinical resources. From the outset of this, we are interested in how local, regional, and national organizers maneuver to standardize while applying OpenEHR technology.

Libraries for Software Use on Peregrine | High-Performance Computing | NREL

Science.gov Websites

-specific libraries. Libraries List Name Description BLAS Basic Linear Algebra Subroutines, libraries only managing hierarchically structured data. LAPACK Standard Netlib offering for computational linear algebra

Zinc-binding Domain of the Bacteriophage T7 DNA Primase Modulates Binding to the DNA Template*

PubMed Central

Lee, Seung-Joo; Zhu, Bin; Akabayov, Barak; Richardson, Charles C.

2012-01-01

The zinc-binding domain (ZBD) of prokaryotic DNA primases has been postulated to be crucial for recognition of specific sequences in the single-stranded DNA template. To determine the molecular basis for this role in recognition, we carried out homolog-scanning mutagenesis of the zinc-binding domain of DNA primase of bacteriophage T7 using a bacterial homolog from Geobacillus stearothermophilus. The ability of T7 DNA primase to catalyze template-directed oligoribonucleotide synthesis is eliminated by substitution of any five-amino acid residue-long segment within the ZBD. The most significant defect occurs upon substitution of a region (Pro-16 to Cys-20) spanning two cysteines that coordinate the zinc ion. The role of this region in primase function was further investigated by generating a protein library composed of multiple amino acid substitutions for Pro-16, Asp-18, and Asn-19 followed by genetic screening for functional proteins. Examination of proteins selected from the screening reveals no change in sequence-specific recognition. However, the more positively charged residues in the region facilitate DNA binding, leading to more efficient oligoribonucleotide synthesis on short templates. The results suggest that the zinc-binding mode alone is not responsible for sequence recognition, but rather its interaction with the RNA polymerase domain is critical for DNA binding and for sequence recognition. Consequently, any alteration in the ZBD that disturbs its conformation leads to loss of DNA-dependent oligoribonucleotide synthesis. PMID:23024359

Spectroscopic Classification of AT2016fij as a Normal Type Ia Supernova

NASA Astrophysics Data System (ADS)

Shivvers, I.; Yuk, H.; Kelly, P.; Stahl, B.; Filippenko, A. V.

2016-09-01

We report that a CCD spectrum (range 350-1050 nm) of AT2016fij was obtained on Aug. 27.5 UT with the 3-m Shane reflector (+Kast) at Lick Observatory. We classified the event via cross-correlation with a library of supernova spectra using the "SuperNova IDentification" code (SNID; Blondin & Tonry 2007, Ap.J. 666, 1024) including the updated templates of Silverman et al. (2012, MNRAS, 425, 1789) and Liu & Modjaz (2014, arXiv:1405.1437).

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…

PDF Version of EPA Communication Product Standards Stylebook

EPA Pesticide Factsheets

This stylebook provides style and format guidance for most media, including print documents, audiovisual, broadcast, presentation and exhibit work. Also find templates and samples, copyright requirements, publishing information, and logo use standards.

Predicting the accuracy of ligand overlay methods with Random Forest models.

PubMed

Nandigam, Ravi K; Evans, David A; Erickson, Jon A; Kim, Sangtae; Sutherland, Jeffrey J

2008-12-01

The accuracy of binding mode prediction using standard molecular overlay methods (ROCS, FlexS, Phase, and FieldCompare) is studied. Previous work has shown that simple decision tree modeling can be used to improve accuracy by selection of the best overlay template. This concept is extended to the use of Random Forest (RF) modeling for template and algorithm selection. An extensive data set of 815 ligand-bound X-ray structures representing 5 gene families was used for generating ca. 70,000 overlays using four programs. RF models, trained using standard measures of ligand and protein similarity and Lipinski-related descriptors, are used for automatically selecting the reference ligand and overlay method maximizing the probability of reproducing the overlay deduced from X-ray structures (i.e., using rmsd < or = 2 A as the criteria for success). RF model scores are highly predictive of overlay accuracy, and their use in template and method selection produces correct overlays in 57% of cases for 349 overlay ligands not used for training RF models. The inclusion in the models of protein sequence similarity enables the use of templates bound to related protein structures, yielding useful results even for proteins having no available X-ray structures.

[Review of digital ground object spectral library].

PubMed

Zhou, Xiao-Hu; Zhou, Ding-Wu

2009-06-01

A higher spectral resolution is the main direction of developing remote sensing technology, and it is quite important to set up the digital ground object reflectance spectral database library, one of fundamental research fields in remote sensing application. Remote sensing application has been increasingly relying on ground object spectral characteristics, and quantitative analysis has been developed to a new stage. The present article summarized and systematically introduced the research status quo and development trend of digital ground object reflectance spectral libraries at home and in the world in recent years. Introducing the spectral libraries has been established, including desertification spectral database library, plants spectral database library, geological spectral database library, soil spectral database library, minerals spectral database library, cloud spectral database library, snow spectral database library, the atmosphere spectral database library, rocks spectral database library, water spectral database library, meteorites spectral database library, moon rock spectral database library, and man-made materials spectral database library, mixture spectral database library, volatile compounds spectral database library, and liquids spectral database library. In the process of establishing spectral database libraries, there have been some problems, such as the lack of uniform national spectral database standard and uniform standards for the ground object features as well as the comparability between different databases. In addition, data sharing mechanism can not be carried out, etc. This article also put forward some suggestions on those problems.

Standards of Practice for California Community College Library Faculty and Programs

ERIC Educational Resources Information Center

Academic Senate for California Community Colleges, 2010

2010-01-01

Libraries and library faculty play a significant role in supporting college curriculum and helping students succeed academically. In particular, libraries are the primary location both physically and remotely for supporting faculty and students in their research and information needs. Over the years, this role of libraries and library faculty has…

The Design of a Templated C++ Small Vector Class for Numerical Computing

NASA Technical Reports Server (NTRS)

Moran, Patrick J.

2000-01-01

We describe the design and implementation of a templated C++ class for vectors. The vector class is templated both for vector length and vector component type; the vector length is fixed at template instantiation time. The vector implementation is such that for a vector of N components of type T, the total number of bytes required by the vector is equal to N * size of (T), where size of is the built-in C operator. The property of having a size no bigger than that required by the components themselves is key in many numerical computing applications, where one may allocate very large arrays of small, fixed-length vectors. In addition to the design trade-offs motivating our fixed-length vector design choice, we review some of the C++ template features essential to an efficient, succinct implementation. In particular, we highlight some of the standard C++ features, such as partial template specialization, that are not supported by all compilers currently. This report provides an inventory listing the relevant support currently provided by some key compilers, as well as test code one can use to verify compiler capabilities.

Library Instruction and Information Literacy-2001.

ERIC Educational Resources Information Center

Johnson, Anna Marie; Rader, Hannelore B.

2002-01-01

Presents a bibliography of literature published during 2001 relating to library instruction and information literacy, the majority of which dealt with the implementation of the Association of College and Research Libraries (ACRL) standards for information literacy in higher education. Also includes school libraries, public libraries, special…

School Library Media Centers in a Statewide Network.

ERIC Educational Resources Information Center

Fox, Carol

1990-01-01

Description of library services in Illinois focuses on school libraries and youth services. Topics discussed include multitype library systems; automation; youth services consultants; data collection for youth services; resource sharing for schools; promotion of reading and library programs; communications networks; and standards and certification…

Cataloguing Standards; The Report of the Canadian Task Group on Cataloguing Standards.

ERIC Educational Resources Information Center

National Library of Canada, Ottawa (Ontario).

Following the recommendations of the National Conference on Cataloguing Standards held at the National Library of Canada in May 1970, a Canadian Task Group on Cataloguing Standards was set up to study and identify present deficiencies in the organizing and processing of Canadian material, and the cataloging problems of Canadian libraries, and to…

Gauging User Interest in Non-Traditional Library Resources

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

Sandberg, Tami; Abbott, Jennifer

The National Renewable Energy Laboratory (NREL) is a government funded research laboratory based in Golden, Colorado. In addition to collecting traditional library resources such as journals, conference proceedings, and print and electronic books, the library also spends a significant portion of its collection development funds on resources not often found in many libraries: technical industry standards (e.g., ISO, IEC, ASTM, IEEE) and energy-related market reports. Assessing user needs for these resources is difficult for a number of reasons, particularly because standardized usage statistics are lacking or non-existent. Standards and market reports are generally costly and include fairly restrictive license agreements,more » which increase the importance of making informed collection development decisions. This presentation will discuss the NREL Library's current collection assessment and development practices as they relate to these unique resources.« less

System and Method for Providing a Climate Data Analytic Services Application Programming Interface Distribution Package

NASA Technical Reports Server (NTRS)

Tamkin, Glenn S. (Inventor); Duffy, Daniel Q. (Inventor); Schnase, John L. (Inventor)

2016-01-01

A system, method and computer-readable storage devices for providing a climate data analytic services application programming interface distribution package. The example system can provide various components. The system provides a climate data analytic services application programming interface library that enables software applications running on a client device to invoke the capabilities of a climate data analytic service. The system provides a command-line interface that provides a means of interacting with a climate data analytic service by issuing commands directly to the system's server interface. The system provides sample programs that call on the capabilities of the application programming interface library and can be used as templates for the construction of new client applications. The system can also provide test utilities, build utilities, service integration utilities, and documentation.

By-product formation in repetitive PCR amplification of DNA libraries during SELEX.

PubMed

Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

2014-01-01

The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.

ISO 9000: The Librarian's Role.

ERIC Educational Resources Information Center

Dobson, Chris; Ernst, Carolyn

1999-01-01

Describes the special library's role in implementing ISO 9000 (i.e., a series of international quality-assurance standards developed by the International Organization of Standards). Topics discussed include document and data control, keeping the standards current, documentation of procedures, the ISO 9000 audit, and benefits for the library. (MES)

Inside Prison Libraries.

ERIC Educational Resources Information Center

Vogel, Brenda; And Others

1989-01-01

Issues related to prison libraries are discussed in six articles. Topics covered include the history of American penitentiary ideology; standards for prison libraries; the controversy as to whether prison libraries should serve prisoners or be used as penological tools; and the lack of knowledge about prison libraries within the general library…

Library Education: Struggling to Meet the Needs of the Profession.

ERIC Educational Resources Information Center

Bohannan, April

1991-01-01

Discussion of complaints about library education covers historical perspectives as well as current trends. Topics discussed include library school closings; curriculum; skills and knowledge employers want recent graduates to have; American Library Association (ALA) standards; student perspectives; university views of library schools and faculty;…

Library Information-Processing System

NASA Technical Reports Server (NTRS)

1985-01-01

System works with Library of Congress MARC II format. System composed of subsystems that provide wide range of library informationprocessing capabilities. Format is American National Standards Institute (ANSI) format for machine-readable bibliographic data. Adaptable to any medium-to-large library.

Theoretical accuracy in cosmological growth estimation

NASA Astrophysics Data System (ADS)

Bose, Benjamin; Koyama, Kazuya; Hellwing, Wojciech A.; Zhao, Gong-Bo; Winther, Hans A.

2017-07-01

We elucidate the importance of the consistent treatment of gravity-model specific nonlinearities when estimating the growth of cosmological structures from redshift space distortions (RSD). Within the context of standard perturbation theory (SPT), we compare the predictions of two theoretical templates with redshift space data from COLA (comoving Lagrangian acceleration) simulations in the normal branch of DGP gravity (nDGP) and general relativity (GR). Using COLA for these comparisons is validated using a suite of full N-body simulations for the same theories. The two theoretical templates correspond to the standard general relativistic perturbation equations and those same equations modeled within nDGP. Gravitational clustering nonlinear effects are accounted for by modeling the power spectrum up to one-loop order and redshift space clustering anisotropy is modeled using the Taruya, Nishimichi and Saito (TNS) RSD model. Using this approach, we attempt to recover the simulation's fiducial logarithmic growth parameter f . By assigning the simulation data with errors representing an idealized survey with a volume of 10 Gpc3/h3 , we find the GR template is unable to recover fiducial f to within 1 σ at z =1 when we match the data up to kmax=0.195 h /Mpc . On the other hand, the DGP template recovers the fiducial value within 1 σ . Further, we conduct the same analysis for sets of mock data generated for generalized models of modified gravity using SPT, where again we analyze the GR template's ability to recover the fiducial value. We find that for models with enhanced gravitational nonlinearity, the theoretical bias of the GR template becomes significant for stage IV surveys. Thus, we show that for the future large data volume galaxy surveys, the self-consistent modeling of non-GR gravity scenarios will be crucial in constraining theory parameters.

Impact of a Structured Reporting Template on Adherence to Prostate Imaging Reporting and Data System Version 2 and on the Diagnostic Performance of Prostate MRI for Clinically Significant Prostate Cancer.

PubMed

Shaish, Hiram; Feltus, Whitney; Steinman, Jonathan; Hecht, Elizabeth; Wenske, Sven; Ahmed, Firas

2018-05-01

The aim of this study was to assess the impact of a structured reporting template on adherence to the Prostate Imaging Reporting and Data System (PI-RADS) version 2 lexicon and on the diagnostic performance of prostate MRI to detect clinically significant prostate cancer (CS-PCa). An imaging database was searched for consecutive patients who underwent prostate MRI followed by MRI-ultrasound fusion biopsy from October 2015 through October 2017. The initial MRI reporting template used included only subheadings. In July 2016, the template was changed to a standardized PI-RADS-compliant structured template incorporating dropdown menus. Lesion, patient characteristics, pathology, and adherence to the PI-RADS lexicon were extracted from MRI reports and patient charts. Diagnostic performance of prostate MRI to detect CS-PCa using combined ultrasound-MRI fusion and systematic biopsy as a reference standard was assessed. Three hundred twenty-four lesions in 202 patients (average age, 67 years; average prostate-specific antigen level, 5.9 ng/mL) were analyzed, including 217 MRI peripheral zone (PZ) lesions, 84 MRI non-PZ lesions, and 23 additional PZ lesions found on systematic biopsy but missed on MRI. Thirty-three percent (106 of 324) were CS-PCa. Adherence to the PI-RADS lexicon improved from 32.9% (50 of 152) to 88.4% (152 of 172) (P < .0001) after introduction of the structured template. The sensitivity of prostate MRI for CS-PCa in the PZ increased from 53% to 70% (P = .011). There was no significant change in specificity (60% versus 55%, P = .458). A structured template with dropdown menus incorporating the PI-RADS lexicon and classification rules improves adherence to PI-RADS and may increase the diagnostic performance of prostate MRI for CS-PCa. Copyright © 2018 American College of Radiology. Published by Elsevier Inc. All rights reserved.

A novel use of the discrete templated notes within an electronic health record software to monitor resident supervision.

PubMed

Ban, Vin Shen; Madden, Christopher J; Browning, Travis; O'Connell, Ellen; Marple, Bradley F; Moran, Brett

2017-04-01

Monitoring the supervision of residents can be a challenging task. We describe our experience with the implementation of a templated note system for documenting procedures with the aim of enabling automated, discrete, and standardized capture of documentation of supervision of residents performing floor-based procedures, with minimal extra effort from the residents. Procedural note templates were designed using the standard existing template within a commercial electronic health record software. Templates for common procedures were created such that residents could document every procedure performed outside of the formal procedural areas. Automated reports were generated and letters were sent to noncompliers. A total of 27 045 inpatient non-formal procedural area procedures were recorded from August 2012 to June 2014. Compliance with NoteWriter template usage averaged 86% in the first year and increased to 94.6% in the second year ( P  = .0055). Initially, only 12.5% of residents documented supervision of any form. By the end of the first year, this was above 80%, with the gains maintained into the second year and beyond. Direct supervision was documented to have occurred where required in 62.8% in the first year and increased to 99.8% in the second year ( P  = .0001) after the addition of hard stops. Notification of attendings prior to procedures was documented 100% of the time by September 2013. Letters sent to errant residents decreased from 3.6 to 0.83 per 100 residents per week. The templated procedure note system with hard stops and integrated reporting can successfully be used to improve monitoring of resident supervision. This has potential impact on resident education and patient safety. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PubMed Central

Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R.

2015-01-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/. PMID:26037908

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

PubMed

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R

2015-09-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cell-free translational screening of an expression sequence tag library of Clonorchis sinensis for novel antigen discovery.

PubMed

Kasi, Devi; Catherine, Christy; Lee, Seung-Won; Lee, Kyung-Ho; Kim, Yu Jung; Ro Lee, Myeong; Ju, Jung Won; Kim, Dong-Myung

2017-05-01

The rapidly evolving cloning and sequencing technologies have enabled understanding of genomic structure of parasite genomes, opening up new ways of combatting parasite-related diseases. To make the most of the exponentially accumulating genomic data, however, it is crucial to analyze the proteins encoded by these genomic sequences. In this study, we adopted an engineered cell-free protein synthesis system for large-scale expression screening of an expression sequence tag (EST) library of Clonorchis sinensis to identify potential antigens that can be used for diagnosis and treatment of clonorchiasis. To allow high-throughput expression and identification of individual genes comprising the library, a cell-free synthesis reaction was designed such that both the template DNA and the expressed proteins were co-immobilized on the same microbeads, leading to microbead-based linkage of the genotype and phenotype. This reaction configuration allowed streamlined expression, recovery, and analysis of proteins. This approach enabled us to identify 21 antigenic proteins. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:832-837, 2017. © 2017 American Institute of Chemical Engineers.

Mechanization of library procedures in the medium-sized medical library. 8. Computer applications in hospital departmental libraries.

PubMed

Howard, E; Kharibian, G

1972-07-01

To test the hypothesis that a standard library system could be designed for hospital departmental libraries, a system was developed and partially tested for four departmental libraries in the Washington University School of Medicine and Associated Hospitals. The system from determination of needs through design and evaluation, is described. The system was limited by specific constraints to control of the monograph collection. Products of control include catalog cards, accessions list, new book list, location list, fund list, missing book list, and discard book list. Sample data form and pages from a procedure manual are given, and conversion from a manual to an automated system is outlined. The question of standardization of library records and procedures is discussed, with indications of the way in which modular design, as utilized in this system, could contribute to greater flexibility in design of future systems. Reference is made to anticipating needs for organizing departmental libraries in developing regional medical library programs and to exploring the role of the departmental library in a medical library network.

