[cDNA library construction from panicle meristem of finger millet].

PubMed

Radchuk, V; Pirko, Ia V; Isaenkov, S V; Emets, A I; Blium, Ia B

2014-01-01

The protocol for production of full-size cDNA using SuperScript Full-Length cDNA Library Construction Kit II (Invitrogen) was tested and high quality cDNA library from meristematic tissue of finger millet panicle (Eleusine coracana (L.) Gaertn) was created. The titer of obtained cDNA library comprised 3.01 x 10(5) CFU/ml in avarage. In average the length of cDNA insertion consisted about 1070 base pairs, the effectivity of cDNA fragment insertions--99.5%. The selective sequencing of cDNA clones from created library was performed. The sequences of cDNA clones were identified with usage of BLAST-search. The results of cDNA library analysis and selective sequencing represents prove good functionality and full length character of inserted cDNA clones. Obtained cDNA library from meristematic tissue of finger millet panicle represents good and valuable source for isolation and identification of key genes regulating metabolism and meristematic development and for mining of new molecular markers to conduct out high quality genetic investigations and molecular breeding as well.

The Use of EST Expression Matrixes for the Quality Control of Gene Expression Data

PubMed Central

Milnthorpe, Andrew T.; Soloviev, Mikhail

2012-01-01

EST expression profiling provides an attractive tool for studying differential gene expression, but cDNA libraries' origins and EST data quality are not always known or reported. Libraries may originate from pooled or mixed tissues; EST clustering, EST counts, library annotations and analysis algorithms may contain errors. Traditional data analysis methods, including research into tissue-specific gene expression, assume EST counts to be correct and libraries to be correctly annotated, which is not always the case. Therefore, a method capable of assessing the quality of expression data based on that data alone would be invaluable for assessing the quality of EST data and determining their suitability for mRNA expression analysis. Here we report an approach to the selection of a small generic subset of 244 UniGene clusters suitable for identification of the tissue of origin for EST libraries and quality control of the expression data using EST expression information alone. We created a small expression matrix of UniGene IDs using two rounds of selection followed by two rounds of optimisation. Our selection procedures differ from traditional approaches to finding “tissue-specific” genes and our matrix yields consistency high positive correlation values for libraries with confirmed tissues of origin and can be applied for tissue typing and quality control of libraries as small as just a few hundred total ESTs. Furthermore, we can pick up tissue correlations between related tissues e.g. brain and peripheral nervous tissue, heart and muscle tissues and identify tissue origins for a few libraries of uncharacterised tissue identity. It was possible to confirm tissue identity for some libraries which have been derived from cancer tissues or have been normalised. Tissue matching is affected strongly by cancer progression or library normalisation and our approach may potentially be applied for elucidating the stage of normalisation in normalised libraries or for cancer staging. PMID:22412959

Construction of high quality Gateway™ entry libraries and their application to yeast two-hybrid for the monocot model plant Brachypodium distachyon.

PubMed

Cao, Shuanghe; Siriwardana, Chamindika L; Kumimoto, Roderick W; Holt, Ben F

2011-05-19

Monocots, especially the temperate grasses, represent some of the most agriculturally important crops for both current food needs and future biofuel development. Because most of the agriculturally important grass species are difficult to study (e.g., they often have large, repetitive genomes and can be difficult to grow in laboratory settings), developing genetically tractable model systems is essential. Brachypodium distachyon (hereafter Brachypodium) is an emerging model system for the temperate grasses. To fully realize the potential of this model system, publicly accessible discovery tools are essential. High quality cDNA libraries that can be readily adapted for multiple downstream purposes are a needed resource. Additionally, yeast two-hybrid (Y2H) libraries are an important discovery tool for protein-protein interactions and are not currently available for Brachypodium. We describe the creation of two high quality, publicly available Gateway™ cDNA entry libraries and their derived Y2H libraries for Brachypodium. The first entry library represents cloned cDNA populations from both short day (SD, 8/16-h light/dark) and long day (LD, 20/4-h light/dark) grown plants, while the second library was generated from hormone treated tissues. Both libraries have extensive genome coverage (~5 × 107 primary clones each) and average clone lengths of ~1.5 Kb. These entry libraries were then used to create two recombination-derived Y2H libraries. Initial proof-of-concept screens demonstrated that a protein with known interaction partners could readily re-isolate those partners, as well as novel interactors. Accessible community resources are a hallmark of successful biological model systems. Brachypodium has the potential to be a broadly useful model system for the grasses, but still requires many of these resources. The Gateway™ compatible entry libraries created here will facilitate studies for multiple user-defined purposes and the derived Y2H libraries can be immediately applied to large scale screening and discovery of novel protein-protein interactions. All libraries are freely available for distribution to the research community.

Introducing the National Library for Health Skin Conditions Specialist Library.

PubMed

Grindlay, Douglas; Boulos, Maged N Kamel; Williams, Hywel C

2005-04-26

This paper introduces the new National Library for Health Skin Conditions Specialist Library http://www.library.nhs.uk/skin. The aims, scope and audience of the new NLH Skin Conditions Specialist Library, and the composition and functions of its core Project Team, Editorial Team and Stakeholders Group are described. The Library's collection building strategy, resource and information types, editorial policies, quality checklist, taxonomy for content indexing, organisation and navigation, and user interface are all presented in detail. The paper also explores the expected impact and utility of the new Library, as well as some possible future directions for further development. The Skin Conditions Specialist Library is not just another new Web site that dermatologists might want to add to their Internet favourites then forget about it. It is intended to be a practical, "one-stop shop" dermatology information service for everyday practical use, offering high quality, up-to-date resources, and adopting robust evidence-based and knowledge management approaches.

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

PubMed Central

LeProust, Emily M.; Peck, Bill J.; Spirin, Konstantin; McCuen, Heather Brummel; Moore, Bridget; Namsaraev, Eugeni; Caruthers, Marvin H.

2010-01-01

We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology). PMID:20308161

Shoestring Digital Library: If Existing Digital Library Software Doesn't Suit Your Needs, Create Your Own

ERIC Educational Resources Information Center

Weber, Jonathan

2006-01-01

Creating a digital library might seem like a task best left to a large research collection with a vast staff and generous budget. However, tools for successfully creating digital libraries are getting easier to use all the time. The explosion of people creating content for the web has led to the availability of many high-quality applications and…

High-throughput continuous hydrothermal synthesis of an entire nanoceramic phase diagram.

PubMed

Weng, Xiaole; Cockcroft, Jeremy K; Hyett, Geoffrey; Vickers, Martin; Boldrin, Paul; Tang, Chiu C; Thompson, Stephen P; Parker, Julia E; Knowles, Jonathan C; Rehman, Ihtesham; Parkin, Ivan; Evans, Julian R G; Darr, Jawwad A

2009-01-01

A novel High-Throughput Continuous Hydrothermal (HiTCH) flow synthesis reactor was used to make directly and rapidly a 66-sample nanoparticle library (entire phase diagram) of nanocrystalline Ce(x)Zr(y)Y(z)O(2-delta) in less than 12 h. High resolution PXRD data were obtained for the entire heat-treated library (at 1000 degrees C/1 h) in less than a day using the new robotic beamline I11, located at Diamond Light Source (DLS). This allowed Rietveld-quality powder X-ray diffraction (PXRD) data collection of the entire 66-sample library in <1 day. Consequently, the authors rapidly mapped out phase behavior and sintering behaviors for the entire library. Out of the entire 66-sample heat-treated library, the PXRD data suggests that 43 possess the fluorite structure, of which 30 (out of 36) are ternary compositions. The speed, quantity and quality of data obtained by our new approach, offers an exciting new development which will allow structure-property relationships to be accessed for nanoceramics in much shorter time periods.

The Gender and Science Digital Library: Affecting Student Achievement in Science.

ERIC Educational Resources Information Center

Nair, Sarita

2003-01-01

Describes the Gender and Science Digital Library (GSDL), an online collection of high-quality, interactive science resources that are gender-fair, inclusive, and engaging to students. Considers use by teachers and school library media specialists to encourage girls to enter careers in science, technology, engineering, and math (STEM). (LRW)

Introducing the National Library for Health Skin Conditions Specialist Library

PubMed Central

Grindlay, Douglas; Boulos, Maged N Kamel; Williams, Hywel C

2005-01-01

Background This paper introduces the new National Library for Health Skin Conditions Specialist Library . Description The aims, scope and audience of the new NLH Skin Conditions Specialist Library, and the composition and functions of its core Project Team, Editorial Team and Stakeholders Group are described. The Library's collection building strategy, resource and information types, editorial policies, quality checklist, taxonomy for content indexing, organisation and navigation, and user interface are all presented in detail. The paper also explores the expected impact and utility of the new Library, as well as some possible future directions for further development. Conclusion The Skin Conditions Specialist Library is not just another new Web site that dermatologists might want to add to their Internet favourites then forget about it. It is intended to be a practical, "one-stop shop" dermatology information service for everyday practical use, offering high quality, up-to-date resources, and adopting robust evidence-based and knowledge management approaches. PMID:15854224

Do quality improvement systems improve health library services? A systematic review.

PubMed

Gray, Hannah; Sutton, Gary; Treadway, Victoria

2012-09-01

A turbulent financial and political climate requires health libraries to be more accountable than ever. Quality improvement systems are widely considered a 'good thing to do', but do they produce useful outcomes that can demonstrate value? To undertake a systematic review to identify which aspects of health libraries are being measured for quality, what tools are being used and what outcomes are reported following utilisation of quality improvement systems. Many health libraries utilise quality improvement systems without translating the data into service improvements. Included studies demonstrate that quality improvement systems produce valuable outcomes including a positive impact on strategic planning, promotion, new and improved services and staff development. No impact of quality improvement systems on library users or patients is reported in the literature. The literature in this area is sparse and requires updating. We recommend further primary research is conducted in health libraries focusing upon the outcomes of utilising quality improvement systems. An exploration of quality improvement systems in other library sectors may also provide valuable insight for health libraries. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

Construction of high-quality Caco-2 three-frame cDNA library and its application to yeast two-hybrid for the human astrovirus protein-protein interaction.

PubMed

Zhao, Wei; Li, Xin; Liu, Wen-Hui; Zhao, Jian; Jin, Yi-Ming; Sui, Ting-Ting

2014-09-01

Human epithelial colorectal adenocarcinoma (Caco-2) cells are widely used as an in vitro model of the human small intestinal mucosa. Caco-2 cells are host cells of the human astrovirus (HAstV) and other enteroviruses. High quality cDNA libraries are pertinent resources and critical tools for protein-protein interaction research, but are currently unavailable for Caco-2 cells. To construct a three-open reading frame, full length-expression cDNA library from the Caco-2 cell line for application to HAstV protein-protein interaction screening, total RNA was extracted from Caco-2 cells. The switching mechanism at the 5' end of the RNA transcript technique was used for cDNA synthesis. Double-stranded cDNA was digested by Sfi I and ligated to reconstruct a pGADT7-Sfi I three-frame vector. The ligation mixture was transformed into Escherichia coli HST08 premium electro cells by electroporation to construct the primary cDNA library. The library capacity was 1.0×10(6)clones. Gel electrophoresis results indicated that the fragments ranged from 0.5kb to 4.2kb. Randomly picked clones show that the recombination rate was 100%. The three-frame primary cDNA library plasmid mixture (5×10(5)cfu) was also transformed into E. coli HST08 premium electro cells, and all clones were harvested to amplify the cDNA library. To detect the sufficiency of the cDNA library, HAstV capsid protein as bait was screened and tested against the Caco-2 cDNA library by a yeast two-hybrid (Y2H) system. A total of 20 proteins were found to interact with the capsid protein. These results showed that a high-quality three-frame cDNA library from Caco-2 cells was successfully constructed. This library was efficient for the application to the Y2H system, and could be used for future research. Copyright © 2014 Elsevier B.V. All rights reserved.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

PubMed

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

A Collaborative Inquiry into Museum and Library Early Learning Services

ERIC Educational Resources Information Center

Sirinides, Phil; Fink, Ryan; DuBois, Tesla

2016-01-01

As states, cities, and communities take a more active role in ensuring that all children have access to high quality experiences and opportunities to learn, many are looking to museums and libraries as part of the early childhood education system. Museums and libraries can play a critical role in these efforts, and there is clear momentum and…

Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning.

PubMed

Lehtonen, Soili I; Taskinen, Barbara; Ojala, Elina; Kukkurainen, Sampo; Rahikainen, Rolle; Riihimäki, Tiina A; Laitinen, Olli H; Kulomaa, Markku S; Hytönen, Vesa P

2015-01-01

Efficient and robust subcloning is essential for the construction of high-diversity DNA libraries in the field of directed evolution. We have developed a more efficient method for the subcloning of DNA-shuffled libraries by employing recombination cloning (Gateway). The Gateway cloning procedure was performed directly after the gene reassembly reaction, without additional purification and amplification steps, thus simplifying the conventional DNA shuffling protocols. Recombination-based cloning, directly from the heterologous reassembly reaction, conserved the high quality of the library and reduced the time required for the library construction. The described method is generally compatible for the construction of DNA-shuffled gene libraries. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Construction of CRISPR Libraries for Functional Screening.

PubMed

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

2018-01-01

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

Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata.

PubMed

Gao, Jin-Xin; Jing, Jing; Yu, Chuan-Jin; Chen, Jie

2015-06-01

Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×10(5) transformants/3 μg pGADT7-Rec. The titer of the primary cDNA library was 2.5×10(8) cfu/mL. The numbers for the cDNA library was 2.46×10(5). Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.

PubMed

Shave, Steven; Mann, Stefan; Koszela, Joanna; Kerr, Alastair; Auer, Manfred

2018-01-01

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

Amino acid substitutions in random mutagenesis libraries: lessons from analyzing 3000 mutations.

PubMed

Zhao, Jing; Frauenkron-Machedjou, Victorine Josiane; Kardashliev, Tsvetan; Ruff, Anna Joëlle; Zhu, Leilei; Bocola, Marco; Schwaneberg, Ulrich

2017-04-01

The quality of amino acid substitution patterns in random mutagenesis libraries is decisive for the success in directed evolution campaigns. In this manuscript, we provide a detailed analysis of the amino acid substitutions by analyzing 3000 mutations of three random mutagenesis libraries (1000 mutations each; epPCR with a low-mutation and a high-mutation frequency and SeSaM-Tv P/P) employing lipase A from Bacillus subtilis (bsla). A comparison of the obtained numbers of beneficial variants in the mentioned three random mutagenesis libraries with a site saturation mutagenesis (SSM) (covering the natural diversity at each amino acid position of BSLA) concludes the diversity analysis. Seventy-six percent of the SeSaM-Tv P/P-generated substitutions yield chemically different amino acid substitutions compared to 64% (epPCR-low) and 69% (epPCR-high). Unique substitutions from one amino acid to others are termed distinct amino acid substitutions. In the SeSaM-Tv P/P library, 35% of all theoretical distinct amino acid substitutions were found in the 1000 mutation library compared to 25% (epPCR-low) and 26% (epPCR-high). Thirty-six percent of distinct amino acid substitutions found in SeSaM-Tv P/P were unobtainable by epPCR-low. Comparison with the SSM library showed that epPCR-low covers 15%, epPCR-high 18%, and SeSaM-Tv P/P 21% of obtainable beneficial amino acid positions. In essence, this study provides first insights on the quality of epPCR and SeSaM-Tv P/P libraries in terms of amino acid substitutions, their chemical differences, and the number of obtainable beneficial amino acid positions.

The contribution of hospital library information services to clinical care: a study in eight hospitals.

PubMed Central

King, D N

1987-01-01

Hospital health sciences libraries represent, for the vast majority of health professionals, the most accessible source for library information and services. Most health professionals do not have available the specialized services of a clinical medical librarian, and rely instead upon general information services for their case-related information needs. The ability of the hospital library to meet these needs and the impact of the information on quality patient care have not been previously examined. A study was conducted in eight hospitals in the Chicago area as a quality assurance project. A total of 176 physicians, nurses, and other health professionals requested information from their hospital libraries related to a current case or clinical situation. They then assessed the quality of information received, its cognitive value, its contribution to patient care, and its impact on case management. Nearly two-thirds of the respondents asserted that they would definitely or probably handle their cases differently as a result of the information provided by the library. Almost all rated the libraries' performance and response highly. An overview of the context and purpose of the study, its methods, selected results, limitations, and conclusions are presented here, as is a review of selected earlier research. PMID:3450340

Curatr: a web application for creating, curating and sharing a mass spectral library.

PubMed

Palmer, Andrew; Phapale, Prasad; Fay, Dominik; Alexandrov, Theodore

2018-04-15

We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation spectra for multiple adducts. An intuitive interface helps users to select high quality spectra that are stored along with searchable molecular information, the providence of each standard and experimental metadata. Curatr supports exports to several standard formats for use with third party software or submission to repositories. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library http://curatr.mcf.embl.de. Source code and example data are at http://github.com/alexandrovteam/curatr/. palmer@embl.de. Supplementary data are available at Bioinformatics online.

The Gaia FGK benchmark stars. High resolution spectral library

NASA Astrophysics Data System (ADS)

Blanco-Cuaresma, S.; Soubiran, C.; Jofré, P.; Heiter, U.

2014-06-01

Context. An increasing number of high-resolution stellar spectra is available today thanks to many past and ongoing spectroscopic surveys. Consequently, numerous methods have been developed to perform an automatic spectral analysis on a massive amount of data. When reviewing published results, biases arise and they need to be addressed and minimized. Aims: We are providing a homogeneous library with a common set of calibration stars (known as the Gaia FGK benchmark stars) that will allow us to assess stellar analysis methods and calibrate spectroscopic surveys. Methods: High-resolution and signal-to-noise spectra were compiled from different instruments. We developed an automatic process to homogenize the observed data and assess the quality of the resulting library. Results: We built a high-quality library that will facilitate the assessment of spectral analyses and the calibration of present and future spectroscopic surveys. The automation of the process minimizes the human subjectivity and ensures reproducibility. Additionally, it allows us to quickly adapt the library to specific needs that can arise from future spectroscopic analyses. Based on NARVAL and HARPS data obtained within the Gaia Data Processing and Analysis Consortium (DPAC) and coordinated by the GBOG (Ground-Based Observations for Gaia) working group, and on data retrieved from the ESO-ADP database.The library of spectra is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/566/A98

Increasing the use of 'smart' pump drug libraries by nurses: a continuous quality improvement project.

PubMed

Harding, Andrew D

2012-01-01

The use of infusion pumps that incorporate "smart" technology (smart pumps) can reduce the risks associated with receiving IV therapies. Smart pump technology incorporates safeguards such as a list of high-alert medications, soft and hard dosage limits, and a drug library that can be tailored to specific patient care areas. Its use can help to improve patient safety and to avoid potentially catastrophic harm associated with medication errors. But when one independent community hospital in Massachusetts switched from older mechanical pumps to smart pumps, it neglected to assign an "owner" to oversee the implementation process. One result was that nurses were using the smart pump library for only 37% of all infusions.To increase pump library usage percentage-thereby reducing the risks associated with infusion and improving patient safety-the hospital undertook a continuous quality improvement project over a four-month period in 2009. With the involvement of direct care nurses, and using quantitative data available from the smart pump software, the nursing quality and pharmacy quality teams identified ways to improve pump and pump library use. A secondary goal was to calculate the hospital's return on investment for the purchase of the smart pumps. Several interventions were developed and, on the first of each month, implemented. By the end of the project, pump library usage had nearly doubled; and the hospital had completely recouped its initial investment.

Construction of human antibody gene libraries and selection of antibodies by phage display.

PubMed

Frenzel, André; Kügler, Jonas; Wilke, Sonja; Schirrmann, Thomas; Hust, Michael

2014-01-01

Antibody phage display is the most commonly used in vitro selection technology and has yielded thousands of useful antibodies for research, diagnostics, and therapy.The prerequisite for successful generation and development of human recombinant antibodies using phage display is the construction of a high-quality antibody gene library. Here, we describe the methods for the construction of human immune and naive scFv gene libraries.The success also depends on the panning strategy for the selection of binders from these libraries. In this article, we describe a panning strategy that is high-throughput compatible and allows parallel selection in microtiter plates.

Construction of a filamentous phage display peptide library.

PubMed

Fagerlund, Annette; Myrset, Astrid Hilde; Kulseth, Mari Ann

2014-01-01

The concept of phage display is based on insertion of random oligonucleotides at an appropriate location within a structural gene of a bacteriophage. The resulting phage will constitute a library of random peptides displayed on the surface of the bacteriophages, with the encoding genotype packaged within each phage particle. Using a phagemid/helper phage system, the random peptides are interspersed between wild-type coat proteins. Libraries of phage-expressed peptides may be used to search for novel peptide ligands to target proteins. The success of finding a peptide with a desired property in a given library is highly dependent on the diversity and quality of the library. The protocols in this chapter describe the construction of a high-diversity library of phagemid vector encoding fusions of the phage coat protein pVIII with random peptides, from which a phage library displaying random peptides can be prepared.

Working with Students.

ERIC Educational Resources Information Center

Mizer, Linda; And Others

1990-01-01

Includes 12 articles that suggest activities to involve junior and senior high school students with their school libraries. Suggestions include a program to promote the reading of quality books; the use of questionnaires to improve individualized service; a checklist for book fairs; library clubs; student book reviewers; booktalks; research…

Using Web sites on quality health care for teaching consumers in public libraries.

PubMed

Oermann, Marilyn H; Lesley, Marsha L; VanderWal, Jillon S

2005-01-01

More and more consumers are searching the Internet for health information. Health Web sites vary in quality, though, and not all consumers are aware of the need to evaluate the information they find on the Web. Nurses and other health providers involved in patient education can evaluate Web sites and suggest quality sites for patients to use. This article describes a project we implemented in 2 public libraries to educate consumers about quality health care and patient safety using Web sites that we had evaluated earlier. Participants (n = 103) completed resources on health care quality, questions patients should ask about their diagnoses and treatment options, changes in Medicare and Medicare options or ways to make their health benefits work for them, and tips to help prevent medical errors. Most consumers were highly satisfied with the Web sites and the information they learned on quality care from these resources. Many participants did not have Internet access at home or work and instead used the library to search the Web. Information about the Web sites used in this project and other sites on quality care can be made available in libraries and community settings and as part of patient education resources in hospitals. The Web provides easy access for consumers to information about patient safety initiatives and health care quality in general.

Assembling short reads from jumping libraries with large insert sizes.

PubMed

Vasilinetc, Irina; Prjibelski, Andrey D; Gurevich, Alexey; Korobeynikov, Anton; Pevzner, Pavel A

2015-10-15

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies. We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads. Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades. ap@bioinf.spbau.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Chat reference service in medical libraries: part 2--Trends in medical school libraries.

PubMed

Dee, Cheryl R

2003-01-01

An increasing number of medical school libraries offer chat service to provide immediate, high quality information at the time and point of need to students, faculty, staff, and health care professionals. Part 2 of Chat Reference Service in Medical Libraries presents a snapshot of the current trends in chat reference service in medical school libraries. In late 2002, 25 (21%) medical school libraries provided chat reference. Trends in chat reference services in medical school libraries were compiled from an exploration of medical school library Web sites and informal correspondence from medical school library personnel. Many medical libraries are actively investigating and planning new chat reference services, while others have decided not to pursue chat reference at this time. Anecdotal comments from medical school library staff provide insights into chat reference service.

Science and Engineering Library and Information Service Development in Support of Research and Development in Indonesia; Report to the Chairman of the Indonesian Institute of Sciences (LIPI).

ERIC Educational Resources Information Center

Shank, Russell

Access to scientific and technical information is essential to the conduct of high quality research and development work. Indonesia's scientists and engineers in Government research institutes are generally not being well-served by their own libraries. The most serious deficiencies are: (1) inadequately trained library staffs, (2) lack of…

Improving the Quality of University Libraries through Citation Mining and Analysis Using Two New Dissertation Bibliometric Assessment Tools

ERIC Educational Resources Information Center

Tunon, Johanna; Brydges, Bruce

2005-01-01

University libraries are becoming increasingly aware of the need to assess the quality of students' information literacy and library research skills and to use this assessment data to effectively improve the quality of university library services to graduate programs. However, libraries have had difficulties finding ways to accomplish this both…

The Organizational Role of Web Services

ERIC Educational Resources Information Center

Mitchell, Erik

2011-01-01

The workload of Web librarians is already split between Web-related and other library tasks. But today's technological environment has created new implications for existing services and new demands for staff time. It is time to reconsider how libraries can best allocate resources to provide effective Web services. Delivering high-quality services…

Safeguarding Copyrighted Contents: Digital Libraries and Intellectual Property Management. CWRU's Rights Management System.

ERIC Educational Resources Information Center

Alrashid, Tareq M.; Barker, James A.; Christian, Brian S.; Cox, Steven C.; Rabne, Michael W.; Slotta, Elizabeth A.; Upthegrove, Luella R.

1998-01-01

Describes Case Western Reserve University's (CWRU's) digital library project that examines the networked delivery of full-text materials and high-quality images to provide students excellent supplemental instructional resources delivered directly to their dormitory rooms. Reviews intellectual property (IP) management requirements and describes…

Eating and Reading in the Library.

ERIC Educational Resources Information Center

Trelease, Jim; Krashen, Stephen

1996-01-01

This article, citing the example of large bookselling chains who offer cafes in their stores, advocates the provision of food and drink in school libraries as well. High-quality food, made available by vending machine, would increase levels of wellness, energy, and teachability. Protests involving mess, lack of money, and difficulties with parents…

Young Adults Deserve the Best: YALSA's Competencies in Action

ERIC Educational Resources Information Center

Flowers, Sarah

2010-01-01

As high school enrollment continues to rise, the need for effective librarianship serving young adults is greater than ever before. "Young Adults Deserve the Best: Competencies for Librarians Serving Youth," developed by Young Adult Library Services Association (YALSA), is a document outlining areas of focus for providing quality library service…

The Cost of Quality--Its Application to Libraries.

ERIC Educational Resources Information Center

Franklin, Brinley

1994-01-01

Examines the conceptual basis for the cost of quality and its application to libraries. The framework for analysis of this conceptual basis includes definitions of the cost of quality; a brief historical review of the cost of quality; and the application of quality cost to libraries, including an explanation of how quality costs respond to quality…

Streamlined approach to high-quality purification and identification of compound series using high-resolution MS and NMR.

PubMed

Mühlebach, Anneke; Adam, Joachim; Schön, Uwe

2011-11-01

Automated medicinal chemistry (parallel chemistry) has become an integral part of the drug-discovery process in almost every large pharmaceutical company. Parallel array synthesis of individual organic compounds has been used extensively to generate diverse structural libraries to support different phases of the drug-discovery process, such as hit-to-lead, lead finding, or lead optimization. In order to guarantee effective project support, efficiency in the production of compound libraries has been maximized. As a consequence, also throughput in chromatographic purification and analysis has been adapted. As a recent trend, more laboratories are preparing smaller, yet more focused libraries with even increasing demands towards quality, i.e. optimal purity and unambiguous confirmation of identity. This paper presents an automated approach how to combine effective purification and structural conformation of a lead optimization library created by microwave-assisted organic synthesis. The results of complementary analytical techniques such as UHPLC-HRMS and NMR are not only regarded but even merged for fast and easy decision making, providing optimal quality of compound stock. In comparison with the previous procedures, throughput times are at least four times faster, while compound consumption could be decreased more than threefold. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Academic Libraries and Quality: An Analysis and Evaluation Framework

ERIC Educational Resources Information Center

Atkinson, Jeremy

2017-01-01

The paper proposes and describes a framework for academic library quality to be used by new and more experienced library practitioners and by others involved in considering the quality of academic libraries' services and provision. The framework consists of eight themes and a number of questions to examine within each theme. The framework was…

Effects of argument quality, source credibility and self-reported diabetes knowledge on message attitudes: an experiment using diabetes related messages.

PubMed

Lin, Tung-Cheng; Hwang, Lih-Lian; Lai, Yung-Jye

2017-05-17

Previous studies have reported that credibility and content (argument quality) are the most critical factors affecting the quality of health information and its acceptance and use; however, this causal relationship merits further investigation in the context of health education. Moreover, message recipients' prior knowledge may moderate these relationships. This study used the elaboration likelihood model to determine the main effects of argument quality, source credibility and the moderating effect of self-reported diabetes knowledge on message attitudes. A between-subjects experimental design using an educational message concerning diabetes for manipulation was applied to validate the effects empirically. A total of 181 participants without diabetes were recruited from the Department of Health, Taipei City Government. Four group messages were manipulated in terms of argument quality (high and low) × source credibility (high and low). Argument quality and source credibility of health information significantly influenced the attitude of message recipients. The participants with high self-reported knowledge participants exhibited significant disapproval for messages with low argument quality. Effective health information should provide objective descriptions and cite reliable sources; in addition, it should provide accurate, customised messages for recipients who have high background knowledge level and ability to discern message quality. © 2017 Health Libraries Group Health Information & Libraries Journal.

Determination of a Screening Metric for High Diversity DNA Libraries.

PubMed

Guido, Nicholas J; Handerson, Steven; Joseph, Elaine M; Leake, Devin; Kung, Li A

2016-01-01

The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

Rethinking Customer Service Training: A Curricular Solution to a Familiar Problem

ERIC Educational Resources Information Center

Epps, Sharon K.; Kidd, Judith; Negro, Toni; Sayles, Sheridan L.

2016-01-01

High-quality customer service is an important aim of the library experience. Its importance is evidenced by attention given to the topic in scholarly literature and academic conference proceedings. This article describes the challenging process of creating and delivering a blended customer service training curriculum to all library staff working…

A highly functional synthetic phage display library containing over 40 billion human antibody clones.

PubMed

Weber, Marcel; Bujak, Emil; Putelli, Alessia; Villa, Alessandra; Matasci, Mattia; Gualandi, Laura; Hemmerle, Teresa; Wulhfard, Sarah; Neri, Dario

2014-01-01

Several synthetic antibody phage display libraries have been created and used for the isolation of human monoclonal antibodies. The performance of antibody libraries, which is usually measured in terms of their ability to yield high-affinity binding specificities against target proteins of interest, depends both on technical aspects (such as library size and quality of cloning) and on design features (which influence the percentage of functional clones in the library and their ability to be used for practical applications). Here, we describe the design, construction and characterization of a combinatorial phage display library, comprising over 40 billion human antibody clones in single-chain fragment variable (scFv) format. The library was designed with the aim to obtain highly stable antibody clones, which can be affinity-purified on protein A supports, even when used in scFv format. The library was found to be highly functional, as >90% of randomly selected clones expressed the corresponding antibody. When selected against more than 15 antigens from various sources, the library always yielded specific and potent binders, at a higher frequency compared to previous antibody libraries. To demonstrate library performance in practical biomedical research projects, we isolated the human antibody G5, which reacts both against human and murine forms of the alternatively spliced BCD segment of tenascin-C, an extracellular matrix component frequently over-expressed in cancer and in chronic inflammation. The new library represents a useful source of binding specificities, both for academic research and for the development of antibody-based therapeutics.

A Highly Functional Synthetic Phage Display Library Containing over 40 Billion Human Antibody Clones

PubMed Central

Weber, Marcel; Bujak, Emil; Putelli, Alessia; Villa, Alessandra; Matasci, Mattia; Gualandi, Laura; Hemmerle, Teresa; Wulhfard, Sarah; Neri, Dario

2014-01-01

Several synthetic antibody phage display libraries have been created and used for the isolation of human monoclonal antibodies. The performance of antibody libraries, which is usually measured in terms of their ability to yield high-affinity binding specificities against target proteins of interest, depends both on technical aspects (such as library size and quality of cloning) and on design features (which influence the percentage of functional clones in the library and their ability to be used for practical applications). Here, we describe the design, construction and characterization of a combinatorial phage display library, comprising over 40 billion human antibody clones in single-chain fragment variable (scFv) format. The library was designed with the aim to obtain highly stable antibody clones, which can be affinity-purified on protein A supports, even when used in scFv format. The library was found to be highly functional, as >90% of randomly selected clones expressed the corresponding antibody. When selected against more than 15 antigens from various sources, the library always yielded specific and potent binders, at a higher frequency compared to previous antibody libraries. To demonstrate library performance in practical biomedical research projects, we isolated the human antibody G5, which reacts both against human and murine forms of the alternatively spliced BCD segment of tenascin-C, an extracellular matrix component frequently over-expressed in cancer and in chronic inflammation. The new library represents a useful source of binding specificities, both for academic research and for the development of antibody-based therapeutics. PMID:24950200

SeSaM-Tv-II generates a protein sequence space that is unobtainable by epPCR.

PubMed

Mundhada, Hemanshu; Marienhagen, Jan; Scacioc, Andreea; Schenk, Alexander; Roccatano, Danilo; Schwaneberg, Ulrich

2011-07-04

Generating high-quality mutant libraries in which each amino acid is equally targeted and substituted in a chemically diverse manner is crucial to obtain improved variants in small mutant libraries. The sequence saturation mutagenesis method (SeSaM-Tv(+) ) offers the opportunity to generate such high-quality mutant libraries by introducing consecutive mutations and by enriching transversions. In this study, automated gel electrophoresis, real-time quantitative PCR, and a phosphorimager quantification system were developed and employed to optimize each step of previously reported SeSaM-Tv(+) method. Advancements of the SeSaM-Tv(+) protocol and the use of a novel DNA polymerase quadrupled the number of transversions, by doubling the fraction of consecutive mutations (from 16.7 to 37.1 %). About 33 % of all amino acid substitutions observed in a model library are rarely introduced by epPCR methods, and around 10 % of all clones carried amino acid substitutions that are unobtainable by epPCR. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

PubMed

Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

2015-01-01

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Service Quality: An Unobtrusive Investigation of Interlibrary Loan in Large Public Libraries in Canada.

ERIC Educational Resources Information Center

Hebert, Francoise

1994-01-01

Describes a study that investigated the quality of interlibrary loan services in Canadian public libraries from the library's and the user's perspectives and then compared results. Measures of interlibrary loan performance are reviewed; an alternative conceptualization of service quality is discussed; and SERVQUAL, a measure of service quality, is…

Orientation and Functions of Library in Quality Education of College

ERIC Educational Resources Information Center

Yang, Lan

2011-01-01

Quality education is the core of college education. Libraries are the second class for students due to the extremely important position and function in quality education. Libraries are the best place for cultivating students' morals, the important front for improving students' scientific and cultural qualities, and the effective facilities for…

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Earth science photographs from the U.S. Geological Survey Library

USGS Publications Warehouse

McGregor, Joseph K.; Abston, Carl C.

1995-01-01

This CD-ROM set contains 1,500 scanned photographs from the U.S. Geological Survey Library for use as a photographic glossary of elementary geologic terms. Scholars are encouraged to copy these public domain images into their reports or databases to enhance their presentations. High-quality prints and (or) slides are available upon request from the library. This CD-ROM was produced in accordance with the ISO 9660 standard; however, it is intended for use on DOS-based computer systems only.

MATH77, Version 4.0

NASA Technical Reports Server (NTRS)

Lawson, Charles L.; Krogh, Fred; Van Snyder, W.; Oken, Carol A.; Mccreary, Faith A.; Lieske, Jay H.; Perrine, Jack; Coffin, Ralph S.; Wayne, Warren J.

1994-01-01

MATH77 is high-quality library of ANSI FORTRAN 77 subprograms implementing contemporary algorithms for basic computational processes of science and engineering. Release 4.0 of MATH77 contains 454 user-callable and 136 lower-level subprograms. MATH77 release 4.0 subroutine library designed to be usable on any computer system supporting full ANSI standard FORTRAN 77 language.

Japanese Manga in Translation and American Graphic Novels: A Preliminary Examination of the Collections in 44 Academic Libraries

ERIC Educational Resources Information Center

Masuchika, Glenn; Boldt, Gail

2010-01-01

American graphic novels are increasingly recognized as high-quality literature and an interesting genre for academic study. Graphic novels of Japan, called manga, have established a strong foothold in American culture. This preliminary survey of 44 United States university libraries demonstrates that Japanese manga in translation are consistently…

Library and information services: impact on patient care quality.

