North Carolina: Statewide Automation and Connectivity Efforts.

ERIC Educational Resources Information Center

Christian, Elaine J., Ed.

1996-01-01

Describes statewide information automation and connectivity efforts in North Carolina. Highlights include Triangle Research Libraries Network Document Delivery System; cooperative networking projects; public library connectivity to the state library; rural access projects; community college automation; K-12 technology plans; electronic government…

Identifying and Articulating Library Connections to Student Success

ERIC Educational Resources Information Center

Massengale, Lisa; Piotrowski, Pattie; Savage, Devin

2016-01-01

Engaging in ongoing assessment is key to libraries demonstrating their value to their institutions. This study is an initial step in a STEM library's long-term goal of measuring the library's connection to, and impact on, student academic success markers such as retention and persistence. Initial results showed that any library usage was always…

EAST ELEVATION OF ERIE PUBLIC LIBRARY. NOTE THE CONNECTING GLASS ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

EAST ELEVATION OF ERIE PUBLIC LIBRARY. NOTE THE CONNECTING GLASS ATRIUM JOINING THE FORMER LIBRARY WITH THE FEDERAL COURTHOUSE AND BAKER BUILDING, CREATING THE NEW ERIE FEDERAL COMPLEX IN 2003-2004. - Erie Public Library, 3 Park Row, Erie, Erie County, PA

Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries

PubMed Central

Bassik, Michael C.; Lebbink, Robert Jan; Churchman, L. Stirling; Ingolia, Nicholas T.; Patena, Weronika; LeProust, Emily M.; Schuldiner, Maya; Weissman, Jonathan S.; McManus, Michael T.

2009-01-01

Short hairpin RNA (shRNA) libraries are limited by the low efficacy of many shRNAs, giving false negatives, and off-target effects, giving false positives. Here we present a strategy for rapidly creating expanded shRNA pools (∼30 shRNAs/gene) that are analyzed by deep-sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of whether a gene is a true hit. PMID:19448642

Telecommunications Options Connect OCLC and Libraries to the Future: The Co-Evolution of OCLC Connectivity Options and the Library Computing Environment.

ERIC Educational Resources Information Center

Breeding, Marshall

1998-01-01

The Online Computer Library Center's (OCLC) access options have kept pace with the evolving trends in telecommunications and the library computing environment. As libraries deploy microcomputers and develop networks, OCLC offers access methods consistent with these environments. OCLC works toward reorienting its network paradigm through TCP/IP…

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

PubMed

Ghodasara, Amar; Voigt, Christopher A

2017-07-27

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

The Policy Implications of Internet Connectivity in Public Libraries

ERIC Educational Resources Information Center

Jaeger, Paul T.; Bertot, John Carlo; McClure, Charles R.; Langa, Lesley A.

2006-01-01

The provision of public Internet access and related networked services by public libraries is affected by a number of information policy issues. This article analyzes the policy dimensions of Internet connectivity in public libraries in light of the data and findings from a national survey of public libraries conducted by the authors of this…

Monosynaptic rabies virus reveals premotor network organization and synaptic specificity of cholinergic partition cells.

PubMed

Stepien, Anna E; Tripodi, Marco; Arber, Silvia

2010-11-04

Movement is the behavioral output of neuronal activity in the spinal cord. Motor neurons are grouped into motor neuron pools, the functional units innervating individual muscles. Here we establish an anatomical rabies virus-based connectivity assay in early postnatal mice. We employ it to study the connectivity scheme of premotor neurons, the neuronal cohorts monosynaptically connected to motor neurons, unveiling three aspects of organization. First, motor neuron pools are connected to segmentally widely distributed yet stereotypic interneuron populations, differing for pools innervating functionally distinct muscles. Second, depending on subpopulation identity, interneurons take on local or segmentally distributed positions. Third, cholinergic partition cells involved in the regulation of motor neuron excitability segregate into ipsilaterally and bilaterally projecting populations, the latter exhibiting preferential connections to functionally equivalent motor neuron pools bilaterally. Our study visualizes the widespread yet precise nature of the connectivity matrix for premotor interneurons and reveals exquisite synaptic specificity for bilaterally projecting cholinergic partition cells. Copyright © 2010 Elsevier Inc. All rights reserved.

Library Partnerships: Making Connections between School and Public Libraries

ERIC Educational Resources Information Center

Squires, Tasha

2009-01-01

Connecting to share ideas, resources, and programs offers school and public libraries an exciting means of achieving their own goals as well as those of the community at large. In this timely guide, young adult library consultant Tasha Squires delves into the many possible avenues for partnership, from summer reading programs to book talks to…

[RNA interference library research progress and its application in cancer research].

PubMed

Zhao, Ning; Cai, Li

2013-02-01

RNA interference is a homologous mRNA special degradation phenomenon which is caused by the double-stranded RNA. RNAi library is a pooled library that is artificially constructed using RNAi technology. As RNAi library has made a major breakthrough in the field of genetic research, it has been widely used in the field of medical research, especially in the field of cancer research. This review discussed the research progress of RNAi library and its applications in cancer research.

47 CFR 54.506 - Internal connections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... other schools or libraries (for example, as part of a consortium), the shared services will be... SERVICE Universal Service Support for Schools and Libraries § 54.506 Internal connections. (a) A service... within one or more non-administrative buildings that comprise a single library branch. Discounts are not...

School Library Media Program Connections for Learning.

ERIC Educational Resources Information Center

Bookmark, 1991

1991-01-01

The 29 articles in this theme issue of "The Bookmark" focus on various aspects of school library media programs. The articles are as follows: (1) "School Library Media Program Connections for Learning" (Betty J. Morris); (2) "Humanity and Technology in the School of the Future" (Michael V. McGill); (3) "Community…

Connecting Libraries and Schools with CLASP.

ERIC Educational Resources Information Center

Del Vecchio, Stephen

1993-01-01

Describes the Dewitt Wallace-Reader's Digest Connecting Libraries and Schools Project (CLASP) of the New York Public Library, a cooperative pilot project to encourage reading among children and youth. Sample projects described include summer reading lists, open school night outreach, and outreach to parents. The importance of materials support is…

78 FR 39781 - Consequence Study of a Beyond-Design-Basis Earthquake Affecting the Spent Fuel Pool for a U.S...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-02

... Spent Fuel Pool Study). The purpose of this study was to examine if faster removal of older, colder... NRC Library at http://www.nrc.gov/reading-rm/adams.html . To begin the search, select ``ADAMS Public... of postulated spent fuel pool accidents. The purpose of this study is to examine if faster removal of...

The Veterans Administration Library Network: VALNET.

PubMed Central

van Vuren, D D

1982-01-01

Given substantial federal budget cuts and ever-increasing quantities of print and nonprint material, Veterans Administration (VA) Library Services have pooled their resources in a network to improve the scope and efficiency of the services they provide. The VA Library Network, VALNET, composed of 176 libraries, serves health care facilities throughout the continental United States and Puerto Rico. This paper outlines VALNET's organization and the range of individual VA Library Services. It also describes centrally provided services and resource-sharing tools being developed by the VA, as well as significant sharing arrangement among VA Library Services and between the VA and non-VA libraries. PMID:7052164

Literary Festivals, Library Style: Libraries Can Use Literary Festivals to Secure Their Role as the Ultimate Connection among Readers, Authors, and Books

ERIC Educational Resources Information Center

Dempsey, Beth

2005-01-01

Literary festivals offer a unique proposition to libraries: host one, bring the reading public up-close and personal with writers of all kinds, and they will bask in the glory of that connection. Indeed, festivals can be the pathway for libraries to "own" the literary niche in their community. Bob Cannon, executive director of the Broward County…

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…

Problem Scoping Design Thinking and Close Reading: Makerspaces in the School Library

ERIC Educational Resources Information Center

Blakemore, Megan

2018-01-01

Makerspaces, collaborative workspaces stocked with materials and tools for creating, building, designing, and learning, are becoming more and more common in schools and, in particular, in school libraries. Makerspaces in the school library allow for connections between making and literacy. Indeed, such connections are authentic and natural as…

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

PubMed

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

2015-09-21

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

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.

HYDROLOGY AND LANDSCAPE CONNECTIVITY OF VERNAL POOLS

EPA Science Inventory

Vernal pools are shaped by hydrologic processes which influence many aspects of pool function. The hydrologic budget of a pool can be summarized by a water balance equation that relates changes in the amount of water in the pool to precipitation, ground- and surface-water flows, ...