Collaborative Portfolio's Effect on Library Usage

ERIC Educational Resources Information Center

Bryan, Valerie

2011-01-01

Library resources are expensive and it is the library media specialist's responsibility to ensure that use of the library's resources is maximized to support the School Strategic Plan (SSP). This library usage study examined data on the scheduling of high school classes for research-based assignments, related to content area curriculum standards,…

Comparison of custom to standard TKA instrumentation with computed tomography.

PubMed

Ng, Vincent Y; Arnott, Lindsay; Li, Jia; Hopkins, Ronald; Lewis, Jamie; Sutphen, Sean; Nicholson, Lisa; Reader, Douglas; McShane, Michael A

2014-08-01

There is conflicting evidence whether custom instrumentation for total knee arthroplasty (TKA) improves component position compared to standard instrumentation. Studies have relied on long-limb radiographs limited to two-dimensional (2D) analysis and subjected to rotational inaccuracy. We used postoperative computed tomography (CT) to evaluate preoperative three-dimensional templating and CI to facilitate accurate and efficient implantation of TKA femoral and tibial components. We prospectively evaluated a single-surgeon cohort of 78 TKA patients (51 custom, 27 standard) with postoperative CT scans using 3D reconstruction and contour-matching technology to preoperative imaging. Component alignment was measured in coronal, sagittal and axial planes. Preoperative templating for custom instrumentation was 87 and 79 % accurate for femoral and tibial component size. All custom components were within 1 size except for the tibial component in one patient (2 sizes). Tourniquet time was 5 min longer for custom (30 min) than standard (25 min). In no case was custom instrumentation aborted in favour of standard instrumentation nor was original alignment of custom instrumentation required to be adjusted intraoperatively. There were more outliers greater than 2° from intended alignment with standard instrumentation than custom for both components in all three planes. Custom instrumentation was more accurate in component position for tibial coronal alignment (custom: 1.5° ± 1.2°; standard: 3° ± 1.9°; p = 0.0001) and both tibial (custom: 1.4° ± 1.1°; standard: 16.9° ± 6.8°; p < 0.0001) and femoral (custom: 1.2° ± 0.9°; standard: 3.1° ± 2.1°; p < 0.0001) rotational alignment, and was similar to standard instrumentation in other measurements. When evaluated with CT, custom instrumentation performs similar or better to standard instrumentation in component alignment and accurately templates component size. Tourniquet time was mildly increased for custom compared to standard.

Meeting the New AASL Standards for the 21st-Century Learner via Big6 Problem Solving

ERIC Educational Resources Information Center

Needham, Joyce

2010-01-01

"AASL Standards for the 21st-Century Learner." New standards for library media programs! What does it mean to practicing library media specialists? Does this mean they must abandon all the strategies, activities, and lessons they have developed based upon "Information Power's Information Literacy Standards for Student Learning" and create all new…

76 FR 11337 - Presidential Library Facilities; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... Presidential Library Facilities; Correction AGENCY: National Archives and Records Administration. ACTION... and design standards for Presidential libraries and information required in NARA's reports to Congress... Presidential library. DATES: This regulation is effective March 2, 2011. FOR FURTHER INFORMATION CONTACT: Laura...

Computers and Libraries-A Reply

ERIC Educational Resources Information Center

Salton, Gerard

1971-01-01

A consideration of the various possibilities which are available for improving library operations and collection control makes it plain that the response of the library community ought to be towards greater cooperation among library centers and more extensive standardization. (31 references) (Author)

libdrdc: software standards library

NASA Astrophysics Data System (ADS)

Erickson, David; Peng, Tie

2008-04-01

This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

End-user satisfaction analysis on library management system unnes using technology acceptance model towards national standard of integrated library

NASA Astrophysics Data System (ADS)

Hardyanto, W.; Purwinarko, A.; Adhi, M. A.

2018-03-01

The library which is the gate of the University should be supported by the existence of an adequate information system, to provide excellent service and optimal to every user. Library management system that has been in existence since 2009 needs to be re-evaluated so that the system can meet the needs of both operator and Unnes user in particular, and users from outside Unnes in general. This study aims to evaluate and improve the existing library management system to produce a system that is accountable and able to meet the needs of end users, as well as produce a library management system that is integrated Unnes. Research is directed to produce evaluation report with Technology Acceptance Model (TAM) approach and library management system integrated with the national standard.

Ideas for the rapid development of the structural models in mechanical engineering

NASA Astrophysics Data System (ADS)

Oanta, E.; Raicu, A.; Panait, C.

2017-08-01

Conceiving computer based instruments is a long run concern of the authors. Some of the original solutions are: optimal processing of the large matrices, interfaces between the programming languages, approximation theory using spline functions, numerical programming increased accuracy based on the extended arbitrary precision libraries. For the rapid development of the models we identified the following directions: atomization, ‘librarization’, parameterization, automatization and integration. Each of these directions has some particular aspects if we approach mechanical design problems or software development. Atomization means a thorough top-down decomposition analysis which offers an insight regarding the basic features of the phenomenon. Creation of libraries of reusable mechanical parts and libraries of programs (data types, functions) save time, cost and effort when a new model must be conceived. Parameterization leads to flexible definition of the mechanical parts, the values of the parameters being changed either using a dimensioning program or in accord to other parts belonging to the same assembly. The resulting templates may be also included in libraries. Original software applications are useful for the model’s input data generation, to input the data into CAD/FEA commercial applications and for the data integration of the various types of studies included in the same project.

Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries.

PubMed

Randrianjatovo-Gbalou, Irina; Rosario, Sandrine; Sismeiro, Odile; Varet, Hugo; Legendre, Rachel; Coppée, Jean-Yves; Huteau, Valérie; Pochet, Sylvie; Delarue, Marc

2018-05-21

Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family. One mutant exhibited a high tolerance towards ribonucleotides (NTPs) and displayed an efficient ribonucleotidyltransferase activity that resulted in the assembly of long RNA polymers. HPLC analysis and RNA sequencing of the products were used to quantify the incorporation of the four NTPs as a function of initial NTP concentrations and established the randomness of each generated nucleic acid sequence. The same mutant revealed a propensity to accept other modified nucleotides and to extend them in long fragments. Hence, this mutant can deliver random natural and modified RNA polymers libraries ready to use for SELEX, with custom lengths and balanced or unbalanced ratios.

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins.

PubMed

Holland, Erika G; Buhr, Diane L; Acca, Felicity E; Alderman, Dawn; Bovat, Kristin; Busygina, Valeria; Kay, Brian K; Weiner, Michael P; Kiss, Margaret M

2013-08-30

Affinity maturation is an important part of the recombinant antibody development process. There are several well-established approaches for generating libraries of mutated antibody genes for affinity maturation, but these approaches are generally too laborious or expensive to allow high-throughput, parallel processing of multiple antibodies. Here, we describe a scalable approach that enables the generation of libraries with greater than 10(8) clones from a single Escherichia coli transformation. In our method, a mutated DNA fragment is produced using PCR conditions that promote nucleotide misincorporation into newly synthesized DNA. In the PCR reaction, one of the primers contains at least three phosphorothioate linkages at its 5' end, and treatment of the PCR product with a 5' to 3' exonuclease is used to preferentially remove the strand synthesized with the non-modified primer, resulting in a single-stranded DNA fragment. This fragment then serves as a megaprimer to prime DNA synthesis on a uracilated, circular, single-stranded template in a Kunkel-like mutagenesis reaction that biases nucleotide base-changes between the megaprimer and uracilated DNA sequence in favor of the in vitro synthesized megaprimer. This method eliminates the inefficient subcloning steps that are normally required for the construction of affinity maturation libraries from randomly mutagenized antibody genes. Copyright © 2013. Published by Elsevier B.V.

G STL: the geostatistical template library in C++

NASA Astrophysics Data System (ADS)

Remy, Nicolas; Shtuka, Arben; Levy, Bruno; Caers, Jef

2002-10-01

The development of geostatistics has been mostly accomplished by application-oriented engineers in the past 20 years. The focus on concrete applications gave birth to many algorithms and computer programs designed to address different issues, such as estimating or simulating a variable while possibly accounting for secondary information such as seismic data, or integrating geological and geometrical data. At the core of any geostatistical data integration methodology is a well-designed algorithm. Yet, despite their obvious differences, all these algorithms share many commonalities on which to build a geostatistics programming library, lest the resulting library is poorly reusable and difficult to expand. Building on this observation, we design a comprehensive, yet flexible and easily reusable library of geostatistics algorithms in C++. The recent advent of the generic programming paradigm allows us elegantly to express the commonalities of the geostatistical algorithms into computer code. Generic programming, also referred to as "programming with concepts", provides a high level of abstraction without loss of efficiency. This last point is a major gain over object-oriented programming which often trades efficiency for abstraction. It is not enough for a numerical library to be reusable, it also has to be fast. Because generic programming is "programming with concepts", the essential step in the library design is the careful identification and thorough definition of these concepts shared by most geostatistical algorithms. Building on these definitions, a generic and expandable code can be developed. To show the advantages of such a generic library, we use G STL to build two sequential simulation programs working on two different types of grids—a surface with faults and an unstructured grid—without requiring any change to the G STL code.

A systematic review of the evidence for topical use of ginger.

PubMed

Ding, Mingshuang; Leach, Matthew J; Bradley, Helen

2013-01-01

The use of ginger as a topical intervention is widely advocated in the popular media. However, there has been no attempt to date to synthesize the evidence for topically administered ginger. To systematically review and synthesize the best available evidence of effectiveness for topical ginger in any condition. CAM on PubMed, CINAHL, Google Scholar, MEDLINE, National Library of Australia, The Cochrane Library, TRIP, pertinent texts, and bibliographies of relevant papers. Data sources were systematically searched for studies investigating the clinical effectiveness of topical ginger, in any form and for any condition, regardless of study design. Studies were limited to those published between 1980 and 2010, and published in English, Mandarin, Cantonese, or Taiwanese. Data were extracted by two authors, independently, using standardized templates. Four studies met the inclusion criteria, including three randomized controlled trials and one non-randomized controlled trial. All studies differed in terms of study population, outcome measures, comparative interventions, and dose and form of ginger used, and thus, were not amenable to meta-analysis. Findings from all trials favored usage of ginger for most outcomes. However, the small sample sizes and inadequate methodological reporting indicate a high risk of bias and the need for caution when interpreting these results. Few studies have investigated the effectiveness of topically administered ginger for any condition. Until the findings of these studies are corroborated by more robust research, and the safety of ginger is adequately established, clinicians should remain cautious about using topical ginger in clinical practice. © 2013 Elsevier Inc. All rights reserved.

Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN.

PubMed

Hao, Jie; Liebeke, Manuel; Astle, William; De Iorio, Maria; Bundy, Jacob G; Ebbels, Timothy M D

2014-01-01

Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.

Systematic searching for theory to inform systematic reviews: is it feasible? Is it desirable?

PubMed

Booth, Andrew; Carroll, Christopher

2015-09-01

In recognising the potential value of theory in understanding how interventions work comes a challenge - how to make identification of theory less haphazard? To explore the feasibility of systematic identification of theory. We searched PubMed for published reviews (1998-2012) that had explicitly sought to identify theory. Systematic searching may be characterised by a structured question, methodological filters and an itemised search procedure. We constructed a template (BeHEMoTh - Behaviour of interest; Health context; Exclusions; Models or Theories) for use when systematically identifying theory. The authors tested the template within two systematic reviews. Of 34 systematic reviews, only 12 reviews (35%) reported a method for identifying theory. Nineteen did not specify how they identified studies containing theory. Data were unavailable for three reviews. Candidate terms include concept(s)/conceptual, framework(s), model(s), and theory/theories/theoretical. Information professionals must overcome inadequate reporting and the use of theory out of context. The review team faces an additional concern in lack of 'theory fidelity'. Based on experience with two systematic reviews, the BeHEMoTh template and procedure offers a feasible and useful approach for identification of theory. Applications include realist synthesis, framework synthesis or review of complex interventions. The procedure requires rigorous evaluation. © 2015 Health Libraries Group.

Viral assembly of oriented quantum dot nanowires

NASA Astrophysics Data System (ADS)

Mao, Chuanbin; Flynn, Christine E.; Hayhurst, Andrew; Sweeney, Rozamond; Qi, Jifa; Georgiou, George; Iverson, Brent; Belcher, Angela M.

2003-06-01

The highly organized structure of M13 bacteriophage was used as an evolved biological template for the nucleation and orientation of semiconductor nanowires. To create this organized template, peptides were selected by using a pIII phage display library for their ability to nucleate ZnS or CdS nanocrystals. The successful peptides were expressed as pVIII fusion proteins into the crystalline capsid of the virus. The engineered viruses were exposed to semiconductor precursor solutions, and the resultant nanocrystals that were templated along the viruses to form nanowires were extensively characterized by using high-resolution analytical electron microscopy and photoluminescence. ZnS nanocrystals were well crystallized on the viral capsid in a hexagonal wurtzite or a cubic zinc blende structure, depending on the peptide expressed on the viral capsid. Electron diffraction patterns showed single-crystal type behavior from a polynanocrystalline area of the nanowire formed, suggesting that the nanocrystals on the virus were preferentially oriented with their [001] perpendicular to the viral surface. Peptides that specifically directed CdS nanocrystal growth were also engineered into the viral capsid to create wurtzite CdS virus-based nanowires. Lastly, heterostructured nucleation was achieved with a dual-peptide virus engineered to express two distinct peptides within the same viral capsid. This work represents a genetically controlled biological synthesis route to a semiconductor nanoscale heterostructure.

Learning-based meta-algorithm for MRI brain extraction.

PubMed

Shi, Feng; Wang, Li; Gilmore, John H; Lin, Weili; Shen, Dinggang

2011-01-01

Multiple-segmentation-and-fusion method has been widely used for brain extraction, tissue segmentation, and region of interest (ROI) localization. However, such studies are hindered in practice by their computational complexity, mainly coming from the steps of template selection and template-to-subject nonlinear registration. In this study, we address these two issues and propose a novel learning-based meta-algorithm for MRI brain extraction. Specifically, we first use exemplars to represent the entire template library, and assign the most similar exemplar to the test subject. Second, a meta-algorithm combining two existing brain extraction algorithms (BET and BSE) is proposed to conduct multiple extractions directly on test subject. Effective parameter settings for the meta-algorithm are learned from the training data and propagated to subject through exemplars. We further develop a level-set based fusion method to combine multiple candidate extractions together with a closed smooth surface, for obtaining the final result. Experimental results show that, with only a small portion of subjects for training, the proposed method is able to produce more accurate and robust brain extraction results, at Jaccard Index of 0.956 +/- 0.010 on total 340 subjects under 6-fold cross validation, compared to those by the BET and BSE even using their best parameter combinations.

Viral assembly of oriented quantum dot nanowires.

PubMed

Mao, Chuanbin; Flynn, Christine E; Hayhurst, Andrew; Sweeney, Rozamond; Qi, Jifa; Georgiou, George; Iverson, Brent; Belcher, Angela M

2003-06-10

The highly organized structure of M13 bacteriophage was used as an evolved biological template for the nucleation and orientation of semiconductor nanowires. To create this organized template, peptides were selected by using a pIII phage display library for their ability to nucleate ZnS or CdS nanocrystals. The successful peptides were expressed as pVIII fusion proteins into the crystalline capsid of the virus. The engineered viruses were exposed to semiconductor precursor solutions, and the resultant nanocrystals that were templated along the viruses to form nanowires were extensively characterized by using high-resolution analytical electron microscopy and photoluminescence. ZnS nanocrystals were well crystallized on the viral capsid in a hexagonal wurtzite or a cubic zinc blende structure, depending on the peptide expressed on the viral capsid. Electron diffraction patterns showed single-crystal type behavior from a polynanocrystalline area of the nanowire formed, suggesting that the nanocrystals on the virus were preferentially oriented with their [001] perpendicular to the viral surface. Peptides that specifically directed CdS nanocrystal growth were also engineered into the viral capsid to create wurtzite CdS virus-based nanowires. Lastly, heterostructured nucleation was achieved with a dual-peptide virus engineered to express two distinct peptides within the same viral capsid. This work represents a genetically controlled biological synthesis route to a semiconductor nanoscale heterostructure.

Innovation in Library Education: Historical X-Files on Technology, People, and Change.

ERIC Educational Resources Information Center

Carmichael, James V., Jr.

1998-01-01

Discusses the history of library education and library educators. Highlights include Melvil Dewey's proposal for formal library education, the earlier apprentice system, obstacles to formal education, changes in attitudes toward patrons, accreditation, standards, and technological changes. (LRW)

Broadband moth-eye antireflection coatings on silicon

NASA Astrophysics Data System (ADS)

Sun, Chih-Hung; Jiang, Peng; Jiang, Bin

2008-02-01

We report a bioinspired templating technique for fabricating broadband antireflection coatings that mimic antireflective moth eyes. Wafer-scale, subwavelength-structured nipple arrays are directly patterned on silicon using spin-coated silica colloidal monolayers as etching masks. The templated gratings exhibit excellent broadband antireflection properties and the normal-incidence specular reflection matches with the theoretical prediction using a rigorous coupled-wave analysis (RCWA) model. We further demonstrate that two common simulation methods, RCWA and thin-film multilayer models, generate almost identical prediction for the templated nipple arrays. This simple bottom-up technique is compatible with standard microfabrication, promising for reducing the manufacturing cost of crystalline silicon solar cells.

Using Standardized Lexicons for Report Template Validation with LexMap, a Web-based Application.

PubMed

Hostetter, Jason; Wang, Kenneth; Siegel, Eliot; Durack, Jeremy; Morrison, James J

2015-06-01

An enormous amount of data exists in unstructured diagnostic and interventional radiology reports. Free text or non-standardized terminologies limit the ability to parse, extract, and analyze these report data elements. Medical lexicons and ontologies contain standardized terms for relevant concepts including disease entities, radiographic technique, and findings. The use of standardized terms offers the potential to improve reporting consistency and facilitate computer analysis. The purpose of this project was to implement an interface to aid in the creation of standards-compliant reporting templates for use in interventional radiology. Non-standardized procedure report text was analyzed and referenced to RadLex, SNOMED-CT, and LOINC. Using JavaScript, a web application was developed which determined whether exact terms or synonyms in reports existed within these three reference resources. The NCBO BioPortal Annotator web service was used to map terms, and output from this application was used to create an interactive annotated version of the original report. The application was successfully used to analyze and modify five distinct reports for the Society of Interventional Radiology's standardized reporting project.