PubMed

Marshall, Joanne Gard; Morgan, Jennifer Craft; Thompson, Cheryl A; Wells, Amber L

2014-01-01

The purpose of this paper is to explore library and information service impact on patient care quality. A large-scale critical incident survey of physicians and residents at 56 library sites serving 118 hospitals in the USA and Canada. Respondents were asked to base their answers on a recent incident in which they had used library resources to search for information related to a specific clinical case. Of 4,520 respondents, 75 percent said that they definitely or probably handled patient care differently using information obtained through the library. In a multivariate analysis, three summary clinical outcome measures were used as value and impact indicators: first, time saved; second, patient care changes; and third, adverse events avoided. The outcomes were examined in relation to four information access methods: first, asking librarian for assistance; second, performing search in a physical library; third, searching library's web site; or fourth, searching library resources on an institutional intranet. All library access methods had consistently positive relationships with the clinical outcomes, providing evidence that library services have a positive impact on patient care quality. Electronic collections and services provided by the library and the librarian contribute to patient care quality.

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

Construction of a scFv Library with Synthetic, Non-combinatorial CDR Diversity.

PubMed

Bai, Xuelian; Shim, Hyunbo

2017-01-01

Many large synthetic antibody libraries have been designed, constructed, and successfully generated high-quality antibodies suitable for various demanding applications. While synthetic antibody libraries have many advantages such as optimized framework sequences and a broader sequence landscape than natural antibodies, their sequence diversities typically are generated by random combinatorial synthetic processes which cause the incorporation of many undesired CDR sequences. Here, we describe the construction of a synthetic scFv library using oligonucleotide mixtures that contain predefined, non-combinatorially synthesized CDR sequences. Each CDR is first inserted to a master scFv framework sequence and the resulting single-CDR libraries are subjected to a round of proofread panning. The proofread CDR sequences are assembled to produce the final scFv library with six diversified CDRs.

Quality Management and Building Government Information Services.

ERIC Educational Resources Information Center

Farrell, Maggie

1998-01-01

Discusses serving library-patron needs in terms of customer service and quality control. Highlights include tools for measuring the quality of service (e.g., the SERVQUAL survey), advisory boards or focus groups, library "service statements," changing patron needs, new information formats, and justifying depository library services. (JAK)

An Exploratory Study of the Relationship between Academic Library Work Experience and Perceptions of Leadership Skill Development Relevant to Academic Library Directorship

ERIC Educational Resources Information Center

Harris-Keith, Colleen Susan

2015-01-01

Though research into academic library director leadership has established leadership skills and qualities required for success, little research has been done to establish where in their career library directors were most likely to acquire those skills and qualities. This research project surveyed academic library directors at Carnegie-designated…

Indoor air pollution and preventions in college libraries

NASA Astrophysics Data System (ADS)

Yang, Zengzhang

2017-05-01

The college library is a place where it gets the comparatively high density of students often staying long time with it. Therefore, the indoor air quality will affect directly reading effect and physical health of teachers and students in colleges and universities. The paper analyzes the influenced factors in indoor air pollution of the library from the selection of green-environmental decorating materials and furniture, good ventilation maintaining, electromagnetic radiation reducing, regular disinfection, indoor green building and awareness of health and environmental protection strengthening etc. six aspects to put forward the ideas for preventions of indoor air pollution and construction of the green low-carbon library.

Mass Spectral Library Quality Assurance by Inter-Library Comparison

NASA Astrophysics Data System (ADS)

Wallace, William E.; Ji, Weihua; Tchekhovskoi, Dmitrii V.; Phinney, Karen W.; Stein, Stephen E.

2017-04-01

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared, the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided.

Mass Spectral Library Quality Assurance by Inter-Library Comparison

PubMed Central

Wallace, W.E.; Ji, W.; Tchekhovskoi, D.V.; Phinney, K.W.; Stein, S.E.

2017-01-01

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided. PMID:28127680

Measuring Customer Satisfaction and Quality of Service in Special Libraries.

ERIC Educational Resources Information Center

White, Marilyn Domas; Abels, Eileen G.; Nitecki, Danuta

This project tested the appropriateness of SERVQUAL (i.e., an instrument widely used in the service industry for assessing service quality based on repeated service encounters rather than a particular service encounter) to measure service quality in special libraries and developed a modified version for special libraries. SERVQUAL is based on an…

Business Students' Perception of University Library Service Quality and Satisfaction

ERIC Educational Resources Information Center

Hsu, Maxwell K.; Cummings, Richard G.; Wang, Stephen W.

2014-01-01

The main purpose of this study is to examine the college students' perception of library services, and to what extent the quality of library services influences students' satisfaction. The findings depict the relationship between academic libraries and their users in today's digital world and identify critical factors that may sustain a viable…

Academic Library Spaces: Advancing Student Success and Helping Students Thrive

ERIC Educational Resources Information Center

Spencer, Mary Ellen; Watstein, Sarah Barbara

2017-01-01

Are today's academic libraries really designed for learning? Do library spaces impact student learning? Intending to spark broader and more informed dialogue about the relationship between the quality of learning and the quality of academic library spaces in higher education, the authors consider the concept of space as service; student learning…

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Martinez, Misti A.; Carpenter, Kristin L.; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo J.; Tabb, David L.

2012-01-01

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines. PMID:22217208

Software Quality Assurance and Verification for the MPACT Library Generation Process

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

Liu, Yuxuan; Williams, Mark L.; Wiarda, Dorothea

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

Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries.

PubMed

Shinozuka, Hiroshi; Forster, John W

2016-01-01

Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time. Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX Connect(TM) Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C. Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R (2) > 0.77), and that observed from MiSeq sequencing (R (2) = 0.82). Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.

Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening

PubMed Central

Dandapani, Sivaraman; Rosse, Gerard; Southall, Noel; Salvino, Joseph M.; Thomas, Craig J.

2015-01-01

The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition. PMID:26705509

Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening.

PubMed

Dandapani, Sivaraman; Rosse, Gerard; Southall, Noel; Salvino, Joseph M; Thomas, Craig J

The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.

Evaluating One-Shot Library Sessions: Impact on the Quality and Diversity of Student Source Use

ERIC Educational Resources Information Center

Howard, Kristina; Nicholas, Thomas; Hayes, Tish; Appelt, Christopher W.

2014-01-01

This article examines the presumption that library research workshops will increase the quality, quantity and diversity of sources students use. This study compares bibliographies of research papers written by freshman composition students who received a library research session to those of students who did not receive any library instruction. Our…

Using SERVQUAL in health libraries across Somerset, Devon and Cornwall.

PubMed

Martin, Susan

2003-03-01

This study provides the results of a survey conducted in the autumn of 2001 by ten NHS library services across Somerset, Devon and Cornwall. The aim of the project was to measure the service quality of each individual library and to provide an overall picture of the quality of library services within the south-west peninsula. The survey was based on SERVQUAL, a diagnostic tool developed in the 1980s, which measures service quality in terms of customer expectations and perceptions of service. The survey results have provided the librarians with a wealth of information about service quality. The service as a whole is perceived to be not only meeting but also exceeding expectations in terms of reliability, responsiveness, empathy and assurance. For the first time, the ten health library services can measure their own service quality as well as benchmark themselves against others.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

PubMed Central

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow. PMID:25565494

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

PubMed

Grayson, Phil; Sin, Simon Y W; Sackton, Timothy B; Edwards, Scott V

2017-01-01

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

[Construction and characterization of a cDNA library from human liver tissue of cirrhosis].

PubMed

Chen, Xiao-hong; Chen, Zhi; Chen, Feng; Zhu, Hai-hong; Zhou, Hong-juan; Yao, Hang-ping

2005-03-01

To construct a cDNA library from human liver tissue of cirrhosis. The total RNA from human liver tissue of cirrhosis was extracted using Trizol method, and the mRNA was purified using mRNA purification kit. SMART technique and CDSIII/3' primer were used for first-strand cDNA synthesis. Long distance PCR was then used to synthesize the double-strand cDNA that was then digested by proteinase K and Sfi I, and was fractionated by CHOMA SPIN-400 column. The cDNA fragments longer than 0.4 kb were collected and ligated to lambdaTripl Ex2 vector. Then lambda-phage packaging reaction and library amplification were performed. The qualities of both unamplified and amplified cDNA libraries was strictly checked by conventional titer determination. Eleven plaques were randomly picked and tested using PCR with universal primers derived from the sequence flanking the vector. The titers of unamplifed and amplified libraries were 1.03 x 10(6) pfu/ml and 1.36 x 10(9) pfu/ml respectively. The percentages of recombinants from both libraries were 97.24 % in unamplified library and 99.02 % in amplified library. The lengths of the inserts were 1.02 kb in average (36.36 % 1 approximately equals 2 kb and 63.64 % 0.5 approximately equals 1.0 kb). A high quality cDNA library from human liver tissue of cirrhosis was constructed successfully, which can be used for screening and cloning new special genes associated with the occurrence of cirrhosis.

Rating the Quality of Open Textbooks: How Reviewer and Text Characteristics Predict Ratings

ERIC Educational Resources Information Center

Fischer, Lane; Ernst, David; Mason, Stacie

2017-01-01

Using data collected from peer reviews for Open Textbook Library titles, this paper explores questions about rating the quality of open textbooks. The five research questions addressed the relationship between textbook and reviewer characteristics and ratings. Although reviewers gave textbooks high ratings generally, reviewers identified…

Automated design of degenerate codon libraries.

PubMed

Mena, Marco A; Daugherty, Patrick S

2005-12-01

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

Generation and analysis of expressed sequence tags from a cDNA library of the fruiting body of Ganoderma lucidum

PubMed Central

2010-01-01

Background Little genomic or trancriptomic information on Ganoderma lucidum (Lingzhi) is known. This study aims to discover the transcripts involved in secondary metabolite biosynthesis and developmental regulation of G. lucidum using an expressed sequence tag (EST) library. Methods A cDNA library was constructed from the G. lucidum fruiting body. Its high-quality ESTs were assembled into unique sequences with contigs and singletons. The unique sequences were annotated according to sequence similarities to genes or proteins available in public databases. The detection of simple sequence repeats (SSRs) was preformed by online analysis. Results A total of 1,023 clones were randomly selected from the G. lucidum library and sequenced, yielding 879 high-quality ESTs. These ESTs showed similarities to a diverse range of genes. The sequences encoding squalene epoxidase (SE) and farnesyl-diphosphate synthase (FPS) were identified in this EST collection. Several candidate genes, such as hydrophobin, MOB2, profilin and PHO84 were detected for the first time in G. lucidum. Thirteen (13) potential SSR-motif microsatellite loci were also identified. Conclusion The present study demonstrates a successful application of EST analysis in the discovery of transcripts involved in the secondary metabolite biosynthesis and the developmental regulation of G. lucidum. PMID:20230644

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.

SOA-based digital library services and composition in biomedical applications.

PubMed

Zhao, Xia; Liu, Enjie; Clapworthy, Gordon J; Viceconti, Marco; Testi, Debora

2012-06-01

Carefully collected, high-quality data are crucial in biomedical visualization, and it is important that the user community has ready access to both this data and the high-performance computing resources needed by the complex, computational algorithms that will process it. Biological researchers generally require data, tools and algorithms from multiple providers to achieve their goals. This paper illustrates our response to the problems that result from this. The Living Human Digital Library (LHDL) project presented in this paper has taken advantage of Web Services to build a biomedical digital library infrastructure that allows clinicians and researchers not only to preserve, trace and share data resources, but also to collaborate at the data-processing level. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Health sciences library outreach to family caregivers: a call to service.

PubMed

Howrey, Mary M

2018-04-01

This commentary discusses the information needs of family caregivers and care recipients in the United States. Health sciences library services and outreach activities that support family caregivers include: (1) advocacy, (2) resource building, and (3) programming and education. Ethical issues related to the privacy and confidentiality of clients are outlined in the commentary for information service providers. Also, continuing professional education resources are identified to assist librarians in providing high-quality information services for this special family caregiver population, such as those designed by the National Library of Medicine (NLM) through the NLM 4 Caregivers program.

Health sciences library outreach to family caregivers: a call to service

PubMed Central

Howrey, Mary M.

2018-01-01

This commentary discusses the information needs of family caregivers and care recipients in the United States. Health sciences library services and outreach activities that support family caregivers include: (1) advocacy, (2) resource building, and (3) programming and education. Ethical issues related to the privacy and confidentiality of clients are outlined in the commentary for information service providers. Also, continuing professional education resources are identified to assist librarians in providing high-quality information services for this special family caregiver population, such as those designed by the National Library of Medicine (NLM) through the NLM 4 Caregivers program. PMID:29632449

The High Level Data Reduction Library

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

LibQUAL+[TM]: A Methodological Suite; Reliability and Structure of LibQUAL+[TM] Scores: Measuring Perceived Library Service Quality; Score Norms for Improving Library Service Quality: A LibQUAL+[TM] Study; ARL Index and Other Validity Correlates of LibQUAL+[TM] Scores.

ERIC Educational Resources Information Center

Heath, Fred M.; Thompson, Bruce; Cook, Colleen; Thompson, Russel L.; Kyrillidou, Martha

2002-01-01

Includes four articles that discuss LibQUAL+[TM], a collaborative effort of the Association of Research Libraries and Texas A&M University responding to the need for greater accountability in measuring the delivery of library services to research library users. Discusses the reliability of LibQUAL+[TM] scores in measuring perceived library…

75 FR 22120 - Notice of Roundtables and Request for Comments on Enhancement in the Quality of Patents and on...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-27

... quality and the metrics the USPTO should use to measure progress. The roundtables are open to the public... will be held at the Los Angeles Public Library--Central Library, which is located at 630 W. 5th Street... USPTO is conducting two roundtables, one at the Los Angeles Public Library--Central Library facility...

Next-generation sequencing library construction on a surface.

PubMed

Feng, Kuan; Costa, Justin; Edwards, Jeremy S

2018-05-30

Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been steadily improved, and the entire process is currently relatively straightforward. However, NGS instrumentation still requires upfront library preparation, which can be a laborious process, requiring significant hands-on time. Herein, we present a simple but robust approach to streamline library preparation by utilizing surface bound transposases to construct DNA libraries directly on a flowcell surface. The surface bound transposases directly fragment genomic DNA while simultaneously attaching the library molecules to the flowcell. We sequenced and analysed a Drosophila genome library generated by this surface tagmentation approach, and we showed that our surface bound library quality was comparable to the quality of the library from a commercial kit. In addition to the time and cost savings, our approach does not require PCR amplification of the library, which eliminates potential problems associated with PCR duplicates. We described the first study to construct libraries directly on a flowcell. We believe our technique could be incorporated into the existing Illumina sequencing pipeline to simplify the workflow, reduce costs, and improve data quality.

Evolutionary concepts in biobanking - the BC BioLibrary

PubMed Central

2009-01-01

Background Medical research to improve health care faces a major problem in the relatively limited availability of adequately annotated and collected biospecimens. This limitation is creating a growing gap between the pace of scientific advances and successful exploitation of this knowledge. Biobanks are an important conduit for transfer of biospecimens (tissues, blood, body fluids) and related health data to research. They have evolved outside of the historical source of tissue biospecimens, clinical pathology archives. Research biobanks have developed advanced standards, protocols, databases, and mechanisms to interface with researchers seeking biospecimens. However, biobanks are often limited in their capacity and ability to ensure quality in the face of increasing demand. Our strategy to enhance both capacity and quality in research biobanking is to create a new framework that repatriates the activity of biospecimen accrual for biobanks to clinical pathology. Methods The British Columbia (BC) BioLibrary is a framework to maximize the accrual of high-quality, annotated biospecimens into biobanks. The BC BioLibrary design primarily encompasses: 1) specialized biospecimen collection units embedded within clinical pathology and linked to a biospecimen distribution system that serves biobanks; 2) a systematic process to connect potential donors with biobanks, and to connect biobanks with consented biospecimens; and 3) interdisciplinary governance and oversight informed by public opinion. Results The BC BioLibrary has been embraced by biobanking leaders and translational researchers throughout BC, across multiple health authorities, institutions, and disciplines. An initial pilot network of three Biospecimen Collection Units has been successfully established. In addition, two public deliberation events have been held to obtain input from the public on the BioLibrary and on issues including consent, collection of biospecimens and governance. Conclusion The BC BioLibrary framework addresses common issues for clinical pathology, biobanking, and translational research across multiple institutions and clinical and research domains. We anticipate that our framework will lead to enhanced biospecimen accrual capacity and quality, reduced competition between biobanks, and a transparent process for donors that enhances public trust in biobanking. PMID:19909513

Students' Perceived Quality of Library Facilities and Services in Nigerian Private Universities

ERIC Educational Resources Information Center

Oluwunmi, A. O.; Durodola, O. D.; Ajayi, C. A.

2016-01-01

In a highly competitive academic environment, students are becoming more selective and demanding in their choice of University. Hence, it is essential for educational institutions, particularly privately-owned institutions, to be interested in getting feedback on the quality of their facilities and services. With a focus on four private…

Positioning Open Access Journals in a LIS Journal Ranking

ERIC Educational Resources Information Center

Xia, Jingfeng

2012-01-01

This research uses the h-index to rank the quality of library and information science journals between 2004 and 2008. Selected open access (OA) journals are included in the ranking to assess current OA development in support of scholarly communication. It is found that OA journals have gained momentum supporting high-quality research and…

Acoustic Sample Deposition MALDI-MS (ASD-MALDI-MS): A Novel Process Flow for Quality Control Screening of Compound Libraries.

PubMed

Chin, Jefferson; Wood, Elizabeth; Peters, Grace S; Drexler, Dieter M

2016-02-01

In the early stages of drug discovery, high-throughput screening (HTS) of compound libraries against pharmaceutical targets is a common method to identify potential lead molecules. For these HTS campaigns to be efficient and successful, continuous quality control of the compound collection is necessary and crucial. However, the large number of compound samples and the limited sample amount pose unique challenges. Presented here is a proof-of-concept study for a novel process flow for the quality control screening of small-molecule compound libraries that consumes only minimal amounts of samples and affords compound-specific molecular data. This process employs an acoustic sample deposition (ASD) technique for the offline sample preparation by depositing nanoliter volumes in an array format onto microscope glass slides followed by matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis. An initial study of a 384-compound array employing the ASD-MALDI-MS workflow resulted in a 75% first-pass positive identification rate with an analysis time of <1 s per sample. © 2015 Society for Laboratory Automation and Screening.

Evaluation of the quality of the college library websites in Iranian medical Universities based on the Stover model.

PubMed

Nasajpour, Mohammad Reza; Ashrafi-Rizi, Hasan; Soleymani, Mohammad Reza; Shahrzadi, Leila; Hassanzadeh, Akbar

2014-01-01

Today, the websites of college and university libraries play an important role in providing the necessary services for clients. These websites not only allow the users to access different collections of library resources, but also provide them with the necessary guidance in order to use the information. The goal of this study is the quality evaluation of the college library websites in Iranian Medical Universities based on the Stover model. This study uses an analytical survey method and is an applied study. The data gathering tool is the standard checklist provided by Stover, which was modified by the researchers for this study. The statistical population is the college library websites of the Iranian Medical Universities (146 websites) and census method was used for investigation. The data gathering method was a direct access to each website and filling of the checklist was based on the researchers' observations. Descriptive and analytical statistics (Analysis of Variance (ANOVA)) were used for data analysis with the help of the SPSS software. The findings showed that in the dimension of the quality of contents, the highest average belonged to type one universities (46.2%) and the lowest average belonged to type three universities (24.8%). In the search and research capabilities, the highest average belonged to type one universities (48.2%) and the lowest average belonged to type three universities. In the dimension of facilities provided for the users, type one universities again had the highest average (37.2%), while type three universities had the lowest average (15%). In general the library websites of type one universities had the highest quality (44.2%), while type three universities had the lowest quality (21.1%). Also the library websites of the College of Rehabilitation and the College of Paramedics, of the Shiraz University of Medical Science, had the highest quality scores. The results showed that there was a meaningful difference between the quality of the college library websites and the university types, resulting in college libraries of type one universities having the highest average score and the college libraries of type three universities having the lowest score.

Evaluation of the quality of the college library websites in Iranian medical Universities based on the Stover model

PubMed Central

Nasajpour, Mohammad Reza; Ashrafi-rizi, Hasan; Soleymani, Mohammad Reza; Shahrzadi, Leila; Hassanzadeh, Akbar

2014-01-01

Introduction: Today, the websites of college and university libraries play an important role in providing the necessary services for clients. These websites not only allow the users to access different collections of library resources, but also provide them with the necessary guidance in order to use the information. The goal of this study is the quality evaluation of the college library websites in Iranian Medical Universities based on the Stover model. Material and Methods: This study uses an analytical survey method and is an applied study. The data gathering tool is the standard checklist provided by Stover, which was modified by the researchers for this study. The statistical population is the college library websites of the Iranian Medical Universities (146 websites) and census method was used for investigation. The data gathering method was a direct access to each website and filling of the checklist was based on the researchers’ observations. Descriptive and analytical statistics (Analysis of Variance (ANOVA)) were used for data analysis with the help of the SPSS software. Findings: The findings showed that in the dimension of the quality of contents, the highest average belonged to type one universities (46.2%) and the lowest average belonged to type three universities (24.8%). In the search and research capabilities, the highest average belonged to type one universities (48.2%) and the lowest average belonged to type three universities. In the dimension of facilities provided for the users, type one universities again had the highest average (37.2%), while type three universities had the lowest average (15%). In general the library websites of type one universities had the highest quality (44.2%), while type three universities had the lowest quality (21.1%). Also the library websites of the College of Rehabilitation and the College of Paramedics, of the Shiraz University of Medical Science, had the highest quality scores. Discussion: The results showed that there was a meaningful difference between the quality of the college library websites and the university types, resulting in college libraries of type one universities having the highest average score and the college libraries of type three universities having the lowest score. PMID:25540794

Think Quality! The Deming Approach Does Work in Libraries.

ERIC Educational Resources Information Center

Mackey, Terry; Mackey, Kitty

1992-01-01

Presents W. Edwards Deming's Total Quality Management method and advocates its adoption in libraries. The 14 points that form the basis of Deming's philosophy are discussed in the context of the library setting. A flow chart of the reference process and user survey questions are included. (MES)

Library Users' Service Desires: A LibQUAL+ Study

ERIC Educational Resources Information Center

Thompson, Bruce; Kyrillidou, Martha; Cook, Colleen

2008-01-01

The present study was conducted to explore library users' desired service quality levels on the twenty-two core LibQUAL+ items. Specifically, we explored similarities and differences in users' desired library service quality levels across user groups (i.e., undergraduate students, graduate students, and faculty), across geographic locations (i.e.,…

Service Quality: A Concept not Fully Explored.

ERIC Educational Resources Information Center

Hernon, Peter; Nitecki, Danuta A.

2001-01-01

Examines the concept of service quality in libraries. Highlights include assessment; service quality versus user satisfaction; measuring service quality, including SERVQUAL; planning; experiences at Texas A& M University in cooperation with ARL (Association of Research Libraries) that resulted in LibQUAL+; and conceptual issues. (Contains 54…

Study of college library appealing information system: A case of Longyan University

NASA Astrophysics Data System (ADS)

Liao, Jin-Hui

2014-10-01

The complaints from the readers at university libraries mainly focus on the aspects of service attitude, quality of service, reading environment, the management system, etc. Librarians should realize that reader complaints can actually promote the role of the library service and communicate with readers who complain in a friendly manner. In addition, the Longyan University library should establish an internal management system, improve library hardware facilities, improve the quality of librarians and optimize the knowledge structure of librarians, so as to improve the quality of the service for readers and reduce complaints. Based on this point, we have designed an appealing information system in cryptography machine basis, to provide readers online, remote and anonymous complaint functions.

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

PubMed Central

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

2012-01-01

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

A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.

PubMed

Gòdia, Marta; Mayer, Fabiana Quoos; Nafissi, Julieta; Castelló, Anna; Rodríguez-Gil, Joan Enric; Sánchez, Armand; Clop, Alex

2018-04-26

The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPure TM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing. Our results show that pig SRR (~22%) is lower than in other mammalian species and that it is not significantly dependent of the sperm quality parameters analyzed in our study. Moreover, no relationship between the RNA yield per sperm cell and sperm phenotypes was found. We compared a RNA-seq library preparation kit optimized for low amounts of fragmented RNA with a standard kit designed for high amount and quality of input RNA and found that for sperm, a protocol designed to work on low-quality RNA is essential. We also compared two small RNA-seq kits and did not find substantial differences in their performance. We propose the methodological workflow described for the RNA-seq screening of the boar spermatozoa transcriptome. FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous RNA; Mt rRNA: mitochondrial ribosomal RNA; Mt tRNA: mitochondrial transference RNA; OAZ3: ornithine decarboxylase antizyme 3; ORT: osmotic resistance test; piRNA: Piwi-interacting RNA; PRM1: protamine 1; PTPRC: protein tyrosine phosphatase receptor type C; rRNA: ribosomal RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; SRR: sperm recovery rate; tRNA: transfer RNA.

Service Quality and Customer Satisfaction: An Assessment and Future Directions.

ERIC Educational Resources Information Center

Hernon, Peter; Nitecki, Danuta A.; Altman, Ellen

1999-01-01

Reviews the literature of library and information science to examine issues related to service quality and customer satisfaction in academic libraries. Discusses assessment, the application of a business model to higher education, a multiple constituency approach, decision areas regarding service quality, resistance to service quality, and future…

Quality Management and Self Assessment Tools for Public Libraries.

ERIC Educational Resources Information Center

Evans, Margaret Kinnell

This paper describes a two-year study by the British Library Research and Innovation Centre that examined the potential of self-assessment for public library services. The approaches that formed the basis for the investigation were the Business Excellence Model, the Quality Framework, and the Democratic Approach. Core values were identified by…

University Rankings: How Well Do They Measure Library Service Quality?

ERIC Educational Resources Information Center

Jackson, Brian

2015-01-01

University rankings play an increasingly large role in shaping the goals of academic institutions and departments, while removing universities themselves from the evaluation process. This study compares the library-related results of two university ranking publications with scores on the LibQUAL+™ survey to identify if library service quality--as…

Psychometric Properties of Scores from the Web-based LibQUAL+ Study of Perceptions of Library Service Quality.

ERIC Educational Resources Information Center

Cook, Colleen; Thompson, Bruce

2001-01-01

Investigated the psychometric integrity of scores from the LibQUAL+ evaluation of perceived library service quality conducted by ARL (Association of Research Libraries). Examines score structure, score reliability, score correlation and concurrent validity coefficients, scale means, and scale standardized norms, and considers the potential of the…

LISTENing to healthcare students: the impact of new library facilities on the quality of services.

PubMed

Haldane, Graham C

2003-06-01

Following a low assessment of 'Learning resources' provision by the Quality Assurance Agency, the librarian of Homerton College, School of Health Studies commenced the LISTEN Project, a long-term study to monitor the effects of planned interventions on the quality of library provision. Surveys of entry-to-register student nurses & midwives were conducted in 1999 and 2001 by extensive questionnaires, inviting Likert-scaled and free text responses. Following a college relocation, students made greater than expected use of a new health studies library in Cambridge, and significantly less use of the local teaching hospital library. Using both a satisfaction index and a non-parametric test of mean scores, student evaluation of library services in Cambridge significantly improved following relocation. The physical accommodation and location of library services remain important to healthcare students. Identifiable improvements to the quality of services, however, will overcome initial resistance to change. Education providers must ensure the best mix of physical and electronic services for students who spend much of their time on clinical placement.

A standard for measuring metadata quality in spectral libraries

NASA Astrophysics Data System (ADS)

Rasaiah, B.; Jones, S. D.; Bellman, C.

2013-12-01

A standard for measuring metadata quality in spectral libraries Barbara Rasaiah, Simon Jones, Chris Bellman RMIT University Melbourne, Australia barbara.rasaiah@rmit.edu.au, simon.jones@rmit.edu.au, chris.bellman@rmit.edu.au ABSTRACT There is an urgent need within the international remote sensing community to establish a metadata standard for field spectroscopy that ensures high quality, interoperable metadata sets that can be archived and shared efficiently within Earth observation data sharing systems. Metadata are an important component in the cataloguing and analysis of in situ spectroscopy datasets because of their central role in identifying and quantifying the quality and reliability of spectral data and the products derived from them. This paper presents approaches to measuring metadata completeness and quality in spectral libraries to determine reliability, interoperability, and re-useability of a dataset. Explored are quality parameters that meet the unique requirements of in situ spectroscopy datasets, across many campaigns. Examined are the challenges presented by ensuring that data creators, owners, and data users ensure a high level of data integrity throughout the lifecycle of a dataset. Issues such as field measurement methods, instrument calibration, and data representativeness are investigated. The proposed metadata standard incorporates expert recommendations that include metadata protocols critical to all campaigns, and those that are restricted to campaigns for specific target measurements. The implication of semantics and syntax for a robust and flexible metadata standard are also considered. Approaches towards an operational and logistically viable implementation of a quality standard are discussed. This paper also proposes a way forward for adapting and enhancing current geospatial metadata standards to the unique requirements of field spectroscopy metadata quality. [0430] BIOGEOSCIENCES / Computational methods and data processing [0480] BIOGEOSCIENCES / Remote sensing [1904] INFORMATICS / Community standards [1912] INFORMATICS / Data management, preservation, rescue [1926] INFORMATICS / Geospatial [1930] INFORMATICS / Data and information governance [1946] INFORMATICS / Metadata [1952] INFORMATICS / Modeling [1976] INFORMATICS / Software tools and services [9810] GENERAL OR MISCELLANEOUS / New fields

Modification and identification of a vector for making a large phage antibody library.

PubMed

Zhang, Guo-min; Chen, Yü-ping; Guan, Yuan-zhi; Wang, Yan; An, Yun-qing

2007-11-20

The large phage antibody library is used to obtain high-affinity human antibody, and the Loxp/cre site-specific recombination system is a potential method for constructing a large phage antibody library. In the present study, a phage antibody library vector pDF was reconstructed to construct diabody more quickly and conveniently without injury to homologous recombination and the expression function of the vector and thus to integrate construction of the large phage antibody library with the preparation of diabodies. scFv was obtained by overlap polymerase chain reaction (PCR) amplification with the newly designed VL and VH extension primers. loxp511 was flanked by VL and VH and the endonuclease ACC III encoding sequences were introduced on both sides of loxp511. scFv was cloned into the vector pDF to obtain the vector pDscFv. The vector expression function was identified and the feasibility of diabody preparation was evaluated. A large phage antibody library was constructed in pDscFv. Several antigens were used to screen the antibody library and the quality of the antibody library was evaluated. The phage antibody library expression vector pDscFv was successfully constructed and confirmed to express functional scFv. The large phage antibody library constructed using this vector was of high diversity. Screening of the library on 6 antigens confirmed the generation of specific antibodies to these antigens. Two antibodies were subjected to enzymatic digestion and were prepared into diabody with functional expression. The reconstructed vector pDscFv retains its recombination capability and expression function and can be used to construct large phage antibody libraries. It can be used as a convenient and quick method for preparing diabodies after simple enzymatic digestion, which facilitates clinical trials and application of antibody therapy.

Benchmarking, Total Quality Management, and Libraries.

ERIC Educational Resources Information Center

Shaughnessy, Thomas W.

1993-01-01

Discussion of the use of Total Quality Management (TQM) in higher education and academic libraries focuses on the identification, collection, and use of reliable data. Methods for measuring quality, including benchmarking, are described; performance measures are considered; and benchmarking techniques are examined. (11 references) (MES)

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

PubMed Central

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

2017-01-01

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

Closing the Gap: The Maturing of Quality Assurance in Australian University Libraries

ERIC Educational Resources Information Center

Tang, Karen

2012-01-01

A benchmarking review of the quality assurance practices of the libraries of the Australian Technology Network conducted in 2006 revealed exemplars of best practice, but also sector-wide gaps. A follow-up review in 2010 indicated the best practices that remain relevant. While some gaps persist, there has been improvement across the libraries and…

Improving Library Service Quality to Graduate Students: LibQual+[TM] Survey Results in a Practical Setting

ERIC Educational Resources Information Center

Jankowska, Maria Anna; Hertel, Karen; Young, Nancy J.

2006-01-01

The LibQUAL+[TM] survey was conducted to determine user satisfaction and expectations concerning library service quality. The results of the "22 items and a box" constituted a rich source of information for the University of Idaho (UI) Library's strategic planning process. Focusing on graduate students, this study used three…

Assessing the Quality of Academic Libraries on the Web: The Development and Testing of Criteria.

ERIC Educational Resources Information Center

Chao, Hungyune

2002-01-01

This study develops and tests an instrument useful for evaluating the quality of academic library Web sites. Discusses criteria for print materials and human-computer interfaces; user-based perspectives; the use of factor analysis; a survey of library experts; testing reliability through analysis of variance; and regression models. (Contains 53…

Structure of Perceptions of Service Quality in Libraries: A LibQUAL+ Study.

ERIC Educational Resources Information Center

Thompson, Bruce; Cook, Colleen; Heath, Fred

2003-01-01

Used confirmatory factor analysis to evaluate the score integrity of LibQUALl+, an instrument to measure perceptions of library service quality. Results for 60,027 graduate and undergraduate students suggest that the model implied by LibQUAL is reasonable and invariant across independent samples and fits all three major subgroups of library users.…

Comparison of the efficiency of antibody selection from semi-synthetic scFv and non-immune Fab phage display libraries against protein targets for rapid development of diagnostic immunoassays.

PubMed

Chan, Conrad E Z; Chan, Annie H Y; Lim, Angeline P C; Hanson, Brendon J

2011-10-28

Rapid development of diagnostic immunoassays against novel emerging or genetically modified pathogens in an emergency situation is dependent on the timely isolation of specific antibodies. Non-immune antibody phage display libraries are an efficient in vitro method for selecting monoclonal antibodies and hence ideal in these circumstances. Such libraries can be constructed from a variety of sources e.g. B cell cDNA or synthetically generated, and use a variety of antibody formats, typically scFv or Fab. However, antibody source and format can impact on the quality of antibodies generated and hence the effectiveness of this methodology for the timely production of antibodies. We have carried out a comparative screening of two antibody libraries, a semi-synthetic scFv library and a human-derived Fab library against the protective antigen toxin component of Bacillus anthracis and the epsilon toxin of Clostridium botulinum. We have shown that while the synthetic library produced a diverse collection of specific scFv-phage, these contained a high frequency of unnatural amber stops and glycosylation sites which limited their conversion to IgG, and also a high number which lost specificity when expressed as IgG. In contrast, these limitations were overcome by the use of a natural human library. Antibodies from both libraries could be used to develop sandwich ELISA assays with similar sensitivity. However, the ease and speed with which full-length IgG could be generated from the human-derived Fab library makes screening this type of library the preferable method for rapid antibody generation for diagnostic assay development. Copyright © 2011 Elsevier B.V. All rights reserved.

Library Computing.

ERIC Educational Resources Information Center

Goodgion, Laurel; And Others

1986-01-01

Eight articles in special supplement to "Library Journal" and "School Library Journal" cover a computer program called "Byte into Books"; microcomputers and the small library; creating databases with students; online searching with a microcomputer; quality automation software; Meckler Publishing Company's…

MyTeachingPartner-Secondary. What Works Clearinghouse Intervention Report [Revised

ERIC Educational Resources Information Center

What Works Clearinghouse, 2015

2015-01-01

MyTeachingPartner-Secondary (MTP-S) is a professional development program that aims to increase student learning and development through improved teacher-student interactions. Through the program, middle and high school teachers access a video library featuring examples of high-quality interactions and receive individualized, web-based coaching…

The Future of Catalogers and Cataloging.

ERIC Educational Resources Information Center

Holley, Robert P.

1981-01-01

Future emphasis in cataloging will be on the sharing of high quality bibliographic records through a national network. As original cataloging decreases, catalogers, rather than disappearing, will more likely be managers of the library's bibliographic control system. (Author/RAA)

Awards and Recognition

MedlinePlus

... this page, please enable JavaScript. Produced by the world's largest medical library, MedlinePlus offers high-quality, up-to-date health information on over 1000 different diseases, conditions, and wellness issues. With over 1 million daily visitors, MedlinePlus provides ...

A universal phage display system for the seamless construction of Fab libraries.

PubMed

Nelson, Renae S; Valadon, Philippe

2017-11-01

The construction of Fab phage libraries requires the cloning of domains from both the light and the heavy chain of antibodies. Despite the advent of powerful strategies such as splicing-by-overlap extension PCR, obtaining high quality libraries with excellent coverage remains challenging. Here, we explored the use of type IIS restriction enzymes for the seamless cloning of Fab libraries. We analyzed human, murine and rabbit germline antibody repertoires and identified combinations of restriction enzymes that exhibit very few or no recognition sites in the antibody sequences. We describe three phagemid vectors, pUP-22Hb, pUP-22Mc and pUP-22Rc, which were employed for cloning the Fab repertoire of these hosts using BsmBI and SapI (human) or SapI alone (mouse and rabbit). Using human serum albumin as a model immunization, we built a mouse/human chimeric Fab library and a mouse Fab library in a single step ligation and successfully panned multiple cognate antibodies. The overall process is highly scalable and faster than PCR-based techniques, with a Fab insertion success rate of around 80%. By using carefully chosen overhangs on each end of the antibody domains, this approach paves the way to the universal, sequence- and vector-independent cloning and reformatting of antibody libraries. Copyright © 2017 Elsevier B.V. All rights reserved.