Working Connections: Suzan Lee--UBS Securities LLC, New York

ERIC Educational Resources Information Center

Library Journal, 2004

2004-01-01

This article is about Suzan Lee of UBS Securities LLC in New York, a person who is dedicated to connecting aspiring professionals to opportunities in the world of special libraries. In 1999, Lee realized that most library students had only one resource for internships--their library schools--and that these offerings focused largely on public and…

Supporting Creativity in School Libraries: Finding, Sharing, and Connecting

ERIC Educational Resources Information Center

Techman, Melissa

2014-01-01

Creativity is about openness and connection, it signals the chance to get ideas, share ideas, and try new things or put together old things in new ways. Libraries have always had the potential to source and support creative activities. Public library events and opportunities bring together people, ideas, and stuff (whether fabric, paint, wood,…

HYDROLOGY AND LANDSCAPE CONNECTIVITY OF VERNAL POOLS OF THE GLACIATED NORTHEAST

EPA Science Inventory

The hydrologic budget of a vernal pool influences many aspects of pool function and is the basis for pool life. Although alternating wet and dry periods occur in most wetlands, vernal pools can experience extreme moisture fluctuations. This variability results from intra- and i...

Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages

PubMed Central

Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

2012-01-01

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing. PMID:23202944

Sandia National Laboratories: CRISPR genome-editing technology

Science.gov Websites

boom sets records, forges ties "Like a jar of jellybeans, a pooled CRISPR library is a complex like individually wrapped and labeled jellybeans. When you identify a particular CRISPR of interest arrayed libraries, the CRISPR of interest is already labeled, therefore hit identification is much easier

36 CFR 702.5 - Gambling.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Gambling. 702.5 Section 702.5 Parks, Forests, and Public Property LIBRARY OF CONGRESS CONDUCT ON LIBRARY PREMISES § 702.5 Gambling. Participation in any illegal gambling, such as the operation of gambling devices, the conduct of an illegal pool...

36 CFR 702.5 - Gambling.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Gambling. 702.5 Section 702.5 Parks, Forests, and Public Property LIBRARY OF CONGRESS CONDUCT ON LIBRARY PREMISES § 702.5 Gambling. Participation in any illegal gambling, such as the operation of gambling devices, the conduct of an illegal pool...

36 CFR 702.5 - Gambling.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Gambling. 702.5 Section 702.5 Parks, Forests, and Public Property LIBRARY OF CONGRESS CONDUCT ON LIBRARY PREMISES § 702.5 Gambling. Participation in any illegal gambling, such as the operation of gambling devices, the conduct of an illegal pool...

36 CFR 702.5 - Gambling.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Gambling. 702.5 Section 702.5 Parks, Forests, and Public Property LIBRARY OF CONGRESS CONDUCT ON LIBRARY PREMISES § 702.5 Gambling. Participation in any illegal gambling, such as the operation of gambling devices, the conduct of an illegal pool...

Efficient generation of connectivity in neuronal networks from simulator-independent descriptions

PubMed Central

Djurfeldt, Mikael; Davison, Andrew P.; Eppler, Jochen M.

2014-01-01

Simulator-independent descriptions of connectivity in neuronal networks promise greater ease of model sharing, improved reproducibility of simulation results, and reduced programming effort for computational neuroscientists. However, until now, enabling the use of such descriptions in a given simulator in a computationally efficient way has entailed considerable work for simulator developers, which must be repeated for each new connectivity-generating library that is developed. We have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeler's needs. We have used the connection generator interface to connect C++ and Python implementations of the previously described connection-set algebra to the NEST simulator. We also demonstrate how the simulator-independent modeling framework PyNN can transparently take advantage of this, passing a connection description through to the simulator layer for rapid processing in C++ where a simulator supports the connection generator interface and falling-back to slower iteration in Python otherwise. A set of benchmarks demonstrates the good performance of the interface. PMID:24795620

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.

PubMed

Trümbach, Dietrich; Pfeiffer, Susanne; Poppe, Manuel; Scherb, Hagen; Doll, Sebastian; Wurst, Wolfgang; Schick, Joel A

2017-11-25

As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import. We demonstrate the capabilities of ENCoRE to interrogate results from a pooled CRISPR cellular viability screen following Tumor Necrosis Factor-alpha challenge. The results not only identified stereotypical players in extrinsic apoptotic signaling but two as yet uncharacterized members of the extrinsic apoptotic cascade, Smg7 and Ces2a. We further validated and characterized cell lines containing mutations in these genes against a panel of cell death stimuli and involvement in p53 signaling. In summary, this software enables bench scientists with sensitive data or without access to informatic cores to rapidly interpret results from large scale experiments resulting from pooled CRISPR/Cas9 library screens.

Out from behind the Byline: The Secret Life of the Reviewer Revealed

ERIC Educational Resources Information Center

Surges, Carol S.

2009-01-01

Hundreds of people work to bring each issue of "Library Media Connection" to readers filled with current articles on the always changing work and role of the school library media specialist. A majority of that group are the reviewers. As reviewers for "Library Media Connection" they work as volunteers. So what keeps them performing this task month…

Connecting the Nation: Classrooms, Libraries, and Health Care Organizations in the Information Age. Update 1995.

ERIC Educational Resources Information Center

Gonzalez, Emilio

Connecting every classroom, library, hospital, and clinic in the United States to the National Information Infrastructure (NII) is a priority for the Clinton Administration. This document provides a status report on this initiative by drawing from current data regarding Internet connectivity, a benchmark for NII access. Chapter 1 of the report…

Development of High Throughput Process for Constructing 454 Titanium and Illumina Libraries

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

Deshpande, Shweta; Hack, Christopher; Tang, Eric

2010-05-28

We have developed two processes with the Biomek FX robot to construct 454 titanium and Illumina libraries in order to meet the increasing library demands. All modifications in the library construction steps were made to enable the adaptation of the entire processes to work with the 96-well plate format. The key modifications include the shearing of DNA with Covaris E210 and the enzymatic reaction cleaning and fragment size selection with SPRI beads and magnetic plate holders. The construction of 96 Titanium libraries takes about 8 hours from sheared DNA to ssDNA recovery. The processing of 96 Illumina libraries takes lessmore » time than that of the Titanium library process. Although both processes still require manual transfer of plates from robot to other work stations such as thermocyclers, these robotic processes represent about 12- to 24-folds increase of library capacity comparing to the manual processes. To enable the sequencing of many libraries in parallel, we have also developed sets of molecular barcodes for both library types. The requirements for the 454 library barcodes include 10 bases, 40-60percent GC, no consecutive same base, and no less than 3 bases difference between barcodes. We have used 96 of the resulted 270 barcodes to construct libraries and pool to test the ability of accurately assigning reads to the right samples. When allowing 1 base error occurred in the 10 base barcodes, we could assign 99.6percent of the total reads and 100percent of them were uniquely assigned. As for the Illumina barcodes, the requirements include 4 bases, balanced GC, and at least 2 bases difference between barcodes. We have begun to assess the ability to assign reads after pooling different number of libraries. We will discuss the progress and the challenges of these scale-up processes.« less

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.

CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries.

PubMed

Heigwer, Florian; Zhan, Tianzuo; Breinig, Marco; Winter, Jan; Brügemann, Dirk; Leible, Svenja; Boutros, Michael

2016-03-24

Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.

Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon.

PubMed

Song, Beng-Kah; Nadarajah, Kalaivani; Romanov, Michael N; Ratnam, Wickneswari

2005-01-01

The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were developed from the publicly available genomic sequences of the cultivated rice, O. sativa, to generate 20 overgo probes for a 1-Mb region that encompasses a yield enhancement QTL yld1.1 in O. rufipogon. The advantages of a high similarity in melting temperature, hybridization kinetics and specific activities of overgos further enabled a pooling strategy for library screening by filter hybridization. Two pools of ten overgos each were hybridized to high-density filters representing the O. rufipogon genomic BAC library. These screening tests succeeded in providing 69 PCR-verified positive hits from a total of 23,040 BAC clones of the entire O. rufipogon library. A minimal tilling path of clones was generated to contribute to a fully covered BAC-contig map of the targeted 1-Mb region. The developed protocol for overgo design based on O. sativa sequences as a comparative genomic framework, and the pooled overgo hybridization screening technique are suitable means for high-resolution physical mapping and the identification of BAC candidates for sequencing.

High-resolution mapping and sequence analysis of 597 cDNA clones transcribed from the 1 Mb region in human chromosome 4q16.3 containing Huntington disease gene

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

Hadano, S.; Ishida, Y.; Tomiyasu, H.