To the Geoportal and Beyond! Preparing the Earth Observing Laboratory's Datasets for Inter-Repository Discovery

NASA Astrophysics Data System (ADS)

Gordon, S.; Dattore, E.; Williams, S.

2014-12-01

Even when a data center makes it's datasets accessible, they can still be hard to discover if the user is unaware of the laboratory or organization the data center supports. NCAR's Earth Observing Laboratory (EOL) is no exception. In response to this problem and as an inquiry into the feasibility of inter-connecting all of NCAR's repositories at a discovery layer, ESRI's Geoportal was researched. It was determined that an implementation of Geoportal would be a good choice to build a proof of concept model of inter-repository discovery around. This collaborative project between the University of Illinois and NCAR is coordinated through the Data Curation Education in Research Centers program. This program is funded by the Institute of Museum and Library Services.Geoportal is open source software. It serves as an aggregation point for metadata catalogs of earth science datasets, with a focus on geospatial information. EOL's metadata is in static THREDDS catalogs. Geoportal can only create records from a THREDDS Data Server. The first step was to make EOL metadata more accessible by utilizing the ISO 19115-2 standard. It was also decided to create DIF records so EOL datasets could be ingested in NASA's Global Change Master Directory (GCMD). To offer records for harvest, it was decided to develop an OAI-PMH server. To make a compliant server, the OAI_DC standard was also implemented. A server was written in Perl to serve a set of static records. We created a sample set of records in ISO 19115-2, FGDC, DIF, and OAI_DC. We utilized GCMD shared vocabularies to enhance discoverability and precision. The proof of concept was tested and verified by having another NCAR laboratory's Geoportal harvest our sample set. To prepare for production, templates for each standard were developed and mapped to the database. These templates will help the automated creation of records. Once the OAI-PMH server is re-written in a Grails framework a dynamic representation of EOL's metadata will be available for harvest. EOL will need to develop an implementation of a Geoportal and point GCMD to the OAI-PMH server. We will also seek out partnerships with other earth science and related discipline repositories that can communicate by OAI-PMH or Geoportal so that the scientific community will benefit from more discoverable data.

Questions and Answers on Library Law: The Fair Labor Standards Act, Part I.

ERIC Educational Resources Information Center

Uhler, Scott; Petsche, Janet; Allison, Rinda; Henn, Kathleen

2000-01-01

Discusses the Fair Labor Standards Act (FLSA), which sets the minimum wage and standards for overtime pay and child labor, as well as prohibiting unequal pay based on gender. Explains the three categories of exempt employees and considers whether any library employees may fall into these categories. (LRW)

Library Functions, Scholarly Communication, and the Foundation of the Digital Library: Laying Claim to the Control Zone.

ERIC Educational Resources Information Center

Atkinson, Ross

1996-01-01

Discussion of academic libraries and online systems focuses on core library services and a digital library which could serve as an alternative publishing mechanism for specialized scholarly communication. Highlights include adding value to sources of information; conflicts, including those with commercial publishers; and standardization and…

E-Books and New Library Service Models: An Analysis of the Impact of E-Book Technology on Academic Libraries.

ERIC Educational Resources Information Center

Jantz, Ronald

2001-01-01

Analyzes the implications of electronic book technology (e-books) on academic libraries. Discusses new business models for publishers, including self-publishing, Internet publishing, and partnerships with libraries as publishers; impact on library services, including cataloging, circulation, and digital preservation; user benefits; standards;…

Networking for Digital Preservation: Current Practice in 15 National Libraries. IFLA Publications 119

ERIC Educational Resources Information Center

Verheul, Ingeborg

2006-01-01

In 2004-2005, The National Library of the Netherlands (Koninklijke Bibliotheek) conducted a survey for the IFLA-CDNL Alliance for Bibliographic Standards (ICABS)--an alliance founded jointly by the International Federation of Library Associations (IFLA), the Conference of Directors of National Libraries (CDNL) and the national libraries of…

Toward a New Evaluation of Neutron Standards

DOE PAGES

Carlson, Allan D.; Pronyaev, Vladimir G.; Capote, Roberto; ...

2016-02-03

Measurements related to neutron cross section standards and certain prompt neutron fission spectra are being evaluated. In addition to the standard cross sections, investigations of reference data that are not as well known as the standards are being considered. We discuss procedures and codes for performing this work. A number of libraries will use the results of this standards evaluation for new versions of their libraries. Most of these data have applications in neutron dosimetry.

School Libraries Empowering Learning: The Australian Landscape.

ERIC Educational Resources Information Center

Todd, Ross J.

2003-01-01

Describes school libraries in Australia. Highlights include the title of teacher librarian and their education; the history of the role of school libraries in Australian education; empowerment; information skills and benchmarks; national standards for school libraries; information literacy; learning outcomes; evidence-based practice; digital…

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

PubMed

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

2008-06-01

During harvest, a variety of plant based contaminants are collected along with cotton lint. The USDA previously created a mid-infrared, attenuated total reflection (ATR), Fourier transform infrared (FT-IR) spectral library of cotton contaminants for contaminant identification as the contaminants have negative impacts on yarn quality. This library has shown impressive identification rates for extremely similar cellulose based contaminants in cases where the library was representative of the samples searched. When spectra of contaminant samples from crops grown in different geographic locations, seasons, and conditions and measured with a different spectrometer and accessories were searched, identification rates for standard search algorithms decreased significantly. Six standard algorithms were examined: dot product, correlation, sum of absolute values of differences, sum of the square root of the absolute values of differences, sum of absolute values of differences of derivatives, and sum of squared differences of derivatives. Four categories of contaminants derived from cotton plants were considered: leaf, stem, seed coat, and hull. Experiments revealed that the performance of the standard search algorithms depended upon the category of sample being searched and that different algorithms provided complementary information about sample identity. These results indicated that choosing a single standard algorithm to search the library was not possible. Three voting scheme algorithms based on result frequency, result rank, category frequency, or a combination of these factors for the results returned by the standard algorithms were developed and tested for their capability to overcome the unpredictability of the standard algorithms' performances. The group voting scheme search was based on the number of spectra from each category of samples represented in the library returned in the top ten results of the standard algorithms. This group algorithm was able to identify correctly as many test spectra as the best standard algorithm without relying on human choice to select a standard algorithm to perform the searches.

Development and implementation of clinical trial protocol templates at the National Institute of Allergy and Infectious Diseases.

PubMed

Bridge, Heather; Smolskis, Mary; Bianchine, Peter; Dixon, Dennis O; Kelly, Grace; Herpin, Betsey; Tavel, Jorge

2009-08-01

A clinical research protocol document must reflect both sound scientific rationale as well as local, national and, when applicable, international regulatory and human subject protections requirements. These requirements originate from a variety of sources, undergo frequent revision and are subject to interpretation. Tools to assist clinical investigators in the production of clinical protocols could facilitate navigating these requirements and ultimately increase the efficiency of clinical research. The National Institute of Allergy and Infectious Diseases (NIAID) developed templates for investigators to serve as the foundation for protocol development. These protocol templates are designed as tools to support investigators in developing clinical protocols. NIAID established a series of working groups to determine how to improve its capacity to conduct clinical research more efficiently and effectively. The Protocol Template Working Group was convened to determine what protocol templates currently existed within NIAID and whether standard NIAID protocol templates should be produced. After review and assessment of existing protocol documents and requirements, the group reached consensus about required and optional content, determined the format and identified methods for distribution as well as education of investigators in the use of these templates. The templates were approved by the NIAID Executive Committee in 2006 and posted as part of the NIAID Clinical Research Toolkit [1] website for broad access. These documents require scheduled revisions to stay current with regulatory and policy changes. The structure of any clinical protocol template, whether comprehensive or specific to a particular study phase, setting or design, affects how it is used by investigators. Each structure presents its own set of advantages and disadvantages. While useful, protocol templates are not stand-alone tools for creating an optimal protocol document, but must be complemented by institutional resources and support. Education and guidance of investigators in the appropriate use of templates is necessary to ensure a complete yet concise protocol document. Due to changing regulatory requirements, clinical protocol templates cannot become static, but require frequent revisions.

A Bayesian approach to the creation of a study-customized neonatal brain atlas

PubMed Central

Zhang, Yajing; Chang, Linda; Ceritoglu, Can; Skranes, Jon; Ernst, Thomas; Mori, Susumu; Miller, Michael I.; Oishi, Kenichi

2014-01-01

Atlas-based image analysis (ABA), in which an anatomical “parcellation map” is used for parcel-by-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain development, aging, and various diseases. The parcellation maps are often created based on common MRI templates, which allow users to transform the template to target images, or vice versa, to perform parcel-by-parcel statistics, and report the scientific findings based on common anatomical parcels. The use of a study-specific template, which represents the anatomical features of the study population better than common templates, is preferable for accurate anatomical labeling; however, the creation of a parcellation map for a study-specific template is extremely labor intensive, and the definitions of anatomical boundaries are not necessarily compatible with those of the common template. In this study, we employed a Volume-based Template Estimation (VTE) method to create a neonatal brain template customized to a study population, while keeping the anatomical parcellation identical to that of a common MRI atlas. The VTE was used to morph the standardized parcellation map of the JHU-neonate-SS atlas to capture the anatomical features of a study population. The resultant “study-customized” T1-weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS atlas, in terms of the registration accuracy. A pronounced increase in the accuracy of cortical parcellation and superior tensor alignment were observed when the customized template was used. With the customized atlas-based analysis, the fractional anisotropy (FA) detected closely approximated the manual measurements. This tool provides a solution for achieving normalization-based measurements with increased accuracy, while reporting scientific findings in a consistent framework. PMID:25026155

Implementation of a lung cancer multidisciplinary team standardised template for reporting to general practitioners: a mixed-method study

PubMed Central

Collett, Gemma K; Brown, Clare M; Shaw, Tim J; White, Kahren M; Beale, Philip J; Anderiesz, Cleola; Barnes, David J

2017-01-01

Objectives Few interventions have been designed that provide standardised information to primary care clinicians about the diagnostic and treatment recommendations resulting from cancer multidisciplinary team (MDT) (tumour board) meetings. This study aimed to develop, implement and evaluate a standardised template for lung cancer MDTs to provide clinical information and treatment recommendations to general practitioners (GPs). Specific objectives were to (1) evaluate template feasibility (acceptability, appropriateness and timeliness) with GPs and (2) document processes of preimplementation, implementation and evaluation within the MDT setting. Design A mixed-method study design using structured interviews with GPs and qualitative documentation of project logs about implementation processes. Setting Two hospitals in Central Sydney, New South Wales, Australia. Participants: 61 GPs evaluated the template. Two lung cancer MDTs, consisting of 33 clinicians, and eight researchers participated in template development and implementation strategy. Results The MDT-reporting template appears to be a feasible way of providing clinical information to GPs following patient presentation at a lung cancer MDT meeting. Ninety-five per cent of GPs strongly agreed or agreed that the standardised template provided useful and relevant information, that it was received in a timely manner (90%) and that the information was easy to interpret and communicate to the patient (84%). Implementation process data show that the investment made in the preimplementation stage to integrate the template into standard work practices was a critical factor in successful implementation. Conclusions This study demonstrates that it is feasible to provide lung cancer MDT treatment recommendations to GPs through implementation of a standardised template. A simple intervention, such as a standardised template, can help to address quality gaps and ensure that timely information is communicated between tertiary and primary care healthcare providers. PMID:29288182

LipidPioneer: A Comprehensive User-Generated Exact Mass Template for Lipidomics

PubMed Central

Ulmer, Candice Z.; Koelmel, Jeremy P.; Ragland, Jared M.; Garrett, Timothy J.

2017-01-01

Lipidomics, the comprehensive measurement of lipid species in a biological system, has promising potential in biomarker discovery and disease etiology elucidation. Advances in chromatographic separation, mass spectrometric techniques, and novel substrate applications continue to expand the number of lipid species observed. The total number and type of lipid species detected in a given sample are generally indicative of the sample matrix examined (e.g. serum, plasma, cells, bacteria, tissue, etc.). Current exact mass lipid libraries are static and represent the most commonly analyzed matrices. It is common practice for users to manually curate their own lists of lipid species and adduct masses; however, this process is time-consuming. LipidPioneer, an interactive template, can be used to generate exact masses and molecular formulas of lipid species that may be encountered in the mass spectrometric analysis of lipid profiles. Over 60 lipid classes are present in the LipidPioneer template, and include several unique lipid species, such as ether-linked lipids and lipid oxidation products. In the template, users can add any fatty acyl constituents without limitation in the number of carbons or degrees of unsaturation. LipidPioneer accepts naming using the lipid class level (sum composition) and the LIPID MAPS notation for fatty acyl structure level. In addition to lipid identification, user generated lipid m/z values can be used to develop inclusion lists for targeted fragmentation experiments. Resulting lipid names and m/z values can be imported into software such as MZmine or Compound Discoverer to automate exact mass searching and isotopic pattern matching across experimental data. PMID:28074328

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.

A practical approach to communicating benefit-risk decisions of medicines to stakeholders.

PubMed

Leong, James; Walker, Stuart; Salek, Sam

2015-01-01

The importance of a framework for a systematic structured assessment of the benefits and risks has been established, but in addition, it is necessary that the benefit-risk decisions and the processes to derive those decisions are documented and communicated to various stakeholders for accountability. Hence there is now a need to find appropriate tools to enhance communication between regulators and other stakeholders, in a manner that would uphold transparency, consistency and standards. A retrospective, non-comparative study was conducted to determine the applicability and practicality of a summary template in documenting benefit-risk assessment and communicating benefit-risk balance and conclusions for reviewers to other stakeholders. The benefit-risk (BR) Summary Template and its User Manual was evaluated by 12 reviewers within a regulatory agency in Singapore, the Health Sciences Authority (HSA). The BR Summary Template was found to be adequate in documenting benefits, risks, relevant summaries and conclusions, while the User Manual was useful in guiding the reviewer in completing the template. The BR Summary Template was also considered a useful tool for communicating benefit-risk decisions to a variety of stakeholders. The use of a template may be of value for the communicating benefit-risk assessment of medicines to stakeholders.

Direct elicitation of template concentration from quantification cycle (Cq) distributions in digital PCR.

PubMed

Mojtahedi, Mitra; Fouquier d'Hérouël, Aymeric; Huang, Sui

2014-01-01

Digital PCR (dPCR) exploits limiting dilution of a template into an array of PCR reactions. From this array the number of reactions that contain at least one (as opposed to zero) initial template is determined, allowing inferring the original template concentration. Here we present a novel protocol to efficiently infer the concentration of a sample and its optimal dilution for dPCR from few targeted qPCR assays. By taking advantage of the real-time amplification feature of qPCR as opposed to relying on endpoint PCR assessment as in standard dPCR prior knowledge of template concentration is not necessary. This eliminates the need for serial dilutions in a separate titration and reduces the number of necessary reactions. We describe the theory underlying our approach and discuss experimental moments that contribute to uncertainty. We present data from a controlled experiment where the initial template concentration is known as proof of principle and apply our method on directly monitoring transcript level change during cell differentiation as well as gauging amplicon numbers in cDNA samples after pre-amplification. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Full stellar kinematical profiles of central parts of nearby galaxies

NASA Astrophysics Data System (ADS)

Vudragović, A.; Samurović, S.; Jovanović, M.

2016-09-01

Context. We present the largest catalog of detailed stellar kinematics of the central parts of nearby galaxies, which includes higher moments of the line-of-sight velocity distribution (LOSVD) function represented by the Gauss-Hermite series. The kinematics is measured on a sample of galaxies selected from the Arecibo Legacy Fast ALFA (Alfalfa) survey using spectroscopy from the Sloan Digital Sky Survey (SDSS DR7). Aims: The SDSS DR7 offers measurements of the LOSVD based on the assumption of a pure Gaussian shape of the broadening function caused by the combination of rotational and random motion of the stars in galaxies. We discuss the consequences of this oversimplification since the velocity dispersion, one of the measured quantities, often serves as the proxy to important modeling parameters such as the black-hole mass and the virial mass of galaxies. Methods: The publicly available pPXF code is used to calculate the full kinematical profile for the sample galaxies including higher moments of their LOSVD. Both observed and synthetic stellar libraries were used and the related template mismatch problem is discussed. Results: For the whole sample of 2180 nearby galaxies reflecting morphological distribution characteristic for the local Universe, we successfully recovered stellar kinematics of their central parts, including higher order moments of the LOSVD function, for signal-to-noise above 50. Conclusions: We show the consequences of the oversimplification of the LOSVD function with Gaussian function on the velocity dispersion for the empirical and the synthetic stellar library. For the empirical stellar library, this approximation leads to an increase in the virial mass of 13% on average, while for the synthetic library the effect is weaker, with an increase of 9% on average. Systematic erroneous estimates of the velocity dispersion comes from the use of the synthetic stellar library instead of the empirical one and is much larger than the value imposed by the use of the Gaussian function. Only after a careful analysis of the template mismatch problem does one need to address the issue of the deviation of the LOSVD from the Gaussian function. We also show that the kurtotic parameter describing symmetrical departures from the Gaussian seems to increase along the continuous morphological sequence from late- to early-type galaxies. The catalog is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/593/A40

Accuracy of femoral templating in reproducing anatomical femoral offset in total hip replacement.