Public Libraries: Responding to Demand.

ERIC Educational Resources Information Center

Annichiarico, Mark; And Others

1993-01-01

Discussion of problems library wholesalers/distributors face trying to fulfill public libraries' needs while adjusting to a changing industry is based on responses by librarians to a survey on library jobbers. Increased services to libraries, electronic ordering, timeliness, stock management, and quality control are addressed; and a chart of…

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

PubMed Central

2011-01-01

Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol. PMID:21205303

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

PubMed

Mora-Castilla, Sergio; To, Cuong; Vaezeslami, Soheila; Morey, Robert; Srinivasan, Srimeenakshi; Dumdie, Jennifer N; Cook-Andersen, Heidi; Jenkins, Joby; Laurent, Louise C

2016-08-01

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing. © 2016 Society for Laboratory Automation and Screening.

The Case for Quality Book Selection.

ERIC Educational Resources Information Center

Bob, Murray C.

1982-01-01

This essay on library book selection critiques Nora Rawlinson's article on practices at the Baltimore County Public Library which appeared in Library Journal, November 15, 1981, p. 2188, and discusses library circulation statistics in relation to book selection. (EJS)

Quality Assurance in Distance Learning Libraries

ERIC Educational Resources Information Center

Tripathi, Manorama; Jeevan, V. K. J.

2009-01-01

Purpose: The paper aims to study how the present distance learning libraries can improve upon their existing services and introduce new ones to enhance quality of services to distance learners. Design/methodology/approach: The paper includes a review of literature on quality assurance in open and distance education in general and student support…

Biomathematical Description of Synthetic Peptide Libraries

PubMed Central

Trepel, Martin

2015-01-01

Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries. PMID:26042419

Federal Public Library Programs in Alabama, 1999.

ERIC Educational Resources Information Center

Alabama Public Library Service, Montgomery.

The Alabama Public Library Service (APLS) is charged with improving library services throughout the state to ensure that all citizens have access to quality library and information services. Part of this charge includes the responsibility for receiving and administering federal funds to the more than 200 public libraries in Alabama. Federal…

A communication library for the parallelization of air quality models on structured grids

NASA Astrophysics Data System (ADS)

Miehe, Philipp; Sandu, Adrian; Carmichael, Gregory R.; Tang, Youhua; Dăescu, Dacian

PAQMSG is an MPI-based, Fortran 90 communication library for the parallelization of air quality models (AQMs) on structured grids. It consists of distribution, gathering and repartitioning routines for different domain decompositions implementing a master-worker strategy. The library is architecture and application independent and includes optimization strategies for different architectures. This paper presents the library from a user perspective. Results are shown from the parallelization of STEM-III on Beowulf clusters. The PAQMSG library is available on the web. The communication routines are easy to use, and should allow for an immediate parallelization of existing AQMs. PAQMSG can also be used for constructing new models.

IFLA General Conference, 1990. Division of Special Libraries: Section of Administrative Libraries; Section of Social Science Libraries; Section of Science and Technology Libraries; Section of Biological and Medical Sciences Libraries; Section of Art Libraries. Booklet 2.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

The 23 papers in this collection were presented at 5 sections of the Division of Special Libraries: (1) "Principles of Government Librarianship" (Hans H. van der Neut); (2) "Strategic Planning as an Instrument of Improving Library Quality" (Maurice B. Line); (3) "Library Staff Development Consultancy: A Means to Achieve a…

The OCLC-SERHOLD connection: an evolution in health sciences union listing.

PubMed Central

Battistella, M S

1991-01-01

The OCLC Union List Subsystem (OCLC ULS) provides a standard, high quality, and widely used means of managing union list data. Over the last several years, OCLC ULS tape products have been used by thirteen health sciences libraries or groups to update SERHOLD. These thirteen libraries or groups were surveyed to examine practices in using OCLC to update SERHOLD. The National Library of Medicine's (NLM) processing of OCLC tape products was assessed to determine how OCLC data are handled by SERHOLD. Most important are the assignment of OCLC holdings symbols, OCLC record selection criteria, tape pull cycles, and the processing of exception reports produced by NLM as a result of tape loads. PMID:1958909

The OCLC-SERHOLD connection: an evolution in health sciences union listing.

PubMed

Battistella, M S

1991-10-01

The OCLC Union List Subsystem (OCLC ULS) provides a standard, high quality, and widely used means of managing union list data. Over the last several years, OCLC ULS tape products have been used by thirteen health sciences libraries or groups to update SERHOLD. These thirteen libraries or groups were surveyed to examine practices in using OCLC to update SERHOLD. The National Library of Medicine's (NLM) processing of OCLC tape products was assessed to determine how OCLC data are handled by SERHOLD. Most important are the assignment of OCLC holdings symbols, OCLC record selection criteria, tape pull cycles, and the processing of exception reports produced by NLM as a result of tape loads.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Association of journal quality indicators with methodological quality of clinical research articles.

PubMed

Lee, Kirby P; Schotland, Marieka; Bacchetti, Peter; Bero, Lisa A

2002-06-05

The ability to identify scientific journals that publish high-quality research would help clinicians, scientists, and health-policy analysts to select the most up-to-date medical literature to review. To assess whether journal characteristics of (1) peer-review status, (2) citation rate, (3) impact factor, (4) circulation, (5) manuscript acceptance rate, (6) MEDLINE indexing, and (7) Brandon/Hill Library List indexing are predictors of methodological quality of research articles, we conducted a cross-sectional study of 243 original research articles involving human subjects published in general internal medical journals. The mean (SD) quality score of the 243 articles was 1.37 (0.22). All journals reported a peer-review process and were indexed on MEDLINE. In models that controlled for article type (randomized controlled trial [RCT] or non-RCT), journal citation rate was the most statistically significant predictor (0.051 increase per doubling; 95% confidence interval [CI], 0.037-0.065; P<.001). In separate analyses by article type, acceptance rate was the strongest predictor for RCT quality (-0.113 per doubling; 95% CI, -0.148 to -0.078; P<.001), while journal citation rate was the most predictive factor for non-RCT quality (0.051 per doubling; 95% CI, 0.044-0.059; P<.001). High citation rates, impact factors, and circulation rates, and low manuscript acceptance rates and indexing on Brandon/Hill Library List appear to be predictive of higher methodological quality scores for journal articles.

Does LibQUAL+[TM] Account for Student Loyalty to a University College Library?

ERIC Educational Resources Information Center

Helgesen, Oyvind; Nesset, Erik

2011-01-01

Purpose: The purpose of this paper is to find out whether LibQUAL+[TM]can account for student loyalty to the library of an institution of higher education. LibQUAL+[TM] is a marketing tool that is used to measure perceived service quality of libraries, and the present analysis aims at validating this service quality instrument within a more…

Massachusetts Libraries: An Alliance for the Future. [Final Report and Executive Summary] for the Massachusetts Board of Library Commissioners.

ERIC Educational Resources Information Center

Griffiths, Jose-Marie; King, Donald W.

A comprehensive study of the current state of library services and library cooperative activities in Massachusetts found that the state's 2,796 public, academic, school, institutional and special libraries make a significant contribution to lifelong learning, to the economy, and to the quality of life. The libraries have a combined collection of…

Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization1

PubMed Central

Yim, Young-Sun; Davis, Georgia L.; Duru, Ngozi A.; Musket, Theresa A.; Linton, Eric W.; Messing, Joachim W.; McMullen, Michael D.; Soderlund, Carol A.; Polacco, Mary L.; Gardiner, Jack M.; Coe, Edward H.

2002-01-01

Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage λ. The results indicate that the libraries are of high quality with low contamination by organellar and λ-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6× coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 × Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 ± 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction. PMID:12481051

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

From Planning to Improvement: Monash University Library's Quality Review

ERIC Educational Resources Information Center

Pernat, Marie

2004-01-01

During 2003, Monash University Library conducted a comprehensive quality review as part of the university's program of reviews. A quality management group was established in September 2002 to drive the process. All staff were given the opportunity to contribute input to the initial self-review. Methods of collecting data, collating responses and…

Distribution and Availability of State and Areawide Water Quality Reports in Oklahoma Libraries.

ERIC Educational Resources Information Center

McClure, Charles R.; Million, Anne

This report examines the distribution and availability of water quality reports in the state of Oklahoma. Based on legislation from the Clean Water Act and regulations from the Environmental Protection Agency's "Public Participation Handbook for Water Quality Management," depository libraries must be established to provide citizen access to…

A Five Year Plan; Pennsylvania Library Development, 1971-1976.

ERIC Educational Resources Information Center

Pennsylvania State Library, Harrisburg.

The objective of Pennsylvania's State Plan for use of Library Services and Construction Act (LSCA) funds is continued development of a statewide system of libraries so that good quality, free, convenient, public library service will be available to every resident of the state. The system consists of: (1) local libraries or bookmobile stops so…

Subtractive transcriptome analysis of leaf and rhizome reveals differentially expressed transcripts in Panax sokpayensis.

PubMed

Gurung, Bhusan; Bhardwaj, Pardeep K; Talukdar, Narayan C

2016-11-01

In the present study, suppression subtractive hybridization (SSH) strategy was used to identify rare and differentially expressed transcripts in leaf and rhizome tissues of Panax sokpayensis. Out of 1102 randomly picked clones, 513 and 374 high quality expressed sequenced tags (ESTs) were generated from leaf and rhizome subtractive libraries, respectively. Out of them, 64.92 % ESTs from leaf and 69.26 % ESTs from rhizome SSH libraries were assembled into different functional categories, while others were of unknown function. In particular, ESTs encoding galactinol synthase 2, ribosomal RNA processing Brix domain protein, and cell division cycle protein 20.1, which are involved in plant growth and development, were most abundant in the leaf SSH library. Other ESTs encoding protein KIAA0664 homologue, ubiquitin-activating enzyme e11, and major latex protein, which are involved in plant immunity and defense response, were most abundant in the rhizome SSH library. Subtractive ESTs also showed similarity with genes involved in ginsenoside biosynthetic pathway, namely farnesyl pyrophosphate synthase, squalene synthase, and dammarenediol synthase. Expression profiles of selected ESTs validated the quality of libraries and confirmed their differential expression in the leaf, stem, and rhizome tissues. In silico comparative analyses revealed that around 13.75 % of unigenes from the leaf SSH library were not represented in the available leaf transcriptome of Panax ginseng. Similarly, around 18.12, 23.75, 25, and 6.25 % of unigenes from the rhizome SSH library were not represented in available root/rhizome transcriptomes of P. ginseng, Panax notoginseng, Panax quinquefolius, and Panax vietnamensis, respectively, indicating a major fraction of novel ESTs. Therefore, these subtractive transcriptomes provide valuable resources for gene discovery in P. sokpayensis and would complement the available transcriptomes from other Panax species.

North Carolina Library Association 1997 Biennial Conference.

ERIC Educational Resources Information Center

North Carolina Libraries, 1997

1997-01-01

Provides summaries of the presentations at the North Carolina Library Association's Biennial Conference, "Choose Quality, Choose Libraries," (Raleigh, NC, October 8-10, 1997). Some of the topics covered include library instruction, Internet access to public documents, outsourcing technical services, copyrights and the Internet, the…

Evaluation of vector-primed cDNA library production from microgram quantities of total RNA.

PubMed

Kuo, Jonathan; Inman, Jason; Brownstein, Michael; Usdin, Ted B

2004-12-15

cDNA sequences are important for defining the coding region of genes, and full-length cDNA clones have proven to be useful for investigation of the function of gene products. We produced cDNA libraries containing 3.5-5 x 10(5) primary transformants, starting with 5 mug of total RNA prepared from mouse pituitary, adrenal, thymus, and pineal tissue, using a vector-primed cDNA synthesis method. Of approximately 1000 clones sequenced, approximately 20% contained the full open reading frames (ORFs) of known transcripts, based on the presence of the initiating methionine residue codon. The libraries were complex, with 94, 91, 83 and 55% of the clones from the thymus, adrenal, pineal and pituitary libraries, respectively, represented only once. Twenty-five full-length clones, not yet represented in the Mammalian Gene Collection, were identified. Thus, we have produced useful cDNA libraries for the isolation of full-length cDNA clones that are not yet available in the public domain, and demonstrated the utility of a simple method for making high-quality libraries from small amounts of starting material.

User experiences of evidence-based online resources for health professionals: User testing of The Cochrane Library

PubMed Central

Rosenbaum, Sarah E; Glenton, Claire; Cracknell, Jane

2008-01-01

Background Evidence-based decision making relies on easy access to trustworthy research results. The Cochrane Library is a key source of evidence about the effect of interventions and aims to "promote the accessibility of systematic reviews to anyone wanting to make a decision about health care". We explored how health professionals found, used and experienced The Library, looking at facets of user experience including findability, usability, usefulness, credibility, desirability and value. Methods We carried out 32 one-hour usability tests on participants from Norway and the UK. Participants both browsed freely and attempted to perform individually tailored tasks while "thinking aloud". Sessions were recorded and viewed in real time by researchers. Transcriptions and videos were reviewed by one researcher and one designer. Findings reported here reflect issues receiving a high degree of saturation and that we judge to be critical to the user experience of evidence-based web sites, based on principles for usability heuristics, web guidelines and evidence-based practice. Results Participants had much difficulty locating both the site and its contents. Non-native English speakers were at an extra disadvantage when retrieving relevant documents despite high levels of English-language skills. Many participants displayed feelings of ineptitude, alienation and frustration. Some made serious mistakes in correctly distinguishing between different information types, for instance reviews, review protocols, and individual studies. Although most expressed a high regard for the site's credibility, some later displayed a mistrust of the independence of the information. Others were overconfident, thinking everything on The Cochrane Library site shared the same level of quality approval. Conclusion Paradoxically, The Cochrane Library, established to support easy access to research evidence, has its own problems of accessibility. Health professionals' experiences of this and other evidence-based online resources can be improved by applying existing principles for web usability, prioritizing the development of simple search functionality, emitting "researcher" jargon, consistent marking of site ownership, and clear signposting of different document types and different content quality. PMID:18662382

Nursing staff connect libraries with improving patient care but not with achieving organisational objectives: a grounded theory approach.

PubMed

Chamberlain, David; Brook, Richard

2014-03-01

Health organisations are often driven by specific targets defined by mission statements, aims and objectives to improve patient care. Health libraries need to demonstrate that they contribute to organisational objectives, but it is not clear how nurses view that contribution. To investigate ward nursing staff motivations, their awareness of ward and organisational objectives; and their attitudes towards the contribution of health library services to improving patient care. Qualitative research using focus group data was combined with content analysis of literature evidence and library statistics (quantitative data). Data were analysed using thematic coding, divided into five group themes: understanding of Trust, Ward and Personal objectives, use of Library, use of other information sources, quality and Issues. Four basic social-psychological processes were then developed. Behaviour indicates low awareness of organisational objectives despite patient-centric motivation. High awareness of library services is shown with some connection made by ward staff between improved knowledge and improved patient care. There was a two-tiered understanding of ward objectives and library services, based on level of seniority. However, evidence-based culture needs to be intrinsic in the organisation before all staff benefit. Libraries can actively engage in this at ward and board level and improve patient care by supporting organisational objectives. © 2014 The author. Health Information and Libraries Journal © 2014 Health Libraries Group.

MISR Regional VBBE Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:   Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional UAE2 Map Projection

Atmospheric Science Data Center

2013-03-26

... Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

Combinatorial Optimization of Heterogeneous Catalysts Used in the Growth of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Cassell, Alan M.; Verma, Sunita; Delzeit, Lance; Meyyappan, M.; Han, Jie

2000-01-01

Libraries of liquid-phase catalyst precursor solutions were printed onto iridium-coated silicon substrates and evaluated for their effectiveness in catalyzing the growth of multi-walled carbon nanotubes (MWNTs) by chemical vapor deposition (CVD). The catalyst precursor solutions were composed of inorganic salts and a removable tri-block copolymer (EO)20(PO)70(EO)20 (EO = ethylene oxide, PO = propylene oxide) structure-directing agent (SDA), dissolved in ethanol/methanol mixtures. Sample libraries were quickly assayed using scanning electron microscopy after CVD growth to identify active catalysts and CVD conditions. Composition libraries and focus libraries were then constructed around the active spots identified in the discovery libraries to understand how catalyst precursor composition affects the yield, density, and quality of the nanotubes. Successful implementation of combinatorial optimization methods in the development of highly active, carbon nanotube catalysts is demonstrated, as well as the identification of catalyst formulations that lead to varying densities and shapes of aligned nanotube towers.

Total Quality Management in Academic Libraries: Initial Implementation Efforts. Proceedings from the International Conference on TQM and Academic Libraries (1st, Washington, D.C., April 20-22, 1994).

ERIC Educational Resources Information Center

Rounds, Laura, Ed.; Matthews, Michael, Ed.

This document contains conference papers, other speeches, and supplementary material from the first International Conference on Total Quality Management (TQM) and Academic Libraries, held in 1994. The conference was comprised of four sessions, and the introductory remarks of each are included, along with transcriptions of each session's…

Perspectives on User Satisfaction Surveys.

ERIC Educational Resources Information Center

Cullen, Rowena

2001-01-01

Discusses academic libraries, digital environments, increasing competition, the relationship between service quality and user satisfaction, and user surveys. Describes the SERVQUAL model that measures service quality and user satisfaction in academic libraries; considers gaps between user expectations and managers' perceptions of user…

Evaluating clinical librarian services: a systematic review.

PubMed

Brettle, Alison; Maden-Jenkins, Michelle; Anderson, Lucy; McNally, Rosalind; Pratchett, Tracey; Tancock, Jenny; Thornton, Debra; Webb, Anne

2011-03-01

  Previous systematic reviews have indicated limited evidence and poor quality evaluations of clinical librarian (CL) services. Rigorous evaluations should demonstrate the value of CL services, but guidance is needed before this can be achieved.   To undertake a systematic review which examines models of CL services, quality, methods and perspectives of clinical librarian service evaluations.   Systematic review methodology and synthesis of evidence, undertaken collaboratively by a group of 8 librarians to develop research and critical appraisal skills.   There are four clear models of clinical library service provision. Clinical librarians are effective in saving health professionals time, providing relevant, useful information and high quality services. Clinical librarians have a positive effect on clinical decision making by contributing to better informed decisions, diagnosis and choice of drug or therapy. The quality of CL studies is improving, but more work is needed on reducing bias and providing evidence of specific impacts on patient care. The Critical Incident Technique as part of a mixed method approach appears to offer a useful approach to demonstrating impact.   This systematic review provides practical guidance regarding the evaluation of CL services. It also provides updated evidence regarding the effectiveness and impact of CL services. The approach used was successful in developing research and critical appraisal skills in a group of librarians. © 2010 The authors. Health Information and Libraries Journal © 2010 Health Libraries Group.

MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences

PubMed Central

Venier, Paola; De Pittà, Cristiano; Bernante, Filippo; Varotto, Laura; De Nardi, Barbara; Bovo, Giuseppe; Roch, Philippe; Novoa, Beatriz; Figueras, Antonio; Pallavicini, Alberto; Lanfranchi, Gerolamo

2009-01-01

Background Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria. Results We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database . Conclusion We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels. PMID:19203376

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

PubMed

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

2017-03-22

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

Alabama Public Library Service, The State Library Agency. 1986 Annual Report.

ERIC Educational Resources Information Center

Alabama Public Library Service, Montgomery.

Designed to provide an overview of the range and quality of services provided by the Alabama Public Library Service (APLS), this annual report focuses on the 1986 activities of APLS; the state's public library directory and statistical report will be published separately. A discussion of the activities of the Library Development Division includes…

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,…

Building Earth's Largest Library: Driving into the Future.

ERIC Educational Resources Information Center

Coffman, Steve

1999-01-01

Examines the Amazon.com online bookstore as a blueprint for designing the world's largest library. Topics include selection; accessibility and convenience; quality of Web sites and search tools; personalized service; library collection development, including interlibrary loan; library catalogs and catalog records; a circulation system; costs;…

Library-Based Learning in an Information Society.

ERIC Educational Resources Information Center

Breivik, Patricia Senn

1986-01-01

The average academic library has great potential for quality nonclassroom learning benefiting students, faculty, alumni, and the local business community. The major detriments are the limited perceptions about libraries and librarians among campus administrators and faculty. Library-based learning should be planned to be assimilated into overall…

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.

Western European Art Foundations and Publishing

ERIC Educational Resources Information Center

King, Lindsay M.; Clement, Russell T.

2011-01-01

Western European art foundations create invaluable opportunities for research and exhibition by artists, curators, and scholars. These activities are often documented and disseminated via high-quality publications. This article highlights an important but under-recognized collecting resource for academic and museum libraries by profiling several…

MISR Regional SAMUM Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

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.

The necessity of measurement.

PubMed

Dudden, Rosalind Farnam

2008-01-01

Measurement of library systems and services is a multidimensional management task. New paradigms of library service and the context in which libraries operate have made it necessary for librarians to find new measures while at the same time keeping the old. Factors that can be measured, such as needs, inputs, quality processes, outputs, quality of service, outcomes, and impacts, are described. This bibliographic essay covers the current trends while leading readers to resources where they can learn more.

Focus on Customer Service. Service Management: How to Plan for it Rather Than Hope for It [and] Learning to Say "Yes": A Customer Service Program for Library Staff [and] Maintaining Momentum in a Quality Improvement Process.

ERIC Educational Resources Information Center

Brewer, Julie; And Others

1995-01-01

Presents three articles that discuss customer service in libraries, with a focus on planning for service management, a customer service program for library staff, and a quality improvement process. Highlights include developing and implementing service strategies, dealing with requests, redefining work relationships, coworkers as customers,…

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.

PubMed

Si, Zengzhi; Du, Bing; Huo, Jinxi; He, Shaozhen; Liu, Qingchang; Zhai, Hong

2016-11-21

Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93-10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library.

PubMed

Hoffberg, Sandra L; Troendle, Nicholas J; Glenn, Travis C; Mahmud, Ousman; Louha, Swarnali; Chalopin, Domitille; Bennetzen, Jeffrey L; Mauricio, Rodney

2018-04-27

The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species. Copyright © 2018, G3: Genes, Genomes, Genetics.

Forward view: advancing health library and knowledge services in England.

PubMed

Lacey Bryant, Sue; Bingham, Helen; Carlyle, Ruth; Day, Alison; Ferguson, Linda; Stewart, David

2018-03-01

This article is the fourth in a series on New Directions. The National Health Service is under pressure, challenged to meet the needs of an ageing population, whilst striving to improve standards and ensure decision making is underpinned by evidence. Health Education England is steering a new course for NHS library and knowledge services in England to ensure access to knowledge and evidence for all decision makers. Knowledge for Healthcare calls for service transformation, role redesign, greater coordination and collaboration. To meet user expectations, health libraries must achieve sustainable, affordable access to digital content. Traditional tasks will progressively become mechanised. Alongside supporting learners, NHS librarians and knowledge specialists will take a greater role as knowledge brokers, delivering business critical services. They will support the NHS workforce to signpost patients and the public to high-quality information. There is a need for greater efficiency and effectiveness through greater co-operation and service mergers. Evaluation of service quality will focus more on outcomes, less on counting. These changes require an agile workforce, fit for the future. There is a bright future in which librarians' expertise is used to mobilise evidence, manage and share knowledge, support patients, carers and families, optimise technology and social media and provide a keystone for improved patient care and safety. © 2018 Health Libraries Group.

Measuring Quality in Special Libraries: Lessons from Service Marketing.

ERIC Educational Resources Information Center

White, Marilyn Domas; Abels, Eileen G.

1995-01-01

Surveys the service marketing literature for models and data-gathering instruments measuring service quality, particularly the instruments SERVQUAL and SERVPERF, and assesses their applicability to special libraries and information centers. Topics include service characteristics and definitions of service; performance-minus-expectations and…

East Asian Collections and Organizational Transformation in Academic Libraries.

ERIC Educational Resources Information Center

Kamada, Hitoshi

2002-01-01

Discusses special aspects of East Asian collections and explores how organizational changes in academic libraries affect them, based on experiences at the University of Arizona. Considers total quality management; continuous quality improvement; teamwork; staffing changes; specialization versus generalization; budgetary restraints and cost…

Alabama Public Library Service Annual Report, 1995.

ERIC Educational Resources Information Center

Alabama Public Library Service, Montgomery.

This annual report summarizes activities of the Alabama Public Library Service (APLS) for the fiscal year 1995. The APLS is charged with improving library services throughout the state to ensure that all citizens have access to quality library and information services. During fiscal year 1995, major building renovations were completed with the…

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,…

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…

Comparing Service Priorities between Staff and Users in Association of Research Libraries (ARL) Member Libraries

ERIC Educational Resources Information Center

Jaggars, Damon E.; Jaggars, Shanna Smith; Duffy, Jocelyn S.

2009-01-01

Using the results for participating Association of Research Libraries from the 2006 LibQUAL+[R] library service quality survey, we examine the service priorities of library staff (for example, whether desired scores for each survey item are above or below average) and the extent to which they are aligned with the priorities of undergraduates,…

Cartographic symbol library considering symbol relations based on anti-aliasing graphic library

NASA Astrophysics Data System (ADS)

Mei, Yang; Li, Lin

2007-06-01

Cartographic visualization represents geographic information with a map form, which enables us retrieve useful geospatial information. In digital environment, cartographic symbol library is the base of cartographic visualization and is an essential component of Geographic Information System as well. Existing cartographic symbol libraries have two flaws. One is the display quality and the other one is relations adjusting. Statistic data presented in this paper indicate that the aliasing problem is a major factor on the symbol display quality on graphic display devices. So, effective graphic anti-aliasing methods based on a new anti-aliasing algorithm are presented and encapsulated in an anti-aliasing graphic library with the form of Component Object Model. Furthermore, cartographic visualization should represent feature relation in the way of correctly adjusting symbol relations besides displaying an individual feature. But current cartographic symbol libraries don't have this capability. This paper creates a cartographic symbol design model to implement symbol relations adjusting. Consequently the cartographic symbol library based on this design model can provide cartographic visualization with relations adjusting capability. The anti-aliasing graphic library and the cartographic symbol library are sampled and the results prove that the two libraries both have better efficiency and effect.

Higher-Order Factor Analysis as a Score Validity Evaluation Tool: An Example with a Measure of Perceptions of Library Service Quality.

ERIC Educational Resources Information Center

Cook, Colleen; Thompson, Bruce

The SERVQUAL measure was developed by A. Parasuraman, L. Berry, and V. Zeithaml (1988) to measure perceptions of service quality, originally in the retailing sector. However, libraries and other educational institutions are also service providers. Librarians in particular have increasingly become interested in measuring quality of service as the…

Comparison of methods for library construction and short read annotation of shellfish viral metagenomes.

PubMed

Wei, Hong-Ying; Huang, Sheng; Wang, Jiang-Yong; Gao, Fang; Jiang, Jing-Zhe

2018-03-01

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI's NR and Uniprot's Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

Developing a long-term condition's information service in collaboration with third sector organisations.

PubMed

McShane, Lesley; Greenwell, Kate; Corbett, Sally; Walker, Richard

2014-06-01

People with long-term conditions need to be signposted to high quality information and advice to understand and manage their condition. Information seeking tools combined with third sector information could help address their information needs. To describe the development and implementation of an information service for people living with long-term conditions at one NHS acute trust in the Northeast of England. An information service was trialled using bespoke information models for three long-term conditions in collaboration with third sector organisations. These guided people to relevant, timely and reliable information. Both clinician and service user questionnaires were used to evaluate satisfaction with the service. Appropriately designed information models can be used interchangeably across all services. Between 75% and 91% of users agreed that they were satisfied with various aspects of the service. Generally, users received relevant, understandable and high quality information at the right time. Nearly all health professionals (94-100%) felt the service was accessible, provided high quality information and did not significantly impact on their consultation time. The developed information service was well received by service users and health professionals. Specifically, the use of information prescriptions and menus facilitated access to information for people with long-term conditions. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Group.

Toward a TQM Paradigm: Using SERVQUAL to Measure Library Service Quality.

ERIC Educational Resources Information Center

Coleman, Vicki; And Others

1997-01-01

Texas A&M University's Evans Library conducted a survey (SERVQUAL) to measure service quality in terms of tangibles (appearance of facilities, equipment, personnel, and communication materials), reliability, responsiveness, assurance, and empathy. Discrepancies between expectations and perceptions were found in reliability, responsiveness,…

Evaluation of School Library Media Centers: Demonstrating Quality.

ERIC Educational Resources Information Center

Everhart, Nancy

2003-01-01

Discusses ways to evaluate school library media programs and how to demonstrate quality. Topics include how principals evaluate programs; sources of evaluative data; national, state, and local instruments; surveys and interviews; Colorado benchmarks; evaluating the use of electronic resources; and computer reporting options. (LRW)

34 CFR 656.22 - What selection criteria does the Secretary use to evaluate an application for an undergraduate...

Code of Federal Regulations, 2014 CFR

2014-07-01

... other libraries or on-line databases and the extent to which teachers, students, and faculty from other... program of high quality; and (2) The extent to which the Center provides academic and career advising...

34 CFR 656.22 - What selection criteria does the Secretary use to evaluate an application for an undergraduate...

Code of Federal Regulations, 2013 CFR

2013-07-01

... other libraries or on-line databases and the extent to which teachers, students, and faculty from other... program of high quality; and (2) The extent to which the Center provides academic and career advising...

34 CFR 656.22 - What selection criteria does the Secretary use to evaluate an application for an undergraduate...

Code of Federal Regulations, 2011 CFR

2011-07-01

... other libraries or on-line databases and the extent to which teachers, students, and faculty from other... program of high quality; and (2) The extent to which the Center provides academic and career advising...

34 CFR 656.22 - What selection criteria does the Secretary use to evaluate an application for an undergraduate...

Code of Federal Regulations, 2012 CFR

2012-07-01

... other libraries or on-line databases and the extent to which teachers, students, and faculty from other... program of high quality; and (2) The extent to which the Center provides academic and career advising...

34 CFR 656.22 - What selection criteria does the Secretary use to evaluate an application for an undergraduate...

Code of Federal Regulations, 2010 CFR

2010-07-01

... other libraries or on-line databases and the extent to which teachers, students, and faculty from other... program of high quality; and (2) The extent to which the Center provides academic and career advising...

MISR Regional INTEX-B Map Projection

Atmospheric Science Data Center

2016-09-28

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

MISR Regional GoMACCS Map Projection

Atmospheric Science Data Center

2017-03-29

... Regional Imagery:  Overview  |  Products  |  Data Quality  | Map Projection |  File Format  |  View Data  |  ... is needed if you are doing high precision work. The packages mentioned about (HDF-EOS library, GCTP, and IDL) all convert to and ...

Issues Facing Academic Library Consortia and Perceptions of Members of the Illinois Digital Academic Library.

ERIC Educational Resources Information Center

Brooks, Sam; Dorst, Thomas J.

2002-01-01

Discusses the role of consortia in academic libraries, specifically the Illinois Digital Academic Library (IDAL), and describes a study conducted by the IDAL that investigated issues surrounding full text database research including stability of content, vendor communication, embargo periods, publisher concerns, quality of content, linking and…

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…

Training for QSC: How McDonald's Makes Library Managers.

ERIC Educational Resources Information Center

Aycock, Anthony

2001-01-01

Written by a former McDonald's manager who earned a master's degree in library science, this article describes how "QSC"--quality, services, and cleanliness--can be applied to libraries in the same way it is used by restaurants. Argues that libraries are simply businesses that cater to customers. (Contains 42 references.) (NB)

The Profiles in Science Digital Library: Behind the Scenes.

PubMed

Gallagher, Marie E; Moffatt, Christie

2012-01-01

This demonstration shows the Profiles in Science ® digital library. Profiles in Science contains digitized selections from the personal manuscript collections of prominent biomedical researchers, medical practitioners, and those fostering science and health. The Profiles in Science Web site is the delivery mechanism for content derived from the digital library system. The system is designed according to our basic principles for digital library development [1]. The digital library includes the rules and software used for digitizing items, creating and editing database records and performing quality control as well as serving the digital content to the public. Among the types of data managed by the digital library are detailed item-level, collection-level and cross-collection metadata, digitized photographs, papers, audio clips, movies, born-digital electronic files, optical character recognized (OCR) text, and annotations (see Figure 1). The digital library also tracks the status of each item, including digitization quality, sensitivity of content, and copyright. Only items satisfying all required criteria are released to the public through the World Wide Web. External factors have influenced all aspects of the digital library's infrastructure.

Changes in the Quality of Paper in French Books, 1860-1914: A Study of Selected Holdings of the Wilson Library, University of North Carolina.

ERIC Educational Resources Information Center

Rutledge, John; Owen, Willy

1983-01-01

This survey of paper quality of French-language holdings in history and literature (1860-1914) at Wilson Library reveals that a serious decline in paper quality in French books began around 1885 and continued through the rest of the period. Data on specific publishers and 14 references are included. (EJS)

Evaluation of a Digital Library by Means of Quality Function Deployment (QFD) and the Kano Model

ERIC Educational Resources Information Center

Garibay, Cecilia; Gutierrez, Humberto; Figueroa, Arturo

2010-01-01

This paper proposes utilizing a combination of the Quality Function Deployment (QFD)-Kano model as a useful tool to evaluate service quality. The digital library of the University of Guadalajara (Mexico) is presented as a case study. Data to feed the QFD-Kano model was gathered by an online questionnaire that was made available to users on the…

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Virtual in-service training from the librarians' point of view in libraries of medical sciences universities in Tehran.

PubMed

Mohaghegh, Niloofar; Raiesi Dehkordi, Puran; Alibeik, MohammadReza; Ghashghaee, Ahmad; Janbozorgi, Mojgan

2016-01-01

Background: In-service training courses are one of the most available programs that are used to improve the quantity and quality level of the staff services in various organizations, including libraries and information centers. With the advent of new technologies in the field of education, the problems and shortcomings of traditional in-service training courses were replaced with virtual ones. This study aimed to evaluate the virtual in-service training courses from the librarians' point of view in libraries of state universities of medical sciences in Tehran. Methods: This was a descriptive- analytical study. The statistical population consisted of all librarians at libraries of universities of medical sciences in Tehran. Out of 103 librarians working in the libraries under the study, 93 (90%) participated in this study. Data were collected, using a questionnaire. Results: The results revealed that 94/6% of librarians were satisfied to participate in virtual in-service training courses. In this study, only 45 out of 93 participants said that the virtual in-service courses were held in their libraries. Of the participants, 75.6% were satisfied with the length of training courses, and one month seemed to be adequate time duration for the librarians to be more satisfied. The satisfaction level of the individuals who participated in in-service courses of the National Library was moderate to high. A total of 84.4% participants announced that the productivity level of the training courses was moderate to high. The most important problem with which the librarians were confronted in virtual in-service training was the "low speed of the internet and inadequate computer substructures". Conclusion: Effectiveness of in-service training courses from librarians' point of view was at an optimal level in the studied libraries.

Virtual in-service training from the librarians' point of view in libraries of medical sciences universities in Tehran

PubMed Central

Mohaghegh, Niloofar; Raiesi Dehkordi, Puran; Alibeik, MohammadReza; Ghashghaee, Ahmad; Janbozorgi, Mojgan

2016-01-01

Background: In-service training courses are one of the most available programs that are used to improve the quantity and quality level of the staff services in various organizations, including libraries and information centers. With the advent of new technologies in the field of education, the problems and shortcomings of traditional in-service training courses were replaced with virtual ones. This study aimed to evaluate the virtual in-service training courses from the librarians' point of view in libraries of state universities of medical sciences in Tehran. Methods: This was a descriptive- analytical study. The statistical population consisted of all librarians at libraries of universities of medical sciences in Tehran. Out of 103 librarians working in the libraries under the study, 93 (90%) participated in this study. Data were collected, using a questionnaire. Results: The results revealed that 94/6% of librarians were satisfied to participate in virtual in-service training courses. In this study, only 45 out of 93 participants said that the virtual in-service courses were held in their libraries. Of the participants, 75.6% were satisfied with the length of training courses, and one month seemed to be adequate time duration for the librarians to be more satisfied. The satisfaction level of the individuals who participated in in-service courses of the National Library was moderate to high. A total of 84.4% participants announced that the productivity level of the training courses was moderate to high. The most important problem with which the librarians were confronted in virtual in-service training was the "low speed of the internet and inadequate computer substructures". Conclusion: Effectiveness of in-service training courses from librarians’ point of view was at an optimal level in the studied libraries. PMID:28491833

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

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

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

DOE PAGES

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina; ...