1994-09-01

To complete a transcription map of the 1 Mb region in human chromosome 4p16.3 containing the Huntington disease (HD) gene, the isolation of cDNA clones are being performed throughout. Our method relies on a direct screening of the cDNA libraries probed with single copy microclones from 3 YAC clones spanning 1 Mbp of the HD gene region. AC-DNAs were isolated by a preparative pulsed-field gel electrophoresis, amplified by both a single unique primer (SUP)-PCR and a linker ligation PCR, and 6 microclone-DNA libraries were generated. Then, 8,640 microclones from these libraries were independently amplified by PCR, and arrayed onto themore » membranes. 800-900 microclones that were not cross-hybridized with total human and yeast genomic DNA, TAC vector DNA, and ribosomal cDNA on a dot hybridization (putatively carrying single copy sequences) were pooled to make 9 probe pools. A total of {approximately}1.8x10{sup 7} plaques from the human brain cDNA libraries was screened with 9 pool-probes, and then 672 positive cDNA clones were obtained. So far, 597 cDNA clones were defined and arrayed onto a map of the 1 Mbp of the HD gene region by hybridization with HD region-specific cosmid contigs and YAC clones. Further characterization including a DNA sequencing and Northern blot analysis is currently underway.« less

Long non-coding RNA XIST predicts worse prognosis in digestive system tumors: a systemic review and meta-analysis.

PubMed

Liu, Xuefang; Ming, Xinliang; Jing, Wei; Luo, Ping; Li, Nandi; Zhu, Man; Yu, Mingxia; Liang, Chunzi; Tu, Jiancheng

2018-05-11

Aims: Increasing studies are indicating that long non-coding RNA X-inactive specific transcript (XIST) is associated with the prognosis of cancer patients. However, the results have been disputed. Therefore, we aimed to further explore the prognostic value and clinical significance of XIST in various types of cancers. Then, we focused our research on the comparison of the predictive value of XIST between digestive system tumors and non-digestive system tumors. Methods: We performed a systematic search by looking up PubMed, Embase, Cochrane Library, Web of Science, and Medline (up to January 3, 2018). Fifteen studies which matched to our inclusion criteria with a total of 920 patients for overall survival and 867 patients for clinicopathological characteristics were included in this meta-analysis. Pooled hazard ratios (HR) and odds ratios (ORs) with their corresponding 95% confidence intervals (95% CIs) were calculated to summarize the effects. Results: Our results suggested that high expression levels of XIST were associated with unfavorable overall survival in cancer patients (pooled HR=1.81, 95% CI: 1.45-2.26). Additionally, we found that XIST was more valuable in digestive system tumors (pooled HR=2.24, 95% CI: 1.73-2.92) than in non-digestive system tumors (pooled HR=1.22, 95% CI: 0.60-2.45). Additionally, elevated expression levels of XIST were connection with distant metastasis and tumor stage. Conclusion: XIST was correlated with poor prognosis, which suggested that XIST might serve as a novel predictive biomarker for cancer patients, especially for patients of digestive system tumors. ©2018 The Author(s).

California: Library Information Technologies.

ERIC Educational Resources Information Center

Will, Barbara, Ed.

1996-01-01

Describes six information technology projects in California libraries, including Internet access in public libraries; digital library developments at the University of California, Berkeley; the World Wide Web home page for the state library; Pacific Bell's role in statewide connectivity; state government initiatives; and services of the state…

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

PubMed Central

Hart, Traver; Tong, Amy Hin Yan; Chan, Katie; Van Leeuwen, Jolanda; Seetharaman, Ashwin; Aregger, Michael; Chandrashekhar, Megha; Hustedt, Nicole; Seth, Sahil; Noonan, Avery; Habsid, Andrea; Sizova, Olga; Nedyalkova, Lyudmila; Climie, Ryan; Tworzyanski, Leanne; Lawson, Keith; Sartori, Maria Augusta; Alibeh, Sabriyeh; Tieu, David; Masud, Sanna; Mero, Patricia; Weiss, Alexander; Brown, Kevin R.; Usaj, Matej; Billmann, Maximilian; Rahman, Mahfuzur; Costanzo, Michael; Myers, Chad L.; Andrews, Brenda J.; Boone, Charles; Durocher, Daniel; Moffat, Jason

2017-01-01

The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines. PMID:28655737

Mass spectrometric screening of ligands with lower off-rate from a clicked-based pooled library.

PubMed

Arai, Satoshi; Hirosawa, Shota; Oguchi, Yusuke; Suzuki, Madoka; Murata, Atsushi; Ishiwata, Shin'ichi; Takeoka, Shinji

2012-08-13

This paper describes a convenient screening method using ion trap electrospray ionization mass spectrometry to classify ligands to a target molecule in terms of kinetic parameters. We demonstrate this method in the screening of ligands to a hexahistidine tag from a pooled library synthesized by click chemistry. The ion trap mass spectrometry analysis revealed that higher stabilities of ligand-target complexes in the gas phase were related to lower dissociation rate constants, i.e., off-rates in solution. Finally, we prepared a fluorescent probe utilizing the ligand with lowest off-rate and succeeded in performing single molecule observations of hexahistidine-tagged myosin V walking on actin filaments.

Alcoholism Detection by Data Augmentation and Convolutional Neural Network with Stochastic Pooling.

PubMed

Wang, Shui-Hua; Lv, Yi-Ding; Sui, Yuxiu; Liu, Shuai; Wang, Su-Jing; Zhang, Yu-Dong

2017-11-17

Alcohol use disorder (AUD) is an important brain disease. It alters the brain structure. Recently, scholars tend to use computer vision based techniques to detect AUD. We collected 235 subjects, 114 alcoholic and 121 non-alcoholic. Among the 235 image, 100 images were used as training set, and data augmentation method was used. The rest 135 images were used as test set. Further, we chose the latest powerful technique-convolutional neural network (CNN) based on convolutional layer, rectified linear unit layer, pooling layer, fully connected layer, and softmax layer. We also compared three different pooling techniques: max pooling, average pooling, and stochastic pooling. The results showed that our method achieved a sensitivity of 96.88%, a specificity of 97.18%, and an accuracy of 97.04%. Our method was better than three state-of-the-art approaches. Besides, stochastic pooling performed better than other max pooling and average pooling. We validated CNN with five convolution layers and two fully connected layers performed the best. The GPU yielded a 149× acceleration in training and a 166× acceleration in test, compared to CPU.

Towards dropout training for convolutional neural networks.

PubMed

Wu, Haibing; Gu, Xiaodong

2015-11-01

Recently, dropout has seen increasing use in deep learning. For deep convolutional neural networks, dropout is known to work well in fully-connected layers. However, its effect in convolutional and pooling layers is still not clear. This paper demonstrates that max-pooling dropout is equivalent to randomly picking activation based on a multinomial distribution at training time. In light of this insight, we advocate employing our proposed probabilistic weighted pooling, instead of commonly used max-pooling, to act as model averaging at test time. Empirical evidence validates the superiority of probabilistic weighted pooling. We also empirically show that the effect of convolutional dropout is not trivial, despite the dramatically reduced possibility of over-fitting due to the convolutional architecture. Elaborately designing dropout training simultaneously in max-pooling and fully-connected layers, we achieve state-of-the-art performance on MNIST, and very competitive results on CIFAR-10 and CIFAR-100, relative to other approaches without data augmentation. Finally, we compare max-pooling dropout and stochastic pooling, both of which introduce stochasticity based on multinomial distributions at pooling stage. Copyright © 2015 Elsevier Ltd. All rights reserved.

75 FR 17584 - Schools and Libraries Universal Service Support Mechanism

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-07

... libraries may receive discounts for eligible telecommunications services, Internet access, and internal... service, Internet access, internal connections, basic maintenance of internal connections, and... VoIP be listed in both the telecommunications and Internet access categories of the ESL, despite the...

Broca’s area network in language function: a pooling-data connectivity study

PubMed Central

Bernal, Byron; Ardila, Alfredo; Rosselli, Monica

2015-01-01

Background and Objective: Modern neuroimaging developments have demonstrated that cognitive functions correlate with brain networks rather than specific areas. The purpose of this paper was to analyze the connectivity of Broca’s area based on language tasks. Methods: A connectivity modeling study was performed by pooling data of Broca’s activation in language tasks. Fifty-seven papers that included 883 subjects in 84 experiments were analyzed. Analysis of Likelihood Estimates of pooled data was utilized to generate the map; thresholds at p < 0.01 were corrected for multiple comparisons and false discovery rate. Resulting images were co-registered into MNI standard space. Results: A network consisting of 16 clusters of activation was obtained. Main clusters were located in the frontal operculum, left posterior temporal region, supplementary motor area, and the parietal lobe. Less common clusters were seen in the sub-cortical structures including the left thalamus, left putamen, secondary visual areas, and the right cerebellum. Conclusion: Broca’s area-44-related networks involved in language processing were demonstrated utilizing a pooling-data connectivity study. Significance, interpretation, and limitations of the results are discussed. PMID:26074842

Missouri Library Connection: A Beginner's Guide to the Bibliofile/Microcomputer System.