PubMed

Davies, H; Foote, J; Spencer, R F

2007-01-01

Restoration of hip biomechanics is a crucial component of successful total hip replacement. Preoperative templating is recommended to ensure that the size and orientation of implants is optimised. We studied how closely natural femoral offset could be reproduced using the manufacturers' templates for 10 femoral stems in common use in the UK. A series of 23 consecutive preoperative radiographs from patients who had undergone unilateral total hip replacement for unilateral osteoarthritis of the hip was employed. The change in offset between the templated position of the best-fitting template and the anatomical centre of the hip was measured. The templates were then ranked according to their ability to reproduce the normal anatomical offset. The most accurate was the CPS-Plus (Root Mean Square Error 2.0 mm) followed in rank order by: C stem (2.16), CPT (2.40), Exeter (3.23), Stanmore (3.28), Charnley (3.65), Corail (3.72), ABG II (4.30), Furlong HAC (5.08) and Furlong modular (7.14). A similar pattern of results was achieved when the standard error of variability of offset was analysed. We observed a wide variation in the ability of the femoral prosthesis templates to reproduce normal femoral offset. This variation was independent of the seniority of the observer. The templates of modern polished tapered stems with high modularity were best able to reproduce femoral offset. The current move towards digitisation of X-rays may offer manufacturers an opportunity to improve template designs in certain instances, and to develop appropriate computer software.

Robotic Needle Guide for Prostate Brachytherapy: Clinical Testing of Feasibility and Performance

PubMed Central

Song, Danny Y; Burdette, Everette C; Fiene, Jonathan; Armour, Elwood; Kronreif, Gernot; Deguet, Anton; Zhang, Zhe; Iordachita, Iulian; Fichtinger, Gabor; Kazanzides, Peter

2010-01-01

Purpose Optimization of prostate brachytherapy is constrained by tissue deflection of needles and fixed spacing of template holes. We developed and clinically tested a robotic guide towards the goal of allowing greater freedom of needle placement. Methods and Materials The robot consists of a small tubular needle guide attached to a robotically controlled arm. The apparatus is mounted and calibrated to operate in the same coordinate frame as a standard template. Translation in x and y directions over the perineum ±40mm are possible. Needle insertion is performed manually. Results Five patients were treated in an IRB-approved study. Confirmatory measurements of robotic movements for initial 3 patients using infrared tracking showed mean error of 0.489 mm (SD 0.328 mm). Fine adjustments in needle positioning were possible when tissue deflection was encountered; adjustments were performed in 54/179 (30.2%) needles placed, with 36/179 (20.1%) adjustments of > 2mm. Twenty-seven insertions were intentionally altered to positions between the standard template grid to improve the dosimetric plan or avoid structures such as pubic bone and blood vessels. Conclusions Robotic needle positioning provided a means of compensating for needle deflections as well as the ability to intentionally place needles into areas between the standard template holes. To our knowledge, these results represent the first clinical testing of such a system. Future work will be incorporation of direct control of the robot by the physician, adding software algorithms to help avoid robot collisions with the ultrasound, and testing the angulation capability in the clinical setting. PMID:20729152

How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation

NASA Astrophysics Data System (ADS)

Giorgino, Toni

2018-07-01

The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation.

By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX

PubMed Central

Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

2014-01-01

The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection. PMID:25490402

The National and University Library in Zagreb: The Goal Is Known--How Can It Be Attained?

ERIC Educational Resources Information Center

Miletic-Vejzovic, Laila

1994-01-01

Provides an overview of the state of libraries and their resources in Croatia. Highlights include destruction of libraries resulting from the war; the need for centralization, uniformity, and standards; the role of the National and University Library; processing library materials; and the development of an automated system and network. (Contains…

Library Manpower, A Preliminary Study of Essential Factors Contributing to Library Staffing Patterns.

ERIC Educational Resources Information Center

Fairholm, G.W.; And Others

This study was conducted to develop quantitative and qualitative productivity standards, work measures, and activity reports to facilitate effective budgeting for library staff in the State University of New York (SUNY) library system. The research methodology used by the study team involved a survey of 11 libraries of the 22 institutions in the…

Library Services for State Government; An Evaluation of the Resources of the Oregon State Library.

ERIC Educational Resources Information Center

Hill, Mildred M.

This study outlines the types of library service required to furnish quality reference services to state agencies. The services provided by the Oregon State Library were evaluated according to the standards established by the American Library Association. Evaluation of the collection for scope and coverage in subject areas of automation,…

cDNA encoding a polypeptide including a hevein sequence

DOEpatents

Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

1993-02-16

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology

PubMed Central

Chappell, James; Jensen, Kirsten; Freemont, Paul S.

2013-01-01

A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. To address this, we have validated a completely in vitro approach for the characterization of DNA regulatory elements using Escherichia coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology. PMID:23371936

A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei

PubMed Central

Pauli, Wolfgang M.; Nili, Amanda N.; Tyszka, J. Michael

2018-01-01

Recent advances in magnetic resonance imaging methods, including data acquisition, pre-processing and analysis, have benefited research on the contributions of subcortical brain nuclei to human cognition and behavior. At the same time, these developments have led to an increasing need for a high-resolution probabilistic in vivo anatomical atlas of subcortical nuclei. In order to address this need, we constructed high spatial resolution, three-dimensional templates, using high-accuracy diffeomorphic registration of T1- and T2- weighted structural images from 168 typical adults between 22 and 35 years old. In these templates, many tissue boundaries are clearly visible, which would otherwise be impossible to delineate in data from individual studies. The resulting delineations of subcortical nuclei complement current histology-based atlases. We further created a companion library of software tools for atlas development, to offer an open and evolving resource for the creation of a crowd-sourced in vivo probabilistic anatomical atlas of the human brain. PMID:29664465

Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?

PubMed

Skolnick, Jeffrey; Zhou, Hongyi

2017-04-20

Despite their different implementations, comparison of the best threading approaches to the prediction of evolutionary distant protein structures reveals that they tend to succeed or fail on the same protein targets. This is true despite the fact that the structural template library has good templates for all cases. Thus, a key question is why are certain protein structures threadable while others are not. Comparison with threading results on a set of artificial sequences selected for stability further argues that the failure of threading is due to the nature of the protein structures themselves. Using a new contact map based alignment algorithm, we demonstrate that certain folds are highly degenerate in that they can have very similar coarse grained fractions of native contacts aligned and yet differ significantly from the native structure. For threadable proteins, this is not the case. Thus, contemporary threading approaches appear to have reached a plateau, and new approaches to structure prediction are required.

An Expert System for Classifying Stars on the MK Spectral Classification System

NASA Astrophysics Data System (ADS)

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

2013-01-01

We will describe an expert computer system designed to classify stellar spectra on the MK Spectral Classification system employing methods similar to those of humans who make direct comparison with the MK classification standards. Like an expert human classifier, MKCLASS first comes up with a rough spectral type, and then refines that type by direct comparison with MK standards drawn from a standards library using spectral criteria appropriate to the spectral class. Certain common spectral-type peculiarities can also be detected by the program. The program is also capable of identifying WD spectra and carbon stars and giving appropriate (but currently approximate) spectral types on the relevant systems. We will show comparisons between spectral types (including luminosity types) performed by MKCLASS and humans. The program currently is capable of competent classifications in the violet-green region, but plans are underway to extend the spectral criteria into the red and near-infrared regions. Two standard libraries with resolutions of 1.8 and 3.6Å are now available, but a higher-resolution standard library, using the new spectrograph on the Vatican Advanced Technology Telescope, is currently under preparation. Once that library is available, MKCLASS and the spectral libraries will be made available to the astronomical community.

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

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

The Next Stage: Moving from Isolated Digital Collections to Interoperable Digital Libraries.

ERIC Educational Resources Information Center

Besser, Howard

2002-01-01

Presents a conceptual framework for digital library development and discusses how to move from isolated digital collections to interoperable digital libraries. Topics include a history of digital libraries; user-centered architecture; stages of technological development; standards, including metadata; and best practices. (Author/LRW)

Satisfaction Formation Processes in Library Users: Understanding Multisource Effects

ERIC Educational Resources Information Center

Shi, Xi; Holahan, Patricia J.; Jurkat, M. Peter

2004-01-01

This study explores whether disconfirmation theory can explain satisfaction formation processes in library users. Both library users' needs and expectations are investigated as disconfirmation standards. Overall library user satisfaction is predicted to be a function of two independent sources--satisfaction with the information product received…

Temple University Libraries in the Mid-Seventies: A Status Report.

ERIC Educational Resources Information Center

Nitecki, Joseph Z.

Present central library operations are discussed in terms of emerging needs and possible direction for future development. Library objectives include acquiring and organizing relevant records of knowledge, and providing satisfactory information service standards. Issues relating to objectives include the library's involvement in planning and…

Partners for Success: A School Library Advocacy Training Program for Principals.

ERIC Educational Resources Information Center

Kachel, Debra E.

2003-01-01

Describes a program developed to help school principals understand the importance of school library media specialists based on "Information Power." Explains modules on academic achievement and school libraries, information literacy and academic standards, library collections and flexible access, and revitalization and evaluation of…

The patients' library movement: an overview of early efforts in the United States to establish organized libraries for hospital patients.

PubMed Central

Panella, N M

1996-01-01

The patients' library movement in the United States, a dynamic, cohesive drive begun and sustained by librarians and physicians, strove to promote placement of organized libraries for patients in hospitals. It took shape in the early years of this century, evolving from its proponents' deeply held conviction that books and reading foster the rehabilitation of sick people. The American Library Association's World War I service to hospitalized military personnel dramatically reinforced the conviction; the post-World War I institution of public library extension services to general hospitals explicitly reflected it. Enormous energy was infused into the patients' library movement. Throughout the first half of this century, there were sustained efforts not only to establish organized libraries for hospitalized people but also to expand and systematically study bibliotherapy and to shape patients' librarianship as a professional specialty. The movement's achievements include the establishment of patients' library committees within national and international associations; impetus for development of academic programs to train patients' librarians; and publication, from 1944 through 1970, of successive sets of standards for hospital patients' libraries. The first of these remain the first standards written and issued by a professional library association for a hospital library. PMID:8938330

Competency-based goals, objectives, and linked evaluations for rheumatology training programs: a standardized template of learning activities from the Carolinas Fellows Collaborative.

PubMed

Criscione-Schreiber, Lisa G; Bolster, Marcy B; Jonas, Beth L; O'Rourke, Kenneth S

2013-06-01

American Council on Graduate Medical Education program requirements mandate that rheumatology training programs have written goals, objectives, and performance evaluations for each learning activity. Since learning activities are similar across rheumatology programs, we aimed to create competency-based goals and objectives (CBGO) and evaluations that would be generalizable nationally. Through an established collaboration of the 4 training programs' directors in North Carolina and South Carolina, we collaboratively composed CBGO and evaluations for each learning activity for rheumatology training programs. CBGO and linked evaluations were written using appropriate verbs based on Bloom's taxonomy. Draft documents were peer reviewed by faculty at the 4 institutions and by members of the American College of Rheumatology (ACR) Clinician Scholar Educator Group. We completed templates of CBGO for core and elective rotations and conferences. Templates detail progressive fellow performance improvement appropriate to educational level. Specific CBGO are mirrored in learning activity evaluations. Templates are easily modified to fit individual program attributes, have been successfully implemented by our 4 programs, and have proven their value in 4 residency review committee reviews. We propose adoption of these template CBGO by the ACR, with access available to all rheumatology training programs. Evaluation forms that exactly reflect stated objectives ensure that trainees are assessed using standardized measures and that trainees are aware of the learning expectations. The objectives mirrored in the evaluations closely align with the proposed milestones for internal medicine training, and will therefore be a useful starting point for creating these milestones in rheumatology. Copyright © 2013 by the American College of Rheumatology.

Mode-dependent templates and scan order for H.264/AVC-based intra lossless coding.

PubMed

Gu, Zhouye; Lin, Weisi; Lee, Bu-Sung; Lau, Chiew Tong; Sun, Ming-Ting

2012-09-01

In H.264/advanced video coding (AVC), lossless coding and lossy coding share the same entropy coding module. However, the entropy coders in the H.264/AVC standard were original designed for lossy video coding and do not yield adequate performance for lossless video coding. In this paper, we analyze the problem with the current lossless coding scheme and propose a mode-dependent template (MD-template) based method for intra lossless coding. By exploring the statistical redundancy of the prediction residual in the H.264/AVC intra prediction modes, more zero coefficients are generated. By designing a new scan order for each MD-template, the scanned coefficients sequence fits the H.264/AVC entropy coders better. A fast implementation algorithm is also designed. With little computation increase, experimental results confirm that the proposed fast algorithm achieves about 7.2% bit saving compared with the current H.264/AVC fidelity range extensions high profile.

The Grid[Way] Job Template Manager, a tool for parameter sweeping

NASA Astrophysics Data System (ADS)

Lorca, Alejandro; Huedo, Eduardo; Llorente, Ignacio M.

2011-04-01

Parameter sweeping is a widely used algorithmic technique in computational science. It is specially suited for high-throughput computing since the jobs evaluating the parameter space are loosely coupled or independent. A tool that integrates the modeling of a parameter study with the control of jobs in a distributed architecture is presented. The main task is to facilitate the creation and deletion of job templates, which are the elements describing the jobs to be run. Extra functionality relies upon the GridWay Metascheduler, acting as the middleware layer for job submission and control. It supports interesting features like multi-dimensional sweeping space, wildcarding of parameters, functional evaluation of ranges, value-skipping and job template automatic indexation. The use of this tool increases the reliability of the parameter sweep study thanks to the systematic bookkeeping of job templates and respective job statuses. Furthermore, it simplifies the porting of the target application to the grid reducing the required amount of time and effort. Program summaryProgram title: Grid[Way] Job Template Manager (version 1.0) Catalogue identifier: AEIE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Apache license 2.0 No. of lines in distributed program, including test data, etc.: 3545 No. of bytes in distributed program, including test data, etc.: 126 879 Distribution format: tar.gz Programming language: Perl 5.8.5 and above Computer: Any (tested on PC x86 and x86_64) Operating system: Unix, GNU/Linux (tested on Ubuntu 9.04, Scientific Linux 4.7, centOS 5.4), Mac OS X (tested on Snow Leopard 10.6) RAM: 10 MB Classification: 6.5 External routines: The GridWay Metascheduler [1]. Nature of problem: To parameterize and manage an application running on a grid or cluster. Solution method: Generation of job templates as a cross product of the input parameter sets. Also management of the job template files including the job submission to the grid, control and information retrieval. Restrictions: The parameter sweep is limited by disk space during generation of the job templates. The wild-carding of parameters cannot be done in decreasing order. Job submission, control and information is delegated to the GridWay Metascheduler. Running time: From half a second in the simplest operation to a few minutes for thousands of exponential sampling parameters.

Free-radical cyclizations onto differently substituted 1,2,3-triazoles installed in sugar templates.

PubMed

Marco-Contelles, J; Rodríguez-Fernández, M

2001-06-01

The synthesis and manipulation of differently substituted 1,2,3-triazoles (7-11 and 12-16) installed in sugar templates gave compounds 29-34 and 44-50, after reaction with tributyltin hydride or tris(trimethylsilyl)silane. Following standard procedures compound 44 was transformed into piperidinose derivative 54. These compounds are chiral, useful building blocks for the synthesis of glycosidase inhibitors of the fused-azole piperidinose type.

Information Power: Student Achievement is the Bottom Line.

ERIC Educational Resources Information Center

Harada, Violet; Donham, Jean

1998-01-01

Focuses on the student-centered "Information Power: Building Partnerships for Learning" mission for school library media programs, and the corresponding information literacy standards. Discusses examples of content-area standards; instructional roles; and three strategies for developing an integrated library media program--collaborating with…

Leveraging Metadata to Create Better Web Services

ERIC Educational Resources Information Center

Mitchell, Erik

2012-01-01

Libraries have been increasingly concerned with data creation, management, and publication. This increase is partly driven by shifting metadata standards in libraries and partly by the growth of data and metadata repositories being managed by libraries. In order to manage these data sets, libraries are looking for new preservation and discovery…

Shared Geospatial Metadata Repository for Ontario University Libraries: Collaborative Approaches

ERIC Educational Resources Information Center

Forward, Erin; Leahey, Amber; Trimble, Leanne

2015-01-01

Successfully providing access to special collections of digital geospatial data in academic libraries relies upon complete and accurate metadata. Creating and maintaining metadata using specialized standards is a formidable challenge for libraries. The Ontario Council of University Libraries' Scholars GeoPortal project, which created a shared…

The Role of the Library in Distance Education.

ERIC Educational Resources Information Center

Rodrigues, Helena F.

1996-01-01

Discusses the evolving role of academic libraries in providing products and services to distance learners. Guided by accreditation standards, libraries are examining how well their services satisfy the unique needs of these students. Gives examples of library policies and procedures, highlights Internet significance, and discusses future trends in…

Service Standards for the Mobile/Social Library

ERIC Educational Resources Information Center

Thomas, Lisa Carlucci

2010-01-01

Customer service is at the core of everything librarians do in libraries. They strive to create positive customer relationships and to provide added value to the library services offered to their patrons. Emerging technologies offer opportunities for creative integration with library services. Staff should be encouraged to explore, learn, and…

Evaluating Library Staff: A Performance Appraisal System.

ERIC Educational Resources Information Center

Belcastro, Patricia

This manual provides librarians and library managers with a performance appraisal system that measures staff fairly and objectively and links performance to the goals of the library. The following topics are addressed: (1) identifying expectations for quality service or standards of performance; (2) the importance of a library's code of service,…

Six-Year Planning Report for Crosby Library, Gonzaga University.

ERIC Educational Resources Information Center

Gonzaga Univ., Spokane, WA.

A response to a call for six-year planning documents from Gonzaga University's instructional units, this report is divided into five broad sections: (1) library collections, an assessment of Crosby Library's holdings and comparison with the overall quantitative standards established by the Association of College and Research Libraries; (2) library…

Library Automation: Guidelines to Costing.

ERIC Educational Resources Information Center

Ford, Geoffrey

As with all new programs, the costs associated with library automation must be carefully considered before implementation. This document suggests guidelines to be followed and areas to be considered in the costing of library procedures. An existing system model has been suggested as a standard (Appendix A) and a classification of library tasks…

School Libraries and Student Learning: A Guide for School Leaders

ERIC Educational Resources Information Center

Morris, Rebecca J.

2015-01-01

Innovative, well-designed school library programs can be critical resources for helping students meet high standards of college and career readiness. In "School Libraries and Student Learning", Rebecca J. Morris shows how school leaders can make the most of their school libraries to support ambitious student learning. She offers…

School Library Renaissance in Baltimore County: An Open-and-Shut Case for Library Funding.