2017-03-01

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

Diagnostic accuracy of scapular physical examination tests for shoulder disorders: a systematic review.

PubMed

Wright, Alexis A; Wassinger, Craig A; Frank, Mason; Michener, Lori A; Hegedus, Eric J

2013-09-01

To systematically review and critique the evidence regarding the diagnostic accuracy of physical examination tests for the scapula in patients with shoulder disorders. A systematic, computerised literature search of PubMED, EMBASE, CINAHL and the Cochrane Library databases (from database inception through January 2012) using keywords related to diagnostic accuracy of physical examination tests of the scapula. The Quality Assessment of Diagnostic Accuracy Studies tool was used to critique the quality of each paper. Eight articles met the inclusion criteria; three were considered to be of high quality. Of the three high-quality studies, two were in reference to a 'diagnosis' of shoulder pain. Only one high-quality article referenced specific shoulder pathology of acromioclavicular dislocation with reported sensitivity of 71% and 41% for the scapular dyskinesis and SICK scapula test, respectively. Overall, no physical examination test of the scapula was found to be useful in differentially diagnosing pathologies of the shoulder.

Using Digital Videos to Enhance Teacher Preparation

ERIC Educational Resources Information Center

Dymond, Stacy K.; Bentz, Johnell L.

2006-01-01

The technology to produce high quality, digital videos is widely available, yet its use in teacher preparation remains largely overlooked. A digital video library was created to augment instruction in a special education methods course for preservice elementary education teachers. The videos illustrated effective strategies for working with…

Creating a State-Wide Virtual Health Library: The Michigan Experience.

ERIC Educational Resources Information Center

Brenneise, Harvey

The AccessMichigan Electronic Community Health Information Initiative (AMECHII) is a response to a recommendation of the Michigan Information Technology Commission Report recommending improved access to high-quality health care information for all Michigan stakeholders. This project is multi-type, including public, general academic, academic…

Scaling up the 454 Titanium Library Construction and Pooling of Barcoded Libraries

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

Phung, Wilson; Hack, Christopher; Shapiro, Harris

2009-03-23

We have been developing a high throughput 454 library construction process at the Joint Genome Institute to meet the needs of de novo sequencing a large number of microbial and eukaryote genomes, EST, and metagenome projects. We have been focusing efforts in three areas: (1) modifying the current process to allow the construction of 454 standard libraries on a 96-well format; (2) developing a robotic platform to perform the 454 library construction; and (3) designing molecular barcodes to allow pooling and sorting of many different samples. In the development of a high throughput process to scale up the number ofmore » libraries by adapting the process to a 96-well plate format, the key process change involves the replacement of gel electrophoresis for size selection with Solid Phase Reversible Immobilization (SPRI) beads. Although the standard deviation of the insert sizes increases, the overall quality sequence and distribution of the reads in the genome has not changed. The manual process of constructing 454 shotgun libraries on 96-well plates is a time-consuming, labor-intensive, and ergonomically hazardous process; we have been experimenting to program a BioMek robot to perform the library construction. This will not only enable library construction to be completed in a single day, but will also minimize any ergonomic risk. In addition, we have implemented a set of molecular barcodes (AKA Multiple Identifiers or MID) and a pooling process that allows us to sequence many targets simultaneously. Here we will present the testing of pooling a set of selected fosmids derived from the endomycorrhizal fungus Glomus intraradices. By combining the robotic library construction process and the use of molecular barcodes, it is now possible to sequence hundreds of fosmids that represent a minimal tiling path of this genome. Here we present the progress and the challenges of developing these scaled-up processes.« less

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

PubMed Central

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

2009-01-01

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

Immune-Related Transcriptome of Coptotermes formosanus Shiraki Workers: The Defense Mechanism

PubMed Central

Hussain, Abid; Li, Yi-Feng; Cheng, Yu; Liu, Yang; Chen, Chuan-Cheng; Wen, Shuo-Yang

2013-01-01

Formosan subterranean termites, Coptotermes formosanus Shiraki, live socially in microbial-rich habitats. To understand the molecular mechanism by which termites combat pathogenic microbes, a full-length normalized cDNA library and four Suppression Subtractive Hybridization (SSH) libraries were constructed from termite workers infected with entomopathogenic fungi (Metarhizium anisopliae and Beauveria bassiana), Gram-positive Bacillus thuringiensis and Gram-negative Escherichia coli, and the libraries were analyzed. From the high quality normalized cDNA library, 439 immune-related sequences were identified. These sequences were categorized as pattern recognition receptors (47 sequences), signal modulators (52 sequences), signal transducers (137 sequences), effectors (39 sequences) and others (164 sequences). From the SSH libraries, 27, 17, 22 and 15 immune-related genes were identified from each SSH library treated with M. anisopliae, B. bassiana, B. thuringiensis and E. coli, respectively. When the normalized cDNA library was compared with the SSH libraries, 37 immune-related clusters were found in common; 56 clusters were identified in the SSH libraries, and 259 were identified in the normalized cDNA library. The immune-related gene expression pattern was further investigated using quantitative real time PCR (qPCR). Important immune-related genes were characterized, and their potential functions were discussed based on the integrated analysis of the results. We suggest that normalized cDNA and SSH libraries enable us to discover functional genes transcriptome. The results remarkably expand our knowledge about immune-inducible genes in C. formosanus Shiraki and enable the future development of novel control strategies for the management of Formosan subterranean termites. PMID:23874972

The Land of Confusion? High School Students and Their Use of the World Wide Web for Research.

ERIC Educational Resources Information Center

Lorenzen, Michael

2002-01-01

Examines high school students' use of the World Wide Web to complete assignments. Findings showed the students used a good variety of resources, including libraries and the World Wide Web, to find information for assignments. However, students were weak at determining the quality of the information found on web sites. Students did poorly at…

Pros and Cons of Internet2 Videoconferencing as a New Generation Distance Education Tool

ERIC Educational Resources Information Center

Ozkan, Betul C.

2005-01-01

Internet2 is one of the newer ways of videoconferencing in American universities. Over 200 universities in the United States collaborate with each other through these high-quality Internet lines. K-12 schools and libraries nationwide have also started taking advantage of this fiber optic, high-capacity speedy network. However, the term Internet2,…

SU-G-BRB-02: An Open-Source Software Analysis Library for Linear Accelerator Quality Assurance

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

Kerns, J; Yaldo, D

Purpose: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. Methods: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence. The analysis library was built using the general programming language Python. Each test was analyzed with the library algorithms and compared to manual measurements taken at the timemore » of acquisition. Results: VMAT QA results agreed within 0.1% between the library and manual measurements. Machine logs (dynalogs & trajectory logs) were successfully parsed; mechanical axis positions were verified for accuracy and MLC fluence agreed well with EPID measurements. CBCT QA measurements were within 10 HU and 0.2mm where applicable. Winston Lutz isocenter size measurements were within 0.2mm of TrueBeam’s Machine Performance Check. Starshot analysis was within 0.2mm of the Winston Lutz results for the same conditions. Picket fence images with and without a known error showed that the library was capable of detecting MLC offsets within 0.02mm. Conclusion: A new routine QA software library has been benchmarked and is available for use by the community. The library is open-source and extensible for use in larger systems.« less

USGS Digital Spectral Library splib06a

USGS Publications Warehouse

Clark, Roger N.; Swayze, Gregg A.; Wise, Richard A.; Livo, K. Eric; Hoefen, Todd M.; Kokaly, Raymond F.; Sutley, Stephen J.

2007-01-01

Introduction We have assembled a digital reflectance spectral library that covers the wavelength range from the ultraviolet to far infrared along with sample documentation. The library includes samples of minerals, rocks, soils, physically constructed as well as mathematically computed mixtures, plants, vegetation communities, microorganisms, and man-made materials. The samples and spectra collected were assembled for the purpose of using spectral features for the remote detection of these and similar materials. Analysis of spectroscopic data from laboratory, aircraft, and spacecraft instrumentation requires a knowledge base. The spectral library discussed here forms a knowledge base for the spectroscopy of minerals and related materials of importance to a variety of research programs being conducted at the U.S. Geological Survey. Much of this library grew out of the need for spectra to support imaging spectroscopy studies of the Earth and planets. Imaging spectrometers, such as the National Aeronautics and Space Administration (NASA) Airborne Visible/Infra Red Imaging Spectrometer (AVIRIS) or the NASA Cassini Visual and Infrared Mapping Spectrometer (VIMS) which is currently orbiting Saturn, have narrow bandwidths in many contiguous spectral channels that permit accurate definition of absorption features in spectra from a variety of materials. Identification of materials from such data requires a comprehensive spectral library of minerals, vegetation, man-made materials, and other subjects in the scene. Our research involves the use of the spectral library to identify the components in a spectrum of an unknown. Therefore, the quality of the library must be very good. However, the quality required in a spectral library to successfully perform an investigation depends on the scientific questions to be answered and the type of algorithms to be used. For example, to map a mineral using imaging spectroscopy and the mapping algorithm of Clark and others (1990a, 2003b), one simply needs a diagnostic absorption band. The mapping system uses continuum-removed reference spectral features fitted to features in observed spectra. Spectral features for such algorithms can be obtained from a spectrum of a sample containing large amounts of contaminants, including those that add other spectral features, as long as the shape of the diagnostic feature of interest is not modified. If, however, the data are needed for radiative transfer models to derive mineral abundances from reflectance spectra, then completely uncontaminated spectra are required. This library contains spectra that span a range of quality, with purity indicators to flag spectra for (or against) particular uses. Acquiring spectral measurements and performing sample characterizations for this library has taken about 15 person-years of effort. Software to manage the library and provide scientific analysis capability is provided (Clark, 1980, 1993). A personal computer (PC) reader for the library is also available (Livo and others, 1993). The program reads specpr binary files (Clark, 1980, 1993) and plots spectra. Another program that reads the specpr format is written in IDL (Kokaly, 2005). In our view, an ideal spectral library consists of samples covering a very wide range of materials, has large wavelength range with very high precision, and has enough sample analyses and documentation to establish the quality of the spectra. Time and available resources limit what can be achieved. Ideally, for each mineral, the sample analysis would include X-ray diffraction (XRD), electron microprobe (EM) or X-ray fluorescence (XRF), and petrographic microscopic analyses. For some minerals, such as iron oxides, additional analyses such as Mossbauer would be helpful. We have found that to make the basic spectral measurements, provide XRD, EM or XRF analyses, and microscopic analyses, document the results, and complete an entry of one spectral library sample, all takes about

Insights into Library Services and Users from Qualitative Research.

ERIC Educational Resources Information Center

Lincoln, Yvonna S.

2002-01-01

Describes a study that used interview data to adapt SERVQUAL, a survey to determine customer perceptions of service quality, to LibQUAL[TM], a Web-based survey to investigate users' perceptions of library service quality. Offers hypotheses regarding how data was categorized as it was. (Author/LRW)

Applying GRA and QFD to Improve Library Service Quality

ERIC Educational Resources Information Center

Chen, Yen-Ting; Chou, Tsung-Yu

2011-01-01

This paper applied Grey Relational Analysis (GRA) to Quality Function Deployment (QFD) to identify service improvement techniques for an academic library. First, reader needs and their importance, and satisfaction degrees were examined via questionnaires. Second, the service improvement techniques for satisfying the reader needs were developed by…

Managing Service Quality with the Balanced Scorecard.

ERIC Educational Resources Information Center

Poll, Roswitha

In order to evaluate and utilize library data for the management process, a German project, sponsored by the German Research Council, uses the Balanced Scorecard as the concept for integrated quality management. Performance indicators across the following four perspectives are combined to produce a balanced evaluation of the library: (1) users,…

Total Quality Management in Libraries: A Sourcebook.

ERIC Educational Resources Information Center

O'Neil, Rosanna M., Comp.

Total Quality Management (TQM) brings together the best aspects of organizational excellence by driving out fear, offering customer-driven products and services, doing it right the first time by eliminating error, and maintaining inventory control without waste. Libraries are service organizations which are constantly trying to improve service.…

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

PubMed

Kresse, Stine H; Namløs, Heidi M; Lorenz, Susanne; Berner, Jeanne-Marie; Myklebost, Ola; Bjerkehagen, Bodil; Meza-Zepeda, Leonardo A

2018-01-01

Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.

Alabama Public Library Service, 1987 Annual Report.

ERIC Educational Resources Information Center

Alabama Public Library Service, Montgomery.

Designed to provide an overview of the range and quality of services provided by the Alabama Public Library Service (APLS), this annual report focuses on the 1987 activities of APLS. A report on the activities of the Library Development Division shows the allocation of state aid and Library Services and Construction Act (LCSA) Titles I and III…

Law Firms and Public Libraries.

ERIC Educational Resources Information Center

Fong, Colin

1997-01-01

Summarizes sources of legal information in New South Wales and outlines the libraries' driving motivations, access policies, and practices. Also highlights the important value-added service professional library staff contribute to both the quality and quantity of information delivery in this discipline. (Author/AEF)

Deconstructing Cancer Patient Information Seeking in a Consumer Health Library Toward Developing a Virtual Information Consult for Cancer Patients and Their Caregivers: A Qualitative, Instrumental Case Study

PubMed Central

Abdelmutti, Nazek; Giuliani, Meredith E; Snow, Michelle; McCurdie, Tara; Pulandiran, Menaka; Urowitz, Sara; Wiljer, David

2017-01-01

Background Cancer patients and their caregivers want information about their disease and are interested in finding health information online. Despite the abundance of cancer information online, it is often fragmented, its quality is highly variable, and it can be difficult to navigate without expert-level knowledge of the cancer system. The Patient & Family Library at the Princess Margaret Cancer Centre offers a broad collection of high-quality cancer health information and staff are available to help patrons refine their questions and explore information needs that they may not have considered. Objective The purpose of this research study was to deconstruct patrons’ information-seeking behaviors in the library to assess the feasibility of replicating the services provided in the library through a Web app, extending the service beyond the walls of the cancer centre. The specific aims of this research were to understand (1) how patrons approach information seeking in the library (interface design), (2) how patrons communicate their informational needs (information categorization and metadata requirements), and (3) what resources are provided to address the patrons’ information needs (collection development). Methods We employed a qualitative, instrumental case study to deconstruct patrons’ health information-seeking behavior. The study population included patients, the librarian, and library volunteers. Ethnographic observation was conducted at the library over 3 days and key informant interviews with library staff were conducted to address the first aim. A closed card-sorting activity was conducted to address the second aim and the library shift logs and Search Request Forms (SRFs) were reviewed to address the third aim. Results A total of 55 interactions were recorded during the ethnographic observation and nine semistructured interviews were conducted during the key informant interviews. Seven library patron personas were identified: (1) Newbie, (2) Seasoned, (3) Direct, (4) Window Shopper, (5) Collector, (6) Information Seeker, and (7) Distressed. A total of 83 participants completed the closed card-sorting exercise. The participants’ conceptual clusters within the similarity matrix overlapped with the groupings created by the librarian, with a few differences. A total of 161 entries in the library shift log and 65 SRFs were analyzed to determine what resources were given to patrons. Most resources that patrons received were available online (61%), although almost half of these required special access (47%). Conclusions The study findings suggest it is possible to replicate library functions in a Web app with a few exceptions that cannot be replicated online. These elements include access to journal articles or other content behind paywalls and the librarian’s ability to encourage further discussion through empathy and active listening. Discussion with the librarian could serve to refine and predict needs through observing information seekers and to provide immediate connection to spiritual care and psychosocial support for patrons in distress. PMID:28539305

Information Literacy for First-Year Students: An Embedded Curriculum Approach

ERIC Educational Resources Information Center

Andrews, T.; Patil, R.

2007-01-01

The ability to access, evaluate and synthesise high-quality research material is the backbone of critical thinking in academic and professional contexts for Engineers and Industrial Designers. This is the premise upon which teaching and library staff developed Information Literacy (IL) components in Engineering & Industrial Design Practice--a…

ION COMPOSITION ELUCIDATION (ICE): AN INVESTIGATIVE TOOL FOR CHARACTERIZATION AND IDENTIFICATION OF COMPOUNDS OF REGULATORY IMPORTANCE

EPA Science Inventory

Ion Composition Elucidation (ICE) often leads to identification of compounds and provides high quality evidence for tracking compounds to their sources. Mass spectra for most organic compounds are not found in mass spectral libraries used to tentatively identify analytes. In addi...

Design and Development of Web-Based Information Literacy Tutorials

ERIC Educational Resources Information Center

Su, Shiao-Feng; Kuo, Jane

2010-01-01

The current study conducts a thorough content analysis of recently built or up-to-date high-quality web-based information literacy tutorials contributed by academic libraries in a peer-reviewed database, PRIMO. This research analyzes the topics/skills PRIMO tutorials consider essential and the teaching strategies they consider effective. The…

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

PubMed

Hulse-Kemp, Amanda M; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A; Jaffe, David; Williams, Stephen R; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C; Church, Deanna M; Van Deynze, Allen

2018-01-01

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available  de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

Managing Academic Libraries with Fewer Resources.

ERIC Educational Resources Information Center

Riggs, Donald E.

1992-01-01

A discussion of academic library management during retrenchment looks at a variety of issues, including staffing needs in the labor-intensive library environment, acquisitions budgeting, interlibrary cooperation (ownership vs. access to resources), entrepreneurship and strategic planning for problem solving, and use of total quality management…

Measuring Effectiveness in a Virtual Library

ERIC Educational Resources Information Center

Finch, Jannette L.

2010-01-01

Measuring quality of service in academic libraries traditionally includes quantifiable data such as collection size, staff counts, circulation numbers, reference service statistics, qualitative analyses of customer satisfaction, shelving accuracy, and building comfort. In the libraries of the third millennium, virtual worlds, Web content and…

Benchmarking and Its Relevance to the Library and Information Sector. Interim Findings of "Best Practice Benchmarking in the Library and Information Sector," a British Library Research and Development Department Project.

ERIC Educational Resources Information Center

Kinnell, Margaret; Garrod, Penny

This British Library Research and Development Department study assesses current activities and attitudes toward quality management in library and information services (LIS) in the academic sector as well as the commercial/industrial sector. Definitions and types of benchmarking are described, and the relevance of benchmarking to LIS is evaluated.…

"We Don't Do Public Libraries Like We Used to": Attitudes to Public Library Buildings in the UK at the Start of the 21st Century

ERIC Educational Resources Information Center

Black, Alistair

2011-01-01

Although the quality, performance and future of public library services in the UK is a matter of debate, there is little doubt that in recent years, despite claims relating to the emergence of a cyber-society, interest in library buildings and the library as "place" has been intense, almost matching that seen during the Carnegie era of…

Academic Libraries and the Research Quality Framework

ERIC Educational Resources Information Center

Haddow, Gaby

2007-01-01

The Federal Government is introducing a new funding model for research in Australian higher education institutions, the Research Quality Framework (RQF). This paper provides an overview of the RQF and looks at possible impacts of the RQF on academic libraries in Australia. These impacts are drawn from experience at one Australian university,…

Performance, Process, and Costs: Managing Service Quality with the Balanced Scorecard.

ERIC Educational Resources Information Center

Poll, Roswitha

2001-01-01

Describes a cooperative project among three German libraries that used the Balanced Scorecard as a concept for an integrated quality management system. Considers performance indicators across four perspectives that will help academic libraries establish an integrated controlling system and to collect and evaluate performance as well as cost data…

Measuring Perceptual (In) Congruence between Information Service Providers and Users

ERIC Educational Resources Information Center

Boyce, Crystal

2017-01-01

Library quality is no longer evaluated solely on the value of its collections, as user perceptions of service quality play an increasingly important role in defining overall library value. This paper presents a retooling of the LibQUAL+ survey instrument, blending the gap measurement model with perceptual congruence model studies from information…

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.

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

PubMed Central

2010-01-01

Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts. PMID:20089148

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

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

Kim, Kang Seog

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

School Library Research from around the World: Where It's Been and Where It's Headed

ERIC Educational Resources Information Center

Gavigan, Karen

2018-01-01

Although their research agendas may vary widely, school library researchers from around the world share the common goal of conducting studies designed to advance the field of school librarianship. International school library scholars are united in their efforts to prove that quality school library programs can have a significant impact on student…

Evaluation of Library Utilization by Students Enrolled in External Degree Programme in University of Nairobi, Kenya

ERIC Educational Resources Information Center

Gor, Peter Ochieng

2012-01-01

With the increasing popularity of distance education, focus has turned to the role of libraries in distance learning process. It is widely agreed that like their campus-based counterparts, distance education learners need adequate library services if they are to gain quality education. This study sought to examine library utilization by students…

Survey of the Use of Slide/Tape Presentations for Orientation and Instruction Purposes in Academic Libraries.

ERIC Educational Resources Information Center

Hardesty, Larry

Eighty-eight academic libraries were surveyed to determine what kinds of slide/tape library instruction materials are available for purchase or loan. The conclusions reached were: (1) there are less than a dozen libraries that have produced presentations of sufficient quality and adaptability to be widely used; and (2) the slide/tape format…

Chandler Public Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

ERIC Educational Resources Information Center

Drake, Karen; Rodriguez, Leonard

This final performance report for the Chandler Public Library literacy project for fiscal year 1992 begins with a section that provides quantitative data. The next section compares actual accomplishments to the project goal--to improve the quality of life for illiterate, semiliterate, and non-English-speaking citizens by providing a comprehensive…

Initial Ada components evaluation

NASA Technical Reports Server (NTRS)

Moebes, Travis

1989-01-01

The SAIC has the responsibility for independent test and validation of the SSE. They have been using a mathematical functions library package implemented in Ada to test the SSE IV and V process. The library package consists of elementary mathematical functions and is both machine and accuracy independent. The SSE Ada components evaluation includes code complexity metrics based on Halstead's software science metrics and McCabe's measure of cyclomatic complexity. Halstead's metrics are based on the number of operators and operands on a logical unit of code and are compiled from the number of distinct operators, distinct operands, and total number of occurrences of operators and operands. These metrics give an indication of the physical size of a program in terms of operators and operands and are used diagnostically to point to potential problems. McCabe's Cyclomatic Complexity Metrics (CCM) are compiled from flow charts transformed to equivalent directed graphs. The CCM is a measure of the total number of linearly independent paths through the code's control structure. These metrics were computed for the Ada mathematical functions library using Software Automated Verification and Validation (SAVVAS), the SSE IV and V tool. A table with selected results was shown, indicating that most of these routines are of good quality. Thresholds for the Halstead measures indicate poor quality if the length metric exceeds 260 or difficulty is greater than 190. The McCabe CCM indicated a high quality of software products.

Digitizing an Analog Radiography Teaching File Under Time Constraint: Trade-Offs in Efficiency and Image Quality.

PubMed

Loehfelm, Thomas W; Prater, Adam B; Debebe, Tequam; Sekhar, Aarti K

2017-02-01

We digitized the radiography teaching file at Black Lion Hospital (Addis Ababa, Ethiopia) during a recent trip, using a standard digital camera and a fluorescent light box. Our goal was to photograph every radiograph in the existing library while optimizing the final image size to the maximum resolution of a high quality tablet computer, preserving the contrast resolution of the radiographs, and minimizing total library file size. A secondary important goal was to minimize the cost and time required to take and process the images. Three workers were able to efficiently remove the radiographs from their storage folders, hang them on the light box, operate the camera, catalog the image, and repack the radiographs back to the storage folder. Zoom, focal length, and film speed were fixed, while aperture and shutter speed were manually adjusted for each image, allowing for efficiency and flexibility in image acquisition. Keeping zoom and focal length fixed, which kept the view box at the same relative position in all of the images acquired during a single photography session, allowed unused space to be batch-cropped, saving considerable time in post-processing, at the expense of final image resolution. We present an analysis of the trade-offs in workflow efficiency and final image quality, and demonstrate that a few people with minimal equipment can efficiently digitize a teaching file library.

ION COMPOSITION ELUCIDATION (ICE): A HIGH ...

EPA Pesticide Factsheets

Identifying compounds found in the environment without knowledge of their origin is a very difficult analytical problem. Comparison of the low resolution mass spectrum of a compound with those in the NIST or Wiley mass spectral libraries can provide a tentative identification when the mass spectrum is free of interferences, at least several prominent ions are observed in the mass spectrum, the mass spectrum is in the library, and only one plausible match is found. Because these libraries contain only 226,334 distinct compounds (1) compared to the 16 million compounds that have been synthesized or isolated from natural sources (2), most compounds are not found in the libraries. In addition, most compounds are ionic, too polar, too thermolabile, or too high in mass to traverse a GC column or to volatilize from a probe. For these compounds, liquid sample introduction with electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) provides few fragment ions for pattern matching, and adduct ions complicate the mass spectra. Commercial ESI and APCI mass spectral libraries are not available. Consequently, low resolution mass spectrometry cannot identify most compounds-. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support

Leadership Qualities of Assistant/Associate Directors.

ERIC Educational Resources Information Center

Bailey, Martha J.

1992-01-01

Describes job responsibilities of assistant/associate library directors. Changes affecting libraries as a result of automation and their impact on management are discussed, and two studies of public and academic libraries that examined ratings of managerial skills and competencies by directors and assistant directors are reviewed. (nine…

Collection Evaluation in Research Libraries: The Search for Quality, Consistency, and System in Collection Development.

ERIC Educational Resources Information Center

Mosher, Paul H.

1979-01-01

Reviews the history, literature, and methodology of collection evaluation or assessment in American research libraries; discusses current problems, tools, and methodology of evaluation; and describes an ongoing collection evaluation program at the Stanford University Libraries. (Author/MBR)

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

PubMed

Heredia, Nicholas J

2018-01-01

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

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

The Development of Performance Indicators for Prison Libraries.

ERIC Educational Resources Information Center

Lithgow, Susan D.

This report describes a study to investigate the improved efficiency and effectiveness of prison library provision in England and Wales, through the development and validation of relevant performance indicators to be used as part of quality assurance programs. Prison libraries perform important educational, rehabilitative, and recreational…

Benchmark for Strategic Performance Improvement.

ERIC Educational Resources Information Center

Gohlke, Annette

1997-01-01

Explains benchmarking, a total quality management tool used to measure and compare the work processes in a library with those in other libraries to increase library performance. Topics include the main groups of upper management, clients, and staff; critical success factors for each group; and benefits of benchmarking. (Author/LRW)

Reliability and Validity of SERVQUAL Scores Used To Evaluate Perceptions of Library Service Quality.

ERIC Educational Resources Information Center

Thompson, Bruce; Cook, Colleen

Research libraries are increasingly supplementing collection counts with perceptions of service quality as indices of status and productivity. The present study was undertaken to explore the reliability and validity of scores from the SERVQUAL measurement protocol (A. Parasuraman and others, 1991), which has previously been used in this type of…

Evaluating the Impact of Library Instruction Methods on the Quality of Student Research.

ERIC Educational Resources Information Center

Ackerson, Linda G.; Young, Virgina E.

1994-01-01

A three-year study at the University of Alabama compared a traditional lecture method for teaching library research skills with a course-integrated, computer-enhanced approach by assessing each method's impact on the quality of bibliographies from engineering students' term papers. In four of the five semesters, no significant differences were…

A Critique of Books for College Libraries, 2d ed.

ERIC Educational Resources Information Center

Pownall, David E.

The second edition of "Books for College Libraries," a six-volume work listing 38,651 titles is flawed, although it shows merit, and should be useful. Quality of selections and coverage range from good through excellent to superb. The primary flaws relate to the quality and extent of selections, particularly for such disciplines as history and…

Google vs. the Library (Part III): Assessing the Quality of Sources Found by Undergraduates

ERIC Educational Resources Information Center

Georgas, Helen

2015-01-01

This study assesses and compares the quality of sources found by undergraduate students when doing research using both Google and a library (federated) search tool. Thirty undergraduates were asked to find four sources (one book, two articles, and one additional source of their choosing) related to a selected research topic. Students used both…

Designing a curriculum on Internet health resources for deaf high school students.

PubMed

Gregg, Amy L; Wozar, Jody A; Wessel, Charles B; Epstein, Barbara A

2002-10-01

This paper examines the integration of instruction about quality health resources on the Internet into the health curriculum of a specialized high school for students with hearing disabilities. The Health Sciences Library System (HSLS) at the University of Pittsburgh has formed a partnership with the Western Pennsylvania School for the Deaf (WPSD). This project was partially funded through a subcontract with the National Library of Medicine. As one component of its Health Information for the Public project, HSLS formed a partnership with the WPSD. This partnership allowed for a librarian to provide instruction to health education and learning center teachers and students at WPSD about health resources on the Internet. This paper describes the planning process, curriculum development, and challenges encountered. These challenges include student knowledge of English as a second language, the need for a sign language interpreter, students' third-to-fourth-grade reading levels, and the need for appropriate visual presentations to accompany the audio counterpart. The partnership formed between HSLS and WPSD improved deaf high school students' ability to locate quality health information on the Internet. A pre-class survey and post-class survey were used to determine the impact of the instruction.

Journal Quality in the Asian Region: Results of a Pilot Study for the IFLA Round Table of Library and Information Science Journals.

ERIC Educational Resources Information Center

Gorman, G. E.; Calvert, Philip J.

This paper reports on a pilot project in Asia sponsored by the IFLA (International Federation of Library Associations and institutions) Round Table of Library and Information Science Journals that had the following objectives: to identify the most commonly accepted criteria for evaluating LIS (Library and Information Science) journals; to evaluate…

Characteristics of knowledge content in a curated online evidence library.

PubMed

Varada, Sowmya; Lacson, Ronilda; Raja, Ali S; Ip, Ivan K; Schneider, Louise; Osterbur, David; Bain, Paul; Vetrano, Nicole; Cellini, Jacqueline; Mita, Carol; Coletti, Margaret; Whelan, Julia; Khorasani, Ramin

2018-05-01

To describe types of recommendations represented in a curated online evidence library, report on the quality of evidence-based recommendations pertaining to diagnostic imaging exams, and assess underlying knowledge representation. The evidence library is populated with clinical decision rules, professional society guidelines, and locally developed best practice guidelines. Individual recommendations were graded based on a standard methodology and compared using chi-square test. Strength of evidence ranged from grade 1 (systematic review) through grade 5 (recommendations based on expert opinion). Finally, variations in the underlying representation of these recommendations were identified. The library contains 546 individual imaging-related recommendations. Only 15% (16/106) of recommendations from clinical decision rules were grade 5 vs 83% (526/636) from professional society practice guidelines and local best practice guidelines that cited grade 5 studies (P < .0001). Minor head trauma, pulmonary embolism, and appendicitis were topic areas supported by the highest quality of evidence. Three main variations in underlying representations of recommendations were "single-decision," "branching," and "score-based." Most recommendations were grade 5, largely because studies to test and validate many recommendations were absent. Recommendation types vary in amount and complexity and, accordingly, the structure and syntax of statements they generate. However, they can be represented in single-decision, branching, and score-based representations. In a curated evidence library with graded imaging-based recommendations, evidence quality varied widely, with decision rules providing the highest-quality recommendations. The library may be helpful in highlighting evidence gaps, comparing recommendations from varied sources on similar clinical topics, and prioritizing imaging recommendations to inform clinical decision support implementation.

Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands.

PubMed

Phipps, M Lisa; Lillo, Antoinetta M; Shou, Yulin; Schmidt, Emily N; Paavola, Chad D; Naranjo, Leslie; Bemdich, Sara; Swanson, Basil I; Bradbury, Andrew R M; Martinez, Jennifer S

2016-01-01

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The "helper cell" packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.

A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.

PubMed

Brouilette, Scott; Kuersten, Scott; Mein, Charles; Bozek, Monika; Terry, Anna; Dias, Kerith-Rae; Bhaw-Rosun, Leena; Shintani, Yasunori; Coppen, Steven; Ikebe, Chiho; Sawhney, Vinit; Campbell, Niall; Kaneko, Masahiro; Tano, Nobuko; Ishida, Hidekazu; Suzuki, Ken; Yashiro, Kenta

2012-10-01

Deep sequencing of single cell-derived cDNAs offers novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-seq analysis requires multiple steps with consequent sample loss and stochastic variation at each step significantly affecting output. Thus, a simpler and better protocol is desirable. The recently developed hyperactive Tn5-mediated library preparation, which brings high quality libraries, is likely one of the solutions. Here, we tested the applicability of hyperactive Tn5-mediated library preparation to deep sequencing of single cell cDNA, optimized the protocol, and compared it with the conventional method based on sonication. This new technique does not require any expensive or special equipment, which secures wider availability. A library was constructed from only 100 ng of cDNA, which enables the saving of precious specimens. Only a few steps of robust enzymatic reaction resulted in saved time, enabling more specimens to be prepared at once, and with a more reproducible size distribution among the different specimens. The obtained RNA-seq results were comparable to the conventional method. Thus, this Tn5-mediated preparation is applicable for anyone who aims to carry out deep sequencing for single cell cDNAs. Copyright © 2012 Wiley Periodicals, Inc.

Sequence evaluation of four specific cDNA libraries for developmental genomics of sunflower.

PubMed

Tamborindeguy, C; Ben, C; Liboz, T; Gentzbittel, L

2004-04-01

Four different cDNA libraries were constructed from sunflower protoplasts growing under embryogenic and non-embryogenic conditions: one standard library from each condition and two subtractive libraries in opposite sense. A total of 22,876 cDNA clones were obtained and 4800 ESTs were sequenced, giving rise to 2479 high quality ESTs representing an unigene set of 1502 sequences. This set was compared with ESTs represented in public databases using the programs BLASTN and BLASTX, and its members were classified according to putative function using the catalog in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Some 33% of sequences failed to align with existing plant ESTs and therefore represent putative novel genes. The libraries show a low level of redundancy and, on average, 50% of the present ESTs have not been previously reported for sunflower. Several potentially interesting genes were identified, based on their homology with genes involved in animal zygotic division or plant embryogenesis. We also identified two ESTs that show significantly different levels of expression under embryogenic and non-embryogenic conditions. The libraries described here represent an original and valuable resource for the discovery of yet unknown genes putatively involved in dicot embryogenesis and improving our knowledge of the mechanisms involved in polarity acquisition by plant embryos.

Re-inventing Data Libraries: Ensuring Continuing Access To Curated (Value-added) Data

NASA Astrophysics Data System (ADS)

Burnhill, P.; Medyckyj-Scott, D.

2008-12-01

How many years of inexperience do we need in using, and in particular sharing, digital data generated by others? That history pre-dates, but must also gain leverage from, the emergence of the digital library. Much of this sharing was done within research groups but recent attention to spatial data infrastructure highlights the importance of achieving several 'right mixes': * between Internet-standards, geo-specific referencing, and domain-specific vocabulary (cf ontology); * between attention to user-focus'd services and machine-to-machine interoperability; * between the demands of current high-quality services, the practice of data curation, and the need for long term preservation. This presentation will draw upon ideas and experience data library services in research universities, a national (UK) academic data centre, and developments in digital curation. It will be argued that the 1980s term 'data library' has some polemic value in that we have yet to learn what it means to 'do library' for data: more than "a bit like inter-galactic library loan", perhaps. Illustration will be drawn from multi-faceted database of digitized boundaries (UKBORDERS), through the first Internet map delivery of national mapping agency data (Digimap), to strategic positioning to help geo-enable academic and scientific data and so enhance research (in the UK, in Europe, and beyond).

Creating an Information Literate School: Information Literacy in Action.

ERIC Educational Resources Information Center

Batz, Linda; Rosenberg, Harlene

1999-01-01

Describes an award-winning instructional media center (IMC) at a New Jersey high school. The IMC (library) is the school's hub from 7:15 a.m. to 6 p.m., and has dial-in access. This information-literacy program emphasizes total-quality-management principles, ongoing professional development, teacher support, and information skills instruction.…

The Annotated Bibliography and Citation Behavior: Enhancing Student Scholarship in an Undergraduate Biology Course

ERIC Educational Resources Information Center

Flaspohler, Molly R.; Rux, Erika M.; Flaspohler, John A.

2007-01-01

Contemporary undergraduates in the biological sciences have unprecedented access to scientific information. Although many of these students may be savvy technologists, studies from the field of library and information science consistently show that undergraduates often struggle to locate, evaluate, and use high-quality, reputable sources of…

The ARL Scholars Portal Initiative.