ERIC Educational Resources Information Center

Raithel, Frederick J.; Foster, Paul

In 1988, the Missouri State Library offered microcomputers to Missouri public libraries to help them implement a retrospective conversion of their cataloging system to an online system called Bibliofile. The goal of the State Library was to create and maintain a Union Catalog for Missouri libraries. This guide provides Missouri library personnel…

The Librarian Who Loves "LibraryThing"

ERIC Educational Resources Information Center

Sibley, Roberta

2008-01-01

"LibraryThing" is a great way for library media specialists to keep track of the books they personally read. "LibraryThing" allows them to create a personal library, give their books tags, choose book covers, give star ratings, generate citations, and review books. Library media specialists can also connect to other readers and see their reviews.…

Using graph approach for managing connectivity in integrative landscape modelling

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Military Interoperable Digital Hospital Testbed (MIDHT)

DTIC Science & Technology

2013-10-01

activities are selected highlights completed by Northrop Grumman during the year. Cycle 4 development: - Increased the max_allowed_packet size in MySQL ...deployment with the Java install that is required by CONNECT v3.3.1.3. - Updated the MIDHT code base to work with the CONNECT v.3.3.1.3 Core Libraries...Provided TATRC the CONNECTUniversalClientGUI binaries for use with CONNECT v3.3.1.3 − Created and deployed a common Java library for the CONNECT

Synthesis of Enantiomerically Pure 6-Substituted-Piperazine-2-Acetic Acid Esters as Intermediates for Library Production.

PubMed

Chamakuri, Srinivas; Jain, Prashi; Guduru, Shiva Krishna Reddy; Arney, Joseph Winston; MacKenzie, Kevin; Santini, Conrad; Young, Damian W

2018-05-11

Amino acids from the chiral pool have been used to produce a 24-member branch of 2,6-disubstituted piperazine scaffolds suitable for use in compound library production. Each scaffold was obtained as a single absolute stereoisomer in multi-gram quantities. Stereochemistry was confirmed by 2D NMR protocols and enantiomeric purity was determined by chiral HPLC. The scaffolds are intended for use as intermediates in parallel synthesis of small-molecule libraries.

Cable Library Survey Results.

ERIC Educational Resources Information Center

Public Service Satellite Consortium, Washington, DC.

This report summarizes a survey of 198 libraries which had been identified as potential cable libraries which assessed: (1) to what extent a national satellite cable library network might already be in technical existence, (2) how many libraries are connected to cooperative cable companies with satellite hardware and excess receiver capacity, and…

Investigating the Relationship of Library Usage to Student Outcomes

ERIC Educational Resources Information Center

Stemmer, John K.; Mahan, David M.

2016-01-01

This study connects library user surveys, a common library assessment technique, to institutional data to demonstrate the value an academic library brings to student learning and student outcomes. Using regression techniques, the study identifies multiple significant correlations, both positive and negative, between student use of the library and…

Connecting the Library's Patron Database to Campus Administrative Software: Simplifying the Library's Accounts Receivable Process

ERIC Educational Resources Information Center

Oliver, Astrid; Dahlquist, Janet; Tankersley, Jan; Emrich, Beth

2010-01-01

This article discusses the processes that occurred when the Library, Controller's Office, and Information Technology Department agreed to create an interface between the Library's Innovative Interfaces patron database and campus administrative software, Banner, using file transfer protocol, in an effort to streamline the Library's accounts…

What's a School Librarian's Favorite Preposition? Evidence in, of, and for Practice

ERIC Educational Resources Information Center

Richey, Jennifer; Cahill, Maria

2015-01-01

School librarians, professional library literature, and scholarly library literature tout the benefits of schools staffed with certified school librarians. However, recent reductions in library funding and elimination of school library positions suggest stakeholders do not connect the school library program to positive student learning outcomes.…

Library of the Year 2008: Laramie County Library System, Wyoming--The Impact Library

ERIC Educational Resources Information Center

Berry, John N., III

2008-01-01

This article features Laramie County Library System (LCLS) of Cheyenne, Wyoming, which is named as Gale/"Library Journal" 2008 Library of the Year. It is not just strong, effective publicity or the fine new building or even a staff built around its ability to connect with the people, although all of those things add to the impact of…

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

PubMed

Marine, Rachel; McCarren, Coleen; Vorrasane, Vansay; Nasko, Dan; Crowgey, Erin; Polson, Shawn W; Wommack, K Eric

2014-01-30

Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.

View of Powell Library main reading room ceiling; suspension system ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of Powell Library main reading room ceiling; suspension system above ceiling showing close-up connection. - University of California Los Angeles, Powell Library, Westwood, Los Angeles, Los Angeles County, CA

Mimotope mapping as a complementary strategy to define allergen IgE-epitopes: peach Pru p 3 allergen as a model.

PubMed

Pacios, Luis F; Tordesillas, Leticia; Cuesta-Herranz, Javier; Compes, Esther; Sánchez-Monge, Rosa; Palacín, Arantxa; Salcedo, Gabriel; Díaz-Perales, Araceli

2008-04-01

Lipid transfer proteins (LTPs) are the major allergens of Rosaceae fruits in the Mediterranean area. Pru p 3, the LTP and major allergen of peach, is a suitable model for studying food allergy and amino acid sequences related with its IgE-binding capacity. In this work, we sought to map IgE mimotopes on the structure of Pru p 3, using the combination of a random peptide phage display library and a three-dimensional modelling approach. Pru p 3-specific IgE was purified from 2 different pools of sera from peach allergic patients grouped by symptoms (OAS-pool or SYS-pool), and used for screening of a random dodecapeptide phage display library. Positive clones were further confirmed by ELISA assays testing individual sera from each pool. Three-dimensional modelling allowed location of mimotopes based on analysis of electrostatic properties and solvent exposure of the Pru p 3 surface. Twenty-one phage clones were selected using Pru p 3-specific IgE, 9 of which were chosen using OAS-specific IgE while the other 12 were selected with systemic-specific IgE. Peptide alignments revealed consensus sequences for each pool: L37 R39 T40 P42 D43 R44 A46 P70 S76 P78 Y79 for OAS-IgE, and N35 N36 L37 R39 T40 D43 A46 S76 I77 P78 for systemic-IgE. These 2 consensus sequences were mapped on the same surface of Pru p 3, corresponding to the helix 2-loop-helix 3 region and part of the non-structured C-terminal coil. Thus, 2 relevant conformational IgE-binding regions of Pru p 3 were identified using a random peptide phage display library. Mimotopes can be used to study the interaction between allergens and IgE, and to accelerate the process to design new vaccines and new immunotherapy strategies.

Real Time with the Librarian: Using Web Conferencing Software to Connect to Distance Students

ERIC Educational Resources Information Center

Riedel, Tom; Betty, Paul

2013-01-01

A pilot program to provide real-time library webcasts to Regis University distance students using Adobe Connect software was initiated in fall of 2011. Previously, most interaction between librarians and online students had been accomplished by asynchronous discussion threads in the Learning Management System. Library webcasts were offered in…

How To Integrate and Manage New Technology in the Library.

ERIC Educational Resources Information Center

Becker, Joseph

1983-01-01

As technology permeates the special library, new requirements will emerge to integrate staff, equipment, and systems and establish connections between information resources and people. Being library managers in special libraries of tomorrow means mastering fundamentals of cost accounting, strategic planning, technological change, and behavioral…

Connecting Library Use to Student Success

ERIC Educational Resources Information Center

LeMaistre, Tiffany; Shi, Qingmin; Thanki, Sandip

2018-01-01

This study investigated the relationship between use of online library resources and student success at a small, teaching-focused, baccalaureate college. Researchers also measured whether library users were representative of the student population. Use of online library resources was a significant predictor of semester grade point average (GPA),…

36 CFR 701.6 - Loans of library materials for blind and other physically handicapped persons.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Loans of library materials... Property LIBRARY OF CONGRESS PROCEDURES AND SERVICES § 701.6 Loans of library materials for blind and other physically handicapped persons. (a) Program. In connection with the Library's program of service under the...