ERIC Educational Resources Information Center

Curtis, Della

2000-01-01

Explains how Baltimore County secondary school libraries increased their funding and staffing levels. Discusses a partnership with Towson University for staffing needs; the role of technology; the development of online learning modules; marketing efforts; state standards for library collections; and collection analysis criteria. (LRW)

Content Metadata Standards for Marine Science: A Case Study

USGS Publications Warehouse

Riall, Rebecca L.; Marincioni, Fausto; Lightsom, Frances L.

2004-01-01

The U.S. Geological Survey developed a content metadata standard to meet the demands of organizing electronic resources in the marine sciences for a broad, heterogeneous audience. These metadata standards are used by the Marine Realms Information Bank project, a Web-based public distributed library of marine science from academic institutions and government agencies. The development and deployment of this metadata standard serve as a model, complete with lessons about mistakes, for the creation of similarly specialized metadata standards for digital libraries.

Low-template methods yield limited extra information for PowerPlex® Fusion 6C profiling.

PubMed

Duijs, Francisca; van de Merwe, Linda; Sijen, Titia; Benschop, Corina C G

2018-06-01

Advances in autosomal DNA profiling systems enable analyzing increased numbers of short tandem repeat (STR) loci in one reaction. Increasing the number of STR loci increases the amount of information that may be obtained from a (crime scene) sample. In this study, we examined whether even more allelic information can be obtained by applying low-template methods. To this aim, the performance of the PowerPlex® Fusion 6C STR typing system was assessed when increasing the number of PCR cycles or enhancing the capillary electrophoresis (CE) injection settings. Results show that applying these low-template methods yields limited extra information and comes at cost of more background noise. In addition, the gain in detection of alleles was much smaller when compared to the gain when applying low-template methods to the 15-loci AmpFLSTR® NGM™ system. Consequently, the PowerPlex® Fusion 6C STR typing system was implemented using standard settings only; low-template methods were not implemented for our routine forensic casework. Copyright © 2018 Elsevier B.V. All rights reserved.

Academic Libraries in Iran

ERIC Educational Resources Information Center

Deale, H. Vail

1973-01-01

Iranian librarianship is in the embryonic stages of development, especially with respect to modern and functional academic libraries. In three major areas--personnel, resources, and physical facilities--the academic libraries are deficient compared with Western standards. (16 references) (Author)

Media Standards.

ERIC Educational Resources Information Center

North Clackamas School District 12, Milwaukie, OR.

Guidelines for library media services for the North Clackamas School District were developed by two teams representing the elementary, junior high, and senior high schools. These minimum standards describe the goals and objectives for library media services to students, staff, and community; the operation of the media centers; and the audiovisual…

International Standardization of Library and Documentation Techniques.

ERIC Educational Resources Information Center

International Federation for Documentation, The Hague (Netherlands).

This comparative study of the national and international standards, rules and regulations on library and documentation techniques adopted in various countries was conducted as a preliminary step in determining the minimal bases for facilitating national and international cooperation between documentalists and librarians. The study compares and…

The Vendors' Corner--The Request for Proposal.

ERIC Educational Resources Information Center

Sugnet, Chris; And Others

1987-01-01

Several online vendors address the issue of RFPs (requests for proposals) for library systems, discussing the documents' style, technical standards, library expectations, liabilities associated with using this procedure, factors in the decision to bid, and the need for a standardized document and national clearinghouse. (CLB)

Spreadsheets for Analyzing and Optimizing Space Missions

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Agrawal, Anil K.; Czikmantory, Akos J.; Weisbin, Charles R.; Hua, Hook; Neff, Jon M.; Cowdin, Mark A.; Lewis, Brian S.; Iroz, Juana; Ross, Rick

2009-01-01

XCALIBR (XML Capability Analysis LIBRary) is a set of Extensible Markup Language (XML) database and spreadsheet- based analysis software tools designed to assist in technology-return-on-investment analysis and optimization of technology portfolios pertaining to outer-space missions. XCALIBR is also being examined for use in planning, tracking, and documentation of projects. An XCALIBR database contains information on mission requirements and technological capabilities, which are related by use of an XML taxonomy. XCALIBR incorporates a standardized interface for exporting data and analysis templates to an Excel spreadsheet. Unique features of XCALIBR include the following: It is inherently hierarchical by virtue of its XML basis. The XML taxonomy codifies a comprehensive data structure and data dictionary that includes performance metrics for spacecraft, sensors, and spacecraft systems other than sensors. The taxonomy contains >700 nodes representing all levels, from system through subsystem to individual parts. All entries are searchable and machine readable. There is an intuitive Web-based user interface. The software automatically matches technologies to mission requirements. The software automatically generates, and makes the required entries in, an Excel return-on-investment analysis software tool. The results of an analysis are presented in both tabular and graphical displays.

Program Helps Standardize Documentation Of Software

NASA Technical Reports Server (NTRS)

Howe, G.

1994-01-01

Intelligent Documentation Management System, IDMS, computer program developed to assist project managers in implementing information system documentation standard known as NASA-STD-2100-91, NASA STD, COS-10300, of NASA's Software Management and Assurance Program. Standard consists of data-item descriptions or templates, each of which governs particular component of software documentation. IDMS helps program manager in tailoring documentation standard to project. Written in C language.

High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2.

PubMed

Abécassis, V; Pompon, D; Truan, G

2000-10-15

The design of a family shuffling strategy (CLERY: Combinatorial Libraries Enhanced by Recombination in Yeast) associating PCR-based and in vivo recombination and expression in yeast is described. This strategy was tested using human cytochrome P450 CYP1A1 and CYP1A2 as templates, which share 74% nucleotide sequence identity. Construction of highly shuffled libraries of mosaic structures and reduction of parental gene contamination were two major goals. Library characterization involved multiprobe hybridization on DNA macro-arrays. The statistical analysis of randomly selected clones revealed a high proportion of chimeric genes (86%) and a homogeneous representation of the parental contribution among the sequences (55.8 +/- 2.5% for parental sequence 1A2). A microtiter plate screening system was designed to achieve colorimetric detection of polycyclic hydrocarbon hydroxylation by transformed yeast cells. Full sequences of five randomly picked and five functionally selected clones were analyzed. Results confirmed the shuffling efficiency and allowed calculation of the average length of sequence exchange and mutation rates. The efficient and statistically representative generation of mosaic structures by this type of family shuffling in a yeast expression system constitutes a novel and promising tool for structure-function studies and tuning enzymatic activities of multicomponent eucaryote complexes involving non-soluble enzymes.

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening

PubMed Central

2017-01-01

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing. PMID:28199790

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening.

PubMed

MacConnell, Andrew B; Price, Alexander K; Paegel, Brian M

2017-03-13

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing.

An Inventory of Library Services and Resources of the State of Washington, 1965.

ERIC Educational Resources Information Center

Bevis, L. Dorothy

This survey of current library resources and services in Washington is based on questionnaires; visits to public, university, college and community college libraries in the state; and statistics from state and national governmental sources. The inventories of public and academic libraries include discussions of standards applicable to the…

The Practicing Librarian: Public Library Parking Needs.

ERIC Educational Resources Information Center

Galvin, Hoyt

1978-01-01

Suggests standards for the numbers of parking spaces needed for a public library. From the annual Library Journal public library construction questionnaires, data were available on the number of parking spaces and the square foot size of the buildings reported; information on estimated needs was collected from the librarians in charge of each…

Handbook of Standard Terminology for Reporting and Recording Information about Libraries.

ERIC Educational Resources Information Center

Jones, Dennis P.; And Others

Intended to foster a common language for information exchange about library operations and resources, this handbook provides library managers, boards of trustees, and other library decisionmakers with guidance in identifying items of information from which to obtain factual and comparative data for (1) developing policies and decisions; (2)…

Benchmarking Reference Desk Service in Academic Health Science Libraries: A Preliminary Survey.

ERIC Educational Resources Information Center

Robbins, Kathryn; Daniels, Kathleen

2001-01-01

This preliminary study was designed to benchmark patron perceptions of reference desk services at academic health science libraries, using a standard questionnaire. Responses were compared to determine the library that provided the highest-quality service overall and along five service dimensions. All libraries were rated very favorably, but none…

The University Library: A Study of Services Offered the Blind.

ERIC Educational Resources Information Center

Parkin, Derral

A survey based on the American Library Association's "Standards for Library Services for the Blind and Visually Handicapped" (1966) was sent to 65 four year universities in Utah, Idaho, Wyoming, Colorado, New Mexico, Nevada, Montana, and Arizona. Libraries were asked how many blind patrons they had and what services and facilities were…

Archives, accessibility, and advocacy: a case study of strategies for creating and maintaining relevance

PubMed Central

Welch, Jennifer M; Hoffius, Susan D; Fox, E. Brooke

2011-01-01

Question/Objective: How can a special collection maintain or increase its profile in its parent institution, when that parent institution emphasizes scientific and clinical learning? Setting/Context: The Waring Historical Library, Medical University of South Carolina (MUSC), preserves and promotes the history of health sciences at MUSC and in South Carolina. As a state entity, MUSC has suffered significant budget cuts for the past several years. In this climate, the Waring had to find ways to maintain relevance in the MUSC community. Methods: The Waring partnered with the MUSC College of Nursing to explore new ways to build institutional allies. By combining traditional archival administration with innovative uses of digital collections aimed at institutional promotion and outreach, the Waring's digital library became an advocacy tool that led to the Waring's enhanced value to its parent institution. Outcomes: The Waring Library is a resource for MUSC development and alumni relations. Tangible outcomes include additional funding from grants, increased staff, no loss of institutional funding, increased access to collections, increased accessions, cultivation of institutional allies for long-term support of the Waring, and development of a template for future partnerships. PMID:21243056

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.

PubMed

Rozenberg, Andrey; Leese, Florian; Weiss, Linda C; Tollrian, Ralph

2016-01-01

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

Investigating the effect of sputtering conditions on the physical properties of aluminum thin film and the resulting alumina template

NASA Astrophysics Data System (ADS)

Taheriniya, Shabnam; Parhizgar, Sara Sadat; Sari, Amir Hossein

2018-06-01

To study the alumina template pore size distribution as a function of Al thin film grain size distribution, porous alumina templates were prepared by anodizing sputtered aluminum thin films. To control the grain size the aluminum samples were sputtered with the rate of 0.5, 1 and 2 Å/s and the substrate temperature was either 25, 75 or 125 °C. All samples were anodized for 120 s in 1 M sulfuric acid solution kept at 1 °C while a 15 V potential was being applied. The standard deviation value for samples deposited at room temperature but with different rates is roughly 2 nm in both thin film and porous template form but it rises to approximately 4 nm with substrate temperature. Samples with the average grain size of 13, 14, 18.5 and 21 nm respectively produce alumina templates with an average pore size of 8.5, 10, 15 and 16 nm in that order which shows the average grain size limits the average pore diameter in the resulting template. Lateral correlation length and grain boundary effect are other factors that affect the pore formation process and pore size distribution by limiting the initial current density.

Solid-phase synthesis of molecularly imprinted nanoparticles.

PubMed

Canfarotta, Francesco; Poma, Alessandro; Guerreiro, Antonio; Piletsky, Sergey

2016-03-01

Molecularly imprinted polymers (MIPs) are synthetic materials, generally based on acrylic or methacrylic monomers, that are polymerized in the presence of a specific target molecule called the 'template' and capable of rebinding selectively to this target molecule. They have the potential to be low-cost and robust alternatives to biomolecules such as antibodies and receptors. When prepared by traditional synthetic methods (i.e., with free template in solution), their usefulness has been limited by high binding site heterogeneity, the presence of residual template and the fact that the production methods are complex and difficult to standardize. To overcome some of these limitations, we developed a method for the synthesis of MIP nanoparticles (nanoMIPs) using an innovative solid-phase approach, which relies on the covalent immobilization of the template molecules onto the surface of a solid support (glass beads). The obtained nanoMIPs are virtually free of template and demonstrate high affinity for the target molecule (e.g., melamine and trypsin in our published work). Because of an affinity separation step performed on the solid phase after polymerization, poor binders and unproductive polymer are removed, so the final product has more uniform binding characteristics. The overall protocol, starting from the immobilization of the template onto the solid phase and including the purification and characterization of the nanoparticles, takes up to 1 week.

Public Access Workstations in the Library: New Trends.

ERIC Educational Resources Information Center

Beecher, Henry

1991-01-01

Discusses the use of microcomputer-based workstations that are provided for public access in libraries. Criteria for workstations are discussed, including standard hardware, open-design software, scalable interface, and connectivity options for networking; systems that provide full-text access are described; and the need for standards is…

37 CFR 251.38 - Billing and commitment to standards.

Code of Federal Regulations, 2011 CFR

2011-07-01

... standards. 251.38 Section 251.38 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS... performed during each hour or day charged. (d) Except for support services provided by the Library of Congress, arbitrators shall perform their own work, including research, analysis of the record, and...

37 CFR 251.38 - Billing and commitment to standards.

Code of Federal Regulations, 2010 CFR

2010-07-01

... standards. 251.38 Section 251.38 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS... performed during each hour or day charged. (d) Except for support services provided by the Library of Congress, arbitrators shall perform their own work, including research, analysis of the record, and...

The detection and upgrade rates of prostate adenocarcinoma following transperineal template-guided prostate biopsy – a tertiary referral centre experience

PubMed Central

Telford, Robert; Viney, Richard; Patel, Prashant

2016-01-01

Introduction We aim to present transperineal template-guided prostate biopsy (template biopsy) outcomes at a tertiary referral centre. Furthermore, to identify the detection rate of prostate cancer in those with a previous negative transrectal ultrasound guided prostate biopsy and the upgrade rate of those on active surveillance for Gleason 3 + 3 = 6 prostate adenocarcinoma. Material and methods We conducted a prospective study of 200 consecutive men who underwent template biopsy over a 22-month period in a tertiary referral centre, using a standard 24 region template prostate biopsy technique. Indications and histology results, as well as complications, were recorded. Results Median age was 67 years and median PSA was 10 ng/mL. Overall detection rate was 47%. 39.5% of cases with previous negative transrectal biopsies were found to have prostate adenocarcinoma. 47.5% of cases on active surveillance for Gleason 3 + 3 = 6 prostate adenocarcinoma were upgraded. The most frequent complication was acute urinary retention at a rate of 12.5%, however, the use of a single prophylactic dose of tamsulosin was found to be beneficial, with 13 cases needed to treat to prevent one episode. Conclusions Template biopsies are safe and efficacious with an overall detection rate of 47% in the present series. Due to the high detection rate, one must consider template biopsy following one negative transrectal biopsy where there is persistent clinical suspicion. Furthermore, those considering active surveillance for Gleason 3 + 3 = 6 disease should be offered template biopsy to confirm the grade of their disease. PMID:27123325

Cross-linked nanoassemblies from poly(ethylene glycol)-poly(aspartate) block copolymers as stable supramolecular templates for particulate drug delivery.

PubMed

Lee, Hyun Jin; Bae, Younsoo

2011-07-11

Block copolymer cross-linked nanoassemblies (CNAs) were developed as stable supramolecular templates for particulate drug delivery. Poly(ethylene glycol)-poly(aspartate) [PEG-p(Asp)] block copolymers, consisting of PEG (5 or 12 kDa) and Asp (5, 14, 25, 33, and 37 repeating units), were used as scaffolds and grafts in combination to prepare a nanoassembly library of grafted nanoassemblies (GNAs) and CNAs. Four synthesis routes were tested to maximize the number of drug-binding Asp units per nanoassembly. Grafting-onto-scaffold and grafting-from-scaffold methods were used for GNA synthesis. Either partially or completely deprotected PEG-p(Asp) was cross-linked with diamine compounds to prepare CNAs. (1)H NMR and GPC measurements showed that GNAs and CNAs contained the maximum 183 and 253 Asp units, respectively. Initial screening of the nanoassemblies revealed that GNAs would be impractical for further development as drug carriers due to variable grafting efficiency and low product yields. CNAs were obtained in high yields and identified as a promising supramolecular template that can entrap and release ionizable drugs (doxorubicin), enhancing the particle stability of nanoassemblies in the pharmaceutically relevant pH ranges between 4 and 9. Light scattering measurements demonstrated that the particle size of CNAs remained uniform before and after drug entrapment, causing neither aggregation nor dissociation (<5 mg/mL).

The Weakest Link: Library Catalogs.

ERIC Educational Resources Information Center

Young, Terrence E., Jr.

2002-01-01

Describes methods of correcting MARC records in online public access catalogs in school libraries. Highlights include in-house methods; professional resources; conforming to library cataloging standards; vendor services, including Web-based services; software specifically developed for record cleanup; and outsourcing. (LRW)

Mechanism of chimera formation during the Multiple Displacement Amplification reaction.

PubMed

Lasken, Roger S; Stockwell, Timothy B

2007-04-12

Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2-21 nucleotides (nts) in the new templates. Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

Performing label-fusion-based segmentation using multiple automatically generated templates.

PubMed

Chakravarty, M Mallar; Steadman, Patrick; van Eede, Matthijs C; Calcott, Rebecca D; Gu, Victoria; Shaw, Philip; Raznahan, Armin; Collins, D Louis; Lerch, Jason P

2013-10-01

Classically, model-based segmentation procedures match magnetic resonance imaging (MRI) volumes to an expertly labeled atlas using nonlinear registration. The accuracy of these techniques are limited due to atlas biases, misregistration, and resampling error. Multi-atlas-based approaches are used as a remedy and involve matching each subject to a number of manually labeled templates. This approach yields numerous independent segmentations that are fused using a voxel-by-voxel label-voting procedure. In this article, we demonstrate how the multi-atlas approach can be extended to work with input atlases that are unique and extremely time consuming to construct by generating a library of multiple automatically generated templates of different brains (MAGeT Brain). We demonstrate the efficacy of our method for the mouse and human using two different nonlinear registration algorithms (ANIMAL and ANTs). The input atlases consist a high-resolution mouse brain atlas and an atlas of the human basal ganglia and thalamus derived from serial histological data. MAGeT Brain segmentation improves the identification of the mouse anterior commissure (mean Dice Kappa values (κ = 0.801), but may be encountering a ceiling effect for hippocampal segmentations. Applying MAGeT Brain to human subcortical structures improves segmentation accuracy for all structures compared to regular model-based techniques (κ = 0.845, 0.752, and 0.861 for the striatum, globus pallidus, and thalamus, respectively). Experiments performed with three manually derived input templates suggest that MAGeT Brain can approach or exceed the accuracy of multi-atlas label-fusion segmentation (κ = 0.894, 0.815, and 0.895 for the striatum, globus pallidus, and thalamus, respectively). Copyright © 2012 Wiley Periodicals, Inc.