ERIC Educational Resources Information Center

Jackson, Mary E.

2002-01-01

Describes an initiative of the Association of Research Libraries (ARL), the Scholars Portal Initiative, a three-year collaborative effort which seeks to provide tools for an academic community to have a single point of access on the Web to find high-quality information resources and to deliver the information and related services directly to the…

A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

PubMed Central

Sattin, Eleonora; Andreani, Nadia A.; Carraro, Lisa; Lucchini, Rosaria; Fasolato, Luca; Telatin, Andrea; Balzan, Stefania; Novelli, Enrico; Simionati, Barbara; Cardazzo, Barbara

2016-01-01

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples. PMID:27582735

Using the Gamma-Poisson Model to Predict Library Circulations.

ERIC Educational Resources Information Center

Burrell, Quentin L.

1990-01-01

Argues that the gamma mixture of Poisson processes, for all its perceived defects, can be used to make predictions regarding future library book circulations of a quality adequate for general management requirements. The use of the model is extensively illustrated with data from two academic libraries. (Nine references) (CLB)

Library Educators' Awareness and Evaluation of National Audiovisual Center Materials.

ERIC Educational Resources Information Center

Palmer, Joseph W.

1980-01-01

Describes a survey of 18 library schools conducted to determine if faculty are familiar with audiovisual materials available from the National Audiovisual Center, and how these materials are rated in quality. Results indicate that there is a need for more descriptive and evaluative information to reach library educators. (BK)

How To Become a Great Public Space.

ERIC Educational Resources Information Center

Block, Marylaine

2003-01-01

Presents interviews with Fred Kent, founder of the Project for Public Spaces (PPS) and Phil Myrick, PPS's assistant vice president, about transforming libraries into desirable public spaces. Discusses qualities people value in public spaces; great library buildings and what they are doing right; the first thing library directors should do when…

Web 2.0 and Nigerian Academic Librarians

ERIC Educational Resources Information Center

Adekunmisi, Sowemimo Ronke; Odunewu, Abiodun Olusegun

2016-01-01

Web 2.0 applications to library services are aimed at enhancing the provision of relevant and cost-effective information resources for quality education and research. Despite the richness of these web applications and their enormous impact on library and information services as recorded in the developed world, Nigerian academic libraries are yet…

Outsourcing in American Libraries--An Overview.

ERIC Educational Resources Information Center

Bordeianu, Sever; Benaud, Claire-Lise

1997-01-01

Discusses the state of outsourcing in American libraries. Highlights include objectives (to reduce cost, increase the quality of service, and achieve a better price/performance objective); operations that can be outsourced; pros and cons; changes in the way library personnel view their work; outsourcing in special, public, academic, and federal…

TQM--Will It Work in Your Library?

ERIC Educational Resources Information Center

Butcher, Karyle

Scarce resources, changing customer expectation, and the changing role of top management are all factors that have contributed to the implementation of total quality management (TQM) in libraries. Instructional articles, conferences, and videos can alleviate some concerns of cost and time commitment. Many libraries already practice some of the…

IFLA General Conference, 1985. Opening and Plenary Sessions. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

Remarks by Dr. John Brademas, President of New York University, address the meeting theme--"Libraries and the Universal Availability of Information"--with special attention to research libraries and their service to scholars, the quality of public and school libraries, the plight of non-readers, the role of governments in supporting…

Influencing Database Use in Public Libraries.

ERIC Educational Resources Information Center

Tenopir, Carol

1999-01-01

Discusses results of a survey of factors influencing database use in public libraries. Highlights the importance of content; ease of use; and importance of instruction. Tabulates importance indications for number and location of workstations, library hours, availability of remote login, usefulness and quality of content, lack of other databases,…

Making the Most of Libraries in the Search for Academic Excellence.

ERIC Educational Resources Information Center

Breivik, Patricia Senn

1987-01-01

The role of libraries in the search for quality education was addressed in the Carnegie Foundation's report, "College," and at the first higher education conference on academic libraries. Information literacy and policy, campus organizational issues, and programs in economic development support, active learning, and faculty development…

Developing a quality assurance program for online services.

PubMed Central

Humphries, A W; Naisawald, G V

1991-01-01

A quality assurance (QA) program provides not only a mechanism for establishing training and competency standards, but also a method for continuously monitoring current service practices to correct shortcomings. The typical QA cycle includes these basic steps: select subject for review, establish measurable standards, evaluate existing services using the standards, identify problems, implement solutions, and reevaluate services. The Claude Moore Health Sciences Library (CMHSL) developed a quality assurance program for online services designed to evaluate services against specific criteria identified by research studies as being important to customer satisfaction. These criteria include reliability, responsiveness, approachability, communication, and physical factors. The application of these criteria to the library's existing online services in the quality review process is discussed with specific examples of the problems identified in each service area, as well as the solutions implemented to correct deficiencies. The application of the QA cycle to an online services program serves as a model of possible interventions. The use of QA principles to enhance online service quality can be extended to other library service areas. PMID:1909197

Developing a quality assurance program for online services.

PubMed

Humphries, A W; Naisawald, G V

1991-07-01

A quality assurance (QA) program provides not only a mechanism for establishing training and competency standards, but also a method for continuously monitoring current service practices to correct shortcomings. The typical QA cycle includes these basic steps: select subject for review, establish measurable standards, evaluate existing services using the standards, identify problems, implement solutions, and reevaluate services. The Claude Moore Health Sciences Library (CMHSL) developed a quality assurance program for online services designed to evaluate services against specific criteria identified by research studies as being important to customer satisfaction. These criteria include reliability, responsiveness, approachability, communication, and physical factors. The application of these criteria to the library's existing online services in the quality review process is discussed with specific examples of the problems identified in each service area, as well as the solutions implemented to correct deficiencies. The application of the QA cycle to an online services program serves as a model of possible interventions. The use of QA principles to enhance online service quality can be extended to other library service areas.

[Advantages and disadvantages of different methods for the implementation and the support of standard operating procedures: From PDF files to an app- and webbased SOP management system].

PubMed

Bauer, M; Riech, S; Brandes, I; Waeschle, R M

2015-11-01

The quality assurance of care and patient safety, with increasing cost pressure and performance levels is of major importance in the high-risk and high cost area of the operating room (OR). Standard operating procedures (SOP) are an established tool for structuring and standardization of the clinical treatment pathways and show multiple benefits for quality assurance and process optimization. An internal project was initiated in the department of anesthesiology and a continuous improvement process was carried out to build up a comprehensive SOP library. In the first step the spectrum of procedures in anesthesiology was transferred to PDF-based SOPs. The further development to an app-based SOP library (Aesculapp) was due to the high resource expenditure for the administration and maintenance of the large PDF-based SOP collection and to deficits in the mobile availability. The next developmental stage, the SOP healthcare information assistant (SOPHIA) included a simplified and advanced update feature, an archive feature previously missing and notably the possibility to share the SOP library with other departments including the option to adapt each SOP to the individual situation. A survey of the personnel showed that the app-based allocation of SOPs (Aesculapp, SOPHIA) had a higher acceptance than the PDF-based developmental stage SOP form. The SOP management system SOPHIA combines the benefits of the forerunner version Aesculapp with improved options for intradepartmental maintenance and administration of the SOPs and the possibility of an export and editing function for interinstitutional exchange of SOPs.

The Screening Compound Collection: A Key Asset for Drug Discovery.

PubMed

Boss, Christoph; Hazemann, Julien; Kimmerlin, Thierry; von Korff, Modest; Lüthi, Urs; Peter, Oliver; Sander, Thomas; Siegrist, Romain

2017-10-25

In this case study on an essential instrument of modern drug discovery, we summarize our successful efforts in the last four years toward enhancing the Actelion screening compound collection. A key organizational step was the establishment of the Compound Library Committee (CLC) in September 2013. This cross-functional team consisting of computational scientists, medicinal chemists and a biologist was endowed with a significant annual budget for regular new compound purchases. Based on an initial library analysis performed in 2013, the CLC developed a New Library Strategy. The established continuous library turn-over mode, and the screening library size of 300'000 compounds were maintained, while the structural library quality was increased. This was achieved by shifting the selection criteria from 'druglike' to 'leadlike' structures, enriching for non-flat structures, aiming for compound novelty, and increasing the ratio of higher cost 'Premium Compounds'. Novel chemical space was gained by adding natural compounds, macrocycles, designed and focused libraries to the collection, and through mutual exchanges of proprietary compounds with agrochemical companies. A comparative analysis in 2016 provided evidence for the positive impact of these measures. Screening the improved library has provided several highly promising hits, including a macrocyclic compound, that are currently followed up in different Hit-to-Lead and Lead Optimization programs. It is important to state that the goal of the CLC was not to achieve higher HTS hit rates, but to increase the chances of identified hits to serve as the basis of successful early drug discovery programs. The experience gathered so far legitimates the New Library Strategy.

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

PubMed Central

2011-01-01

Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

User library service expectations in health science vs. other settings: a LibQUAL+ Study.

PubMed

Thompson, Bruce; Kyrillidou, Martha; Cook, Colleen

2007-12-01

To explore how the library service expectations and perceptions of users might differ across health-related libraries as against major research libraries not operating in a medical context; to determine whether users of medical libraries demand better library service quality, because the inability of users to access needed literature promptly may lead to a patient who cannot be properly diagnosed, or a diagnosis that cannot be properly treated. We compared LibQUAL+ total and subscale scores across three groups of US, Canadian and British libraries for this purpose. Anticipated differences in expectations for health as other library settings did not emerge. The expectations and perceptions are similar across different types of health science library settings, hospital and academic, and across other general research libraries.

User account | National Agricultural Library

Science.gov Websites

Skip to main content Home National Agricultural Library United States Department of Agriculture Ag | Agricultural Research Service | Plain Language | FOIA | Accessibility Statement | Information Quality | Privacy

Genome sequencing of a single tardigrade Hypsibius dujardini individual

PubMed Central

Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

2016-01-01

Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies. PMID:27529330

Genome sequencing of a single tardigrade Hypsibius dujardini individual.

PubMed

Arakawa, Kazuharu; Yoshida, Yuki; Tomita, Masaru

2016-08-16

Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies.

Screening strategies to identify new chemical diversity for drug development to treat kinetoplastid infections.

PubMed

Don, Rob; Ioset, Jean-Robert

2014-01-01

The Drugs for Neglected Diseases initiative (DNDi) has defined and implemented an early discovery strategy over the last few years, in fitting with its virtual R&D business model. This strategy relies on a medium- to high-throughput phenotypic assay platform to expedite the screening of compound libraries accessed through its collaborations with partners from the pharmaceutical industry. We review the pragmatic approaches used to select compound libraries for screening against kinetoplastids, taking into account screening capacity. The advantages, limitations and current achievements in identifying new quality series for further development into preclinical candidates are critically discussed, together with attractive new approaches currently under investigation.

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.

What criteria do consumer health librarians use to develop library collections? a phenomenological study.

PubMed

Papadakos, Janet; Trang, Aileen; Wiljer, David; Cipolat Mis, Chiara; Cyr, Alaina; Friedman, Audrey Jusko; Mazzocut, Mauro; Snow, Michelle; Raivich, Valeria; Catton, Pamela

2014-04-01

The criteria for determining whether resources are included in consumer health library collections are summarized in institutional collection development policies (CDPs). Evidence suggests that CDPs do not adequately capture all of these criteria. The aim of this study was to describe the resource review experience of librarians and compare it to what is described in CDPs. A phenomenological approach was used to explore and describe the process. Four consumer health librarians independently evaluated cancer-related consumer health resources and described their review process during a semi-structured telephone interview. Afterward, these librarians completed online questionnaires about their approaches to collection development. CDPs from participating libraries, interview transcripts, and questionnaire data were analyzed. Researchers summarized the findings, and participating librarians reviewed results for validation. Librarians all utilized similar criteria, as documented in their CDPs; however, of thirteen criteria described in the study, only four were documented in CDPs. CDPs for consumer health libraries may be missing important criteria that are considered integral parts of the collection development process. A better understanding of the criteria and contextual factors involved in the collection development process can assist with establishing high-quality consumer health library collections.

What criteria do consumer health librarians use to develop library collections? a phenomenological study*

PubMed Central

Papadakos, Janet; Trang, Aileen; Wiljer, David; Mis, Chiara Cipolat; Cyr, Alaina; Friedman, Audrey Jusko; Mazzocut, Mauro; Snow, Michelle; Raivich, Valeria; Catton, Pamela

2014-01-01

Objectives: The criteria for determining whether resources are included in consumer health library collections are summarized in institutional collection development policies (CDPs). Evidence suggests that CDPs do not adequately capture all of these criteria. The aim of this study was to describe the resource review experience of librarians and compare it to what is described in CDPs. Methods: A phenomenological approach was used to explore and describe the process. Four consumer health librarians independently evaluated cancer-related consumer health resources and described their review process during a semi-structured telephone interview. Afterward, these librarians completed online questionnaires about their approaches to collection development. CDPs from participating libraries, interview transcripts, and questionnaire data were analyzed. Researchers summarized the findings, and participating librarians reviewed results for validation. Results: Librarians all utilized similar criteria, as documented in their CDPs; however, of thirteen criteria described in the study, only four were documented in CDPs. Conclusions: CDPs for consumer health libraries may be missing important criteria that are considered integral parts of the collection development process. Implications: A better understanding of the criteria and contextual factors involved in the collection development process can assist with establishing high-quality consumer health library collections. PMID:24860261

Deconstructing Cancer Patient Information Seeking in a Consumer Health Library Toward Developing a Virtual Information Consult for Cancer Patients and Their Caregivers: A Qualitative, Instrumental Case Study.

PubMed

Papadakos, Janet; Trang, Aileen; Cyr, Alaina B; Abdelmutti, Nazek; Giuliani, Meredith E; Snow, Michelle; McCurdie, Tara; Pulandiran, Menaka; Urowitz, Sara; Wiljer, David

2017-05-24

Cancer patients and their caregivers want information about their disease and are interested in finding health information online. Despite the abundance of cancer information online, it is often fragmented, its quality is highly variable, and it can be difficult to navigate without expert-level knowledge of the cancer system. The Patient & Family Library at the Princess Margaret Cancer Centre offers a broad collection of high-quality cancer health information and staff are available to help patrons refine their questions and explore information needs that they may not have considered. The purpose of this research study was to deconstruct patrons' information-seeking behaviors in the library to assess the feasibility of replicating the services provided in the library through a Web app, extending the service beyond the walls of the cancer centre. The specific aims of this research were to understand (1) how patrons approach information seeking in the library (interface design), (2) how patrons communicate their informational needs (information categorization and metadata requirements), and (3) what resources are provided to address the patrons' information needs (collection development). We employed a qualitative, instrumental case study to deconstruct patrons' health information-seeking behavior. The study population included patients, the librarian, and library volunteers. Ethnographic observation was conducted at the library over 3 days and key informant interviews with library staff were conducted to address the first aim. A closed card-sorting activity was conducted to address the second aim and the library shift logs and Search Request Forms (SRFs) were reviewed to address the third aim. A total of 55 interactions were recorded during the ethnographic observation and nine semistructured interviews were conducted during the key informant interviews. Seven library patron personas were identified: (1) Newbie, (2) Seasoned, (3) Direct, (4) Window Shopper, (5) Collector, (6) Information Seeker, and (7) Distressed. A total of 83 participants completed the closed card-sorting exercise. The participants' conceptual clusters within the similarity matrix overlapped with the groupings created by the librarian, with a few differences. A total of 161 entries in the library shift log and 65 SRFs were analyzed to determine what resources were given to patrons. Most resources that patrons received were available online (61%), although almost half of these required special access (47%). The study findings suggest it is possible to replicate library functions in a Web app with a few exceptions that cannot be replicated online. These elements include access to journal articles or other content behind paywalls and the librarian's ability to encourage further discussion through empathy and active listening. Discussion with the librarian could serve to refine and predict needs through observing information seekers and to provide immediate connection to spiritual care and psychosocial support for patrons in distress. ©Janet Papadakos, Aileen Trang, Alaina B Cyr, Nazek Abdelmutti, Meredith E Giuliani, Michelle Snow, Tara McCurdie, Menaka Pulandiran, Sara Urowitz, David Wiljer. Originally published in JMIR Cancer (http://cancer.jmir.org), 24.05.2017.

A Guide to the Librarian's Responsibility in Achieving Quality in Lighting and Ventilation.

ERIC Educational Resources Information Center

Mason, Ellsworth

1967-01-01

Quality, not intensity, is the keystone to good library lighting. The single most important problem in lighting is glare caused by extremely intense centers of light. Multiple interfiling of light rays is a factor required in library lighting. A fixture that diffuses light well is basic when light emerges from the fixture. It scatters widely,…

The Impact of Information Behavior in Academic Library Service Quality: A Case Study of the Science and Technology Area in Spain

ERIC Educational Resources Information Center

Pinto, Maria; Fernandez-Marcial, Viviana; Gomez-Camarero, Carmen

2010-01-01

This research explores the extent of service quality in Spanish university science and technology libraries, based on the expectations and perceptions of their users: faculty and researchers. Users' information behavior is analyzed with the specially designed BiQual tool, which reveals specific needs such as the greater importance of electronic…

Outsourcing Photocopying in a Library: One Experience.

ERIC Educational Resources Information Center

Wittorf, Robert

1998-01-01

Describes the process for outsourcing photocopying including developing a clear request for proposal, monitoring and responding to vendor performance, and ensuring quality controls in academic libraries. (Author/PEN)

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

NASA Astrophysics Data System (ADS)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.

Changing the Concept and Measure of Service Quality in Academic Libraries.

ERIC Educational Resources Information Center

Nitecki, Danuta A.

1996-01-01

The diagnostic instrument SERVQUAL has been developed to measure customer expectations and perceptions of service. This article describes a study that investigated how applicable SERVQUAL is to academic libraries and how influential the study's findings might be in changing concepts of the management of academic library services. Two SERVQUAL…

Closing the Gap: Public Libraries and Senior Learners

ERIC Educational Resources Information Center

Welliver, Hilary

2017-01-01

This executive position paper (EPP) examines the gap in Delaware's public library services to senior citizens engaged in lifelong learning. Re-envisioning the public library as a center that provides support of lifelong learning for the whole individual and improving the quality of life for Kent County's seniors is one approach that may keep…

Self-Service Charge Systems: Current Technological Applications and Their Implications for the Future Library.

ERIC Educational Resources Information Center

Mardikian, Jackie

1995-01-01

Discusses a possible shift to self-service check-out systems for academic library patrons. Provides an annotated bibliography of 51 items that discuss the impact of self-service technology on the quality of service and customer satisfaction in libraries, service sectors, banking, and the vending industry. (LRW)

Library Web Sites in Pakistan: An Analysis of Content

ERIC Educational Resources Information Center

Qutab, Saima; Mahmood, Khalid

2009-01-01

Purpose: The purpose of this paper is to investigate library web sites in Pakistan, to analyse their content and navigational strengths and weaknesses and to give recommendations for developing better web sites and quality assessment studies. Design/methodology/approach: Survey of web sites of 52 academic, special, public and national libraries in…

Library Services in Institutions for Mentally and Developmentally Disabled Adults.

ERIC Educational Resources Information Center

Ensor, Pat

To improve the quality of life of institutionalized individuals, libraries can serve as a constructive escape mechanism for dealing with stress, a representation of external reality, and a therapeutic agent, in addition to offering bibliotherapy. Ideally, the library should be an integral part of the institution and provide a user-appropriate…

Students' Perception on Library Service Quality: A Qualitative Study of IIUM Library

ERIC Educational Resources Information Center

Ahmed, Selim; Islam, Rafikul

2012-01-01

Academic libraries are currently facing their greatest challenge since the explosion in tertiary education and academic publishing, which began after World War II. The global digital revolution is affecting both the traditional forms of the creation, organisation, and dissemination of knowledge, and the world of tertiary education itself. In the…

The Case for Creating a Scholars Portal to the Web: A White Paper.

ERIC Educational Resources Information Center

Campbell, Jerry D.

2001-01-01

Considers the need for reliable, scholarly access to the Web and suggests that the Association for Research Libraries, in partnership with OCLC and the Library of Congress, develop a so-called scholar's portal. Topics include quality content; enhanced library services; and gateway functions, including access to commercial databases and focused…

[Construction of forward and reverse subtracted cDNA libraries between muscle tissue of Meishan and Landrace pigs].

PubMed

Xu, De-Quan; Zhang, Yi-Bing; Xiong, Yuan-Zhu; Gui, Jian-Fang; Jiang, Si-Wen; Su, Yu-Hong

2003-07-01

Using suppression subtractive hybridization (SSH) technique, forward and reverse subtracted cDNA libraries were constructed between Longissimus muscles from Meishan and Landrace pigs. A housekeeping gene, G3PDH, was used to estimate the efficiency of subtractive cDNA. In two cDNA libraries, G3PDH was subtracted very efficiently at appropriate 2(10) and 2(5) folds, respectively, indicating that some differentially expressed genes were also enriched at the same folds and the two subtractive cDNA libraries were very successful. A total of 709 and 673 positive clones were isolated from forward and reverse subtracted cDNA libraries, respectively. Analysis of PCR showed that most of all plasmids in the clones contained 150-750 bp inserts. The construction of subtractive cDNA libraries between muscle tissue from different pig breeds laid solid foundations for isolating and identifying the genes determining muscle growth and meat quality, which will be important to understand the mechanism of muscle growth, determination of meat quality and practice of molecular breeding.

Deep sequencing in library selection projects: what insight does it bring?

PubMed

Glanville, J; D'Angelo, S; Khan, T A; Reddy, S T; Naranjo, L; Ferrara, F; Bradbury, A R M

2015-08-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deep sequencing in library selection projects: what insight does it bring?

PubMed Central

Glanville, J; D’Angelo, S; Khan, T.A.; Reddy, S. T.; Naranjo, L.; Ferrara, F.; Bradbury, A.R.M.

2015-01-01

High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology. PMID:26451649

An efficient field and laboratory workflow for plant phylotranscriptomic projects1

PubMed Central

Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Timoneda, Alfonso; Feng, Tao; Marx, Hannah E.; Walker, Joseph F.; Smith, Stephen A.

2017-01-01

Premise of the study: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. Methods and Results: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms. These included difficult mucilaginous tissues such as those of Cactaceae and Droseraceae. Conclusions: Our workflow is not only cost effective (ca. $270 per sample, as of August 2016, from tissue to reads) and time efficient (less than 50 h for 10–12 samples including all laboratory work and sample curation), but also has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds. PMID:28337391

Capillary Flow Layer-by-Layer: A Microfluidic Platform for the High-Throughput Assembly and Screening of Nanolayered Film Libraries

PubMed Central

2015-01-01

Layer-by-layer (LbL) assembly is a powerful tool with increasing real world applications in energy, biomaterials, active surfaces, and membranes; however, the current state of the art requires individual sample construction using large quantities of material. Here we describe a technique using capillary flow within a microfluidic device to drive high-throughput assembly of LbL film libraries. This capillary flow layer-by-layer (CF-LbL) method significantly reduces material waste, improves quality control, and expands the potential applications of LbL into new research spaces. The method can be operated as a simple lab benchtop apparatus or combined with liquid-handling robotics to extend the library size. Here we describe and demonstrate the technique and establish its ability to recreate and expand on the known literature for film growth and morphology. We use the same platform to assay biological properties such as cell adhesion and proliferation and ultimately provide an example of the use of this approach to identify LbL films for surface-based DNA transfection of commonly used cell types. PMID:24836460

Constructing and detecting a cDNA library for mites.

PubMed

Hu, Li; Zhao, YaE; Cheng, Juan; Yang, YuanJun; Li, Chen; Lu, ZhaoHui

2015-10-01

RNA extraction and construction of complementary DNA (cDNA) library for mites have been quite challenging due to difficulties in acquiring tiny living mites and breaking their hard chitin. The present study is to explore a better method to construct cDNA library for mites that will lay the foundation on transcriptome and molecular pathogenesis research. We selected Psoroptes cuniculi as an experimental subject and took the following steps to construct and verify cDNA library. First, we combined liquid nitrogen grinding with TRIzol for total RNA extraction. Then, switching mechanism at 5' end of the RNA transcript (SMART) technique was used to construct full-length cDNA library. To evaluate the quality of cDNA library, the library titer and recombination rate were calculated. The reliability of cDNA library was detected by sequencing and analyzing positive clones and genes amplified by specific primers. The results showed that the RNA concentration was 836 ng/μl and the absorbance ratio at 260/280 nm was 1.82. The library titer was 5.31 × 10(5) plaque-forming unit (PFU)/ml and the recombination rate was 98.21%, indicating that the library was of good quality. In the 33 expressed sequence tags (ESTs) of P. cuniculi, two clones of 1656 and 1658 bp were almost identical with only three variable sites detected, which had an identity of 99.63% with that of Psoroptes ovis, indicating that the cDNA library was reliable. Further detection by specific primers demonstrated that the 553-bp Pso c II gene sequences of P. cuniculi had an identity of 98.56% with those of P. ovis, confirming that the cDNA library was not only reliable but also feasible.

The use of PacBio and Hi-C data in denovo assembly of the goat genome

USDA-ARS?s Scientific Manuscript database

Generating de novo reference genome assemblies for non-model organisms is a laborious task that often requires a large amount of data from several sequencing platforms and cytogenetic surveys. By using PacBio sequence data and new library creation techniques, we present a de novo, high quality refer...

A Kind of Transformation of Information Service--Science and Technology Novelty Search in Chinese University Libraries

ERIC Educational Resources Information Center

Aiguo, Li

2007-01-01

Science and Technology Novelty Search (S&TNS) is a special information consultation service developed as part of the Chinese Sci-Tech system. The author introduces the concept of S&TNS, and explains its role, and the role of the university library in the process. A quality control model to improve the quality of service of the S&TNS at…

Beyond helper phage: Using "helper cells" to select peptide affinity ligands

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

Phipps, Mary Lisa; Lillo, Antoinetta M.; Shou, Yulin

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report onmore » the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.« less

Beyond helper phage: Using "helper cells" to select peptide affinity ligands

DOE PAGES

Phipps, Mary Lisa; Lillo, Antoinetta M.; Shou, Yulin; ...

2016-09-14

Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report onmore » the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.« less

Collection policy management for the Kuopio University and Kuopio University Hospital, Finland: detecting the needs of users and developing high-quality collections.

PubMed

Kananen, Jukka; Ovaska, Tuulevi; Saarti, Jarmo

2006-09-01

This article discusses the collection policies of a university library in a modern digital environment. A brief description of national collection policy decisions in Finland is provided. The rapid evolution and growth of scientific publication places new demands on building a collection in a health and bioscience orientated university, and it requires an evidence-based approach to support effective service processes. The aim of the study was to identify the needs of the university's students and staff. Usage statistics were surveyed and analysed. Both usage statistics and user surveys indicate that the library use is divided half-and-half between the traditional use of printed material and library premises and the modern use of digital materials via the Web. The former is mainly the way that the students and hospital staff use the library, and the latter can be viewed as the researchers' way of using the library. Librarians and information specialists act in this as service providers and/or guides and tutors to the end-users. These results, however, must be validated with a longer timescale data collation and analysis, both of which are an ongoing process within the library. It is important that requirements and needs of the library's users are monitored regularly and acquisition policies are updated frequently. It also seems that the needs have changed quite dramatically in response to modern ways of disseminating publications, but this supposition will require further study.

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

PubMed

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

2018-03-01

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

[Building Mass Spectrometry Spectral Libraries of Human Cancer Cell Lines].

PubMed

Faktor, J; Bouchal, P

Cancer research often focuses on protein quantification in model cancer cell lines and cancer tissues. SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), the state of the art method, enables the quantification of all proteins included in spectral library. Spectral library contains fragmentation patterns of each detectable protein in a sample. Thorough spectral library preparation will improve quantitation of low abundant proteins which usually play an important role in cancer. Our research is focused on the optimization of spectral library preparation aimed at maximizing the number of identified proteins in MCF-7 breast cancer cell line. First, we optimized the sample preparation prior entering the mass spectrometer. We examined the effects of lysis buffer composition, peptide dissolution protocol and the material of sample vial on the number of proteins identified in spectral library. Next, we optimized mass spectrometry (MS) method for spectral library data acquisition. Our thorough optimized protocol for spectral library building enabled the identification of 1,653 proteins (FDR < 1%) in 1 µg of MCF-7 lysate. This work contributed to the enhancement of protein coverage in SWATH digital biobanks which enable quantification of arbitrary protein from physically unavailable samples. In future, high quality spectral libraries could play a key role in preparing of patient proteome digital fingerprints.Key words: biomarker - mass spectrometry - proteomics - digital biobanking - SWATH - protein quantificationThis work was supported by the project MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 7. 5. 2016Accepted: 9. 6. 2016.

A New Culture of Assessment: Preliminary Report on the ARL SERVQUAL Survey.

ERIC Educational Resources Information Center

Cook, Colleen; Heath, Fred; Thompson, Bruce

Texas A&M University and the Association of Research Libraries (ARL) under the New Measures initiative are engaged in a project to evaluate service quality in research libraries using an augmented SERVQUAL instrument. In spring 2000, 13 ARL libraries in North America invited a random sample of students and faculty to take the survey through…

Disturbingly Weak: The Current State of Financial Management Education in Library and Information Science Curricula

ERIC Educational Resources Information Center

Burger, Robert H.; Kaufman, Paula T.; Atkinson, Amy L.

2015-01-01

Financial management skills are necessary for responsible library management. In light of the profession's current emphasis on financial literacy, the authors posed four questions: (1) to what extent are library and information science schools providing courses in financial management for their graduates; (2) what is the quality and quantity of…

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…

Faculty Perception of Information Control Using LibQUAL+[TM] Indicators

ERIC Educational Resources Information Center

Kayongo, Jessica; Jones, Sherri

2008-01-01

The LibQUAL+[TM] survey was used in 2006 to assess library service quality at the University of Notre Dame. While results showed that the Libraries were meeting users' expectations for service in most areas, a closer examination of the data revealed dissatisfaction from a subgroup of users in one particular dimension of library services. This…

4/4/2018: The Ag Data Commons Metrics | National Agricultural Library

Science.gov Websites

Skip to main content Home National Agricultural Library United States Department of Agriculture Ag | Agricultural Research Service | Plain Language | FOIA | Accessibility Statement | Information Quality | Privacy

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.

Evaluation of products and services of a nursing library: user satisfaction.

PubMed

Cozin, Sheila Kátia; Turrini, Ruth Natalia Teresa

2008-01-01

The goal of the study was to evaluate the quality of the services provided by the library at the Nursing School of the University of São Paulo. A questionnaire evaluating users' satisfaction with the service was employed, covering five quality components: tangibles, reliability, responsiveness, assurance and empathy. The Satisfaction Rate was calculated through the degree of importance in relation to satisfaction. The analysis of the open-ended answers was quanti-qualitative. For Reliability and Empathy, the users showed dissatisfaction with the training for bibliographic research and the librarian's willingness to meet the clients' information needs, respectively. Responsiveness did not fully satisfy the users, disagreeing with the providers. However, both agreed that the archives are outdated. Among the tangible aspects, equipment and noise were criticized most often. The results show that the library offers good service quality to its users.

The ToxCast Chemical Landscape - Paving the Road to 21st ...

EPA Pesticide Factsheets

The ToxCast high-throughput screening (HTS) program within the U.S. Environmental Protection Agency (EPA) was launched in 2007. Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay endpoints. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in public release of screening data at the end of 2013. Concurrently, a larger EPA library of 3726 chemicals (including the Phase II chemicals) was undergoing screening in the cross-federal agency Tox21 HTS project. Four years later, Phase III of EPA’s ToxCast program is actively screening a diverse library consisting of more than 3800 chemicals, 96% of which are also undergoing Tox21 screening. The majority of ToxCast studies, to date, have focused on using HTS results to build biologically based models for predicting in vivo toxicity endpoints. The focus of the present article, in contrast, is on the EPA chemical library underpinning these efforts. A history of the phased construction of EPA’s ToxCast library is presented, considering factors influencing chemical selection as well as the various quality measures implemented. Next, Chemical Abstracts Service Registry Numbers (CASRN), which were used to compile initial chemical nominations for ToxCast testing, are used to assess overlaps of the current ToxCast library with important toxicity, regulatory, and exposure inventories. Lastly, ToxCast chemicals are described in terms of generaliz

Clinical data miner: an electronic case report form system with integrated data preprocessing and machine-learning libraries supporting clinical diagnostic model research.

PubMed

Installé, Arnaud Jf; Van den Bosch, Thierry; De Moor, Bart; Timmerman, Dirk

2014-10-20

Using machine-learning techniques, clinical diagnostic model research extracts diagnostic models from patient data. Traditionally, patient data are often collected using electronic Case Report Form (eCRF) systems, while mathematical software is used for analyzing these data using machine-learning techniques. Due to the lack of integration between eCRF systems and mathematical software, extracting diagnostic models is a complex, error-prone process. Moreover, due to the complexity of this process, it is usually only performed once, after a predetermined number of data points have been collected, without insight into the predictive performance of the resulting models. The objective of the study of Clinical Data Miner (CDM) software framework is to offer an eCRF system with integrated data preprocessing and machine-learning libraries, improving efficiency of the clinical diagnostic model research workflow, and to enable optimization of patient inclusion numbers through study performance monitoring. The CDM software framework was developed using a test-driven development (TDD) approach, to ensure high software quality. Architecturally, CDM's design is split over a number of modules, to ensure future extendability. The TDD approach has enabled us to deliver high software quality. CDM's eCRF Web interface is in active use by the studies of the International Endometrial Tumor Analysis consortium, with over 4000 enrolled patients, and more studies planned. Additionally, a derived user interface has been used in six separate interrater agreement studies. CDM's integrated data preprocessing and machine-learning libraries simplify some otherwise manual and error-prone steps in the clinical diagnostic model research workflow. Furthermore, CDM's libraries provide study coordinators with a method to monitor a study's predictive performance as patient inclusions increase. To our knowledge, CDM is the only eCRF system integrating data preprocessing and machine-learning libraries. This integration improves the efficiency of the clinical diagnostic model research workflow. Moreover, by simplifying the generation of learning curves, CDM enables study coordinators to assess more accurately when data collection can be terminated, resulting in better models or lower patient recruitment costs.

Novel method for high-throughput colony PCR screening in nanoliter-reactors

PubMed Central

Walser, Marcel; Pellaux, Rene; Meyer, Andreas; Bechtold, Matthias; Vanderschuren, Herve; Reinhardt, Richard; Magyar, Joseph; Panke, Sven; Held, Martin

2009-01-01

We introduce a technology for the rapid identification and sequencing of conserved DNA elements employing a novel suspension array based on nanoliter (nl)-reactors made from alginate. The reactors have a volume of 35 nl and serve as reaction compartments during monoseptic growth of microbial library clones, colony lysis, thermocycling and screening for sequence motifs via semi-quantitative fluorescence analyses. nl-Reactors were kept in suspension during all high-throughput steps which allowed performing the protocol in a highly space-effective fashion and at negligible expenses of consumables and reagents. As a first application, 11 high-quality microsatellites for polymorphism studies in cassava were isolated and sequenced out of a library of 20 000 clones in 2 days. The technology is widely scalable and we envision that throughputs for nl-reactor based screenings can be increased up to 100 000 and more samples per day thereby efficiently complementing protocols based on established deep-sequencing technologies. PMID:19282448

Designing a curriculum on Internet health resources for deaf high school students*

PubMed Central

Gregg, Amy L.; Wozar, Jody A.; Wessel, Charles B.; Epstein, Barbara A.

2002-01-01

Purpose: This paper examines the integration of instruction about quality health resources on the Internet into the health curriculum of a specialized high school for students with hearing disabilities. Setting/Participants/Resources: The Health Sciences Library System (HSLS) at the University of Pittsburgh has formed a partnership with the Western Pennsylvania School for the Deaf (WPSD). Brief Description: This project was partially funded through a subcontract with the National Library of Medicine. As one component of its Health Information for the Public project, HSLS formed a partnership with the WPSD. This partnership allowed for a librarian to provide instruction to health education and learning center teachers and students at WPSD about health resources on the Internet. This paper describes the planning process, curriculum development, and challenges encountered. These challenges include student knowledge of English as a second language, the need for a sign language interpreter, students' third-to-fourth-grade reading levels, and the need for appropriate visual presentations to accompany the audio counterpart. Results/Outcome: The partnership formed between HSLS and WPSD improved deaf high school students' ability to locate quality health information on the Internet. Evaluation Method: A pre-class survey and post-class survey were used to determine the impact of the instruction. PMID:12398249

[Health and quality of life of medical residents].