36 CFR 701.6 - Loans of library materials for blind and other physically handicapped persons.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Loans of library materials... Property LIBRARY OF CONGRESS PROCEDURES AND SERVICES § 701.6 Loans of library materials for blind and other physically handicapped persons. (a) Program. In connection with the Library's program of service under the...

Technology for Libraries.

ERIC Educational Resources Information Center

Phenix, Katharine; And Others

1990-01-01

Five articles discuss information technology in libraries: (1) "Software for Libraries" (Katharine Phenix); (2) "Online Update: European Online Services" (Martin Kesselman); (3) "Connect Time: Online Pricing Breakthroughs" (Barbara Quint); (4) "Microcomputing: Micro Biology Computer Viruses" (James LaRue);…

In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction

PubMed Central

Uhse, Simon; Pflug, Florian G.; Stirnberg, Alexandra; Ehrlinger, Klaus; von Haeseler, Arndt

2018-01-01

Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis, which is a serious bottleneck in complex biological systems. A major impediment to the success of next-generation sequencing (NGS)-based screens for virulence factors is that the genetic material of pathogens is often underrepresented within the eukaryotic host, making detection extremely challenging. We therefore established insertion Pool-Sequencing (iPool-Seq) on maize infected with the biotrophic fungus U. maydis. iPool-Seq features tagmentation, unique molecular barcodes, and affinity purification of pathogen insertion mutant DNA from in vivo-infected tissues. In a proof of concept using iPool-Seq, we identified 28 virulence factors, including 23 that were previously uncharacterized, from an initial pool of 195 candidate effector mutants. Because of its sensitivity and quantitative nature, iPool-Seq can be applied to any insertional mutagenesis library and is especially suitable for genetically complex setups like pooled infections of eukaryotic hosts. PMID:29684023

Effects of riffle length on the short-term movement of fishes among stream pools.

Treesearch

David George Lonzarich; Mary Ruth Elger Lonzrich; Melvin L. Warren

2000-01-01

Recent research has suggested that the within-habitat dynamics of fish populations and assemblages can be affected by the spatial distribution of habitats within streams. In this study, we determined the extent to which pool isolation (length of riffles connecting adjacent pools) influenced fish movement in two Arkansas streams. We marked individuals from 12 pools...

Broadband for Public Libraries: Importance, Issues, and Research Needs

ERIC Educational Resources Information Center

Mandel, Lauren H.; Bishop, Bradley Wade; McClure, Charles R.; Bertot, John Carlo; Jaeger, Paul T.

2010-01-01

U.S. public libraries provide free public internet services to the communities that they serve, but require robust, high-speed broadband internet connections to continue meeting public demands. The 2008-2009 "Public Library Funding & Technology Access Study" ("PLFTAS") illustrates challenges that public libraries encounter in achieving broadband…

Caldecott Connections to Social Studies.

ERIC Educational Resources Information Center

Glandon, Shan

The Caldecott Medal is awarded annually by the Association for Library Service to Children, a division of the American Library Association, to the U.S. artist of the most distinguished picture book for children. This activity book is based on the idea that connections with art teachers are a natural result of a focus on Caldecott Award literature,…

Connecting Libraries with Classrooms: The Curricular Roles of the Media Specialist. Second Edition

ERIC Educational Resources Information Center

Bishop, Kay

2011-01-01

This book provides an in-depth exploration of the topics that are currently relevant in K-12 curricula, including the school librarian's role in dealing with these issues, collaborating with teachers, and connecting to classrooms. The role and responsibilities of the library media specialist in the 21st century continue to expand. Since the…

36 CFR § 701.6 - Loans of library materials for blind and other physically handicapped persons.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Loans of library materials for... Property LIBRARY OF CONGRESS PROCEDURES AND SERVICES § 701.6 Loans of library materials for blind and other physically handicapped persons. (a) Program. In connection with the Library's program of service under the...

26 CFR 1.528-4 - Substantiality test.

Code of Federal Regulations, 2010 CFR

2010-04-01

... residence. Units which are used for purposes auxiliary to residential use (such as laundry areas, swimming... may be used for parking spaces, swimming pools, tennis courts, schools, fire stations, libraries...

Understanding Medical Words: A Tutorial from the National Library of Medicine

MedlinePlus

... Understanding Medical Words: A Tutorial from the National Library of Medicine To use the sharing features on ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Barrow's Living Room: How a Tribal College Library Connects Communities across the Arctic

ERIC Educational Resources Information Center

Hollingsworth, Erin

2015-01-01

More than just storerooms of information, tribal college libraries are gathering spaces that bring people together. The Tuzzy Consortium Library at IIisagvik College builds community by providing services and programs that reflect the values of Alaska's North Slope Iñupiaq people. The college library collaborates with different organizations to…

The Impact of the Academic Library on Student Success: Connecting the Dots

ERIC Educational Resources Information Center

Thorpe, Angie; Lukes, Ria; Bever, Diane J.; He, Yan

2016-01-01

In an age of assessment and accountability, academic libraries feel much pressure to prove their value according to new university measurements of student success. This study describes a methodology for how libraries may examine student interactions with services to assess whether library usage impacts student grade point averages (GPAs) and…

Library Power in Philadelphia: Final Report from Seven Case Studies.

ERIC Educational Resources Information Center

Useem, Elizabeth; Coe, Cati

Library Power seeks to activate an underutilized resource--a school's library program--in ways that promote schoolwide changes in the curriculum and instruction. This three-year initiative of the DeWitt Wallace-Readers' Digest Fund, located in 19 sites across the country, connects elementary and middle school libraries more directly to classroom…

Evaluating Internet Health Information: A Tutorial from the National Library of Medicine

MedlinePlus

... Internet Health Information: A Tutorial from the National Library of Medicine To use the sharing features on ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Library Connection Development.

ERIC Educational Resources Information Center

Berry, John N., III

1990-01-01

The John Wiley and Sons publishing company has made a commitment to publishing more tradebooks for the retail and library marketplace. As part of this expansion, Wiley has strengthened its library sales and promotion efforts and launched new publications and promotions to reach librarians. (MES)

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

Geng, J.; Nlebedim, I. C.; Besser, M. F.

A bulk combinatorial approach for synthesizing alloy libraries using laser engineered net shaping (LENS; i.e., 3D printing) was utilized to rapidly assess material systems for magnetic applications. The LENS system feeds powders in different ratios into a melt pool created by a laser to synthesize samples with bulk (millimeters) dimensions. By analyzing these libraries with autosampler differential scanning calorimeter/thermal gravimetric analysis and vibrating sample magnetometry, we are able to rapidly characterize the thermodynamic and magnetic properties of the libraries. Furthermore, the Fe-Co binary alloy was used as a model system and the results were compared with data in the literature.

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.…

Cryptic Hepatitis B and E in Patients With Acute Hepatitis of Unknown Etiology.

PubMed

Ganova-Raeva, Lilia; Punkova, Lili; Campo, David S; Dimitrova, Zoya; Skums, Pavel; Vu, Nga H; Dat, Do T; Dalton, Harry R; Khudyakov, Yury

2015-12-15

Up to 30% of acute viral hepatitis has no known etiology. To determine the disease etiology in patients with acute hepatitis of unknown etiology (HUE), serum specimens were obtained from 38 patients residing in the United Kingdom and Vietnam and from 26 healthy US blood donors. All specimens tested negative for known viral infections causing hepatitis, using commercially available serological and nucleic acid assays. Specimens were processed by sequence-independent complementary DNA amplification and next-generation sequencing (NGS). Sufficient material for individual NGS libraries was obtained from 12 HUE cases and 26 blood donors; the remaining HUE cases were sequenced as a pool. Read mapping was done by targeted and de novo assembly. Sequences from hepatitis B virus (HBV) were detected in 7 individuals with HUE (58.3%) and the pooled library, and hepatitis E virus (HEV) was detected in 2 individuals with HUE (16.7%) and the pooled library. Both HEV-positive cases were coinfected with HBV. HBV sequences belonged to genotypes A, D, or G, and HEV sequences belonged to genotype 3. No known hepatotropic viruses were detected in the tested normal human sera. NGS-based detection of HBV and HEV infections is more sensitive than using commercially available assays. HBV and HEV may be cryptically associated with HUE. Published by Oxford University Press on behalf of the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Is There a Global Role for Metropolitan City Libraries?