Mechanism of chimera formation during the Multiple Displacement Amplification reaction

PubMed Central

Lasken, Roger S; Stockwell, Timothy B

2007-01-01

Background Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts) in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications. PMID:17430586

Standards for School Library/Media Programs, 1972-75.

ERIC Educational Resources Information Center

Wisconsin State Dept. of Public Instruction, Madison. Div. of Library Services.

To aid elementary, middle, junior high, and high schools in planning an Instructional Materials Center, this handbook presents standards for this modern concept of a school library. The term Instructional Materials Center (IMC) is used throughout to designate a centralized collection of materials, with a staff of professional and clerical…

Common Bibliographic Standards for Baylor University Libraries. Revised.

ERIC Educational Resources Information Center

Scott, Sharon; And Others

Developed by a Baylor University (Texas) Task Force, the revised policies of bibliographic standards for the university libraries provide formats for: (1) archives and manuscript control; (2) audiovisual media; (3) books; (4) machine-readable data files; (5) maps; (6) music scores; (7) serials; and (8) sound recordings. The task force assumptions…

Use Standards to Draw Curriculum Maps

ERIC Educational Resources Information Center

Franklin, Pat; Stephens, Claire Gatrell

2009-01-01

Specific curriculum is taught at every grade level and it is the job of library media specialists to know subject area content. Library media specialists should develop collections to meet the content associated with curriculum standards. To ensure that these collections meet school needs, collection mapping with specific curriculum related to…

MARC: Mrs. Avram's Remarkable Contribution.

ERIC Educational Resources Information Center

Rather, Lucia J.; Wiggins, Beacher

1989-01-01

This discussion of the contributions of Henriette D. Avram to the field of librarianship covers her role in establishing MARC formats as the international standard for library automation and her work in the retrospective conversion of catalogs, establishment of library standards, and creation of information networks. An interview with Dr. Avram is…

A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing

DOE PAGES

Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.; ...

2016-12-21

When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich formore » pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.« less

A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing

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

Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.

When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich formore » pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.« less

Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry.

PubMed

Nour, Hany F; Islam, Tuhidul; Fernández-Lahore, Marcelo; Kuhnert, Nikolai

2012-12-30

Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest. Copyright © 2012 John Wiley & Sons, Ltd.

An Investigation into the Trueness and Precision of Copy Denture Templates Produced by Rapid Prototyping and Conventional Means.

PubMed

Davda, K; Osnes, C; Dillon, S; Wu, J; Hyde, P; Keeling, A

2017-12-01

To assess the trueness and precision of copy denture templates produced using traditional methods and 3D printing. Six copies of a denture were made using: 1. Conventional technique with silicone putty in an impression tray (CT). 2. Conventional technique with no impression tray (CNT). 3. 3D scanning and printing (3D). Scan trueness and precision was investigated by scanning a denture six times and comparing five scans to the sixth. Then the scans of the six CT, CNT and 3D dentures were compared by aligning, in turn, the copies of each denture to the scanned original. Outcome measures were the mean surface-to-surface distance, standard deviation of that distance and the maximum distance. Student's unpaired t-tests with Bonferroni correction were used to analyse the results. The repeated scans of the original denture showed a scan trueness of 0.013mm (SD 0.002) and precision of 0.013mm (SD 0.002). Trueness: CT templates, 0.168mm (0.047), CNT templates 0.195mm (0.034) and 3D 0.103mm (0.021). Precision: CT templates 0.158mm (0.037), CNT 0.233mm (0.073), 3D 0.090mm (0.017). For each outcome measure the 3D templates demonstrated an improvement which was statistically significant (p⟨0.05). 3D printed copy denture templates reproduced the original with greater trueness and precision than conventional techniques. Copyright© 2017 Dennis Barber Ltd.

The More Things Change the More They Stay the Same

ERIC Educational Resources Information Center

Barnett, Cassandra

2015-01-01

Over the last century, school library standards have gone through a number of iterations, and expectations for student learning have evolved. While the school library of today looks and functions differently from the school library of the early 1900s, the vision surprisingly is still very similar. The goal of today's school library is to provide…

Collection overlap in hospital health sciences libraries: a case study.

PubMed

Stroyan, S

1985-10-01

Given similar demographics (age, size, and user population), to what extent do community hospital libraries differ in collection content? It is sometimes assumed that hospital libraries are relatively homogeneous and therefore subject to standardized procedures and collection development guides. This study compares the holdings of two community hospital libraries in Illinois to determine similarities and differences.

How Accessible Are Public Libraries' Web Sites? A Study of Georgia Public Libraries

ERIC Educational Resources Information Center

Ingle, Emma; Green, Ravonne A.; Huprich, Julia

2009-01-01

One issue that public librarians must consider when planning Web site design is accessibility for patrons with disabilities. This article reports a study of Web site accessibility of public libraries in Georgia. The focus of the report is whether public libraries use accessible guidelines and standards in making their Web sites accessible. An…

Proposals for a Dynamic Library. Technical Report.

ERIC Educational Resources Information Center

Salton, Gerard

The current library environment is first examined, and an attempt is made to explain why the standard approaches to the library problem have been less productive than had been anticipated. A new design is then introduced for modern library operations based on a two-fold strategy: on the input side, the widest possible utilization should be made of…

How School Librarians Help Kids Achieve Standards: The Second Colorado Study.

ERIC Educational Resources Information Center

Lance, Keith Curry; Rodney, Marcia J.; Hamilton-Pennell, Christine

In 1993, the Colorado State Library published "The Impact of School Library Media Centers on Academic Achievement." This follow-up study focuses attention on the library media specialist and the services she or he provides throughout the building, rather than just the library media center as a specific place, and emphasizes the fact that…

Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia;

Nucleic acid amplification using modular branched primers

DOEpatents

Ulanovsky, Levy; Raja, Mugasimangalam C.

2001-01-01

Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

The ELF in Your Library.

ERIC Educational Resources Information Center

McKimmie, Tim; Smith, Jeanette

1994-01-01

Presents an overview of the issues related to extremely low frequency (ELF) radiation from computer video display terminals. Highlights include electromagnetic fields; measuring ELF; computer use in libraries; possible health effects; electromagnetic radiation; litigation and legislation; standards and safety; and what libraries can do. (Contains…

Content Management and the Future of Academic Libraries.

ERIC Educational Resources Information Center

Wu, Yuhfen Diana; Liu, Mengxiong

2001-01-01

Discusses Internet-based electronic content management in digital libraries and considers the future of academic libraries. Topics include digital technologies; content management systems; standards; bandwidth; security and privacy concerns; legal matters, including copyrights and ownership; lifecycle; and multilingual access and interface. (LRW)

Helping Students Use Virtual Libraries Effectively.

ERIC Educational Resources Information Center

Fitzgerald, Mary Ann; Galloway, Chad

2001-01-01

Describes a study in which online behavior of high school and undergraduate students using GALILEO (Georgia Library Learning Online), a virtual library, were observed. Topics include cognitive demands; technology literacy; domain knowledge; search strategies; relevance; evaluation of information; information literacy standards; and suggestions to…

Realistic Library Research Methods: Bibliographic Sources Annotated.

ERIC Educational Resources Information Center

Kushon, Susan G.; Wells, Bernice

This guide gives an overview of basic library research methods with emphasis upon developing an understanding of library organization and professional services. Commonly used bibliographic techniques are described for various published and unpublished, print and nonprint materials. Standard reference sources (bibliographies, encyclopedias, annual…

Speaking up for Equity Takes Courage--But the Standards Have Your Back

ERIC Educational Resources Information Center

Lechtenberg, Kate; Phillips, Jeanie

2018-01-01

The National School Library Standards require school librarians to make equity a value that permeates the entire school library community. Creating displays to celebrate diversity is not enough. We cannot allow ourselves to approach diversity as a "social good," in which isolated programs serve marginalized students without challenging…

Teaching Information Ethics to High School Students

ERIC Educational Resources Information Center

Lehman, Kathy

2009-01-01

The new AASL standards clearly spell out ethical responsibilities, which school librarians strive to instill and model as they work with staff and students. In this article, the author presents the AASL standards together with some tips and lesson ideas which she and her library partner have put into practice within their library media program.

International developments in openEHR archetypes and templates.

PubMed

Leslie, Heather

Electronic Health Records (EHRs) are a complex knowledge domain. The ability to design EHRs to cope with the changing nature of health knowledge, and to be shareable, has been elusive. A recent pilot study1 tested the applicability of the CEN 13606 as an electronic health record standard. Using openEHR archetypes and tools2, 650 clinical content specifi cations (archetypes) were created (e.g. for blood pressure) and re-used across all clinical specialties and contexts. Groups of archetypes were aggregated in templates to support clinical information gathering or viewing (e.g. 80 separate archetypes make up the routine antenatal visit record). Over 60 templates were created for use in the emergency department, antenatal care and delivery of an infant, and paediatric hearing loss assessment. The primary goal is to define a logical clinical record architecture for the NHS but potentially, with archetypes as the keystone, shareable EHRs will also be attainable. Archetype and template development work is ongoing, with associated evaluation occurring in parallel.

Strategy for communicating benefit-risk decisions: a comparison of regulatory agencies' publicly available documents

PubMed Central

Leong Wai Yeen, James; Salek, Sam; Walker, Stuart

2014-01-01

The assessment report formats of four major regulatory reference agencies, US Food and Drug Administration, European Medicines Agency, Health Canada, and Australia's Therapeutic Goods Administration were compared to a benefit-risk (BR) documentation template developed by the Centre for Innovation in Regulatory Science and a four-member Consortium on Benefit-Risk Assessment. A case study was also conducted using a US FDA Medical Review, the European Public Assessment Report and Australia's Public Assessment Report for the same product. Compared with the BR Template, existing regulatory report formats are inadequate regarding the listing of benefits and risks, the assigning of relative importance and values, visualization and the utilization of a detailed, systematic, standardized structure. The BR Template is based on the principles of BR assessment common to major regulatory agencies. Given that there are minimal differences among the existing regulatory report formats, it is timely to consider the feasibility of a universal template. PMID:25538620

Structure and Thermoelectric Properties of Bi2−xSbxTe3 Nanowires Grown in Flexible Nanoporous Polycarbonate Templates

PubMed Central

Datta, Anuja; Sangle, Abhijeet; Hardingham, Nick; Cooper, Charles; Kraan, Max; Ritchie, David; Narayan, Vijay; Kar-Narayan, Sohini

2017-01-01

We report the room-temperature growth of vertically aligned ternary Bi2−xSbxTe3 nanowires of diameter ~200 nm and length ~12 µm, within flexible track-etched nanoporous polycarbonate (PC) templates via a one-step electrodeposition process. Bi2−xSbxTe3 nanowires with compositions spanning the entire range from pure Bi2Te3 (x = 0) to pure Sb2Te3 (x = 2) were systematically grown within the nanoporous channels of PC templates from a tartaric–nitric acid based electrolyte, at the end of which highly crystalline nanowires of uniform composition were obtained. Compositional analysis showed that the Sb concentration could be tuned by simply varying the electrolyte composition without any need for further annealing of the samples. Thermoelectric properties of the Bi2−xSbxTe3 nanowires were measured using a standardized bespoke setup while they were still embedded within the flexible PC templates. PMID:28772915

A difference tracking algorithm based on discrete sine transform

NASA Astrophysics Data System (ADS)

Liu, HaoPeng; Yao, Yong; Lei, HeBing; Wu, HaoKun

2018-04-01

Target tracking is an important field of computer vision. The template matching tracking algorithm based on squared difference matching (SSD) and standard correlation coefficient (NCC) matching is very sensitive to the gray change of image. When the brightness or gray change, the tracking algorithm will be affected by high-frequency information. Tracking accuracy is reduced, resulting in loss of tracking target. In this paper, a differential tracking algorithm based on discrete sine transform is proposed to reduce the influence of image gray or brightness change. The algorithm that combines the discrete sine transform and the difference algorithm maps the target image into a image digital sequence. The Kalman filter predicts the target position. Using the Hamming distance determines the degree of similarity between the target and the template. The window closest to the template is determined the target to be tracked. The target to be tracked updates the template. Based on the above achieve target tracking. The algorithm is tested in this paper. Compared with SSD and NCC template matching algorithms, the algorithm tracks target stably when image gray or brightness change. And the tracking speed can meet the read-time requirement.

Generation and evaluation of an ultra-high-field atlas with applications in DBS planning

NASA Astrophysics Data System (ADS)

Wang, Brian T.; Poirier, Stefan; Guo, Ting; Parrent, Andrew G.; Peters, Terry M.; Khan, Ali R.

2016-03-01

Purpose Deep brain stimulation (DBS) is a common treatment for Parkinson's disease (PD) and involves the use of brain atlases or intrinsic landmarks to estimate the location of target deep brain structures, such as the subthalamic nucleus (STN) and the globus pallidus pars interna (GPi). However, these structures can be difficult to localize with conventional clinical magnetic resonance imaging (MRI), and thus targeting can be prone to error. Ultra-high-field imaging at 7T has the ability to clearly resolve these structures and thus atlases built with these data have the potential to improve targeting accuracy. Methods T1 and T2-weighted images of 12 healthy control subjects were acquired using a 7T MR scanner. These images were then used with groupwise registration to generate an unbiased average template with T1w and T2w contrast. Deep brain structures were manually labelled in each subject by two raters and rater reliability was assessed. We compared the use of this unbiased atlas with two other methods of atlas-based segmentation (single-template and multi-template) for subthalamic nucleus (STN) segmentation on 7T MRI data. We also applied this atlas to clinical DBS data acquired at 1.5T to evaluate its efficacy for DBS target localization as compared to using a standard atlas. Results The unbiased templates provide superb detail of subcortical structures. Through one-way ANOVA tests, the unbiased template is significantly (p <0.05) more accurate than a single-template in atlas-based segmentation and DBS target localization tasks. Conclusion The generated unbiased averaged templates provide better visualization of deep brain nuclei and an increase in accuracy over single-template and lower field strength atlases.

An automated method for modeling proteins on known templates using distance geometry.

PubMed

Srinivasan, S; March, C J; Sudarsanam, S

1993-02-01

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.

Social marketing and student documentation of asthma care: a quasi-randomized controlled trial.

PubMed

Gimbel, Ronald W; Olsen, Cara H; Williams, Pamela M; Stephens, Mark B

2012-02-01

The study's objective was to determine the effectiveness of a social marketing intervention in influencing use of a targeted electronic medical record (EMR) template to document a standard asthma encounter. This quasi-randomized controlled trial used intervention groups exposed to an educational workshop on EMR documentation with embedded social marketing messages aimed at persuading behavior. Conducted in July 2009 to June 2010, participants in the study included third-year medical students. The primary outcome was the number of participants using a target EMR template. (Clinicaltrials.gov identifier: NCT01043113). A total of 155 participants randomized across eight clusters. Following the workshop, intervention groups were more likely to use the target asthma template than the control group (PR 3.97, 95% CI=1.34--11.79). At slightly over 30 days following the workshop, the intervention group continued to use the asthma template more often than the control group (PR 2.40, 95% CI=1.10--5.21). Stratifying by gender, intervention group females used the asthma template more after the interventions than control group females (PR 10.79, 95% CI=1.18--64.27). In follow-up at slightly over 30 days after the intervention, intervention group female participant asthma template use continued to be used more than control group females (PR 2.82, 95% CI=1.58--5.02). There were no significant differences in group use of asthma template use by intervention group males immediately after the intervention compared to control group males (PR 2.55, 95% CI=0.80--8.14) or similarly at slightly over 30 day follow-up (PR 2.18, 95% CI=0.74-6.42). Social marketing can effectively influence medical student use of EMR templates for clinical documentation in a controlled setting.

New template family for the detection of gravitational waves from comparable-mass black hole binaries

NASA Astrophysics Data System (ADS)

Porter, Edward K.

2007-11-01

In order to improve the phasing of the comparable-mass waveform as we approach the last stable orbit for a system, various resummation methods have been used to improve the standard post-Newtonian waveforms. In this work we present a new family of templates for the detection of gravitational waves from the inspiral of two comparable-mass black hole binaries. These new adiabatic templates are based on reexpressing the derivative of the binding energy and the gravitational wave flux functions in terms of shifted Chebyshev polynomials. The Chebyshev polynomials are a useful tool in numerical methods as they display the fastest convergence of any of the orthogonal polynomials. In this case they are also particularly useful as they eliminate one of the features that plagues the post-Newtonian expansion. The Chebyshev binding energy now has information at all post-Newtonian orders, compared to the post-Newtonian templates which only have information at full integer orders. In this work, we compare both the post-Newtonian and Chebyshev templates against a fiducially exact waveform. This waveform is constructed from a hybrid method of using the test-mass results combined with the mass dependent parts of the post-Newtonian expansions for the binding energy and flux functions. Our results show that the Chebyshev templates achieve extremely high fitting factors at all post-Newtonian orders and provide excellent parameter extraction. We also show that this new template family has a faster Cauchy convergence, gives a better prediction of the position of the last stable orbit and in general recovers higher Signal-to-Noise ratios than the post-Newtonian templates.

Collection overlap in hospital health sciences libraries: a case study.