PubMed

Lourenção, Luciano Garcia; Moscardini, Airton Camacho; Soler, Zaida Aurora Sperli Geraldes

2010-01-01

This article highlights the relationship between health and quality of life among the resident medical staff. A review was carried out to analyze the content of the relationship under study. Sources for this search were the Virtual Health Library (VHL), by BIREME (Centro Latino-American and Caribbean Center on Health Sciences Information), the Electronic databases Medline (Medical Literature Analysis and Retrieval System On-Line) Lilacs (Literatura Latino-American and Caribbean Health Sciences), SciELO (Scientific Electronic Library Online) and the email address scholar.google.com.br. Descriptors used were: Quality of life, Burnout, Internship and Residency. Planning and analysis of scientific literature, was performed to evaluate and discuss issues presented in the studies related to the subject, considering the distribution of publications according to country of origin, date of publication, source and title, focus of study and main conclusions. Studies published point to high rates of burnout, stress, depression, fatigue and insomnia among medical residents; moreover a lack of coping strategies, the relationship between workload and quality of life, require a change of medical legislation regarding work-based learning. Studies have shown that an adequate training program is needed not only to increase professional qualification and personal quality of life, but also to provide safety during patient treatment. It is known that residency training is stressful; it is nevertheless a process required to prepare for a solid career and personal growth of the young medical staff.

Improving Instruction through a Videotape Library.

ERIC Educational Resources Information Center

Batesky, James

1979-01-01

Videotape and a videotape library can be used to expand the quality of instruction of a physical education program by allowing greater diversity of material taught and increased use of professionals and experts in various sports. (JMF)

Evolution of Reference: A New Service Model for Science and Engineering Libraries

ERIC Educational Resources Information Center

Bracke, Marianne Stowell; Chinnaswamy, Sainath; Kline, Elizabeth

2008-01-01

This article explores the different steps involved in adopting a new service model at the University of Arizona Science-Engineering Library. In a time of shrinking budgets and changing user behavior the library was forced to rethink it reference services to be cost effective and provide quality service at the same time. The new model required…

Building the Service-Based Library Web Site: A Step-by-Step Guide to Design and Options.

ERIC Educational Resources Information Center

Garlock, Kristen L.; Piontek, Sherry

The World Wide Web, with its captivating multimedia features and hypertext capabilities, has brought millions of new users to the Internet. Library staff who could create a home page on the Web could present basic information about the library and its services, showcase its resources, create links to quality material inside and outside the…

77 FR 27111 - Office of Commercial Space Transportation (AST); Notice of Availability of the Final...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-08

... Policy Act of 1969, as amended (NEPA; 42 U.S.C. 4321 et seq.), Council on Environmental Quality NEPA... Base Library, 95 SPTG/SVMG, 5 West Yeager Blvd., Building 2665, Edwards AFB, CA 93524-1295. Kern County Library, Boron Branch, 26967 20 Mule Team Road, Boron, CA 93516. Kern County Library, California City...

The Library as a Humanistic Workplace. A Report to the LAMA Board.

ERIC Educational Resources Information Center

American Library Association, Chicago, IL. Library Administration and Management Association.

While it may seem redundant to be considering the library as a humanistic workplace, since most libraries are probably at the upper end of the quality of workplace life, there is always some room for improvement, making the topic worthy of exploration. The most important consideration in a humanistic workplace is how people are treated. There is a…

Lilead Fellows Program: An Innovative Approach to Professional Development for School Library Leaders

ERIC Educational Resources Information Center

Kodama, Christie; DiScala, Jeffrey; Weeks, Ann Carlson; Barlow, Diane L.; Jacobs, Leah; Hall, Rosemary

2016-01-01

In this article, the authors discuss the Lilead Fellows Program, funded by a grant from the Institute of Museum and Library Services (IMLS). This innovative approach to professional development (PD) is for school district library supervisors. It is based upon widely accepted principles of quality PD, and is in its second year of operation with an…

Do It Right! Best Practices for Serving Young Adults in School and Public Libraries. Teens @ the Library Series.

ERIC Educational Resources Information Center

Jones, Patrick; Shoemaker, Joel

This book explores how librarians can work to strengthen and improve the quality of service to young adults. The introduction is written by Mary Kay Chelton, whose dissertation, "Adult-Adolescent Service Encounters: The Library Context" (1997), inspired this book. The book has 12 chapters. Chapter 1 introduces the provision of best young adult…

Design and implementation of a cloud based lithography illumination pupil processing application

NASA Astrophysics Data System (ADS)

Zhang, Youbao; Ma, Xinghua; Zhu, Jing; Zhang, Fang; Huang, Huijie

2017-02-01

Pupil parameters are important parameters to evaluate the quality of lithography illumination system. In this paper, a cloud based full-featured pupil processing application is implemented. A web browser is used for the UI (User Interface), the websocket protocol and JSON format are used for the communication between the client and the server, and the computing part is implemented in the server side, where the application integrated a variety of high quality professional libraries, such as image processing libraries libvips and ImageMagic, automatic reporting system latex, etc., to support the program. The cloud based framework takes advantage of server's superior computing power and rich software collections, and the program could run anywhere there is a modern browser due to its web UI design. Compared to the traditional way of software operation model: purchased, licensed, shipped, downloaded, installed, maintained, and upgraded, the new cloud based approach, which is no installation, easy to use and maintenance, opens up a new way. Cloud based application probably is the future of the software development.

A novel spectral library workflow to enhance protein identifications.

PubMed

Li, Haomin; Zong, Nobel C; Liang, Xiangbo; Kim, Allen K; Choi, Jeong Ho; Deng, Ning; Zelaya, Ivette; Lam, Maggie; Duan, Huilong; Ping, Peipei

2013-04-09

The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed

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

2018-06-01

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

Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

PubMed

Hoskins, Roger A; Stapleton, Mark; George, Reed A; Yu, Charles; Wan, Kenneth H; Carlson, Joseph W; Celniker, Susan E

2005-12-02

cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequence Tag (EST) sequencing is the method of choice for recovering cDNAs representing many of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a cDNA library at random, and it recovers transcripts with low expression levels inefficiently. We describe a PCR-based method for directed screening of plasmid cDNA libraries. We demonstrate its utility in a screen of libraries used in our Drosophila EST projects for 153 transcription factor genes that were not represented by full-length cDNA clones in our Drosophila Gene Collection. We recovered high-quality, full-length cDNAs for 72 genes and variously compromised clones for an additional 32 genes. The method can be used at any scale, from the isolation of cDNA clones for a particular gene of interest, to the improvement of large gene collections in model organisms and the human. Finally, we discuss the relative merits of directed cDNA library screening and RT-PCR approaches.

The Librarian's Internet Survival Guide: Strategies for the High-Tech Reference Desk.

ERIC Educational Resources Information Center

McDermott, Irene E.; Quint, Barbara, Ed.

This guide discusses the use of the World Wide Web for library reference service. Part 1, "Ready Reference on the Web: Resources for Patrons," contains chapters on searching and meta-searching the Internet, using the Web to find people, news on the Internet, quality reference resources on the Web, Internet sites for kids, free full-text…

Dr. Janie Merkel is interviewed by Ryan Blum and Janice Friend.

PubMed

Merkel, Janie

2007-12-01

Dr. Janie Merkel is the director of Yale's Chemical Genomics Screening Facility, a high-throughput screening laboratory that is part of the Yale University Center for Genomics and Proteomics. The Screening Facility connects Yale researchers with industry-quality robotic machinery and a diverse group of compound libraries, which have been used successfully to link therapeutic targets with potential therapies.

Optimization and high-throughput screening of antimicrobial peptides.

PubMed

Blondelle, Sylvie E; Lohner, Karl

2010-01-01

While a well-established process for lead compound discovery in for-profit companies, high-throughput screening is becoming more popular in basic and applied research settings in academia. The development of combinatorial libraries combined with easy and less expensive access to new technologies have greatly contributed to the implementation of high-throughput screening in academic laboratories. While such techniques were earlier applied to simple assays involving single targets or based on binding affinity, they have now been extended to more complex systems such as whole cell-based assays. In particular, the urgent need for new antimicrobial compounds that would overcome the rapid rise of drug-resistant microorganisms, where multiple target assays or cell-based assays are often required, has forced scientists to focus onto high-throughput technologies. Based on their existence in natural host defense systems and their different mode of action relative to commercial antibiotics, antimicrobial peptides represent a new hope in discovering novel antibiotics against multi-resistant bacteria. The ease of generating peptide libraries in different formats has allowed a rapid adaptation of high-throughput assays to the search for novel antimicrobial peptides. Similarly, the availability nowadays of high-quantity and high-quality antimicrobial peptide data has permitted the development of predictive algorithms to facilitate the optimization process. This review summarizes the various library formats that lead to de novo antimicrobial peptide sequences as well as the latest structural knowledge and optimization processes aimed at improving the peptides selectivity.

Research on Energy-saving Shape Design of High School Library Building in Cold Region

NASA Astrophysics Data System (ADS)

Hui, Zhao; Weishuang, Xie; Zirui, Tong

2017-11-01

Considering climatic characteristics in cold region, existing high school libraries in Changchun are researched according to investigation of real conditions of these library buildings. Mathematical analysis and CAD methods are used to summarize the relation between building shape and building energy saving of high school library. Strategies are put forward for sustainable development of high school library building in cold region, providing reliable design basis for construction of high school libraries in Changchun.

Improving medical education in Kenya: an international collaboration.

PubMed

Mayo, Alexa

2014-04-01

This paper describes a partnership between the University of Nairobi College of Health Sciences (CHS) Library and the University of Maryland Health Sciences and Human Services Library (HS/HSL). The libraries are collaborating to develop best practices for the CHS Library as it meets the challenge of changing medical education information needs in a digital environment. The collaboration is part of a Medical Education Partnership Initiative. The library project has several components: an assessment of the CHS Library, learning visits in the United States and Kenya, development of recommendations to enhance the CHS Library, and ongoing evaluation of the program's progress. Development of new services and expertise at the CHS Library is critical to the project's success. A productive collaboration between the HS/HSL and CHS Library is ongoing. A successful program to improve the quality of medical education will have a beneficial impact on health outcomes in Kenya.

Improving medical education in Kenya: an international collaboration*†

PubMed Central

Mayo, Alexa

2014-01-01

This paper describes a partnership between the University of Nairobi College of Health Sciences (CHS) Library and the University of Maryland Health Sciences and Human Services Library (HS/HSL). The libraries are collaborating to develop best practices for the CHS Library as it meets the challenge of changing medical education information needs in a digital environment. The collaboration is part of a Medical Education Partnership Initiative. The library project has several components: an assessment of the CHS Library, learning visits in the United States and Kenya, development of recommendations to enhance the CHS Library, and ongoing evaluation of the program's progress. Development of new services and expertise at the CHS Library is critical to the project's success. A productive collaboration between the HS/HSL and CHS Library is ongoing. A successful program to improve the quality of medical education will have a beneficial impact on health outcomes in Kenya. PMID:24860265

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

PubMed

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

2018-04-06

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

Selection of Journals for Index Medicus: A Historical Review

PubMed Central

Karel, Leonard

1967-01-01

From the inception of the first Index Medicus, published in 1879, to the present, the National Library of Medicine has been concerned with the quality of journals in the Index. The Library has, therefore, sought advice repeatedly on how best to maintain currency of the Index without sacrificing quality and subject matter balance. Responding to suggestions, the Library decided in June 1964 to base its selection of journals on recommendations made by a panel consisting primarily of extramural consultants widely regarded as specialists in the totality of biomedical literature. Beginning with its first meeting in September 1964, this panel has been fortified in its reviews by advice from subject matter specialists. The panel, by its own wishes, which bear the endorsement of the Board of Regents of the Library, will continue to rely heavily on such expert advice in future evaluations of journals. PMID:6072093

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

PubMed

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

NASA Astrophysics Data System (ADS)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Assessment of Service Desk Quality at an Academic Health Sciences Library.

PubMed

Blevins, Amy E; DeBerg, Jennifer; Kiscaden, Elizabeth

2016-01-01

Due to an identified need for formal assessment, a small team of librarians designed and administered a survey to gauge the quality of customer service at their academic health sciences library. Though results did not drive major changes to services, several important improvements were implemented and a process was established to serve as a foundation for future use. This article details the assessment process used and lessons learned during the project.

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

PubMed

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

2014-04-15

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

Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries

NASA Astrophysics Data System (ADS)

Grünzner, S.; Reddavide, F. V.; Steinfelder, C.; Cui, M.; Busek, M.; Klotzbach, U.; Zhang, Y.; Sonntag, F.

2017-02-01

The fast development of DNA-encoded chemical libraries (DECL) in the past 10 years has received great attention from pharmaceutical industries. It applies the selection approach for small molecular drug discovery. Because of the limited choices of DNA-compatible chemical reactions, most DNA-encoded chemical libraries have a narrow structural diversity and low synthetic yield. There is also a poor correlation between the ranking of compounds resulted from analyzing the sequencing data and the affinity measured through biochemical assays. By combining DECL with dynamical chemical library, the resulting DNA-encoded dynamic library (EDCCL) explores the thermodynamic equilibrium of reversible reactions as well as the advantages of DNA encoded compounds for manipulation/detection, thus leads to enhanced signal-to-noise ratio of the selection process and higher library quality. However, the library dynamics are caused by the weak interactions between the DNA strands, which also result in relatively low affinity of the bidentate interaction, as compared to a stable DNA duplex. To take advantage of both stably assembled dual-pharmacophore libraries and EDCCLs, we extended the concept of EDCCLs to heat-induced EDCCLs (hi-EDCCLs), in which the heat-induced recombination process of stable DNA duplexes and affinity capture are carried out separately. To replace the extremely laborious and repetitive manual process, a fully automated device will facilitate the use of DECL in drug discovery. Herein we describe a novel lab-on-a-chip platform for high throughput drug discovery with hi-EDCCL. A microfluidic system with integrated actuation was designed which is able to provide a continuous sample circulation by reducing the volume to a minimum. It consists of a cooled and a heated chamber for constant circulation. The system is capable to generate stable temperatures above 75 °C in the heated chamber to melt the double strands of the DNA and less than 15 °C in the cooled chamber, to reanneal the reshuffled library. In the binding chamber (the cooled chamber) specific retaining structures are integrated. These hold back beads functionalized with the target protein, while the chamber is continuously flushed with library molecules. Afterwards the whole system can be flushed with buffer to wash out unspecific bound molecules. Finally the protein-loaded beads with attached molecules can be eluted for further investigation.

Development of an Efficient Approach to Perform Neutronics Simulations for Plutonium-238 Production

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

Chandler, David; Ellis, Ronald James

Conversion of 238Pu decay heat into usable electricity is imperative to power National Aeronautics and Space Administration (NASA) deep space exploration missions; however, the current stockpile of 238Pu is diminishing and the quality is less than ideal. In response, the US Department of Energy and NASA have undertaken a program to reestablish a domestic 238Pu production program and a technology demonstration sub-project has been initiated. Neutronics simulations for 238Pu production play a vital role in this project because the results guide reactor safety-basis, target design and optimization, and post-irradiation examination activities. A new, efficient neutronics simulation tool written in Pythonmore » was developed to evaluate, with the highest fidelity possible with approved tools, the time-dependent nuclide evolution and heat deposition rates in 238Pu production targets irradiated in the High Flux Isotope Reactor (HFIR). The Python Activation and Heat Deposition Script (PAHDS) was developed specifically for experiment analysis in HFIR and couples the MCNP5 and SCALE 6.1.3 software quality assured tools to take advantage of an existing high-fidelity MCNP HFIR model, the most up-to-date ORIGEN code, and the most up-to-date nuclear data. Three cycle simulations were performed with PAHDS implementing ENDF/B-VII.0, ENDF/B-VII.1, and the Hybrid Library GPD-Rev0 cross-section libraries. The 238Pu production results were benchmarked against VESTA-obtained results and the impact of various cross-section libraries on the calculated metrics were assessed.« less

Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn)

PubMed Central

Yin, Jingjing; Li, Liangjun; Chen, Xuehao

2013-01-01

Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root. PMID:23840598

Using Localized Survey Items to Augment Standardized Benchmarking Measures: A LibQUAL+[TM] Study

ERIC Educational Resources Information Center

Thompson, Bruce; Cook, Colleen; Kyrillidou, Martha

2006-01-01

The LibQUAL+[TM] protocol solicits open-ended comments from users with regard to library service quality, gathers data on 22 core items, and, at the option of individual libraries, also garners ratings on five items drawn from a pool of more than 100 choices selected by libraries. In this article, the relationship of scores on these locally…

The National Library of Medicine Pill Image Recognition Challenge: An Initial Report.

PubMed

Yaniv, Ziv; Faruque, Jessica; Howe, Sally; Dunn, Kathel; Sharlip, David; Bond, Andrew; Perillan, Pablo; Bodenreider, Olivier; Ackerman, Michael J; Yoo, Terry S

2016-10-01

In January 2016 the U.S. National Library of Medicine announced a challenge competition calling for the development and discovery of high-quality algorithms and software that rank how well consumer images of prescription pills match reference images of pills in its authoritative RxIMAGE collection. This challenge was motivated by the need to easily identify unknown prescription pills both by healthcare personnel and the general public. Potential benefits of this capability include confirmation of the pill in settings where the documentation and medication have been separated, such as in a disaster or emergency; and confirmation of a pill when the prescribed medication changes from brand to generic, or for any other reason the shape and color of the pill change. The data for the competition consisted of two types of images, high quality macro photographs, reference images, and consumer quality photographs of the quality we expect users of a proposed application to acquire. A training dataset consisting of 2000 reference images and 5000 corresponding consumer quality images acquired from 1000 pills was provided to challenge participants. A second dataset acquired from 1000 pills with similar distributions of shape and color was reserved as a segregated testing set. Challenge submissions were required to produce a ranking of the reference images, given a consumer quality image as input. Determination of the winning teams was done using the mean average precision quality metric, with the three winners obtaining mean average precision scores of 0.27, 0.09, and 0.08. In the retrieval results, the correct image was amongst the top five ranked images 43%, 12%, and 11% of the time, out of 5000 query/consumer images. This is an initial promising step towards development of an NLM software system and application-programming interface facilitating pill identification. The training dataset will continue to be freely available online at: http://pir.nlm.nih.gov/challenge/submission.html.

Leveraging OpenStudio's Application Programming Interfaces: Preprint

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

Long, N.; Ball, B.; Goldwasser, D.

2013-11-01

OpenStudio development efforts have been focused on providing Application Programming Interfaces (APIs) where users are able to extend OpenStudio without the need to compile the open source libraries. This paper will discuss the basic purposes and functionalities of the core libraries that have been wrapped with APIs including the Building Model, Results Processing, Advanced Analysis, UncertaintyQuantification, and Data Interoperability through Translators. Several building energy modeling applications have been produced using OpenStudio's API and Software Development Kits (SDK) including the United States Department of Energy's Asset ScoreCalculator, a mobile-based audit tool, an energy design assistance reporting protocol, and a portfolio scalemore » incentive optimization analysismethodology. Each of these software applications will be discussed briefly and will describe how the APIs were leveraged for various uses including high-level modeling, data transformations from detailed building audits, error checking/quality assurance of models, and use of high-performance computing for mass simulations.« less

Past presidents I have known.

PubMed Central

Keys, T E

1998-01-01

This paper is an account of the accomplishments of some of the early past presidents of the Medical Library Association known personally to the author in his career as a medical librarian. It demonstrates the qualities that made these librarians leaders of our profession and also indicates their personal attributes that contributed to the advancement of medical librarianship. It is hoped that the historical presentation of some of the giants of our profession will inspire present and future presidents and other medical librarians with an understanding of some of the qualities necessary to the continuing success of our profession. Sir William Osler, who was a great believer in libraries and librarians and himself a past president of MLA, summed up four qualities in his advice to medical students equally applicable to past and present leadership in the library profession--(1) the art of detachment, (2) the virtue of method, (3) the quality of thoroughness, and (4) the grace of humility (Osler, Sir William. Teacher and Student. In his Aequanimitas: with Other Addresses to Medical Students. 3d ed. Philadelphia, Blakiston Company, 1904. p. 27-31). It is thought that our past presidents possessed all of these qualities. Images PMID:9578938

Past presidents I have known.

PubMed Central

Keys, T E

1975-01-01

This paper is an account of the accomplishments of some of the early past presidents of the Medical Library Association known personally to the author in his career as a medical librarian. It demonstrates the qualities that made these librarians leaders of our profession and also indicates their personal attributes that contributed to the advancement of medical librarianship. It is hoped that the historical presentation of some of the giants of our profession will inspire present and future presidents and other medical librarians with an understanding of some of the qualities necessary to the continuing success of our profession. Sir William Osler, who was a great believer in libraries and librarians and himself a Past President of MLA, summed up four qualities in his advice to medical students equally applicable to past and present leadership in the library profession-(1) the art of detachment, (2) the virtue of method, (3) the quality of thoroughness, (4) the grace of humility (Osler, Sir William. Teacher and Student. In his Aequanimitas: with Other Addresses to Medical Students. 3d ed. Philadelphia, Blakiston Company, 1904. p. 27-31.). It is thought that our past presidents possessed all of these qualities. Images PMID:1089017

Texture Classification by Texton: Statistical versus Binary

PubMed Central

Guo, Zhenhua; Zhang, Zhongcheng; Li, Xiu; Li, Qin; You, Jane

2014-01-01

Using statistical textons for texture classification has shown great success recently. The maximal response 8 (Statistical_MR8), image patch (Statistical_Joint) and locally invariant fractal (Statistical_Fractal) are typical statistical texton algorithms and state-of-the-art texture classification methods. However, there are two limitations when using these methods. First, it needs a training stage to build a texton library, thus the recognition accuracy will be highly depended on the training samples; second, during feature extraction, local feature is assigned to a texton by searching for the nearest texton in the whole library, which is time consuming when the library size is big and the dimension of feature is high. To address the above two issues, in this paper, three binary texton counterpart methods were proposed, Binary_MR8, Binary_Joint, and Binary_Fractal. These methods do not require any training step but encode local feature into binary representation directly. The experimental results on the CUReT, UIUC and KTH-TIPS databases show that binary texton could get sound results with fast feature extraction, especially when the image size is not big and the quality of image is not poor. PMID:24520346

A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms.

PubMed

Sze, Sing-Hoi; Parrott, Jonathan J; Tarone, Aaron M

2017-12-06

While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies.

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

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

A reliable computational workflow for the selection of optimal screening libraries.

PubMed

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic components, it can be easily adapted and reproduced by computational groups interested in rational selection of screening libraries. Furthermore, the workflow could be readily modified to include additional components. This workflow has been routinely used in our laboratory for the selection of libraries in multiple projects and consistently selects libraries which are well balanced across multiple parameters.Graphical abstract.

Promoting Academic Physicists, Their Students, and Their Research through Library Partnerships

NASA Astrophysics Data System (ADS)

Rozum, B.; Wesolek, A.

2012-12-01

At many institutions, attracting and mentoring quality students is of key importance. Through their developing careers, typically under the tutelage of one primary faculty member, students build portfolios, prepare for graduate school, and apply to post-doc programs or faculty positions. Often though, the corpus of that primary faculty member's work is not available in a single location. This is a disadvantage both for current students, who wish to highlight the importance of their work within the context of a research group and for the department, which can miss opportunities to attract high-quality future students. Utah State University Libraries hosts a thriving institutional repository, DigitalCommons@USU, which provides open access to scholarly works, research, reports, publications, and journals produced by Utah State University faculty, staff, and students. The Library and the Physics Department developed a partnership to transcend traditional library repository architecture and emphasize faculty research groups within the department. Previously, only student theses and dissertations were collected, and they were not associated with the department in any way. Now student presentations, papers, and posters appear with other faculty works all in the same research work space. This poster session highlights the features of the University's repository and describes what is required to establish a similar structure at other academic institutions. We anticipate several long-term benefits of this new structure. Students are pleased with the increased visibility of their research and with having an online presence through their "Selected Works" personal author site. Faculty are pleased with the opportunity to highlight their research and the potential to attract new students to their research groups. This new repository model also allows the library to amplify the existing scientific outreach initiatives of the physics department. One example of this is a recent exhibit created in the Library showcasing a student research group's 30-year history of sending payloads into space. The exhibit was a direct result of archiving the work of student researchers in the institutional repository. From the perspective of the Library, the benefits are also impressive. The Library is able to build its institutional repository, develop strong relations with faculty in the Physics Department, and have access to unpublished reports that otherwise might be lost. Establishing research groups' presence in DigitalCommons@USU provided an opportunity to meet with the Physics graduate students to discuss setting up online web portfolios, archiving their publications, and understanding publisher contracts. Developing partnerships between academic units and libraries is one more method to reach out to potential students, promote research, and showcase the talents of faculty and students. Using the Library's institutional repository to do this is beneficial for everyone.

The Unrecognized Crisis: Library Reference Service at the Crossroads.

ERIC Educational Resources Information Center

Hernon, Peter

1986-01-01

Briefly describes fundamental problems with library reference service based on the findings of 20 separate studies using unobtrusive tests. An emphasis on quality of service, realistic goals, and effective managerial strategies are identified as possible resolutions of these problems. (CLB)

Animals & Livestock | National Agricultural Library

Science.gov Websites

Skip to main content Home National Agricultural Library United States Department of Agriculture Ag (maps, tables, graphs), Agricultural Products html National Animal Nutrition Program (NANP) Feed | Agricultural Research Service | Plain Language | FOIA | Accessibility Statement | Information Quality | Privacy

Agonists and Antagonists of Protease-Activated Receptor 2 Discovered within a DNA-Encoded Chemical Library Using Mutational Stabilization of the Target.

PubMed

Brown, Dean G; Brown, Giles A; Centrella, Paolo; Certel, Kaan; Cooke, Robert M; Cuozzo, John W; Dekker, Niek; Dumelin, Christoph E; Ferguson, Andrew; Fiez-Vandal, Cédric; Geschwindner, Stefan; Guié, Marie-Aude; Habeshian, Sevan; Keefe, Anthony D; Schlenker, Oliver; Sigel, Eric A; Snijder, Arjan; Soutter, Holly T; Sundström, Linda; Troast, Dawn M; Wiggin, Giselle; Zhang, Jing; Zhang, Ying; Clark, Matthew A

2018-06-01

The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library. We observed a number of putative ligands enriched upon selection, and subsequent cellular profiling revealed these ligands to comprise both agonists and antagonists. The agonist series shared structural similarity with known agonists. The antagonists were shown to bind in a novel allosteric binding site on the PAR2 protein. This report serves to demonstrate that cell-free affinity selection against GPCRs can be achieved with mutant stabilized protein targets.

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers.

PubMed

Pan, Jin; Wang, Baosheng; Pei, Zhi-Yong; Zhao, Wei; Gao, Jie; Mao, Jian-Feng; Wang, Xiao-Ru

2015-07-01

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking. © 2014 John Wiley & Sons Ltd.

Discovering Drugs with DNA-Encoded Library Technology: From Concept to Clinic with an Inhibitor of Soluble Epoxide Hydrolase.

PubMed

Belyanskaya, Svetlana L; Ding, Yun; Callahan, James F; Lazaar, Aili L; Israel, David I

2017-05-04

DNA-encoded chemical library technology was developed with the vision of its becoming a transformational platform for drug discovery. The hope was that a new paradigm for the discovery of low-molecular-weight drugs would be enabled by combining the vast molecular diversity achievable with combinatorial chemistry, the information-encoding attributes of DNA, the power of molecular biology, and a streamlined selection-based discovery process. Here, we describe the discovery and early clinical development of GSK2256294, an inhibitor of soluble epoxide hydrolase (sEH, EPHX2), by using encoded-library technology (ELT). GSK2256294 is an orally bioavailable, potent and selective inhibitor of sEH that has a long half life and produced no serious adverse events in a first-time-in-human clinical study. To our knowledge, GSK2256294 is the first molecule discovered from this technology to enter human clinical testing and represents a realization of the vision that DNA-encoded chemical library technology can efficiently yield molecules with favorable properties that can be readily progressed into high-quality drugs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physical Analysis of the Complex Rye (Secale cereale L.) Alt4 Aluminium (Aluminum) Tolerance Locus Using a Whole-Genome BAC Library of Rye cv. Blanco

USDA-ARS?s Scientific Manuscript database

Rye is a diploid crop species with many outstanding qualities, and is also important as a source of new traits for wheat and triticale improvement. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies. The library provides a 6 × genome ...

MR 201424 Final Report Addendum

DTIC Science & Technology

2016-09-01

FINAL REPORT ADDENDUM Munitions Classification Library ESTCP Project MR-201424 SEPTEMBER 2016 Mr. Craig Murray Dr. Nagi Khadr Parsons Dr...solver and multi-solver library databases, and only the TEMTADS 2X2 and the MetalMapper advanced TEM systems are supported by UX-Analyze, data on...other steps (section 3.4) before getting into the data collection activities (sections 3.5-3.7). All inversions of library quality data collected over

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

Where Is the Xerox Corporation of the LIS Sector?

ERIC Educational Resources Information Center

Gilchrist, Alan; Brockman, John

1996-01-01

Discusses barriers to the implementation of quality management in the library and information science sector in Europe. Topics include Total Quality Management and other business experiences, an information quality infrastructure, supplier/customer relations, customer satisfaction, and a European Quality Model. (LRW)

What's in Your Techno-Future? Vendors Share Their Views.

ERIC Educational Resources Information Center

Gerber, Carole

1995-01-01

Examines vendors' views on the future of CD-ROM technology. Topics include the library role, single point access, costs, tape backup, user-friendly library automation systems and databases, improved quality, the growth of Internet access, and perspectives on technology in schools. (AEF)

A Mandate for Change in the Library Environment.

ERIC Educational Resources Information Center

Silberman, Richard M.

1993-01-01

The problem of indoor air quality and sick-building syndrome in libraries is explained in terms of human health and comfort and the preservation of books and manuscripts. Ventilation and indoor pollutants are discussed, and a proactive strategy of prevention is recommended. (EAM)

Fragment-based hit identification: thinking in 3D.

PubMed

Morley, Andrew D; Pugliese, Angelo; Birchall, Kristian; Bower, Justin; Brennan, Paul; Brown, Nathan; Chapman, Tim; Drysdale, Martin; Gilbert, Ian H; Hoelder, Swen; Jordan, Allan; Ley, Steven V; Merritt, Andy; Miller, David; Swarbrick, Martin E; Wyatt, Paul G

2013-12-01

The identification of high-quality hits during the early phases of drug discovery is essential if projects are to have a realistic chance of progressing into clinical development and delivering marketed drugs. As the pharmaceutical industry goes through unprecedented change, there are increasing opportunities to collaborate via pre-competitive networks to marshal multifunctional resources and knowledge to drive impactful, innovative science. The 3D Fragment Consortium is developing fragment-screening libraries with enhanced 3D characteristics and evaluating their effect on the quality of fragment-based hit identification (FBHI) projects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis.

PubMed

Pan, Yuchen; Sackmann, Eric K; Wypisniak, Karolina; Hornsby, Michael; Datwani, Sammy S; Herr, Amy E

2016-12-23

High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality - the binding affinity - is quantified through the dissociation constant (K D ) of each recombinant antibody and the target antigen. To characterize the K D of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The K D for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.

Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis

PubMed Central

Pan, Yuchen; Sackmann, Eric K.; Wypisniak, Karolina; Hornsby, Michael; Datwani, Sammy S.; Herr, Amy E.

2016-01-01

High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization. PMID:28008969

Bacterial communities in Great Barrier Reef calcareous sediments: Contrasting 16S rDNA libraries from nearshore and outer shelf reefs

NASA Astrophysics Data System (ADS)

Uthicke, S.; McGuire, K.

2007-03-01

Bacterial communities in eight 16S rDNA clone libraries from calcareous sediments were investigated to provide an assessment of the bacterial diversity on sediments of the Great Barrier Reef (GBR) and to investigate differences due to decreased water quality. Sample effort was spread across two locations on each of four coral reefs, with two reefs located nearshore and two reefs on the outer shelf to allow robust statistical comparison of nearshore reefs (subjected to enhanced runoff) and outer shelf reefs (pristine conditions). Out of 221 non-chimeric sequences, 189 (85.5%) were unique and only one sequence occurred in more than one library. Rarefaction analyses and coverage calculations indicated that only a small fraction of the diversity was sampled. Cluster analyses and comparison to published sequences indicated that sequences retrieved belonged to the α, γ and δ subdivision of the Proteobacteria (6.8, 29.4 and 13.6% of the total, respectively), Cytophaga-Flavobacteria-Bacteroidetes (CFB) group (20.4%), Cyanobacteria (5.4%), Planctomycetaceae (7.7%), Verrucomicrobiaceae (6.8%), Acidobacteriaceae (2.7%). Analysis of Similarity (ANOSIM, based on grouping all retrieved sequences into 9 phylogenetic groups) indicated that subtle differences do exist in the community composition between nearshore and outer shelf reefs. Similarity percentage analysis (SIMPER) indicated that Acidobacteriaceae and Cyanobacteriaceae were the main contributors to the dissimilarity. A significant difference between bacteria on nearshore and outer shelf reefs also existed on the molecular level ( FST = 0.008, p = 0.007 for all samples, 0.006, p = 0.022 when repeated sequences within libraries were removed). Thus, bacterial communities on carbonate sediments investigated were highly diverse and differences in community composition may provide important leads for the search for indicator species or communities for water quality differences.

Quality Work, Quality Control in Technical Services.

ERIC Educational Resources Information Center

Horny, Karen L.

1985-01-01

Quality in library technical services is explored in light of changes produced by automation. Highlights include a definition of quality; new opportunities and shifting priorities; cataloging (fullness of records, heading consistency, accountability, local standards, automated checking); need for new skills (management, staff); and boons of…

Strategic Issues in Quality Management: 1. Theoretical Considerations.

ERIC Educational Resources Information Center

Johannsen, Carl Gustav

1996-01-01

Examines the relationship between strategic management and quality management concepts in a library and information services setting. Conceptual frameworks are presented and a new strategic quality management framework, inspired by the Japanese policy deployment approach, is developed that also discusses total quality management. (Author/LRW)

Catalogers and Competition.

ERIC Educational Resources Information Center

Howden, Norman

1987-01-01

Reports the results of a literature review and a survey of catalogers which were conducted to study the problem of the decline in quantity and quality of applications for entry-level cataloging jobs. Factors studied included: competition between types of library professionals, automation, library education, the women's movement, and library…

Reflections: Management Morphology--How We Got To Be Who We Are.

ERIC Educational Resources Information Center

Hoadley, Irene B.

1999-01-01

Reviews library management issues over the past 25 years. Highlights include library education for managerial skills; on the job training; gender issues; societal factors; Total Quality Management; management changes; and future possibilities, including managerial roles, management models, and organizational structure. (LRW)

Designing and Managing Your Digital Library.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

Discusses digital libraries and Web site design issues. Highlights include accessibility issues, including standards, markup languages like HTML and XML, and metadata; building virtual communities; the use of Web portals for customized delivery of information; quality assurance tools, including data mining; and determining user needs, including…

Computers, Education and the Library at The Bronx High School of Science.

ERIC Educational Resources Information Center

Nachbar, Sondra; Sussman, Valerie

1988-01-01

Describes the services and programs offered by the library at The Bronx High School of Science. Topics discussed include the library collection; a basic library skills mini-course for freshmen and incoming sophomores; current uses of the library's computer system; and plans to automate the library's card catalog and circulation records.…

Transcriptome Analysis of the Octopus vulgaris Central Nervous System

PubMed Central

Zhang, Xiang; Mao, Yong; Huang, Zixia; Qu, Meng; Chen, Jun; Ding, Shaoxiong; Hong, Jingni; Sun, Tiantian

2012-01-01

Background Cephalopoda are a class of Mollusca species found in all the world's oceans. They are an important model organism in neurobiology. Unfortunately, the lack of neuronal molecular sequences, such as ESTs, transcriptomic or genomic information, has limited the development of molecular neurobiology research in this unique model organism. Results With high-throughput Illumina Solexa sequencing technology, we have generated 59,859 high quality sequences from 12,918,391 paired-end reads. Using BLASTx/BLASTn, 12,227 contigs have blast hits in the Swissprot, NR protein database and NT nucleotide database with E-value cutoff 1e−5. The comparison between the Octopus vulgaris central nervous system (CNS) library and the Aplysia californica/Lymnaea stagnalis CNS ESTs library yielded 5.93%/13.45% of O. vulgaris sequences with significant matches (1e−5) using BLASTn/tBLASTx. Meanwhile the hit percentage of the recently published Schistocerca gregaria, Tilapia or Hirudo medicinalis CNS library to the O. vulgaris CNS library is 21.03%–46.19%. We constructed the Phylogenetic tree using two genes related to CNS function, Synaptotagmin-7 and Synaptophysin. Lastly, we demonstrated that O. vulgaris may have a vertebrate-like Blood-Brain Barrier based on bioinformatic analysis. Conclusion This study provides a mass of molecular information that will contribute to further molecular biology research on O. vulgaris. In our presentation of the first CNS transcriptome analysis of O. vulgaris, we hope to accelerate the study of functional molecular neurobiology and comparative evolutionary biology. PMID:22768275

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Access for all? A survey of health librarians in the north-west of England on provision of information to patients.