ERIC Educational Resources Information Center

Mason, Marilyn Gell

1994-01-01

Discusses the potential for linking large metropolitan public libraries to international interlibrary loan networks. Issues involved in international networking, including funding, standards, network connectivity, and protectionism, are discussed. Examples of libraries capable of participating and brief descriptions of their collections are given.…

Flexible CRISPR library construction using parallel oligonucleotide retrieval

PubMed Central

Read, Abigail; Gao, Shaojian; Batchelor, Eric

2017-01-01

Abstract CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval. Together, these resources provide a convenient means for individual labs to generate customized CRISPR libraries of variable size and coverage depth for functional genomics application. PMID:28334828

Books, children, dogs, artists: library programs for the entire family.

PubMed

Haver, Mary Katherine

2014-01-01

The promotion of library resources and services is a continuous process for all libraries, especially hospital family resource center libraries. Like public libraries, a family resource center can utilize programs as a pathway for connecting with and developing awareness of library resources and services available to patient families. This column describes the programs currently offered for All Children's Hospital Johns Hopkins Medicine patient families, marketing initiatives to promote these programs, and utilization of grant funding to supplement a program.

26 CFR 301.7701(i)-3 - Effective dates and duration of taxable mortgage pool classification.

Code of Federal Regulations, 2011 CFR

2011-04-01

... mortgage pool classification. 301.7701(i)-3 Section 301.7701(i)-3 Internal Revenue INTERNAL REVENUE SERVICE... § 301.7701(i)-3 Effective dates and duration of taxable mortgage pool classification. (a) Effective... connected to the entity's issuance of related debt obligations (as defined in paragraph (b)(3) of this...

L.S.C.A. Library Services & Construction Act Report for 1994. Information Partners for the 21st Century.

ERIC Educational Resources Information Center

Michigan Library, Lansing.

This annual report, consisting of 16 district summaries, demonstrates how federal Library Services and Construction Act (LSCA) funds have supported a wide range of 1994 projects to improve services in Michigan libraries. Most often these projects involved getting connected to the Internet, making the library accessible to the handicapped,…

Cultural Connections: Open Your School to the World by Partnering with a Library Abroad

ERIC Educational Resources Information Center

Mann, Carolyn

2005-01-01

What school library media coordinator could resist the opportunity to engage students in a cultural exchange with a library elsewhere in the world? Not this one. When the author saw she could use her library to inspire students in rural North Carolina to broaden their understanding of the world, she leaped at the opportunity. She linked the…

Are Self-Perception Measures Used in School Library Research Transferable to the Context of Public Library Summer Reading Programs?

ERIC Educational Resources Information Center

Arnone, Marilyn P.; Small, Ruth V.; Weng, Shicheng

2016-01-01

Several instruments previously validated for use in school library research were tested for their appropriateness in the context of public libraries' summer reading programs for youth. The researchers were also interested in whether the connection between perceived competence in one's own information skills and perceived competence in one's own…

Freebies for the Library Web.

ERIC Educational Resources Information Center

Perez, Ernest

2000-01-01

Illustrates the possibilities of freely or inexpensively connecting a library to the Internet. Discusses the advertising-supported approach; local resources for free or budget Internet resources; public access catalogs; examples of free Web materials and of libraries that have achieved a low-budget Web presence; building an effective planning…

47 CFR 54.502 - Eligible services.

Code of Federal Regulations, 2012 CFR

2012-10-01

... SERVICE Universal Service Support for Schools and Libraries § 54.502 Eligible services. (a) Supported... comprise a single library branch. Discounts are not available for internal connections in non-instructional buildings of a school or school district, or in administrative buildings of a library, to the extent that a...

Risk of malignancy in ankylosing spondylitis: a systematic review and meta-analysis.

PubMed

Deng, Chuiwen; Li, Wenli; Fei, Yunyun; Li, Yongzhe; Zhang, Fengchun

2016-08-18

Current knowledge about the overall and site-specific risk of malignancy associated with ankylosing spondylitis (AS) is inconsistent. We conducted a systematic review and meta-analysis to address this knowledge gap. Five databases (PubMed, EMBASE, Web of Science, the Cochrane library and the virtual health library) were systematically searched. A manual search of publications within the last 2 years in key journals in the field (Annals of the Rheumatic Diseases, Rheumatology and Arthritis &rheumatology) was also performed. STATA 11.2 software was used to conduct the meta-analysis. After screening, twenty-three studies, of different designs, were eligible for meta-analysis. AS is associated with a 14% (pooled RR 1.14; 95% CI 1.03-1.25) increase in the overall risk for malignancy. Compared to controls, patients with AS are at a specific increased risk for malignancy of the digestive system (pooled RR 1.20; 95% CI 1.01 to 1.42), multiple myelomas (pooled RR 1.92; 95% CI 1.37 to 3.69) and lymphomas (pooled RR 1.32; 95% CI 1.11 to 1.57). On subgroup analysis, evidence from high quality cohort studies indicated that AS patients from Asia are at highest risk for malignancy overall. Confirmation of findings from large-scale longitudinal studies is needed to identify specific risk factors and to evaluate treatment effects.

Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.

PubMed

Baym, Michael; Shaket, Lev; Anzai, Isao A; Adesina, Oluwakemi; Barstow, Buz

2016-11-10

Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction and purification of a curated whole-genome collection of single-gene transposon disruption mutants termed Knockout Sudoku. Using simple combinatorial pooling, a highly oversampled collection of mutants is condensed into a next-generation sequencing library in a single day, a 30- to 100-fold improvement over prior methods. The identities of the mutants in the collection are then solved by a probabilistic algorithm that uses internal self-consistency within the sequencing data set, followed by rapid algorithmically guided condensation to a minimal representative set of mutants, validation, and curation. Starting from a progenitor collection of 39,918 mutants, we compile a quality-controlled knockout collection of the electroactive microbe Shewanella oneidensis MR-1 containing representatives for 3,667 genes that is functionally validated by high-throughput kinetic measurements of quinone reduction.

Connecting to Special Collections of Children's Literature

ERIC Educational Resources Information Center

Brodie, Carolyn S.

2013-01-01

The Kent State University School of Library and Information Science serves as the home for two children's literature special collections. The Reinberger Children's Library Center is located on the third floor of Kent State's University Library and includes the Marantz Picturebook Collection for the Study of Picturebook Art. The Reinberger…

Using Social Networks to Create Powerful Learning Communities

ERIC Educational Resources Information Center

Lenox, Marianne; Coleman, Maurice

2010-01-01

Regular readers of "Computers in Libraries" are aware that social networks are forming increasingly important linkages to professional and personal development in all libraries. Live and virtual social networks have become the new learning playground for librarians and library staff. Social networks have the ability to connect those who are…

Personal Computing and Academic Library Design.

ERIC Educational Resources Information Center

Bazillion, Richard J.

1992-01-01

Notebook computers of increasing power and portability offer unique advantages to library users. Connecting easily to a campus data network, they are small silent work stations capable of drawing information from a variety of sources. Designers of new library buildings may assume that users in growing numbers will carry these multipurpose…

A method for high-throughput production of sequence-verified DNA libraries and strain collections.

PubMed

Smith, Justin D; Schlecht, Ulrich; Xu, Weihong; Suresh, Sundari; Horecka, Joe; Proctor, Michael J; Aiyar, Raeka S; Bennett, Richard A O; Chu, Angela; Li, Yong Fuga; Roy, Kevin; Davis, Ronald W; Steinmetz, Lars M; Hyman, Richard W; Levy, Sasha F; St Onge, Robert P

2017-02-13

The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site-specific recombination to index library DNA, and next-generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost-effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Chemical Biology Probes from Advanced DNA-encoded Libraries.

PubMed

Salamon, Hazem; Klika Škopić, Mateja; Jung, Kathrin; Bugain, Olivia; Brunschweiger, Andreas

2016-02-19

The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.

78 FR 61941 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-07

.... Applicants: Southwest Power Pool, Inc. Description: Revisions to Day-Ahead Virtual Energy Transaction Fee to...: 20130924-5121. Comments Due: 5 p.m. e.t. 10/15/13. The filings are accessible in the Commission's eLibrary...

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.

Library Services Funding Assessment

NASA Technical Reports Server (NTRS)

Lorig, Jonathan A.