PubMed Central

Stroyan, S

1985-01-01

Given similar demographics (age, size, and user population), to what extent do community hospital libraries differ in collection content? It is sometimes assumed that hospital libraries are relatively homogeneous and therefore subject to standardized procedures and collection development guides. This study compares the holdings of two community hospital libraries in Illinois to determine similarities and differences. PMID:4052675

Collaboration: Finding the Teacher, Finding the Topic, Finding the Time

ERIC Educational Resources Information Center

Gess, Angela

2009-01-01

Have you ever had a teacher say, "I'd love to bring my classes to the library more often, but we just don't have enough time because we have to prepare for our state standardized tests?" This response stems from a misconception about the role of library media centers and library media specialists. In some school environments, the library media…

The ACRL framework for information literacy in higher education: implications for health sciences librarianship.

PubMed

Knapp, Maureen; Brower, Stewart

2014-01-01

The Association of College and Research Libraries is developing a new framework of information literacy concepts that will revise and replace the previously adopted standards. This framework consists of six threshold concepts that are more flexible than the original standards, and that work to identify both the function and the feelings behind information literacy education practices. This column outlines the new tentative framework with an eye toward its implications for health sciences libraries, and suggests ways the medical library community might work with this new document.

Local Area Networks.

ERIC Educational Resources Information Center

Nasatir, Marilyn; And Others

1990-01-01

Four papers discuss LANs (local area networks) and library applications: (1) "Institute for Electrical and Electronic Engineers Standards..." (Charles D. Brown); (2) "Facilities Planning for LANs..." (Gail Persky); (3) "Growing up with the Alumni Library: LAN..." (Russell Buchanan); and (4) "Implementing a LAN...at the Health Sciences Library"…

A Bridge to the Future: Observations on Building a Digital Library.

ERIC Educational Resources Information Center

Gaunt, Marianne I.

2002-01-01

The experience of Rutgers University Libraries illustrates the extensive planning, work effort, possibilities, and investment required to develop the digital library. Examines these key areas: organizational structure; staff development needs; facilities and the new digital infrastructure; metadata standards/interoperability; digital collection…

Academic Libraries in Japan

ERIC Educational Resources Information Center

Cullen, Rowena; Nagata, Haruki

2008-01-01

Academic libraries in Japan are well resourced by international standards, and support Japan's internationally recognized research capability well, but there are also ways in which they reflect Japan's strong bureaucratic culture. Recent changes to the status of national university libraries have seen a new interest in customer service, and…

Is There a Global Role for Metropolitan City Libraries?

ERIC Educational Resources Information Center

Mason, Marilyn Gell

1994-01-01

Discusses the potential for linking large metropolitan public libraries to international interlibrary loan networks. Issues involved in international networking, including funding, standards, network connectivity, and protectionism, are discussed. Examples of libraries capable of participating and brief descriptions of their collections are given.…

Microbiological quality of indoor air in university libraries.

PubMed

Hayleeyesus, Samuel Fekadu; Manaye, Abayneh Melaku

2014-05-01

To evaluate the concentration of bacteria and fungi in the indoor environment of Jimma University libraries, so as to estimate the health hazard and to create standards for indoor air quality control. The microbial quality of indoor air of eight libraries of Jimma University was determined. The settle plate method using open Petri-dishes containing different culture media was employed to collect sample twice daily. Isolates were identified according to standard methods. The concentrations of bacteria and fungi aerosols in the indoor environment of the university libraries ranged between 367-2595 CFU/m(3). According to the sanitary standards classification of European Commission, almost all the libraries indoor air of Jimma University was heavily contaminated with bacteria and fungi. In spite of their major source difference, the average fungi density found in the indoor air of libraries did appear to follow the same trend with bacterial density (P=0.001). The bacteria isolates included Micrococcus sp., Staphylococcus aureus, Streptococcus pyogenes, Bacillus sp. and Neisseria sp. while Cladosporium sp., Alternaria sp., Penicillium sp. and Aspergillus sp. were the most isolated fungi. The indoor air of all libraries were in the range above highly contaminated according to European Commission classification and the most isolates are considered as potential candidates involved in the establishment of sick building syndromes and often associated with clinical manifestations like allergy, rhinitis, asthma and conjunctivitis. Thus, attention must be given to control those environmental factors which favor the growth and multiplication of microbes in indoor environment of libraries to safeguard the health of users and workers.

Comprehensive peptidomimetic libraries targeting protein-protein interactions.

PubMed

Whitby, Landon R; Boger, Dale L

2012-10-16

Transient protein-protein interactions (PPIs) are essential components in cellular signaling pathways as well as in important processes such as viral infection, replication, and immune suppression. The unknown or uncharacterized PPIs involved in such interaction networks often represent compelling therapeutic targets for drug discovery. To date, however, the main strategies for discovery of small molecule modulators of PPIs are typically limited to structurally characterized targets. Recent developments in molecular scaffolds that mimic the side chain display of peptide secondary structures have yielded effective designs, but few screening libraries of such mimetics are available to interrogate PPI targets. We initiated a program to prepare a comprehensive small molecule library designed to mimic the three major recognition motifs that mediate PPIs (α-helix, β-turn, and β-strand). Three libraries would be built around templates designed to mimic each such secondary structure and substituted with all triplet combinations of groups representing the 20 natural amino acid side chains. When combined, the three libraries would contain a member capable of mimicking the key interaction and recognition residues of most targetable PPIs. In this Account, we summarize the results of the design, synthesis, and validation of an 8000 member α-helix mimetic library and a 4200 member β-turn mimetic library. We expect that the screening of these libraries will not only provide lead structures against α-helix- or β-turn-mediated protein-protein or peptide-receptor interactions, even if the nature of the interaction is unknown, but also yield key insights into the recognition motif (α-helix or β-turn) and identify the key residues mediating the interaction. Consistent with this expectation, the screening of the libraries against p53/MDM2 and HIV-1 gp41 (α-helix mimetic library) or the opioid receptors (β-turn mimetic library) led to the discovery of library members expected to mimic the known endogenous ligands. These efforts led to the discovery of high-affinity α-helix mimetics (K(i) = 0.7 μM) against HIV-1 gp41 as well as high-affinity and selective β-turn mimetics (K(i) = 80 nM) against the κ-opioid receptor. The results suggest that the use of such comprehensive libraries of peptide secondary structure mimetics, built around effective molecular scaffolds, constitutes a powerful method of interrogating PPIs. These structures provide small molecule modulators of PPI networks for therapeutic target validation, lead compound discovery, and the identification of modulators of biological processes for further study.

SCORE user`s manual

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

Brown, S.A.

SABrE is a set of tools to facilitate the development of portable scientific software and to visualize scientific data. As with most constructs, SABRE has a foundation. In this case that foundation is SCORE. SCORE (SABRE CORE) has two main functions. The first and perhaps most important is to smooth over the differences between different C implementations and define the parameters which drive most of the conditional compilations in the rest of SABRE. Secondly, it contains several groups of functionality that are used extensively throughout SABRE. Although C is highly standardized now, that has not always been the case. Roughlymore » speaking C compilers fall into three categories: ANSI standard; derivative of the Portable C Compiler (Kernighan and Ritchie); and the rest. SABRE has been successfully ported to many ANSI and PCC systems. It has never been successfully ported to a system in the last category. The reason is mainly that the ``standard`` C library supplied with such implementations is so far from true ANSI or PCC standard that SABRE would have to include its own version of the standard C library in order to work at all. Even with standardized compilers life is not dead simple. The ANSI standard leaves several crucial points ambiguous as ``implementation defined.`` Under these conditions one can find significant differences in going from one ANSI standard compiler to another. SCORE`s job is to include the requisite standard headers and ensure that certain key standard library functions exist and function correctly (there are bugs in the standard library functions supplied with some compilers) so that, to applications which include the SCORE header(s) and load with SCORE, all C implementations look the same.« less

SCORE user's manual

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

Brown, S.A.

SABrE is a set of tools to facilitate the development of portable scientific software and to visualize scientific data. As with most constructs, SABRE has a foundation. In this case that foundation is SCORE. SCORE (SABRE CORE) has two main functions. The first and perhaps most important is to smooth over the differences between different C implementations and define the parameters which drive most of the conditional compilations in the rest of SABRE. Secondly, it contains several groups of functionality that are used extensively throughout SABRE. Although C is highly standardized now, that has not always been the case. Roughlymore » speaking C compilers fall into three categories: ANSI standard; derivative of the Portable C Compiler (Kernighan and Ritchie); and the rest. SABRE has been successfully ported to many ANSI and PCC systems. It has never been successfully ported to a system in the last category. The reason is mainly that the standard'' C library supplied with such implementations is so far from true ANSI or PCC standard that SABRE would have to include its own version of the standard C library in order to work at all. Even with standardized compilers life is not dead simple. The ANSI standard leaves several crucial points ambiguous as implementation defined.'' Under these conditions one can find significant differences in going from one ANSI standard compiler to another. SCORE's job is to include the requisite standard headers and ensure that certain key standard library functions exist and function correctly (there are bugs in the standard library functions supplied with some compilers) so that, to applications which include the SCORE header(s) and load with SCORE, all C implementations look the same.« less

Reference standard space hippocampus labels according to the European Alzheimer's Disease Consortium-Alzheimer's Disease Neuroimaging Initiative harmonized protocol: Utility in automated volumetry.

PubMed

Wolf, Dominik; Bocchetta, Martina; Preboske, Gregory M; Boccardi, Marina; Grothe, Michel J

2017-08-01

A harmonized protocol (HarP) for manual hippocampal segmentation on magnetic resonance imaging (MRI) has recently been developed by an international European Alzheimer's Disease Consortium-Alzheimer's Disease Neuroimaging Initiative project. We aimed at providing consensual certified HarP hippocampal labels in Montreal Neurological Institute (MNI) standard space to serve as reference in automated image analyses. Manual HarP tracings on the high-resolution MNI152 standard space template of four expert certified HarP tracers were combined to obtain consensual bilateral hippocampus labels. Utility and validity of these reference labels is demonstrated in a simple atlas-based morphometry approach for automated calculation of HarP-compliant hippocampal volumes within SPM software. Individual tracings showed very high agreement among the four expert tracers (pairwise Jaccard indices 0.82-0.87). Automatically calculated hippocampal volumes were highly correlated (r L/R  = 0.89/0.91) with gold standard volumes in the HarP benchmark data set (N = 135 MRIs), with a mean volume difference of 9% (standard deviation 7%). The consensual HarP hippocampus labels in the MNI152 template can serve as a reference standard for automated image analyses involving MNI standard space normalization. Copyright © 2017 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

DLESE Teaching Box Pilot Project: Developing a Replicable Model for Collaboratively Creating Innovative Instructional Sequences Using Exemplary Resources in the Digital Library for Earth System Education (DLESE)

NASA Astrophysics Data System (ADS)

Weingroff, M.

2004-12-01

Before the advent of digital libraries, it was difficult for teachers to find suitable high-quality resources to use in their teaching. Digital libraries such as DLESE have eased the task by making high quality resources more easily accessible and providing search mechanisms that allow teachers to 'fine tune' the criteria over which they search. Searches tend to return lists of resources with some contextualizing information. However, teachers who are teaching 'out of discipline' or who have minimal training in science often need additional support to know how to use and sequence them. The Teaching Box Pilot Project was developed to address these concerns, bringing together educators, scientists, and instructional designers in a partnership to build an online framework to fully support innovative units of instruction about the Earth system. Each box integrates DLESE resources and activities, teaching tips, standards, concepts, teaching outcomes, reviews, and assessment information. Online templates and best practice guidelines are being developed that will enable teachers to create their own boxes or customize existing ones. Two boxes have been developed so far, one on weather for high school students, and one on the evidence for plate tectonics for middle schoolers. The project has met with significant enthusiasm and interest, and we hope to expand it by involving individual teachers, school systems, pre-service programs, and universities in the development and use of teaching boxes. A key ingredient in the project's success has been the close collaboration between the partners, each of whom has brought unique experiences, perspectives, knowledge, and skills to the project. This first effort involved teachers in the San Francisco Bay area, the University of California Museum of Paleontology, San Francisco State University, U.S. Geological Survey, and DLESE. This poster will allow participants to explore one of the teaching boxes. We will discuss how the boxes were developed, the conditions that engendered successful collaboration and high-quality results, lessons learned, and potential adaptations for networks of user communities, for example, in ocean education or seismology.

Transformation of Human Cathelicidin LL-37 into Selective, Stable, and Potent Antimicrobial Compounds

PubMed Central

2015-01-01

This Letter reports a family of novel antimicrobial compounds obtained by combining peptide library screening with structure-based design. Library screening led to the identification of a human LL-37 peptide resistant to chymotrypsin. This d-amino-acid-containing peptide template was active against Escherichia coli but not methicillin-resistant Staphylococcus aureus (MRSA). It possesses a unique nonclassic amphipathic structure with hydrophobic defects. By repairing the hydrophobic defects, the peptide (17BIPHE2) gained activity against the ESKAPE pathogens, including Enterococcus faecium, S. aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species. In vitro, 17BIPHE2 could disrupt bacterial membranes and bind to DNA. In vivo, the peptide prevented staphylococcal biofilm formation in a mouse model of catheter-associated infection. Meanwhile, it boosted the innate immune response to further combat the infection. Because these peptides are potent, cell-selective, and stable to several proteases, they may be utilized to combat one or more ESKAPE pathogens. PMID:25061850

Differential Gene Expression from Midguts of Refractory and Susceptible Lines of the Mosquito, Aedes aegypti, Infected with Dengue-2 Virus

PubMed Central

Barón, Olga L.; Ursic-Bedoya, Raul J.; Lowenberger, Carl A.; Ocampo, Clara B.

2010-01-01

Suppressive subtractive hybridization was used to evaluate the differential expression of midgut genes of feral populations of Aedes aegypti (Diptera: Culicidae) from Colombia that are naturally refractory or susceptible to Dengue-2 virus infection. A total of 165 differentially expressed sequence tags (ESTs) were identified in the subtracted libraries. The analysis showed a higher number of differentially expressed genes in the susceptible Ae. aegypti individuals than the refractory mosquitoes. The functional annotation of ESTs revealed a broad response in the susceptible library that included immune molecules, metabolic molecules and transcription factors. In the refractory strain, there was the presence of a trypsin inhibitor gene, which could play a role in the infection. These results serve as a template for more detailed studies aiming to characterize the genetic components of refractoriness, which in turn can be used to devise new approaches to combat transmission of dengue fever. PMID:20572793

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

PubMed

Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen; Pandurangan, Arun Prasad; Sahota, Harpal; Topf, Maya

2015-08-01

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

Template directed synthesis of plasmonic gold nanotubes with tunable IR absorbance.

PubMed

Bridges, Colin R; Schon, Tyler B; DiCarmine, Paul M; Seferos, Dwight S

2013-04-01

A nearly parallel array of pores can be produced by anodizing aluminum foils in acidic environments. Applications of anodic aluminum oxide (AAO) membranes have been under development since the 1990's and have become a common method to template the synthesis of high aspect ratio nanostructures, mostly by electrochemical growth or pore-wetting. Recently, these membranes have become commercially available in a wide range of pore sizes and densities, leading to an extensive library of functional nanostructures being synthesized from AAO membranes. These include composite nanorods, nanowires and nanotubes made of metals, inorganic materials or polymers. Nanoporous membranes have been used to synthesize nanoparticle and nanotube arrays that perform well as refractive index sensors, plasmonic biosensors, or surface enhanced Raman spectroscopy (SERS) substrates, as well as a wide range of other fields such as photo-thermal heating, permselective transport, catalysis, microfluidics, and electrochemical sensing. Here, we report a novel procedure to prepare gold nanotubes in AAO membranes. Hollow nanostructures have potential application in plasmonic and SERS sensing, and we anticipate these gold nanotubes will allow for high sensitivity and strong plasmon signals, arising from decreased material dampening.

Application of complex macromolecular architectures for advanced microelectronic materials.

PubMed

Hedrick, James L; Magbitang, Teddie; Connor, Eric F; Glauser, Thierry; Volksen, Willi; Hawker, Craig J; Lee, Victor Y; Miller, Robert D

2002-08-02

The distinctive features of well-defined, three-dimensional macromolecules with topologies designed to enhance solubility and amplify end-group functionality facilitated nanophase morphologies in mixtures with organosilicates and ultimately nanoporous organosilicate networks. Novel macromolecular architectures including dendritic and star-shaped polymers and organic nanoparticles were prepared by a modular approach from several libraries of building blocks including various generations of dendritic initiators and dendrons, selectively placed to amplify functionality and/or arm number, coupled with living polymerization techniques. Mixtures of an organosilicate and the macromolecular template were deposited, cured, and the phase separation of the organic component, organized the vitrifying organosilicate into nanostructures. Removal of the sacrificial macromolecular template, also denoted as porogen, by thermolysis, yielded the desired nanoporous organosilicate, and the size scale of phase separation was strongly dependent on the chain topology. These materials were designed for use as interlayer, ultra-low dielectric insulators for on-chip applications with dielectric constant values as low as 1.5. The porogen design, chemistry and role of polymer architecture on hybrid and pore morphology will be emphasized.

Using archetypes for defining CDA templates.

PubMed

Moner, David; Moreno, Alberto; Maldonado, José A; Robles, Montserrat; Parra, Carlos

2012-01-01

While HL7 CDA is a widely adopted standard for the documentation of clinical information, the archetype approach proposed by CEN/ISO 13606 and openEHR is gaining recognition as a means of describing domain models and medical knowledge. This paper describes our efforts in combining both standards. Using archetypes as an alternative for defining CDA templates permit new possibilities all based on the formal nature of archetypes and their ability to merge into the same artifact medical knowledge and technical requirements for semantic interoperability of electronic health records. We describe the process followed for the normalization of existing legacy data in a hospital environment, from the importation of the HL7 CDA model into an archetype editor, the definition of CDA archetypes and the application of those archetypes to obtain normalized CDA data instances.

Annual Program, 1987. Texas State Library.

ERIC Educational Resources Information Center

Texas State Library, Austin.

This report provides information related to the Texas State Library's fiscal year 1987 Library Services and Construction Act (LSCA) Public Law 84-597, as amended state-administered program. Information is included on: (1) Standard Form 424 for federal assistance; (2) fiscal breakdowns of estimated expenditures; (3) specific requirements for…

Virtual Reference Transcript Analysis: A Few Models.