PubMed

King, Colette; Hornby, Susan

2003-12-01

This study examined the role that health librarians could play in helping patients to find information. A questionnaire survey was sent out to 50 health librarians in the north-west of England. It examined the following: the type of library and users, access to information for patients, librarians' attitudes to provision of information to patients and their knowledge of other sources available to their users. Ninety-seven per cent of librarians said that they could recommend quality information sources to patients, but many suggested that there were practical problems in allowing patients to use health libraries due to lack of appropriate resources, facilities and funding. Advantages of health library involvement in patient information include having a local point of contact for patients and the ability of librarians to find, evaluate and organize good-quality resources. However, health library staff may not have enough time to answer enquiries from the public and may lack training in dealing with patients. Innovation, especially in developing on-line services, could offer a way to provide a service without overloading the physical requirements of a library. Librarians could also collaborate with other staff to improve patient information.

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

PubMed Central

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

2000-01-01

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

Molecular Pathogenesis of Rickettsioses and Development of Novel Anti-Rickettsial Treatment by Combinatorial Peptide-Based Libraries

DTIC Science & Technology

2007-02-01

Rickettsiae are susceptible to few antibiotics including the tetracyclines and chloramphenicol and are highly resistant to beta - lactams and...agents available for rickettsiae and Orientia, emergence of chloramphenicol- and tetracycline -resistant strains of Orientia, and the possibility of...precipitation (RNAqueous-4 PCR, Ambion). RNA quality was verified by UV spectrophotometry and ribosomal RNA band integrity. The TrueLabeling-AMP™ 2.0 kit

DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae

PubMed Central

Ekrem, Torbjørn; Stur, Elisabeth

2017-01-01

Abstract Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences.

Just-in-Time Compound Pooling Increases Primary Screening Capacity without Compromising Screening Quality.

PubMed

Elkin, L L; Harden, D G; Saldanha, S; Ferguson, H; Cheney, D L; Pieniazek, S N; Maloney, D P; Zewinski, J; O'Connell, J; Banks, M

2015-06-01

Compound pooling, or multiplexing more than one compound per well during primary high-throughput screening (HTS), is a controversial approach with a long history of limited success. Many issues with this approach likely arise from long-term storage of library plates containing complex mixtures of compounds at high concentrations. Due to the historical difficulties with using multiplexed library plates, primary HTS often uses a one-compound-one-well approach. However, as compound collections grow, innovative strategies are required to increase the capacity of primary screening campaigns. Toward this goal, we have developed a novel compound pooling method that increases screening capacity without compromising data quality. This method circumvents issues related to the long-term storage of complex compound mixtures by using acoustic dispensing to enable "just-in-time" compound pooling directly in the assay well immediately prior to assay. Using this method, we can pool two compounds per well, effectively doubling the capacity of a primary screen. Here, we present data from pilot studies using just-in-time pooling, as well as data from a large >2-million-compound screen using this approach. These data suggest that, for many targets, this method can be used to vastly increase screening capacity without significant reduction in the ability to detect screening hits. © 2015 Society for Laboratory Automation and Screening.

Health Consumers eHealth Literacy to Decrease Disparities in Accessing eHealth Information.

PubMed

Park, Hyejin; Cormier, Eileen; Glenna, Gordon

2016-01-01

The purpose of this study was to assess the perceived eHealth literacy of a general health consumer population so that health care professionals can effectively address skills gaps in health consumers' ability to access and use high quality online health information. Participants were recruited from three public library branches in a Northeast Florida community. The eHealth literacy scale (eHEALS) was used. The majority of participants (n = 108) reported they knew how and where to find health information and how to use it to make health decisions; knowledge of what health resources were available and confidence in the ability to distinguish high from low quality information was considerably less. The findings suggest the need for eHealth education and support to health consumers from health care professionals, in particular, how to access and evaluate the quality of health information.

Development and Evaluation of a Measure of Library Automation.

ERIC Educational Resources Information Center

Pungitore, Verna L.

1986-01-01

Construct validity and reliability estimates indicate that study designed to measure utilization of automation in public and academic libraries was successful in tentatively identifying and measuring three subdimensions of level of automation: quality of hardware, method of software development, and number of automation specialists. Questionnaire…

A smart use for mobiles.

PubMed

Amani, Sarah; Trueland, Jennifer

A library of NHS-approved mobile phone apps has been launched in response to concerns about the variable quality of health apps. This article describes the latest apps to be included in the library and reveals how nurse Sarah Amani helped to develop an app for mental health service users.

Developing Crash-Resistant Electronic Services.

ERIC Educational Resources Information Center

Almquist, Arne J.

1997-01-01

Libraries' dependence on computers can lead to frustrations for patrons and staff during downtime caused by computer system failures. Advice for reducing the number of crashes is provided, focusing on improved training for systems staff, better management of library systems, and the development of computer systems using quality components which…

Electronic Reference Service: A Teen's Eye View.

ERIC Educational Resources Information Center

Farmer, Lesley S.

2003-01-01

Discusses electronic reference service from a teen's point of view and from the school library media specialist's view. Considers traits that attract teens, including anonymity, speed, and convenience; and explains concerns of media specialists, including quality of electronic resources, how to provide access, library instruction options, and…

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)

Analysis of Environmental Friendly Library Based on the Satisfaction and Service Quality: study at Library “X”

NASA Astrophysics Data System (ADS)

Herdiansyah, Herdis; Satriya Utama, Andre; Safruddin; Hidayat, Heri; Gema Zuliana Irawan, Angga; Immanuel Tjandra Muliawan, R.; Mutia Pratiwi, Diana

2017-10-01

One of the factor that influenced the development of science is the existence of the library, which in this case is the college libraries. Library, which is located in the college environment, aims to supply collections of literatures to support research activities as well as educational for students of the college. Conceptually, every library now starts to practice environmental principles. For example, “X” library as a central library claims to be an environmental friendly library for practicing environmental friendly management, but the X library has not inserted the satisfaction and service aspect to the users, including whether it is true that environmental friendly process is perceived by library users. Satisfaction can be seen from the comparison between expectations and reality of library users. This paper analyzes the level of library user satisfaction with library services in the campus area and the gap between expectations and reality felt by the library users. The result of the research shows that there is a disparity between the hope of library management, which is sustainable and environmentally friendly with the reality in the management of the library, so that it has not given satisfaction to the users yet. The gap value of satisfaction that has the biggest difference is in the library collection with the value of 1.57; while for the smallest gap value is in the same service to all students with a value of 0.67.

Five Librarians Talk about Quality Control and the OCLC Database.

ERIC Educational Resources Information Center

Helge, Brian; And Others

1987-01-01

Five librarians considered authorities on quality cataloging in the OCLC Online Union Catalog were interviewed to obtain their views on the current level of quality control in the OCLC database, the responsibilities of OCLC and individual libraries in improving the quality of records, and the consequences of quality control problems. (CLB)

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications.

PubMed

Verhoeven, Joost Theo Petra; Canuti, Marta; Munro, Hannah J; Dufour, Suzanne C; Lang, Andrew S

2018-04-19

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (<5 US dollars per sample) and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing and microbiome profiling. ViDiT-CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal-cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT-CACTUS demonstrated its validity in a wide range of microbiology applications and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

Key elements of high-quality practice organisation in primary health care: a systematic review.

PubMed

Crossland, Lisa; Janamian, Tina; Jackson, Claire L

2014-08-04

To identify elements that are integral to high-quality practice and determine considerations relating to high-quality practice organisation in primary care. A narrative systematic review of published and grey literature. Electronic databases (PubMed, CINAHL, the Cochrane Library, Embase, Emerald Insight, PsycInfo, the Primary Health Care Research and Information Service website, Google Scholar) were searched in November 2013 and used to identify articles published in English from 2002 to 2013. Reference lists of included articles were searched for relevant unpublished articles and reports. Data were configured at the study level to allow for the inclusion of findings from a broad range of study types. Ten elements were most often included in the existing organisational assessment tools. A further three elements were identified from an inductive thematic analysis of descriptive articles, and were noted as important considerations in effective quality improvement in primary care settings. Although there are some validated tools available to primary care that identify and build quality, most are single-strategy approaches developed outside health care settings. There are currently no validated organisational improvement tools, designed specifically for primary health care, which combine all elements of practice improvement and whose use does not require extensive external facilitation.

A quantitative and qualitative evaluation of reports of clinical trials published in six Brazilian dental journals indexed in the Scientific Electronic Library Online (SciELO)

PubMed Central

de SOUZA, Raphael Freitas; CHAVES, Carolina de Andrade Lima; CHAVES, Carolina de Andrade Lima; CHAVES, Carolina de Andrade Lima; NASSER, Mona; FEDOROWICZ, Zbys

2010-01-01

Open access publishing is becoming increasingly popular within the biomedical sciences. SciELO, the Scientific Electronic Library Online, is a digital library covering a selected collection of Brazilian scientific journals many of which provide open access to full-text articles. This library includes a number of dental journals some of which may include reports of clinical trials in English, Portuguese and/or Spanish. Thus, SciELO could play an important role as a source of evidence for dental healthcare interventions especially if it yields a sizeable number of high quality reports. Objective The aim of this study was to identify reports of clinical trials by handsearching of dental journals that are accessible through SciELO, and to assess the overall quality of these reports. Material and methods Electronic versions of six Brazilian dental Journals indexed in SciELO were handsearched at www.scielo.br in September 2008. Reports of clinical trials were identified and classified as controlled clinical trials (CCTs - prospective, experimental studies comparing 2 or more healthcare interventions in human beings) or randomized controlled trials (RCTs - a random allocation method is clearly reported), according to Cochrane eligibility criteria. Criteria to assess methodological quality included: method of randomization, concealment of treatment allocation, blinded outcome assessment, handling of withdrawals and losses and whether an intention-totreat analysis had been carried out. Results The search retrieved 33 CCTs and 43 RCTs. A majority of the reports provided no description of either the method of randomization (75.3%) or concealment of the allocation sequence (84.2%). Participants and outcome assessors were reported as blinded in only 31.2% of the reports. Withdrawals and losses were only clearly described in 6.5% of the reports and none mentioned an intention-totreat analysis or any similar procedure. Conclusions The results of this study indicate that a substantial number of reports of trials and systematic reviews are available in the dental journals listed in SciELO, and that these could provide valuable evidence for clinical decision making. However, it is clear that the quality of a number of these reports is of some concern and that improvement in the conduct and reporting of these trials could be achieved if authors adhered to internationally accepted guidelines, e.g. the CONSORT statement. PMID:20485919

A quantitative and qualitative evaluation of reports of clinical trials published in six Brazilian dental journals indexed in the Scientific Electronic Library Online (SciELO).

PubMed

de Souza, Raphael Freitas; Chaves, Carolina de Andrade Lima; Nasser, Mona; Fedorowicz, Zbys

2010-01-01

Open access publishing is becoming increasingly popular within the biomedical sciences. SciELO, the Scientific Electronic Library Online, is a digital library covering a selected collection of Brazilian scientific journals many of which provide open access to full-text articles.This library includes a number of dental journals some of which may include reports of clinical trials in English, Portuguese and/or Spanish. Thus, SciELO could play an important role as a source of evidence for dental healthcare interventions especially if it yields a sizeable number of high quality reports. The aim of this study was to identify reports of clinical trials by handsearching of dental journals that are accessible through SciELO, and to assess the overall quality of these reports. Electronic versions of six Brazilian dental Journals indexed in SciELO were handsearched at www.scielo.br in September 2008. Reports of clinical trials were identified and classified as controlled clinical trials (CCTs - prospective, experimental studies comparing 2 or more healthcare interventions in human beings) or randomized controlled trials (RCTs - a random allocation method is clearly reported), according to Cochrane eligibility criteria. CRITERIA TO ASSESS METHODOLOGICAL QUALITY INCLUDED: method of randomization, concealment of treatment allocation, blinded outcome assessment, handling of withdrawals and losses and whether an intention-to-treat analysis had been carried out. The search retrieved 33 CCTs and 43 RCTs. A majority of the reports provided no description of either the method of randomization (75.3%) or concealment of the allocation sequence (84.2%). Participants and outcome assessors were reported as blinded in only 31.2% of the reports. Withdrawals and losses were only clearly described in 6.5% of the reports and none mentioned an intention-to-treat analysis or any similar procedure. The results of this study indicate that a substantial number of reports of trials and systematic reviews are available in the dental journals listed in SciELO, and that these could provide valuable evidence for clinical decision making. However, it is clear that the quality of a number of these reports is of some concern and that improvement in the conduct and reporting of these trials could be achieved if authors adhered to internationally accepted guidelines, e.g. the CONSORT statement.

Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.

PubMed

Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

2014-10-22

In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or natural product-inspired DOS.

College Libraries and Resource Sharing: Testing a Compact Disc Union Catalog.

ERIC Educational Resources Information Center

Townley, Charles T.

1992-01-01

Presents results of an evaluation of C.D. Cat, a CD-ROM union catalog developed by the Associated College Libraries of Central Pennsylvania consortium. Outcomes are reported in the areas of bibliographic quality, user evaluation, public relations strategies, bibliographic instruction, and guidelines for continuing operations. Recommendations are…

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…

Information Source Characteristics and Environmental Scanning by Academic Library Managers

ERIC Educational Resources Information Center

Babalhavaeji, Fahimeh; Farhadpoor, Mohammad Reza

2013-01-01

Purpose: This article examines characteristics of the external environment of library and information centres of Islamic Azad University in Iran, focusing on perceived environmental uncertainty and perceived source accessibility and quality, and their impacts on the amount of scanning and the frequency of information source use. Methods: This…

75 FR 15705 - Columbia Gas Transmission LLC; Notice of Intent To Prepare an Environmental Assessment for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... interest groups; Native American Tribes; other interested parties; and local libraries and newspapers..., and wetlands; Cultural resources; Vegetation and wildlife; Air quality and noise; Endangered and... American Tribes; other interested parties; and local libraries and newspapers. This list also includes all...

Online Searching in the Small College Library--Ten Years Later.

ERIC Educational Resources Information Center

Smith, Scott; Smith, Jane B.

1991-01-01

Reviews experiences with online searching at the Nazareth College library. Topics discussed include user expectations; actual and perceived search quality; the impact of laser printers; growth in online searching; increases in other reference services; the use of CD-ROM technology; and costs and pricing policies. (LRW)

The Library as Factor in Erudition.

ERIC Educational Resources Information Center

Pasiar, Stefan

Libraries have long functioned as institutions which exerted wide-ranging cultural-social activity as determined by the economic and cultural needs of society. Librarianship as an educational factor has become increasingly important during the past half century with respect to its quantitative growth and its quality world-wide. Although the school…

TQM for Libraries.

ERIC Educational Resources Information Center

Rux, Paul

1993-01-01

Discussion of the application of TQM (Total Quality Management) to libraries addresses planning based on customer needs and use of the scientific method to evaluate customer satisfaction. A TQM experiment at Marquette Middle School (Wisconsin) is examined, and ways that TQM was used to meet the needs of homeless students are described. (MES)

Library Services to Distance Learners in the Commonwealth: A Reader.

ERIC Educational Resources Information Center

Watson, Elizabeth F., Ed.; Jagannathan, Neela, Ed.

The provision of good library services is a crucial factor in determining the quality of distance education. This collection of articles acquaints readers with distance librarianship as it is practiced in developed and developing countries throughout the British Commonwealth. The reader includes: "Introduction" (Michael Wooliscroft);…

Celebrating the Freedom To "Read! Learn! Connect! @ the Library."

ERIC Educational Resources Information Center

Symons, Ann K.

1999-01-01

Discusses the importance of librarians being advocates for children and fighting for free and open access to printed and electronic information. Discusses Banned Book Week; intellectual freedom; the American Library Association's four main concerns related to the Internet--access, quality, education, and local control; and the importance of…

Hanging Together To Avoid Hanging Separately: Opportunities for Academic Libraries and Consortia.

ERIC Educational Resources Information Center

Allen, Barbara McFadden; Hirshon, Arnold

1998-01-01

Discusses academic library consortia, examines types of consortia, and presents three case histories (OhioLINK, PALCI and CIC). Highlights include economic competition; changes in information access and delivery; growth of information technology; quality improvement; and future strategies, including pricing models for electronic information,…

Enhancements to the EPANET-RTX (Real-Time Analytics) ...

EPA Pesticide Factsheets

Technical brief and software The U.S. Environmental Protection Agency (EPA) developed EPANET-RTX as a collection of object-oriented software libraries comprising the core data access, data transformation, and data synthesis (real-time analytics) components of a real-time hydraulic and water quality modeling system. While EPANET-RTX uses the hydraulic and water quality solvers of EPANET, the object libraries are a self-contained set of building blocks for software developers. “Real-time EPANET” promises to change the way water utilities, commercial vendors, engineers, and the water community think about modeling.

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.

Key concepts relevant to quality of complex and shared decision-making in health care: a literature review.

PubMed

Dy, Sydney M; Purnell, Tanjala S

2012-02-01

High-quality provider-patient decision-making is key to quality care for complex conditions. We performed an analysis of key elements relevant to quality and complex, shared medical decision-making. Based on a search of electronic databases, including Medline and the Cochrane Library, as well as relevant articles' reference lists, reviews of tools, and annotated bibliographies, we developed a list of key concepts and applied them to a decision-making example. Key concepts identified included provider competence, trustworthiness, and cultural competence; communication with patients and families; information quality; patient/surrogate competence; and roles and involvement. We applied this concept list to a case example, shared decision-making for live donor kidney transplantation, and identified the likely most important concepts as provider and cultural competence, information quality, and communication with patients and families. This concept list may be useful for conceptualizing the quality of complex shared decision-making and in guiding research in this area. Copyright © 2011 Elsevier Ltd. All rights reserved.

Innovative United Kingdom Approaches To Measuring Service Quality.

ERIC Educational Resources Information Center

Winkworth, Ian

2001-01-01

Reports on approaches to measuring the service quality of academic libraries in the United Kingdom. Discusses the role of government and the national background of quality measurement; measurement frameworks; better use of statistics; benchmarking; measuring user satisfaction; and possible future development. (Author/LRW)

The National Transport Code Collaboration Module Library

NASA Astrophysics Data System (ADS)

Kritz, A. H.; Bateman, G.; Kinsey, J.; Pankin, A.; Onjun, T.; Redd, A.; McCune, D.; Ludescher, C.; Pletzer, A.; Andre, R.; Zakharov, L.; Lodestro, L.; Pearlstein, L. D.; Jong, R.; Houlberg, W.; Strand, P.; Wiley, J.; Valanju, P.; John, H. St.; Waltz, R.; Mandrekas, J.; Mau, T. K.; Carlsson, J.; Braams, B.

2004-12-01

This paper reports on the progress in developing a library of code modules under the auspices of the National Transport Code Collaboration (NTCC). Code modules are high quality, fully documented software packages with a clearly defined interface. The modules provide a variety of functions, such as implementing numerical physics models; performing ancillary functions such as I/O or graphics; or providing tools for dealing with common issues in scientific programming such as portability of Fortran codes. Researchers in the plasma community submit code modules, and a review procedure is followed to insure adherence to programming and documentation standards. The review process is designed to provide added confidence with regard to the use of the modules and to allow users and independent reviews to validate the claims of the modules' authors. All modules include source code; clear instructions for compilation of binaries on a variety of target architectures; and test cases with well-documented input and output. All the NTCC modules and ancillary information, such as current standards and documentation, are available from the NTCC Module Library Website http://w3.pppl.gov/NTCC. The goal of the project is to develop a resource of value to builders of integrated modeling codes and to plasma physics researchers generally. Currently, there are more than 40 modules in the module library.

Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens.

PubMed

Prendergast, Emily N; de Souza Fonseca, Marcos Abraão; Dezem, Felipe Segato; Lester, Jenny; Karlan, Beth Y; Noushmehr, Houtan; Lin, Xianzhi; Lawrenson, Kate

2018-01-01

Exosomes are endosome-derived membrane vesicles that contain proteins, lipids, and nucleic acids. The exosomal transcriptome mediates intercellular communication, and represents an understudied reservoir of novel biomarkers for human diseases. Next-generation sequencing enables complex quantitative characterization of exosomal RNAs from diverse sources. However, detailed protocols describing exosome purification for preparation of exosomal RNA-sequence (RNA-Seq) libraries are lacking. Here we compared methods for isolation of exosomes and extraction of exosomal RNA from human cell-free serum, as well as strategies for attaining equal representation of samples within pooled RNA-Seq libraries. We compared commercial precipitation with ultracentrifugation for exosome purification and confirmed the presence of exosomes via both transmission electron microscopy and immunoblotting. Exosomal RNA extraction was compared using four different RNA purification methods. We determined the minimal starting volume of serum required for exosome preparation and showed that high quality exosomal RNA can be isolated from sera stored for over a decade. Finally, RNA-Seq libraries were successfully prepared with exosomal RNAs extracted from human cell-free serum, cataloguing both coding and non-coding exosomal transcripts. This method provides researchers with strategic options to prepare RNA-Seq libraries and compare RNA-Seq data quantitatively from minimal volumes of fresh and archival human cell-free serum for disease biomarker discovery.

Statistical molecular design of balanced compound libraries for QSAR modeling.

PubMed

Linusson, A; Elofsson, M; Andersson, I E; Dahlgren, M K

2010-01-01

A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link chemical features of compounds with activities towards a target macromolecule associated with the initiation or progression of a disease. QSAR models are computed by combining information on the physicochemical and structural features of a library of congeneric compounds, typically assembled from two or more building blocks, and biological data from one or more in vitro assays. Since the models provide information on features affecting the compounds' biological activity they can be used as guides for further optimization. However, in order for a QSAR model to be relevant to the targeted disease, and drug development in general, the compound library used must contain molecules with balanced variation of the features spanning the chemical space believed to be important for interaction with the biological target. In addition, the assays used must be robust and deliver high quality data that are directly related to the function of the biological target and the associated disease state. In this review, we discuss and exemplify the concept of statistical molecular design (SMD) in the selection of building blocks and final synthetic targets (i.e. compounds to synthesize) to generate information-rich, balanced libraries for biological testing and computation of QSAR models.

A Moderate Resolution NIR Spectral Library of Weak-Lined T Tauri Stars

NASA Astrophysics Data System (ADS)

Cooper, Rachel; Covey, K. R.

2013-01-01

We present a spectral library of high-quality moderate resolution (R ~ 3500) NIR spectra for 44 weak-lined T Tauri Stars (WTTS) in the Taurus-Auriga Molecular Cloud. These spectra, obtained with the TripleSpec spectrograph on the Astrophysical Research Consortium (ARC) 3.5 meter telescope, provide full coverage of the J, H, and K near-infrared bands in a single epoch. Analyzing these spectra, along with those of dwarf and giant spectral type standards from the SpeX Spectral Library, we have identified several elemental and molecular absorption lines that vary in strength with respect to each star's spectral type and luminosity class. Calibrating each of these features as a spectral type indicator, we provide a detailed characterization for each of the WTTSs in our sample, identifying each star's NIR spectral type and line-of-sight extinction, estimated both from the shape of the overall continuum and from the fluxes of the Paschen beta and Brackett gamma emission lines. In addition to improving our understanding of the properties of these WTTSs, this well characterized spectral library will be a valuable resource for analyses of the NIR continuum veiling and line emission present in the spectra of accreting classical T Tauri stars. This research was made possible by NSF Grant AST-1004107.

Isolation and purification of RNA from tissues rich in polyphenols, polysaccharides, and pigments of annatto (Bixa orellana L.).

PubMed

Rodrigues, Simone M; Soares, Virgínia L F; de Oliveira, Tahise M; Gesteira, Abelmon S; Otoni, Wagner C; Costa, Marcio G C

2007-11-01

The tropical plant Bixa orellana L. (annatto) produces an array of natural products, including the pigment bixin used in the food and cosmetics industries. In order to understand the biochemical and molecular basis of the biosynthesis of these natural products, a reliable method for isolating high yields of high-quality RNA is required. Here we described a successful and reproducible method for isolation and purification of high-quantity and high-quality RNA from different tissues of annatto. This protocol overcomes the usual problems associated with large amounts of polyphenols, polysaccharides, pigments, and other secondary metabolites that are not easily removed by conventional extraction procedures. Furthermore, the proposed protocol can be easily carried out in any laboratory and it could also be extended to isolate RNA from other plant species showing similar abundance of compounds that interfere with RNA extractions. The yield and quality of the RNA were monitored by spectrophotometric analysis, separation on agarose gel, Reverse Transcription-Polymerase Chain Reaction (RT-PCR), and construction of a cDNA library.

The impact of complaint management and service quality on organizational image: A case study at the Malaysian public university library

NASA Astrophysics Data System (ADS)

Tan, Pei Kian; Mohd Suradi, Nur Riza; Saludin, Mohamad Nasir

2013-04-01

Service failure frequently occurs. This affects customer expectations which lead to complaint. However, not all dissatisfied customers actually complain. Without customer feedback, it would be impossible for a company to know whether they needed a change for improvement. Thus, complaint management brings a learning experience to organization in order to provide better service. Therefore, it is important to identify customer dissatisfaction through a systematic complaint handling or management. The study proposes a model of systematic complaint management which applied to academic library as a tool of service recovery. As such, the main purpose of this study is to investigate the critical success factors of complaint management towards service quality, customer satisfaction, customer loyalty and the impact to organizational image at academic library. Three academic libraries have been identified and selected for this project, the Library of Tun Sri Lanang, UKM, UTeM and UNIMAS. Using the justice theory, this study investigates the perception of customers on complaint management in terms of outcomes they receive, procedures used by organization and interpersonal treatment. In this study, there are five factors of complaint management identified, which includes speed of recovery, management system, empowerment, culture and psychology and tangible compensation. A questionnaire was designed and used as the data gathering instrument. A total of 600 respondents participated in this study. Ten hypotheses were used to test the relationships between complaint management, service quality, customer satisfaction, customer loyalty and organizational image. To measure the construct relationships, Structural Equation Model (SEM) approach was used. The results show that management system (b = 0.210; p < 0.05) exerts the highest positive impact on service quality. It followed by psychology and culture (b = 0.188; p < 0.05), empowerment (b = 0.179; p < 0.05) and tangible compensation (b = 0.175; p < 0.05). However, the empirical results suggest that speed of recovery (b = -0.009; p > 0.05) do not influence service quality. The second part of this study uses confirmatory factor analysis (CFA) to analyze and confirm the conceptual model proposed in this research. The result shows that all the values obtained in this study fits the data reasonably well.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

PubMed

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

Isolation of genes differentially expressed during development and ripening of Fragaria chiloensis fruit by suppression subtractive hybridization.

PubMed

Pimentel, Paula; Salvatierra, Ariel; Moya-León, María Alejandra; Herrera, Raúl

2010-09-15

Fragaria chiloensis, the native Chilean strawberry, is noted for its good fruit quality characters. However, it is a highly perishable fruit due to its rapid softening. With the aim to screen for genes differentially expressed during development and ripening of strawberry fruit, the subtractive suppressive hybridization (SSH) methodology was employed. Six libraries were generated contrasting transcripts from four different developmental stages. A set of 1807 genes was isolated and characterized. In our EST collection, approximately 90% of partial cDNAs showed significant similarity to proteins with known or unknown function registered in databases. Among them, proteins related to protein fate were identified in a large green fruit library and protein related with cellular transport, cell wall-related proteins, and transcription regulators were identified in a ripe fruit library. Thirteen genes were analyzed by qRT-PCR during development and ripening of the Chilean strawberry fruit. The information generated in this study provides new clues to aid the understanding of the ripening process in F. chiloensis fruit. Copyright 2010 Elsevier GmbH. All rights reserved.

Identification and functional analysis of a new glyphosate resistance gene from a fungus cDNA library.

PubMed

Tao, Bo; Shao, Bai-Hui; Qiao, Yu-Xin; Wang, Xiao-Qin; Chang, Shu-Jun; Qiu, Li-Juan

2017-08-01

Glyphosate is a widely used broad spectrum herbicide; however, this limits its use once crops are planted. If glyphosate-resistant crops are grown, glyphosate can be used for weed control in crops. While several glyphosate resistance genes are used in commercial glyphosate tolerant crops, there is interest in identifying additional genes for glyphosate tolerance. This research constructed a high-quality cDNA library form the glyphosate-resistant fungus Aspergillus oryzae RIB40 to identify genes that may confer resistance to glyphosate. Using a medium containing glyphosate (120mM), we screened several clones from the library. Based on a nucleotide sequence analysis, we identified a gene of unknown function (GenBank accession number: XM_001826835.2) that encoded a hypothetical 344-amino acid protein. The gene was named MFS40. Its ORF was amplified to construct an expression vector, pGEX-4T-1-MFS40, to express the protein in Escherichia coli BL21. The gene conferred glyphosate tolerance to E. coli ER2799 cells. Copyright © 2017 Elsevier B.V. All rights reserved.

The Annotated Bibliography and Citation Behavior: Enhancing Student Scholarship in an Undergraduate Biology Course

PubMed Central

Rux, Erika M.; Flaspohler, John A.

2007-01-01

Contemporary undergraduates in the biological sciences have unprecedented access to scientific information. Although many of these students may be savvy technologists, studies from the field of library and information science consistently show that undergraduates often struggle to locate, evaluate, and use high-quality, reputable sources of information. This study demonstrates the efficacy and pedagogical value of a collaborative teaching approach designed to enhance information literacy competencies among undergraduate biology majors who must write a formal scientific research paper. We rely on the triangulation of assessment data to determine the effectiveness of a substantial research paper project completed by students enrolled in an upper-level biology course. After enhancing library-based instruction, adding an annotated bibliography requirement, and using multiple assessment techniques, we show fundamental improvements in students' library research abilities. Ultimately, these improvements make it possible for students to more independently and effectively complete this challenging science-based writing assignment. We document critical information literacy advances in several key areas: student source-type use, annotated bibliography enhancement, plagiarism reduction, as well as student and faculty/librarian satisfaction. PMID:18056306

The Academic Library/High School Library Connection: Needs Assessment and Proposed Model.

ERIC Educational Resources Information Center

LeClercq, Angie

1986-01-01

Recognizing the limited resources available to gifted high school students and inadequate level of information-gathering skills students often bring to college, University of Tennessee-Knoxville was awarded a grant from the Council on Library Resources to develop a model for providing access to research library resources for high school students.…

A survey of collection development for United States Medical Licensing Examination (USMLE) and National Board Dental Examination (NBDE) preparation material.

PubMed

Hendrix, Dean; Hasman, Linda

2008-07-01

The research sought to ascertain medical and dental libraries' collection development policies, evaluation methods, purchase decisions, and issues that relate to print and electronic United States Medical Licensing Examination (USMLE) and National Board Dental Examination (NBDE) preparation materials. The investigators surveyed librarians supporting American Association of Medical Colleges (AAMC)-accredited medical schools (n = 58/125) on the USMLE and librarians supporting American Dental Association (ADA)-accredited dental schools (n = 23/56) on the NBDE. The investigators analyzed the data by cross-tabulating and filtering the results using EFM Continuum web survey software. Investigators also surveyed print and electronic USMLE and NBDE preparation materials from 2004-2007 to determine the number of publications and existence of reviews. A majority of responding AAMC libraries (62%, n = 58) provide at least 1 electronic or online USMLE preparation resource and buy an average of 11.6 print USMLE titles annually. Due to a paucity of NBDE print and electronic resources, ADA libraries bought significantly fewer print resources, and only 1 subscribed to an electronic resource. The most often reported evaluation methods for both populations were feedback from medical or dental students, feedback from medical or dental faculty, and online trials. Some AAMC (10%, n = 58) and ADA libraries (39%, n = 23) libraries reported that no evaluation of these materials occured at their libraries. From 2004-2007, publishers produced 45 USMLE preparation resources (total n = 546) to every 1 NBDE preparation resource (total n = 12). Users' needs, institutional missions and goals, financial status, and official collection policies most often underlie decisions to collect or not collect examination preparation materials. Evaluating the quality of examination preparation materials can be problematic due to lack of published reviews, lack of usability testing by libraries, and librarians' and library users' unfamiliarity with the actual content of examinations. Libraries must integrate faculty and students into the purchase process to make sure examination preparation resources of the highest quality are purchased.

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

PubMed

Olova, Nelly; Krueger, Felix; Andrews, Simon; Oxley, David; Berrens, Rebecca V; Branco, Miguel R; Reik, Wolf

2018-03-15

Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.

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

PubMed

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

2012-12-01

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

Quality evaluation of tandem mass spectral libraries.

PubMed

Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

2011-06-01

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

76 FR 16737 - Notice of Availability of the Draft Environmental Impact Statement for the Proposed South Coast...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

..., visual effects, noise, vibration, cultural resources, air quality, open space, farmland, hazardous... is also available to review at the following locations: 1. State Transportation Library of Massachusetts 10 Park Plaza, 2nd Floor, Boston, MA. 2. Russell Memorial Library, 88 Main Street, Acushnet, MA. 3...

Investing Wisely: Citation Rankings as a Measure of Quality in Library and Information Science Journals

ERIC Educational Resources Information Center

Via, Barbara J.; Schmidle, Deborah J.

2007-01-01

The library and information science field is currently confronted with difficult decisions about how best to allocate acquisition expenditures among increasingly expensive journals. This article measures the return-on-investment of serial expenditures through the use of citation analysis, which is a widely used approach to ascertaining journal…

The Publishing of Library and Information Science Journals in Southeast Asia--An Overview.

ERIC Educational Resources Information Center

Yeow-fei, Jaffe Yee

This paper presents an overview of the present state of the publishing activities of library and information science journals in Southeast Asia, focusing on format, circulation/readership, quality, and editorial focus. It also highlights some of the important titles from Thailand, Malaysia, Singapore, the Philippines, Indonesia, Brunei, Vietnam,…

Understand, Identify, and Respond: The New Focus of Access Services

ERIC Educational Resources Information Center

Rodriguez, Juan Carlos; Meyer, Kristin; Merry, Brian

2017-01-01

Library public services staff have primarily focused on providing services through interactions with their users. Although service quality and customer satisfaction are important in the delivery of these services, the emphasis and nature of the work have often been influenced by a library-centric philosophy rather than a user-centric philosophy.…

Why Outsourcing Happens, and What To Do about It.

ERIC Educational Resources Information Center

White, Herbert S.

2000-01-01

Discusses the concept of outsourcing in libraries and suggests that it is done for the cosmetic appearance of fiscal economies. Highlights include the possibility of achieving better service quality, but at a higher cost; and the importance of keeping management informed about and aware of the value of library services. (LRW)

From Quick Start Teams to Home Teams: The Duke TQM Experience.

ERIC Educational Resources Information Center

Lubans, John; Gordon, Heather

This paper describes the Duke University Libraries' transition in early 1994 from its traditional hierarchical model to an organization emphasizing Total Quality Management (TQM) concepts such as self-managing teams and continuous improvement. Existing conditions at the libraries that played a role in the decision to switch included: (1) rising…

Comparing and using assessments of the value of information to clinical decision-making.

PubMed Central

Urquhart, C J; Hepworth, J B

1996-01-01

This paper discusses the Value project, which assessed the value to clinical decision-making of information supplied by National Health Service (NHS) library and information services. The project not only showed how health libraries in the United Kingdom help clinicians in decision-making but also provided quality assurance guidelines for these libraries to help make their information services more effective. The paper reviews methods and results used in previous studies of the value of health libraries, noting that methodological differences appear to affect the results. The paper also discusses aspects of user involvement, categories of clinical decision-making, the value of information to present and future clinical decisions, and the combination of quantitative and qualitative assessments of value, as applied to the Value project and the studies reviewed. The Value project also demonstrated that the value placed on information depends in part on the career stage of the physician. The paper outlines the structure of the quality assurance tool kit, which is based on the findings and methods used in the Value project. PMID:8913550

Quality assessment of a sample of mobile app-based health behavior change interventions using a tool based on the National Institute of Health and Care Excellence behavior change guidance.