2004-01-01

The Glenn Technical Library is a science and engineering library that primarily supports research activities at the Glenn Research Center, and provides selected services to researchers at all of the NASA research centers. Resources available in the library include books, journals, CD-ROMs, and access to various online sources, as well as live reference and inter-library loan services. The collection contains over 77,000 books, 800,000 research reports, and print or online access to over 1,400 journals. Currently the library operates within the Logistics and Technical Information Division, and is funded as an open-access resource within the GRC. Some of the research units at the GRC have recently requested that the library convert to a "pay-for-services" model, in which individual research units could fund only those journal subscriptions for which they have a specific need. Under this model, the library would always maintain a certain minimum level of pooled-expense services, including the ready reference and book collections, and inter-library loan services. Theoretically the "pay-for-services" model would encourage efficient financial allocation, and minimize the extent to which paid journal subscriptions go unused. However, this model also could potentially negate the benefits of group purchases for journal subscriptions and access. All of the major journal publishers offer package subscriptions that compare favorably in cost with the sum of individual subscription costs for a similar selection of titles. Furthermore, some of these subscription packages are "consortium" purchases that are funded collectively by the libraries at multiple NASA research centers; such consortia1 memberships would be difficult for the library to pay, if enough GRC research units were to withdraw their pooled contributions. cost of collectively-funded journal access with the cost of individual subscriptions. My primary task this summer is to create the cost dataset framework, and collect as much of the relevant data as possible. Hopefully this dataset will permit the research units at the GRC, and library administration as well, to make informed decisions about future library funding. Prior to the creation of the actual dataset, I established a comprehensive list of the library s print and online journal subscriptions. This list will be useful outside the context of the cost analysis project, as an addition to the library website. The cost analysis dataset s primary fields are: journal name, vendor, publisher, ISSN (International Standard Serial Number, to uniquely identify the titles), stand-alone price, and indication as to the presence of the journal in current GRC Technical Library consortium membership subscriptions. The dataset will hopefully facilitate comparisons between the stand-alone journal prices and the cost of shared journal subscriptions for groups of titles.

Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells

PubMed Central

Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

2013-01-01

A major challenge of the postgenomic era is to understand how human genes function together in normal and disease states. In microorganisms, high-density genetic interaction (GI) maps are a powerful tool to elucidate gene functions and pathways. We have developed an integrated methodology based on pooled shRNA screening in mammalian cells for genome-wide identification of genes with relevant phenotypes and systematic mapping of all GIs among them. We recently demonstrated the potential of this approach in an application to pathways controlling the susceptibility of human cells to the toxin ricin. Here we present the complete quantitative framework underlying our strategy, including experimental design, derivation of quantitative phenotypes from pooled screens, robust identification of hit genes using ultra-complex shRNA libraries, parallel measurement of tens of thousands of GIs from a single double-shRNA experiment, and construction of GI maps. We describe the general applicability of our strategy. Our pooled approach enables rapid screening of the same shRNA library in different cell lines and under different conditions to determine a range of different phenotypes. We illustrate this strategy here for single- and double-shRNA libraries. We compare the roles of genes for susceptibility to ricin and Shiga toxin in different human cell lines and reveal both toxin-specific and cell line-specific pathways. We also present GI maps based on growth and ricin-resistance phenotypes, and we demonstrate how such a comparative GI mapping strategy enables functional dissection of physical complexes and context-dependent pathways. PMID:23739767

Nutrient limitations to aquatic production along an alluvial groundwater connectivity gradient in semi-arid northwest Australia

NASA Astrophysics Data System (ADS)

Iles, Jordan; Pettit, Neil; Grierson, Pauline

2017-04-01

Primary production of intermittent streams in hot arid regions, such as the geologically ancient Pilbara region of northwest Australia, is strongly limited by both water and nutrient availability. Pulses of allochthonous materials can be significant source of nutrients and carbon during short periods of connected flow. However, during interflow periods, which may last months to years, surface water retracts to a series of surface disconnected pools, where hydrological processes including hyporheic exchange and evapo-concentration of ions are of increasing importance in maintaining bioavailable nutrients for primary production. In the Pilbara, the persistence of individual pools during interflow periods is strongly linked to local topography and connectivity to alluvial groundwater. We might thus expect that autochthonous production is greater in pools that become disconnected from groundwater due to increased concentration of nutrients. We thus investigated the importance of nitrogen (N) and phosphorus (P) limitations on aquatic production along an alluvial groundwater connectivity gradient. First, we used in-situ bottle incubations and a 13C-enriched NaHCO3 isotopic tracer to measure rates of charophyte and phytoplankton production in response to nutrient amendments. Second, we paired a nutrient diffusing substrata limitation experiment with high performance liquid chromatography to i) identify which nutrient(s) limit periphyton production, and ii) how the periphyton community structure changes within pools along the alluvial gradient. Charophyte production was 2 mg C g-1 DW h-1 while phytoplankton production was orders of magnitude less (˜0.01 mg C g-1 DW h-1). Although charophytes showed no clear respiration response to short-term nutrient addition, productivity was positively correlated to both charophyte N and P content (R2 = 0.65, p < 0.001 and R2 = 0.41, p < 0.001 respectively). This relationship was stronger in pools which were disconnected from alluvial groundwater (N: R2 = 0.92, p < 0.001 and P: R2 = 0.77, p < 0.001). Short-term phytoplankton production was N limited in some pools (F > 7.6, p < 0.009) but this was not directly linked to alluvial connectivity. The chemotaxonomic response of periphyton algae to experimental increases of biologically available N and P showed clear shifts in production and community composition, with nitrogen additions aiding in production, whilst P additions alone did not increase production and in some instances inhibited growth of some taxa. Unique photosynthetic pigment peaks were identified in each sample and matched with published values. Clearly both N and P, along with alluvial groundwater connectivity, have significant and complex roles in regulating production in these pools. Altered hydrology due to changing climate or water abstraction may thus have significant but as yet poorly understood impacts on the ecological functioning of intermittent streams.

What Drives Pakistan’s Interest in Afghanistan?

DTIC Science & Technology

2011-05-19

2010), 13. 172 Kamran Shafi, “Putting on a Brave Face and Standing Tall,” http://www.dawn.com/wps/wcm/connect/dawn-content-library/dawn/the-newspaper...columnists/ kamran -shafi- putting-on-a-brave-face-and-standing-tall-480 (accessed September 10, 2010). 59 include sanctuary, to militant...Shafi, Kamran . “Putting on a Brave Face and Standing Tall.” http://www.dawn.com/wps/wcm/connect/dawn-content-library/dawn/the- newspaper

Electronic Library and Other Technology "Connects" Anchorage Students.

ERIC Educational Resources Information Center

Davis, E. E. (Gene); Scott, Marilynn S.

1986-01-01

The Anchorage, Alaska, School District is dealing with the problem of teaching students about the "information age" through a unique program in their central library system. It was one of the first school districts in the nation to computerize its library and to provide access to computer databases to the students through telephones as…

Time Travel in the Library

ERIC Educational Resources Information Center

Brown, Donna W.

2005-01-01

A Time Travel project in the library gives enthusiasm to students to connect with the past and reinforces their research skills while instilling respect for the past years. The librarian should choose one specific decade to highlight in the library and create an extravaganza that would allow memorabilia from that time period to be located without…

2004 National Awards for Museum & Library Service

ERIC Educational Resources Information Center

Institute of Museum and Library Services, 2004

2004-01-01

The National Awards for Museum and Library Service give national recognition to institutions that play an integral and essential part in our learning society. The awards celebrate the efforts of libraries and museums of all sizes to connect with their increasingly diverse communities and to serve as centers of lifelong learning. As the pace of…

Google Scholar Usage: An Academic Library's Experience

ERIC Educational Resources Information Center

Wang, Ya; Howard, Pamela

2012-01-01

Google Scholar is a free service that provides a simple way to broadly search for scholarly works and to connect patrons with the resources libraries provide. The researchers in this study analyzed Google Scholar usage data from 2006 for three library tools at San Francisco State University: SFX link resolver, Web Access Management proxy server,…

Participatory and Transformative Engagement in Libraries and Museums: Exploring and Expanding the Salzburg Curriculum

ERIC Educational Resources Information Center

Lankes, R. David; Stephens, Michael; Arjona, Melissa

2015-01-01

During a program titled "Libraries and Museums in an Era of Participatory Culture," co-sponsored by the Salzburg Global Seminar (SGS) and the Institute of Museum and Library Services (IMLS), one of the discussion groups developed recommendations for skills needed by librarians and museum professionals in today's connected and…

The Internet: Trends and Directions.

ERIC Educational Resources Information Center

Anderson, Byron

1996-01-01

Examines current trends and directions in information technology and telecommunications. Discusses legislation; mergers and acquisitions; Internet service providers; fiscal control in libraries and the pooling of electronic information access through consortiums; demand for more bandwidth; technology selection; Internet usage patterns; the…

NREL-Led Efforts Help Bring Financing to Solar Projects - Continuum

Science.gov Websites

public investment in solar power? "There's a large pool of money that does not invest in renewable Michael Mendelsohn. To help connect that pool of money with the solar projects that need low-cost

An in vivo library-versus-library selection of optimized protein-protein interactions.