ERIC Educational Resources Information Center

Smyth, Joanne

2003-01-01

Describes the introduction of virtual, or digital, reference service at the University of New Brunswick libraries. Highlights include analyzing transcripts from LIVE (Library Information in a Virtual Environment); reference question types; ACRL (Association of College and Research Libraries) information literacy competency standards; and the Big 6…

5 CFR 7701.101 - Purpose.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Administrative Personnel INSTITUTE OF MUSEUM AND LIBRARY SERVICES SUPPLEMENTAL STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE INSTITUTE OF MUSEUM AND LIBRARY SERVICES § 7701.101 Purpose. In accordance with 5 CFR 2635.105, the regulations of this part apply to employees of the Institute of Museum and Library Services...

5 CFR 7701.101 - Purpose.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Administrative Personnel INSTITUTE OF MUSEUM AND LIBRARY SERVICES SUPPLEMENTAL STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE INSTITUTE OF MUSEUM AND LIBRARY SERVICES § 7701.101 Purpose. In accordance with 5 CFR 2635.105, the regulations of this part apply to employees of the Institute of Museum and Library Services...

5 CFR 7701.101 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Administrative Personnel INSTITUTE OF MUSEUM AND LIBRARY SERVICES SUPPLEMENTAL STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE INSTITUTE OF MUSEUM AND LIBRARY SERVICES § 7701.101 Purpose. In accordance with 5 CFR 2635.105, the regulations of this part apply to employees of the Institute of Museum and Library Services...

5 CFR 7701.101 - Purpose.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Administrative Personnel INSTITUTE OF MUSEUM AND LIBRARY SERVICES SUPPLEMENTAL STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE INSTITUTE OF MUSEUM AND LIBRARY SERVICES § 7701.101 Purpose. In accordance with 5 CFR 2635.105, the regulations of this part apply to employees of the Institute of Museum and Library Services...

5 CFR 7701.101 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Administrative Personnel INSTITUTE OF MUSEUM AND LIBRARY SERVICES SUPPLEMENTAL STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE INSTITUTE OF MUSEUM AND LIBRARY SERVICES § 7701.101 Purpose. In accordance with 5 CFR 2635.105, the regulations of this part apply to employees of the Institute of Museum and Library Services...

Visual Literacy Standards in Higher Education: New Opportunities for Libraries and Student Learning

ERIC Educational Resources Information Center

Hattwig, Denise; Bussert, Kaila; Medaille, Ann; Burgess, Joanna

2013-01-01

Visual literacy is essential for 21st century learners. Across the higher education curriculum, students are being asked to use and produce images and visual media in their academic work, and they must be prepared to do so. The Association of College and Research Libraries has published the "Visual Literacy Competency Standards for Higher…

An Analysis of the Impact of Federated Search Products on Library Instruction Using the ACRL Standards

ERIC Educational Resources Information Center

Cox, Christopher

2006-01-01

Federated search products are becoming more and more prevalent in academic libraries. What are the implications of this phenomenon for instruction librarians? An analysis of federated search products using the "Information Literacy Competency Standards for Higher Education" and a thorough review of the literature offer insight concerning whether…

40 CFR 75.6 - Incorporation by reference.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., phone: 610-832-9585, http://www.astm.org/DIGITAL_LIBRARY/index.shtml. (1) ASTM D129-00, Standard Test... Information Reference Unit of the U.S. EPA, 401 M St., SW., Washington, DC and at the Library (MD-35), U.S... D4052-96 (Reapproved 2002), Standard Test Method for Density and Relative Density of Liquids by Digital...

40 CFR 75.6 - Incorporation by reference.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., phone: 610-832-9585, http://www.astm.org/DIGITAL_LIBRARY/index.shtml. (1) ASTM D129-00, Standard Test... Information Reference Unit of the U.S. EPA, 401 M St., SW., Washington, DC and at the Library (MD-35), U.S... D4052-96 (Reapproved 2002), Standard Test Method for Density and Relative Density of Liquids by Digital...

40 CFR 75.6 - Incorporation by reference.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., phone: 610-832-9585, http://www.astm.org/DIGITAL_LIBRARY/index.shtml. (1) ASTM D129-00, Standard Test... Information Reference Unit of the U.S. EPA, 401 M St., SW., Washington, DC and at the Library (MD-35), U.S... D4052-96 (Reapproved 2002), Standard Test Method for Density and Relative Density of Liquids by Digital...

40 CFR 75.6 - Incorporation by reference.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., phone: 610-832-9585, http://www.astm.org/DIGITAL_LIBRARY/index.shtml. (1) ASTM D129-00, Standard Test... Information Reference Unit of the U.S. EPA, 401 M St., SW., Washington, DC and at the Library (MD-35), U.S... D4052-96 (Reapproved 2002), Standard Test Method for Density and Relative Density of Liquids by Digital...

State of the Nation: A Coast-to-Coast Survey of the Latest Certification Standards

ERIC Educational Resources Information Center

Thomas, Margie

2006-01-01

This article presents the results from a survey that investigated the latest requirements and certification standards for school librarians in each state. In the survey, 42 report they require certification for K-12 library media specialists, meaning that school library candidates must have a bachelor's degree including coursework designed to…

Hospital library resources in Massachusetts: data collection and analysis.

PubMed

McGrath, P J

1980-10-01

Hospitals in the Commonwealth of Massachusetts were surveyed to establish some ranges and baseline statistics for hospital medical information resources. The data were evaluated in terms of theoretical compliance with the Joint Commission on Accreditation of Hospitals standards as well as the more specific proposed appendices to the Canadian Standards for Hospital Libraries. The study quantifies hospital library resources and services in a state with a substantial number of acute care facilities. Of the study universe, 67.6% were judged as meeting either the revised JCAH or the Canadian criteria. The central finding is that the 100- to 299-bed institutions reflect a significant number of deficiencies when evaluated against either quantitative or nonquantitative standards. Further areas of study are suggested.

Evaluation of MRI and cannabinoid type 1 receptor PET templates constructed using DARTEL for spatial normalization of rat brains

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

Kronfeld, Andrea; Müller-Forell, Wibke; Buchholz, Hans-Georg

Purpose: Image registration is one prerequisite for the analysis of brain regions in magnetic-resonance-imaging (MRI) or positron-emission-tomography (PET) studies. Diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL) is a nonlinear, diffeomorphic algorithm for image registration and construction of image templates. The goal of this small animal study was (1) the evaluation of a MRI and calculation of several cannabinoid type 1 (CB1) receptor PET templates constructed using DARTEL and (2) the analysis of the image registration accuracy of MR and PET images to their DARTEL templates with reference to analytical and iterative PET reconstruction algorithms. Methods: Five male Sprague Dawleymore » rats were investigated for template construction using MRI and [{sup 18}F]MK-9470 PET for CB1 receptor representation. PET images were reconstructed using the algorithms filtered back-projection, ordered subset expectation maximization in 2D, and maximum a posteriori in 3D. Landmarks were defined on each MR image, and templates were constructed under different settings, i.e., based on different tissue class images [gray matter (GM), white matter (WM), and GM + WM] and regularization forms (“linear elastic energy,” “membrane energy,” and “bending energy”). Registration accuracy for MRI and PET templates was evaluated by means of the distance between landmark coordinates. Results: The best MRI template was constructed based on gray and white matter images and the regularization form linear elastic energy. In this case, most distances between landmark coordinates were <1 mm. Accordingly, MRI-based spatial normalization was most accurate, but results of the PET-based spatial normalization were quite comparable. Conclusions: Image registration using DARTEL provides a standardized and automatic framework for small animal brain data analysis. The authors were able to show that this method works with high reliability and validity. Using DARTEL templates together with nonlinear registration algorithms allows for accurate spatial normalization of combined MRI/PET or PET-only studies.« less

Design for Progress. A Report of the Workshop in School Library Quarters and Equipment, July 9 to 20, 1962.

ERIC Educational Resources Information Center

Strohecker, Edwin C., Ed.

Significant ideas brought out in the workshop include--(1) that the library is a necessary part of the whole relational structure in education, and (2) that changes in educational programs and methods call for new library planning standards; a library should be able to provide science facilities, audiovisual materials, and a variety of group-work…

Systematic Heuristic Evaluation of Computerized Consultation Order Templates: Clinicians' and Human Factors Engineers' Perspectives.

PubMed

Savoy, April; Patel, Himalaya; Flanagan, Mindy E; Weiner, Michael; Russ, Alissa L

2017-08-01

We assessed the usability of consultation order templates and identified problems to prioritize in design efforts for improving referral communication. With a sample of 26 consultation order templates, three evaluators performed a usability heuristic evaluation. The evaluation used 14 domain-independent heuristics and the following three supplemental references: 1 new domain-specific heuristic, 6 usability goals, and coded clinicians' statements regarding ease of use for 10 sampled templates. Evaluators found 201 violations, a mean of 7.7 violations per template. Minor violations outnumbered major violations almost twofold, 115 (57%) to 62 (31%). Approximately 68% of violations were linked to 5 heuristics: aesthetic and minimalist design (17%), error prevention (16%), consistency and standards (14%), recognition rather than recall (11%), and meet referrers' information needs (10%). Severe violations were attributed mostly to meet referrers' information needs and recognition rather than recall. Recorded violations yielded potential negative consequences for efficiency, effectiveness, safety, learnability, and utility. Evaluators and clinicians demonstrated 80% agreement in usability assessment. Based on frequency and severity of usability heuristic violations, the consultation order templates reviewed may impede clinical efficiency and risk patient safety. Results support the following design considerations: communicate consultants' requirements, facilitate information seeking, and support communication. While the most frequent heuristic violations involved interaction design and presentation, the most severe violations lacked information desired by referring clinicians. Violations related to templates' inability to support referring clinicians' information needs had the greatest potential negative impact on efficiency and safety usability goals. Heuristics should be prioritized in future design efforts.

Novel Human Intervertebral Disc Strain Template to Quantify Regional Three-Dimensional Strains in a Population and Compare to Internal Strains Predicted by a Finite Element Model

PubMed Central

Showalter, Brent L.; DeLucca, John F.; Peloquin, John M.; Cortes, Daniel H.; Yoder, Jonathon H.; Jacobs, Nathan T.; Wright, Alexander C.; Gee, James C.; Vresilovic, Edward J.; Elliott, Dawn M.

2017-01-01

Tissue strain is an important indicator of mechanical function, but is difficult to noninvasively measure in the intervertebral disc. The objective of this study was to generate a disc strain template, a 3D average of disc strain, of a group of human L4–L5 discs loaded in axial compression. To do so, magnetic resonance images of uncompressed discs were used to create an average disc shape. Next, the strain tensors were calculated pixel-wise by using a previously developed registration algorithm. Individual disc strain tensor components were then transformed to the template space and averaged to create the disc strain template. The strain template reduced individual variability while highlighting group trends. For example, higher axial and circumferential strains were present in the lateral and posterolateral regions of the disc, which may lead to annular tears. This quantification of group-level trends in local 3D strain is a significant step forward in the study of disc biomechanics. These trends were compared to a finite element model that had been previously validated against the disc-level mechanical response. Depending on the strain component, 81–99% of the regions within the finite element model had calculated strains within one standard deviation of the template strain results. The template creation technique provides a new measurement technique useful for a wide range of studies, including more complex loading conditions, the effect of disc pathologies and degeneration, damage mechanisms, and design and evaluation of treatments. PMID:26694516

A pilot study to measure marks in children with cerebral palsy using a novel measurement template.

PubMed

Bennett, T; Jellinek, D; Bennett, M

2013-11-01

The primary aim of this pilot study was to trial a method of assessing bruises in a population of disabled children. If the method was found to be sufficiently robust it would be our intention to undertaking a more extensive observational study. Less is known about normal bruising patterns in children with disability than in those without. It is important that the method used to assess bruising is objective and repeatable. In an effort to define and improve repeatability, we employed a novel bruise measurement template which was printed onto transparent acetate sheets. Twenty primary school age children, the majority of whom were non-ambulant and severely disabled with cerebral palsy, underwent full skin examination. The template was used to assess any bruises seen. A comparison was then made between measurements made by experienced paediatricians using the template and using a standard tape measure on a series of bruise images in 25 photographs. The majority of children in our pilot were found to have bruises, with one child having 6 and one 7 bruises. This comparative study showed that the two techniques had a very similar precision and that the template was easy to use. Greater precision would require a tighter measurement protocol, whether with a template or a tape measure. Further evaluation of the application of such a template would be worthwhile. We would suggest that our finding of some bruising in this population of disabled children is borne in mind whenever bruising is found in a non-ambulant child. © 2012 John Wiley & Sons Ltd.

Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides.

PubMed

Kuwahara, Masayasu; Obika, Satoshi; Nagashima, Jun-ichi; Ohta, Yuki; Suto, Yoshiyuki; Ozaki, Hiroaki; Sawai, Hiroaki; Imanishi, Takeshi

2008-08-01

In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.

Work of the Web Weavers: Web Development in Academic Libraries

ERIC Educational Resources Information Center

Bundza, Maira; Vander Meer, Patricia Fravel; Perez-Stable, Maria A.

2009-01-01

Although the library's Web site has become a standard tool for seeking information and conducting research in academic institutions, there are a variety of ways libraries approach the often challenging--and sometimes daunting--process of Web site development and maintenance. Three librarians at Western Michigan University explored issues related…

Library Statistical Data Base Formats and Definitions.

ERIC Educational Resources Information Center

Jones, Dennis; And Others

Represented are the detailed set of data structures relevant to the categorization of information, terminology, and definitions employed in the design of the library statistical data base. The data base, or management information system, provides administrators with a framework of information and standardized data for library management, planning,…

Opening up Library Automation Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Throughout the history of library automation, the author has seen a steady advancement toward more open systems. In the early days of library automation, when proprietary systems dominated, the need for standards was paramount since other means of inter-operability and data exchange weren't possible. Today's focus on Application Programming…

School Libraries and Science Achievement: A View from Michigan's Middle Schools

ERIC Educational Resources Information Center

Mardis, Marcia

2007-01-01

If strong school library media centers (SLMCs) positively impact middle school student reading achievement, as measured on standardized tests, are they also beneficial for middle school science achievement? To answer this question, the researcher built upon the statistical analyses used in previous school library impact studies with qualitative…

Scaling the Library Collection; A Simplified Method for Weighing the Variables

ERIC Educational Resources Information Center

Vagianos, Louis

1973-01-01

On the assumption that the physical properties of any information stock (book, etc.) offer the best foundation on which to develop satisfactory measurements for assessing library operations and developing library procedures, weight is suggested as the most useful variable for assessment and standardization. Advantages of this approach are…

A Resource Guide for Teachers.

ERIC Educational Resources Information Center

Texas State Library, Austin. Div. for the Blind and Physically Handicapped.

The Texas State Library provides services to persons unable to read standard print due to blindness or other visual impairments, including a wide range of large print materials, braille, and recordings. The library also coordinates a reading machine program incorporating 70 sites in public and academic libraries and provides classrooms with books,…

History of Medford School District Library Media Centers.

ERIC Educational Resources Information Center

Wisely, Steve

2002-01-01

Describes the development of library media centers, programs, and staff at the Medford School District (Oregon). Information from the standards and research used to define roles and responsibilities is summarized, and relevant Oregon state educational organizations are listed. Some of the results of the district's well-defined library programs and…

Principles and application of antibody libraries for infectious diseases.

PubMed

Lim, Bee Nar; Tye, Gee Jun; Choong, Yee Siew; Ong, Eugene Boon Beng; Ismail, Asma; Lim, Theam Soon

2014-12-01

Antibodies have been used efficiently for the treatment and diagnosis of many diseases. Recombinant antibody technology allows the generation of fully human antibodies. Phage display is the gold standard for the production of human antibodies in vitro. To generate monoclonal antibodies by phage display, the generation of antibody libraries is crucial. Antibody libraries are classified according to the source where the antibody gene sequences were obtained. The most useful library for infectious diseases is the immunized library. Immunized libraries would allow better and selective enrichment of antibodies against disease antigens. The antibodies generated from these libraries can be translated for both diagnostic and therapeutic applications. This review focuses on the generation of immunized antibody libraries and the potential applications of the antibodies derived from these libraries.

Picture This... Developing Standards for Electronic Images at the National Library of Medicine

PubMed Central

Masys, Daniel R.

1990-01-01

New computer technologies have made it feasible to represent, store, and communicate high resolution biomedical images via electronic means. Traditional two dimensional medical images such as those on printed pages have been supplemented by three dimensional images which can be rendered, rotated, and “dissected” from any point of view. The library of the future will provide electronic access not only to words and numbers, but to pictures, sounds, and other nontextual information. There currently exist few widely-accepted standards for the representation and communication of complex images, yet such standards will be critical to the feasibility and usefulness of digital image collections in the life sciences. The National Library of Medicine is embarked on a project to develop a complete digital volumetric representation of an adult human male and female. This “Visible Human Project” will address the issue of standards for computer representation of biological structure.

Combining Open-Source Packages for Planetary Exploration

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2015-04-01

The science planning of the ESA Rosetta mission has presented challenges which were addressed with combining various open-source software packages, such as the SPICE toolkit, the Python language and the Web graphics library three.js. The challenge was to compute certain parameters from a pool of trajectories and (possible) attitudes to describe the behaviour of the spacecraft. To be able to do this declaratively and efficiently, a C library was implemented that allows to interface the SPICE toolkit for geometrical computations from the Python language and process as much data as possible during one subroutine call. To minimise the lines of code one has to write special care was taken to ensure that the bindings were idiomatic and thus integrate well into the Python language and ecosystem. When done well, this very much simplifies the structure of the code and facilitates the testing for correctness by automatic test suites and visual inspections. For rapid visualisation and confirmation of correctness of results, the geometries were visualised with the three.js library, a popular Javascript library for displaying three-dimensional graphics in a Web browser. Programmatically, this was achieved by generating data files from SPICE sources that were included into templated HTML and displayed by a browser, thus made easily accessible to interested parties at large. As feedback came and new ideas were to be explored, the authors benefited greatly from the design of the Python-to-SPICE library which allowed the expression of algorithms to be concise and easier to communicate. In summary, by combining several well-established open-source tools, we were able to put together a flexible computation and visualisation environment that helped communicate and build confidence in planning ideas.