PubMed

McMillan, Brian; Hickey, Eamonn; Patel, Mahendra G; Mitchell, Caroline

2016-03-01

To quality assess a sample of health behavior change apps from the NHS Apps Library using a rating tool based on the 2014 National Institute for Health and Care Excellence behavior change guidance (NICE BCG). A qualitative analysis of the NICE BCG identified themes and questions for a quality assessment of health behavior change apps. These were refined by further discussion and piloting, and applied by two independent raters to a sample of NHS Library apps (N=49). Disagreements were resolved following discussions with a third rater. Themes identified were; purpose, planning, usability, tailoring, behavior change technique (BCT), maintenance, evaluation, data security and documentation. Overall, purpose of the apps was clear, but evidence for collaboration with users or professionals was lacking. Usability information was poor and tailoring disappointing. Most used recognized BCTs but paid less attention to behavior maintenance than initiation. Information on app evaluation and documentation was sparse. This study furthers the work of the NHS Apps Library, adapting the NICE (2014) behavior change guidance for quality assessment of behavior change apps. This study helps lay the foundations for development of a quality assurance tool for mobile health apps aimed at health behavior change. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

PubMed

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

2017-10-24

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

Novel encoding methods for DNA-templated chemical libraries.

PubMed

Li, Gang; Zheng, Wenlu; Liu, Ying; Li, Xiaoyu

2015-06-01

Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries. Copyright © 2015 Elsevier Ltd. All rights reserved.

Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.

PubMed

Rhodes, Johanna; Beale, Mathew A; Fisher, Matthew C

2014-01-01

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use.

Evaluating High School Libraries: Service Is Top Priority.

ERIC Educational Resources Information Center

Baldwin, Margaret

1988-01-01

Discusses the need for ongoing evaluation within high school libraries to ensure adequate library services, which, in turn, enhance the total educational program. The evaluation of library facilities, collections, and staff is discussed, and an annotated bibliography of evaluation tools is provided. (6 references) (CLB)

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

PubMed

Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

2013-06-01

We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

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

PubMed

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

2006-05-03

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

De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.

PubMed

Tian, Xin-Jie; Long, Yan; Wang, Jiao; Zhang, Jing-Wen; Wang, Yan-Yan; Li, Wei-Min; Peng, Yu-Fa; Yuan, Qian-Hua; Pei, Xin-Wu

2015-01-01

The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model.

PubMed

Maggi, Elaine C; Gravina, Silvia; Cheng, Haiying; Piperdi, Bilal; Yuan, Ziqiang; Dong, Xiao; Libutti, Steven K; Vijg, Jan; Montagna, Cristina

2018-01-01

The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA. The protocol developed produced high quality libraries consistently generating a conversion rate >98% that will be applicable for the analysis of human and mouse plasma or serum to detect tumor-derived changes in DNA methylation.

The Joint European Compound Library: boosting precompetitive research.

PubMed

Besnard, Jérémy; Jones, Philip S; Hopkins, Andrew L; Pannifer, Andrew D

2015-02-01

The Joint European Compound Library (JECL) is a new high-throughput screening collection aimed at driving precompetitive drug discovery and target validation. The JECL has been established with a core of over 321,000 compounds from the proprietary collections of seven pharmaceutical companies and will expand to around 500,000 compounds. Here, we analyse the physicochemical profile and chemical diversity of the core collection, showing that the collection is diverse and has a broad spectrum of predicted biological activity. We also describe a model for sharing compound information from multiple proprietary collections, enabling diversity and quality analysis without disclosing structures. The JECL is available for screening at no cost to European academic laboratories and SMEs through the IMI European Lead Factory (http://www.europeanleadfactory.eu/). Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Microsoft Biology Foundation Applications for High-Throughput Sequencing

PubMed Central

Mercer, S.

2010-01-01

w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

The Digital Library for Earth System Education: A Progress Report from the DLESE Program Center

NASA Astrophysics Data System (ADS)

Marlino, M. R.; Sumner, T. R.; Kelly, K. K.; Wright, M.

2002-12-01

DLESE is a community-owned and governed digital library offering easy access to high quality electronic resources about the Earth system at all educational levels. Currently in its third year of development and operation, DLESE resources are designed to support systemic educational reform, and include web-based teaching resources, tools, and services for the inclusion of data in classroom activities, as well as a "virtual community center" that supports community goals and growth. "Community-owned" and "community-governed" embody the singularity of DLESE through its unique participatory approach to both library building and governance. DLESE is guided by policy development vested in the DLESE Steering Committee, and informed by Standing Committees centered on Collections, Services, Technology, and Users, and community working groups covering a wide variety of interest areas. This presentation highlights both current and projected status of the library and opportunities for community engagement. It is specifically structured to engage community members in the design of the next version of the library release. The current Version 1.0 of the library consists of a web-accessible graphical user interface connected to a database of catalogued educational resources (approximately 3000); a metadata framework enabling resource characterization; a cataloging tool allowing community cataloging and indexing of materials; a search and discovery system allowing browsing based on topic, grade level, and resource type, and permitting keyword and controlled vocabulary-based searches; and a portal website supporting library use, community action, and DLESE partnerships. Future stages of library development will focus on enhanced community collaborative support; development of controlled vocabularies; collections building and community review systems; resource discovery integrating the National Science Education Standards and geography standards; Earth system science vocabulary; georeferenced discovery; and ultimately, AAAS Benchmarks. DLESE is being designed from the outset to support resource discovery across a diverse, federated network of holdings and collections, including the Alexandria Digital Library Earth Prototype (ADL/ADEPT), NASA education collections, the DLESE reviewed collection, and other community-held resources that have been cataloged and indexed as part of the overall DLESE collections.

Automated construction of an intraoperative high-dose-rate treatment plan library for the Varian brachytherapy treatment planning system.

PubMed

Deufel, Christopher L; Furutani, Keith M; Dahl, Robert A; Haddock, Michael G

2016-01-01

The ability to create treatment plans for intraoperative high-dose-rate (IOHDR) brachytherapy is limited by lack of imaging and time constraints. An automated method for creation of a library of high-dose-rate brachytherapy plans that can be used with standard planar applicators in the intraoperative setting is highly desirable. Nonnegative least squares algebraic methods were used to identify dwell time values for flat, rectangular planar applicators. The planar applicators ranged in length and width from 2 cm to 25 cm. Plans were optimized to deliver an absorbed dose of 10 Gy to three different depths from the patient surface: 0 cm, 0.5 cm, and 1.0 cm. Software was written to calculate the optimized dwell times and insert dwell times and positions into a .XML plan template that can be imported into the Varian brachytherapy treatment planning system. The user may import the .XML template into the treatment planning system in the intraoperative setting to match the patient applicator size and prescribed treatment depth. A total of 1587 library plans were created for IOHDR brachytherapy. Median plan generation time was approximately 1 minute per plan. Plan dose was typically 100% ± 1% (mean, standard deviation) of the prescribed dose over the entire length and width of the applicator. Plan uniformity was best for prescription depths of 0 cm and 0.5 cm from the patient surface. An IOHDR plan library may be created using automated methods. Thousands of plan templates may be optimized and prepared in a few hours to accommodate different applicator sizes and treatment depths and reduce treatment planning time. The automated method also enforces dwell time symmetry for symmetrical applicator geometries, which simplifies quality assurance. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Discrete RNA libraries from pseudo-torsional space

PubMed Central

Humphris-Narayanan, Elisabeth

2012-01-01

The discovery that RNA molecules can fold into complex structures and carry out diverse cellular roles has led to interest in developing tools for modeling RNA tertiary structure. While significant progress has been made in establishing that the RNA backbone is rotameric, few libraries of discrete conformations specifically for use in RNA modeling have been validated. Here, we present six libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone, comparable to phi and psi in the protein backbone. We evaluate the ability of each library to represent single nucleotide backbone conformations and we show how individual library fragments can be assembled into dinucleotides that are consistent with established RNA backbone descriptors spanning from sugar to sugar. We then use each library to build all-atom models of 20 test folds and we show how the composition of a fragment library can limit model quality. Despite the limitations inherent in using discretized libraries, we find that several hundred discrete fragments can rebuild RNA folds up to 174 nucleotides in length with atomic-level accuracy (<1.5Å RMSD). We anticipate the libraries presented here could easily be incorporated into RNA structural modeling, analysis, or refinement tools. PMID:22425640

Application Reuse Library for Software, Requirements, and Guidelines

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Thronesbery, Carroll

1994-01-01

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

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

PubMed Central

Herbold, Craig W.; Pelikan, Claus; Kuzyk, Orest; Hausmann, Bela; Angel, Roey; Berry, David; Loy, Alexander

2015-01-01

High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology. PMID:26236305

Medical literature searches: a comparison of PubMed and Google Scholar.

PubMed

Nourbakhsh, Eva; Nugent, Rebecca; Wang, Helen; Cevik, Cihan; Nugent, Kenneth

2012-09-01

Medical literature searches provide critical information for clinicians. However, the best strategy for identifying relevant high-quality literature is unknown. We compared search results using PubMed and Google Scholar on four clinical questions and analysed these results with respect to article relevance and quality. Abstracts from the first 20 citations for each search were classified into three relevance categories. We used the weighted kappa statistic to analyse reviewer agreement and nonparametric rank tests to compare the number of citations for each article and the corresponding journals' impact factors. Reviewers ranked 67.6% of PubMed articles and 80% of Google Scholar articles as at least possibly relevant (P = 0.116) with high agreement (all kappa P-values < 0.01). Google Scholar articles had a higher median number of citations (34 vs. 1.5, P < 0.0001) and came from higher impact factor journals (5.17 vs. 3.55, P = 0.036). PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals. The identification of frequently cited articles using Google Scholar for searches probably has value for initial literature searches. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.

PubMed

Belsare, Ketaki D; Andorfer, Mary C; Cardenas, Frida S; Chael, Julia R; Park, Hyun June; Lewis, Jared C

2017-03-17

Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450 BM3 , pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.

Total Quality Management: A Selected Bibliography

DTIC Science & Technology

1992-03-01

Total Quality Management (TQM) in the Department of Defense is a strategy for continuously improving performance at every level, and in all areas of...reflects selected books, documents, periodical articles, and videos on the subject of Total Quality Management (TQM) in the collection of the U.S. Army War College Library.

Automated stent defect detection and classification with a high numerical aperture optical system

NASA Astrophysics Data System (ADS)

Bermudez, Carlos; Laguarta, Ferran; Cadevall, Cristina; Matilla, Aitor; Ibañez, Sergi; Artigas, Roger

2017-06-01

Stent quality control is a highly critical process. Cardiovascular stents have to be inspected 100% so as no defective stent is implanted in a human body. However, this visual control is currently performed manually and every stent could need tenths of minutes to be inspected. In this paper, a novel optical inspection system is presented. By the combination of a high numerical aperture (NA) optical system, a rotational stage and a line-scan camera, unrolled sections of the outer and inner surfaces of the stent are obtained and image-processed at high speed. Defects appearing in those surfaces and also in the edges are extremely contrasted due to the shadowing effect of the high NA illumination and acquisition approach. Therefore by means of morphological operations and a sensitivity parameter, defects are detected. Based on a trained defect library, a binary classifier sorts each kind of defect through a set of scoring vectors, providing the quality operator with all the required information to finally take a decision. We expect this new approach to make defect detection completely objective and to dramatically reduce the time and cost of stent quality control stage.

Quality ILL Service in the Network of CSIC Libraries: Five Years of Progress.

ERIC Educational Resources Information Center

Malo de Molina y Martin-Montalvo, Teresa; Quintana Martinez, Isabel

1997-01-01

Although Spanish interlibrary loans (ILL) have increased from 100 to 525 per 100,000 inhabitants, there are still many problems to resolve. Examines a plan developed by the Consejo Superior de Investigaciones Cientificas (CSIC) Library Network to improve ILL services. Provides a comparative analysis of ILL services from 1992-1995. Includes charts…

Youth Services Librarians as Managers: A How-To Guide from Budgeting to Personnel.

ERIC Educational Resources Information Center

Staerkel, Kathleen, Comp.; And Others

Administrators of public library youth services departments and managers of school library media centers often rely on broad sources for advice on managing their specialized youth services. This book is designed to assist youth services librarians in becoming well-versed in management skills crucial to the continued existence of quality service to…

Using Formative & Summative Assessment to Evaluate Library Instruction in an Online First Year Writing Course

ERIC Educational Resources Information Center

Haber, Natalie; Mitchell, Tiffany N.

2017-01-01

Ensuring quality library instruction in an online-exclusive First Year Writing (FYW) course is important and challenging. Assessing what the students learned and how is equally important. The authors collaborate and co-teach the information literacy portion of an online-exclusive second semester FYW course at the University of Tennessee at…

The Pragmatic Idealist: Valerie Gross--Howard County Library, Columbia, MD

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

In the two years since Valerie Gross became director of the Howard County Library (HCL), it has won the county's Community Organization of the Year award, its Accessibility Award, and its Chamber of Commerce's Non-Profit Business of the Year ACE award for contributions to education, economic development, and quality of life. And for the first…

Some Problems Involved in the Shared Cataloging Subsystem of the Ohio College Library Center.

ERIC Educational Resources Information Center

Sacco, Margaret T.

This report outlines the development of the Ohio College Library Center (OCLC) and considers some basic problems in OCLC shared cataloging--e.g., the uneven quality of input cataloging and increasing number of duplicate records. Summaries of findings from an OCLC evaluative study and two surveys of shared cataloging are presented. The report…

A Method of Predicting Queuing at Library Online PCs

ERIC Educational Resources Information Center

Beranek, Lea G.

2006-01-01

On-campus networked personal computer (PC) usage at La Trobe University Library was surveyed during September 2005. The survey's objectives were to confirm peak usage times, to measure some of the relevant parameters of online PC usage, and to determine the effect that 24 new networked PCs had on service quality. The survey found that clients…

Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

ERIC Educational Resources Information Center

Dahlen, Sarah P. C.; Hanson, Kathlene

2017-01-01

Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

Library Standards and Guidelines for Institutions Affiliated with or Offering Extension Programs of Andrews University.

ERIC Educational Resources Information Center

Brenneise, Harvey, Ed.; And Others

Andrews University (Michigan), which is sponsored by the General Conference of Seventh-Day Adventists, extends its academic program to 14 other institutions, three in the United States and abroad. The program permits students in other countries to obtain a recognized, quality tertiary or graduate education. Andrews' research library, the James…

Costs of Preservation Microfilming at Research Libraries: A Study of Four Institutions.

ERIC Educational Resources Information Center

Kantor, Paul B.

The purpose of this study was to identify the central values and the range of variability for costs associated with selecting and preparing books for microfilm preservation, filming, and maintaining quality control and adequate records. The study was based on data supplied by the libraries at the University of Chicago and Columbia University, the…

Quality in Context: A Guide to Certification and Registration by the Medical Library Association.

ERIC Educational Resources Information Center

Fitzsimons, Eileen; Mayfield, M. Kent

This guide is designed to assist prospective examinees in preparing for the certification/registration examination of the Medical Library Association (MLA). The format of the examination and the types of questions to be found on the examination are discussed, and suggestions for test preparation are provided. Several practice "mini"…

American Sculpture and the Library of Congress

ERIC Educational Resources Information Center

Somma, Thomas P.

2010-01-01

The Thomas Jefferson Building of the Library of Congress is one of the more significant public structures in American architecture, due for the most part to its wealth and quality of decoration, including an extensive sculptural program executed in 1894-97. The architects entrusted the program to a committee of three prominent sculptors, J. Q. A.…

A HIGH COVERAGE GENOME SEQUENCE FROM AN ARCHAIC DENISOVAN INDIVIDUAL

PubMed Central

Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; Li, Heng; Racimo, Fernando; Mallick, Swapan; Schraiber, Joshua G.; Jay, Flora; Prüfer, Kay; de Filippo, Cesare; Sudmant, Peter H.; Alkan, Can; Fu, Qiaomei; Do, Ron; Rohland, Nadin; Tandon, Arti; Siebauer, Michael; Green, Richard E.; Bryc, Katarzyna; Briggs, Adrian W.; Stenzel, Udo; Dabney, Jesse; Shendure, Jay; Kitzman, Jacob; Hammer, Michael F.; Shunkov, Michael V.; Derevianko, Anatoli P.; Patterson, Nick; Andrés, Aida M.; Eichler, Evan E.; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante

2013-01-01

We present a DNA library preparation method that has allowed us to reconstruct a high coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans. PMID:22936568

Author identities an interoperability problem solved by a collaborative solution

NASA Astrophysics Data System (ADS)

Fleischer, D.; Czerniak, A.; Schirnick, C.

2012-12-01

The identity of authors and data providers is crucial for personalized interoperability. The marketplace of available identifiers is packed and the right choice is getting more and more complicated. Even though there are more then 15 different systems available there are still some under development and proposed to come up by the end of 2012 ('PubMed Central Author ID' and ORCID). Data Management on a scale beyond the size of a single research institute but on the scale of a scientific site including a university with student education program needs to tackle this problem and so did the Kiel Data Management an Infrastructure. The main problem with the identities of researchers is the quite high frequency changes in positions during a scientist life. The required system needed to be a system that already contained the potential of preregistered people with their scientific publications from other countries, institutions and organizations. Scanning the author ID marketplace brought up, that there us a high risk of additional workload to the researcher itself or the administration due to the fact that individuals need to register an ID for themselves or the chosen register is not yet big enough to simply find the right entry. On the other hand libraries deal with authors and their publications now for centuries and they have high quality catalogs with person identities already available. Millions of records internationally mapped are available by collaboration with libraries and can be used in exactly the same scope. The international collaboration between libraries (VIAF) provides a mapping between libraries from the US, CA, UK, FR, GER and many more. The international library author identification system made it possible to actually reach at the first matching a success of 60% of all scientists. The additional advantage is that librarians can finalize the Identity system in a kind of background process. The Kiel Data Management Infrastructure initiated a web service at Kiel for mapping from one ID to another. This web service supports the scientific workflows for automation of the data archiving process at world data archive PANGAEA. The long-lasting concept of the library identifier enables the use of these identifiers beyond the employment period, while it has nothing to do with the institutional IDM. The access rights and ownership of data can be assured for very long time since the national library with its national scope hosts the basic system. Making use of this existing system released resourced planed for this task and enabled the chance of interoperability on an international scale for a regional data management infrastructure.

Software Quality Control at Belle II

NASA Astrophysics Data System (ADS)

Ritter, M.; Kuhr, T.; Hauth, T.; Gebard, T.; Kristof, M.; Pulvermacher, C.; Belle Software Group, II

2017-10-01

Over the last seven years the software stack of the next generation B factory experiment Belle II has grown to over one million lines of C++ and Python code, counting only the part included in offline software releases. There are several thousand commits to the central repository by about 100 individual developers per year. To keep a coherent software stack of high quality that it can be sustained and used efficiently for data acquisition, simulation, reconstruction, and analysis over the lifetime of the Belle II experiment is a challenge. A set of tools is employed to monitor the quality of the software and provide fast feedback to the developers. They are integrated in a machinery that is controlled by a buildbot master and automates the quality checks. The tools include different compilers, cppcheck, the clang static analyzer, valgrind memcheck, doxygen, a geometry overlap checker, a check for missing or extra library links, unit tests, steering file level tests, a sophisticated high-level validation suite, and an issue tracker. The technological development infrastructure is complemented by organizational means to coordinate the development.

Development of a GC-APCI-QTOFMS library for new psychoactive substances and comparison to a commercial ESI library.

PubMed

Mesihää, Samuel; Ketola, Raimo A; Pelander, Anna; Rasanen, Ilpo; Ojanperä, Ilkka

2017-03-01

Gas chromatography coupled to atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (GC-APCI-QTOFMS) was evaluated for the identification of new psychoactive substances (NPS). An in-house high mass resolution GC-APCI-QTOFMS test library was developed for 29 nitrogen-containing drugs belonging mostly to synthetic stimulants. The library was based on 12 intra-day measurements of each compound at three different collision energies, 10, 20 and 40 eV. The in-house library mass spectra were compared to mass spectra from a commercial library constructed by liquid chromatography-electrospray ionization (LC-ESI) QTOFMS. The reversed library search scores between the in-house GC-APCI library and the commercial LC-ESI library were compared once a week during a 5-week period by using data measured by GC-APCI-QTOFMS. The protonated molecule was found for all drugs in the full scan mode, and the drugs were successfully identified by both libraries in the targeted MS/MS mode. The GC-APCI library score averaged over all collision energies was as high as 94.4/100 with a high repeatability, while the LC-ESI library score was also high (89.7/100) with a repeatability only slightly worse. These results highlight the merits of GC-APCI-QTOFMS in the analysis of NPS even in situations where the reference standards are not immediately available, taking advantage of the accurate mass measurement of the protonated molecule and product ions, and comparison to existing soft-ionization mass spectral libraries. Graphical abstract Tandem mass spectra obtained from GC-APCI-QTOFMS are comparable to LC-ESI-QTOFMS library spectra.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization.

PubMed

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P; Mirokhin, Yuri A; Tchekhovskoi, Dmitrii V; Bukhari, Tallat H; Stein, Stephen E

2018-04-01

We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization

PubMed Central

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P.; Mirokhin, Yuri A.; Tchekhovskoi, Dmitrii V.; Bukhari, Tallat H.; Stein, Stephen E.

2018-01-01

ABSTRACT We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins. PMID:29425077

DLA based compressed sensing for high resolution MR microscopy of neuronal tissue

NASA Astrophysics Data System (ADS)

Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

2015-10-01

In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm.

An Online Information Skills Tutorial

ERIC Educational Resources Information Center

Christensen, Joanne; Morgan, Fawn; Kinikin, Janae

2013-01-01

Looking for new way to teach high school students how to use the library and library resources? The HeLIOS (Hemingway Library Information Online Skills) tutorial, an online tool designed specifically for high school students, may be the answer. For the past two years, students at home, in classrooms, and at libraries throughout Utah have used…

An insight into the sialome of Glossina morsitans morsitans

PubMed Central

2010-01-01

Background Blood feeding evolved independently in worms, arthropods and mammals. Among the adaptations to this peculiar diet, these animals developed an armament of salivary molecules that disarm their host's anti-bleeding defenses (hemostasis), inflammatory and immune reactions. Recent sialotranscriptome analyses (from the Greek sialo = saliva) of blood feeding insects and ticks have revealed that the saliva contains hundreds of polypeptides, many unique to their genus or family. Adult tsetse flies feed exclusively on vertebrate blood and are important vectors of human and animal diseases. Thus far, only limited information exists regarding the Glossina sialome, or any other fly belonging to the Hippoboscidae. Results As part of the effort to sequence the genome of Glossina morsitans morsitans, several organ specific, high quality normalized cDNA libraries have been constructed, from which over 20,000 ESTs from an adult salivary gland library were sequenced. These ESTs have been assembled using previously described ESTs from the fat body and midgut libraries of the same fly, thus totaling 62,251 ESTs, which have been assembled into 16,743 clusters (8,506 of which had one or more EST from the salivary gland library). Coding sequences were obtained for 2,509 novel proteins, 1,792 of which had at least one EST expressed in the salivary glands. Despite library normalization, 59 transcripts were overrepresented in the salivary library indicating high levels of expression. This work presents a detailed analysis of the salivary protein families identified. Protein expression was confirmed by 2D gel electrophoresis, enzymatic digestion and mass spectrometry. Concurrently, an initial attempt to determine the immunogenic properties of selected salivary proteins was undertaken. Conclusions The sialome of G. m. morsitans contains over 250 proteins that are possibly associated with blood feeding. This set includes alleles of previously described gene products, reveals new evidence that several salivary proteins are multigenic and identifies at least seven new polypeptide families unique to Glossina. Most of these proteins have no known function and thus, provide a discovery platform for the identification of novel pharmacologically active compounds, innovative vector-based vaccine targets, and immunological markers of vector exposure. PMID:20353571

Evaluation of hydrothermal resources of North Dakota. Phase II. Final report

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

Harris, K.L.; Howell, F.L.; Winczewski, L.M.

1981-06-01

The Phase II activities dealt with three main topical areas: geothermal gradient and heat-flow studies, stratigraphic studies, and water quality studies. Efforts were concentrated on Mesozoic and Cenozoic rocks. The geothermal gradient and heat-flow studies involved running temperature logs in groundwater observation holes in areas of interest, and locating, obtaining access to, and casing holes of convenience to be used as heat-flow determination sites. The stratigraphic and water quality studies involved two main efforts: updating and expanding WELLFILE and assembling a computer library system (WELLCAT) for all water wells drilled in the state. WATERCAT combines data from the United Statesmore » Geological Survey Water Resources Division's WATSTOR and GWST computer libraries; and includes physical, stratigraphic, and water quality data. Goals, methods, and results are presented.« less

JEFF-3.1, ENDF/B-VII and JENDL-3.3 Critical Assemblies Benchmarking With the Monte Carlo Code TRIPOLI

NASA Astrophysics Data System (ADS)

Sublet, Jean-Christophe

2008-02-01

ENDF/B-VII.0, the first release of the ENDF/B-VII nuclear data library, was formally released in December 2006. Prior to this event the European JEFF-3.1 nuclear data library was distributed in April 2005, while the Japanese JENDL-3.3 library has been available since 2002. The recent releases of these neutron transport libraries and special purpose files, the updates of the processing tools and the significant progress in computer power and potency, allow today far better leaner Monte Carlo code and pointwise library integration leading to enhanced benchmarking studies. A TRIPOLI-4.4 critical assembly suite has been set up as a collection of 86 benchmarks taken principally from the International Handbook of Evaluated Criticality Benchmarks Experiments (2006 Edition). It contains cases for a variety of U and Pu fuels and systems, ranging from fast to deep thermal solutions and assemblies. It covers cases with a variety of moderators, reflectors, absorbers, spectra and geometries. The results presented show that while the most recent library ENDF/B-VII.0, which benefited from the timely development of JENDL-3.3 and JEFF-3.1, produces better overall results, it suggest clearly also that improvements are still needed. This is true in particular in Light Water Reactor applications for thermal and epithermal plutonium data for all libraries and fast uranium data for JEFF-3.1 and JENDL-3.3. It is also true to state that other domains, in which Monte Carlo code are been used, such as astrophysics, fusion, high-energy or medical, radiation transport in general benefit notably from such enhanced libraries. It is particularly noticeable in term of the number of isotopes, materials available, the overall quality of the data and the much broader energy range for which evaluated (as opposed to modeled) data are available, spanning from meV to hundreds of MeV. In pointing out the impact of the different nuclear data at the library but also the isotopic levels one could not help noticing the importance and difference of the compensating effects that result from their single usage. Library differences are still important but tend to diminish due to the ever increasing and beneficial worldwide collaboration in the field of nuclear data measurement and evaluations.

Identification of immune protective genes of Eimeria maxima through cDNA expression library screening.

PubMed

Yang, XinChao; Li, MengHui; Liu, JianHua; Ji, YiHong; Li, XiangRui; Xu, LiXin; Yan, RuoFeng; Song, XiaoKai

2017-02-16

Eimeria maxima is one of the most prevalent Eimeria species causing avian coccidiosis, and results in huge economic loss to the global poultry industry. Current control strategies, such as anti-coccidial medication and live vaccines have been limited because of their drawbacks. The third generation anticoccidial vaccines including the recombinant vaccines as well as DNA vaccines have been suggested as a promising alternative strategy. To date, only a few protective antigens of E. maxima have been reported. Hence, there is an urgent need to identify novel protective antigens of E. maxima for the development of neotype anticoccidial vaccines. With the aim of identifying novel protective genes of E. maxima, a cDNA expression library of E. maxima sporozoites was constructed using Gateway technology. Subsequently, the cDNA expression library was divided into 15 sub-libraries for cDNA expression library immunization (cDELI) using parasite challenged model in chickens. Protective sub-libraries were selected for the next round of screening until individual protective clones were obtained, which were further sequenced and analyzed. Adopting the Gateway technology, a high-quality entry library was constructed, containing 9.2 × 10 6 clones with an average inserted fragments length of 1.63 kb. The expression library capacity was 2.32 × 10 7 colony-forming units (cfu) with an average inserted fragments length of 1.64 Kb. The expression library was screened using parasite challenged model in chickens. The screening yielded 6 immune protective genes including four novel protective genes of EmJS-1, EmRP, EmHP-1 and EmHP-2, and two known protective genes of EmSAG and EmCKRS. EmJS-1 is the selR domain-containing protein of E. maxima whose function is unknown. EmHP-1 and EmHP-2 are the hypothetical proteins of E. maxima. EmRP and EmSAG are rhomboid-like protein and surface antigen glycoproteins of E. maxima respectively, and involved in invasion of the parasite. Our results provide a cDNA expression library for further screening of T cell stimulating or inhibiting antigens of E. maxima. Moreover, our results provide six candidate protective antigens for developing new vaccines against E. maxima.

Multiobjective optimization of combinatorial libraries.

PubMed

Agrafiotis, D K

2002-01-01

Combinatorial chemistry and high-throughput screening have caused a fundamental shift in the way chemists contemplate experiments. Designing a combinatorial library is a controversial art that involves a heterogeneous mix of chemistry, mathematics, economics, experience, and intuition. Although there seems to be little agreement as to what constitutes an ideal library, one thing is certain: only one property or measure seldom defines the quality of the design. In most real-world applications, a good experiment requires the simultaneous optimization of several, often conflicting, design objectives, some of which may be vague and uncertain. In this paper, we discuss a class of algorithms for subset selection rooted in the principles of multiobjective optimization. Our approach is to employ an objective function that encodes all of the desired selection criteria, and then use a simulated annealing or evolutionary approach to identify the optimal (or a nearly optimal) subset from among the vast number of possibilities. Many design criteria can be accommodated, including diversity, similarity to known actives, predicted activity and/or selectivity determined by quantitative structure-activity relationship (QSAR) models or receptor binding models, enforcement of certain property distributions, reagent cost and availability, and many others. The method is robust, convergent, and extensible, offers the user full control over the relative significance of the various objectives in the final design, and permits the simultaneous selection of compounds from multiple libraries in full- or sparse-array format.

Hydrogen-bonded turns in proteins: The case for a recount

PubMed Central

Panasik, Nick; Fleming, Patrick J.; Rose, George D.

2005-01-01

β-Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β-turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β-turn. Here, we identify potential hydrogen-bonded β-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither α-helix nor β-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded β-turns. In particular, 33% of coil library residues were classified as β-turns prior to minimization. After minimization, 45% of such residues could be classified as β-turns, with another 8% in 310 helixes (which closely resemble type III β-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure. PMID:16251367

Hydrogen-bonded turns in proteins: the case for a recount.

PubMed

Panasik, Nick; Fleming, Patrick J; Rose, George D

2005-11-01

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

ILP-2 modeling and virtual screening of an FDA-approved library:a possible anticancer therapy.

PubMed

Khalili, Saeed; Mohammadpour, Hemn; Shokrollahi Barough, Mahideh; Kokhaei, Parviz

2016-06-23

The members of the inhibitors of apoptosis protein (IAP) family inhibit diverse components of the caspase signaling pathway, notably caspase 3, 7, and 9. ILP-2 (BIRC-8) is the most recently identified member of the IAPs, mainly interacting with caspase 9. This interaction would eventually lead to death resistance in the case of cancerous cells. Therefore, structural modeling of ILP-2 and finding applicable inhibitors of its interaction with caspase 9 are a compelling challenge. Three main protein modeling approaches along with various model refinement measures were harnessed to achieve a reliable 3D model, using state-of-the-art software. Thereafter, the selected model was employed to perform virtual screening of an FDA approved library. A model built by a combinatorial approach (homology and ab initio approaches) was chosen as the best model. Model refinement processes successfully bolstered the model quality. Virtual screening of the compound library introduced several high affinity inhibitor candidates that interact with functional residues of ILP2. Given the 3D structure of the ILP2 molecule, we found promising inhibitory molecules. In addition to high affinity towards the ILP2 molecule, these molecules interact with residues that play pivotal rules in ILP2-caspase interaction. These molecules would inhibit ILP2-caspase interaction and consequently would lead to reactivated cell apoptosis through the caspases pathway.

Release of the ENDF/B-VII.1 Evaluated Nuclear Data File

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

Brown, David

2012-06-30

The Cross Section Evaluation Working Group (CSEWG) released the ENDF/B-VII.1 library on December 22, 2011. The ENDF/B-VII.1 library is CSEWG's latest recommended evaluated nuclear data file for use in nuclear science and technology applications, and incorporates advances made in the five years since the release of ENDF/B-VII.0, including: many new evaluation in the neutron sublibrary (423 in all and over 190 of these contain covariances), new fission product yields and a greatly improved decay data sublibrary. This summary barely touches on the five years worth of advances present in the ENDF/B-VII.1 library. We expect that these changes will lead tomore » improved integral performance in reactors and other applications. Furthermore, the expansion of covariance data in this release will allow for better uncertainty quantification, reducing design margins and costs. The ENDF library is an ongoing and evolving effort. Currently, the ENDF data community embarking on several parallel efforts to improve library management: (1) The adoption of a continuous integration system to provide evaluators 'instant' feedback on the quality of their evaluations and to provide data users with working 'beta' quality libraries in between major releases. (2) The transition to new hierarchical data format - the Generalized Nuclear Data (GND) format. We expect GND to enable new kinds of evaluated data which cannot be accommodated in the legacy ENDF format. (3) The development of data assimilation and uncertainty propagation techniques to enable the consistent use of integral experimental data in the evaluation process.« less

Empowering your institution through assessment

PubMed Central

Joubert, Douglas J.; Lee, Tamera P.

2007-01-01

Objectives: The objectives of this study are to describe the process of linking Association of Academic Health Sciences Libraries (AAHSL) data with 2002 LibQUAL+ data and to address four analytical questions created by the AAHSL Task Force on Quality Assessment that relate both to user satisfaction and to services provided by AAHSL libraries. Methods: For the thirty-five AAHSL libraries that participated in the 2002 LibQUAL+ survey, nested-effect of variance was analyzed using a linear mixed model. Using the Pearson correlation coefficient, this study explored four questions about the effect of user demographics on perceived levels of satisfaction with library services. Results: The supposition that library user satisfaction may differ according to library institutional reporting structure was unsupported. Regarding effect on mean overall satisfaction, size of library staff is not significant (P = 0.860), number of constituents is slightly significant (P = 0.027), and ratio of staff to constituents has a moderate and significant effect (P = 0.004). Conclusions: From a demographic perspective, the 2002 LibQUAL+ survey represents the largest cross section of AAHSL libraries. Increased understanding of how qualitative assessment can supplement quantitative data supports evidence-based decision-making and practice. It also could promote changes in data collection and usage. PMID:17252066

Empowering your institution through assessment.

PubMed

Joubert, Douglas J; Lee, Tamera P

2007-01-01

The objectives of this study are to describe the process of linking Association of Academic Health Sciences Libraries (AAHSL) data with 2002 LibQUAL+ data and to address four analytical questions created by the AAHSL Task Force on Quality Assessment that relate both to user satisfaction and to services provided by AAHSL libraries. For the thirty-five AAHSL libraries that participated in the 2002 LibQUAL+ survey, nested-effect of variance was analyzed using a linear mixed model. Using the Pearson correlation coefficient, this study explored four questions about the effect of user demographics on perceived levels of satisfaction with library services. The supposition that library user satisfaction may differ according to library institutional reporting structure was unsupported. Regarding effect on mean overall satisfaction, size of library staff is not significant (P = 0.860), number of constituents is slightly significant (P = 0.027), and ratio of staff to constituents has a moderate and significant effect (P = 0.004). From a demographic perspective, the 2002 LibQUAL+ survey represents the largest cross section of AAHSL libraries. Increased understanding of how qualitative assessment can supplement quantitative data supports evidence-based decision-making and practice. It also could promote changes in data collection and usage.

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

PubMed

Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

2016-05-26

Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

PubMed

Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph

2017-06-06

The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.

The Role of Biomedical Librarians in a Local Basic Unit Library Organization.

ERIC Educational Resources Information Center

Taylor, Ruth

The quality of library service in biomedical institutions ultimately depends upon basic unit librarians. Although the hierarchy is necessary, it can only have as much real authority and cooperation as institutions vest in it by their degree of understanding and sense of personal worth. Vital to this is the local peer groups, which serves two basic…