PubMed

Pelletier, J N; Arndt, K M; Plückthun, A; Michnick, S W

1999-07-01

We describe a rapid and efficient in vivo library-versus-library screening strategy for identifying optimally interacting pairs of heterodimerizing polypeptides. Two leucine zipper libraries, semi-randomized at the positions adjacent to the hydrophobic core, were genetically fused to either one of two designed fragments of the enzyme murine dihydrofolate reductase (mDHFR), and cotransformed into Escherichia coli. Interaction between the library polypeptides reconstituted enzymatic activity of mDHFR, allowing bacterial growth. Analysis of the resulting colonies revealed important biases in the zipper sequences relative to the original libraries, which are consistent with selection for stable, heterodimerizing pairs. Using more weakly associating mDHFR fragments, we increased the stringency of selection. We enriched the best-performing leucine zipper pairs by multiple passaging of the pooled, selected colonies in liquid culture, as the best pairs allowed for better bacterial propagation. This competitive growth allowed small differences among the pairs to be amplified, and different sequence positions were enriched at different rates. We applied these selection processes to a library-versus-library sample of 2.0 x 10(6) combinations and selected a novel leucine zipper pair that may be appropriate for use in further in vivo heterodimerization strategies.

Making Choices, Taking Chances, Facing Challenges, Managing Change: The Implementation of a Voice/Video/Data Network at the Alliance Library System.

ERIC Educational Resources Information Center

Wilford, Valerie J.; Logan, Lee; Bell, Lori; Cloyes, Kay

The Alliance Library System (ALS) is one of 12 regional library systems in Illinois, providing a full spectrum of support services for 300 member libraries of all types (public, school, academic, and special) located in west central Illinois. This paper describes the process by which ALS implemented a voice/video/data network connecting their four…

Interior, looking corridor connecting 511 to 515 into Medical Research ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Interior, looking corridor connecting 511 to 515 into Medical Research Library in 516. - Fitzsimons General Hospital, Central Service Building, North of Building No. 511, East of corridor connecting Building 511 to Building 515, Aurora, Adams County, CO

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

PubMed

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans; Swertz, Morris A

2016-07-15

While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect : m.a.swertz@rug.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks

PubMed Central

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K. Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans

2016-01-01

Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect. Contact: m.a.swertz@rug.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153686

Apparatus for draining lower drywell pool water into suppresion pool in boiling water reactor

DOEpatents

Gluntz, Douglas M.

1996-01-01

An apparatus which mitigates temperature stratification in the suppression pool water caused by hot water drained into the suppression pool from the lower drywell pool. The outlet of a spillover hole formed in the inner bounding wall of the suppression pool is connected to and in flow communication with one end of piping. The inlet end of the piping is above the water level in the suppression pool. The piping is routed down the vertical downcomer duct and through a hole formed in the thin wall separating the downcomer duct from the suppression pool water. The piping discharge end preferably has an elevation at or near the bottom of the suppression pool and has a location in the horizontal plane which is removed from the point where the piping first emerges on the suppression pool side of the inner bounding wall of the suppression pool. This enables water at the surface of the lower drywell pool to flow into and be discharged at the bottom of the suppression pool.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

PubMed Central

2011-01-01

Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. PMID:21794110

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

PubMed

Feltus, Frank A; Saski, Christopher A; Mockaitis, Keithanne; Haiminen, Niina; Parida, Laxmi; Smith, Zachary; Ford, James; Staton, Margaret E; Ficklin, Stephen P; Blackmon, Barbara P; Cheng, Chun-Huai; Schnell, Raymond J; Kuhn, David N; Motamayor, Juan-Carlos

2011-07-27

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Dialysis: MedlinePlus Health Topic

MedlinePlus

... Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Prevalence of chronic kidney disease- ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Bone Density: MedinePlus Health Topic

MedlinePlus

... Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Associations between bone-alkaline phosphatase ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Wilms' Tumor: MedlinePlus Health Topic

MedlinePlus

... Articles References and abstracts from MEDLINE/PubMed (National Library of Medicine) Article: Extrarenal teratoma with nephroblastoma in ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Surfing for Knowledge: Virtual Libraries and Books on the Web

ERIC Educational Resources Information Center

Wicks, Pamela

2011-01-01

Virtual environments such as Second Life (SL) may provide a way to connect with today's digital native and increase the readership of the community college student, both in virtual and real world libraries. Many colleges and universities already have a presence in SL. Books and services typically found in a "brick and mortar" library can…

Does Your Library Have an Attitude Problem towards "Marketing"? Revealing Inter-Relationship between Marketing Attitudes and Behaviour

ERIC Educational Resources Information Center

Singh, Rajesh

2009-01-01

This paper attempts to find if there is any connection between the marketing attitudes and behaviour of librarians in thirty-three different libraries of Finland. Based on market-oriented behaviour, three kinds of libraries were found: "strong," "medium" and "weak." The findings indicate a positive relation between…

Reviving a Community's Adult Education Past: A Case Study of the Library's Role in Learning

ERIC Educational Resources Information Center

Irving, Catherine J.

2010-01-01

Amidst calls for libraries to regain their socially progressive roots and connections to community, this study analyzes two interwoven cases of nonformal, community education in northeastern Nova Scotia, initiated by libraries that aimed to revive those links. Through a reading circle and a people's school, librarians used historical materials on…

South Carolina's SC LENDS: Optimizing Libraries, Transforming Lending

ERIC Educational Resources Information Center

Hamby, Rogan; McBride, Ray; Lundberg, Maria

2011-01-01

Since SC LENDS started operating in June 2009, more public libraries have come on board. All of this on the back end connects to a Mozilla-based staff client that has distributions for Mac OS X and Microsoft Windows, using SSL encryption to keep communications secure and private between remote libraries and the servers hosted at a high-end…

Block copolymer libraries: modular versatility of the macromolecular Lego system.

PubMed

Lohmeijer, Bas G G; Wouters, Daan; Yin, Zhihui; Schubert, Ulrich S

2004-12-21

The synthesis and characterization of a new 4 x 4 library of block copolymers based on polystyrene and poly(ethylene oxide) connected by an asymmetrical octahedral bis(terpyridine) ruthenium complex at the block junction are described, while initial studies on the thin film morphology of the components of the library are presented by the use of Atomic Force Microscopy, demonstrating the impact of a library approach to derive structure-property relationships.

Bulk combinatorial synthesis and high throughput characterization for rapid assessment of magnetic materials: Application of laser engineered net shaping (LENS)

DOE PAGES

Geng, J.; Nlebedim, I. C.; Besser, M. F.; ...

2016-04-15

A bulk combinatorial approach for synthesizing alloy libraries using laser engineered net shaping (LENS; i.e., 3D printing) was utilized to rapidly assess material systems for magnetic applications. The LENS system feeds powders in different ratios into a melt pool created by a laser to synthesize samples with bulk (millimeters) dimensions. By analyzing these libraries with autosampler differential scanning calorimeter/thermal gravimetric analysis and vibrating sample magnetometry, we are able to rapidly characterize the thermodynamic and magnetic properties of the libraries. Furthermore, the Fe-Co binary alloy was used as a model system and the results were compared with data in the literature.

Connecting Restricted, High-Availability, or Low-Latency Resources to a Seamless Global Pool for CMS

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Hufnagel, D.; Hurtado Anampa, K.; Jayatilaka, B.; Khan, F.; Larson, K.; Letts, J.; Mascheroni, M.; Mohapatra, A.; Marra Da Silva, J.; Mason, D.; Perez-Calero Yzquierdo, A.; Piperov, S.; Tiradani, A.; Verguilov, V.; CMS Collaboration

2017-10-01

The connection of diverse and sometimes non-Grid enabled resource types to the CMS Global Pool, which is based on HTCondor and glideinWMS, has been a major goal of CMS. These resources range in type from a high-availability, low latency facility at CERN for urgent calibration studies, called the CAF, to a local user facility at the Fermilab LPC, allocation-based computing resources at NERSC and SDSC, opportunistic resources provided through the Open Science Grid, commercial clouds, and others, as well as access to opportunistic cycles on the CMS High Level Trigger farm. In addition, we have provided the capability to give priority to local users of beyond WLCG pledged resources at CMS sites. Many of the solutions employed to bring these diverse resource types into the Global Pool have common elements, while some are very specific to a particular project. This paper details some of the strategies and solutions used to access these resources through the Global Pool in a seamless manner.

Is the time and effort worth it? One library's evaluation of using social networking tools for outreach.

PubMed

Vucovich, Lee A; Gordon, Valerie S; Mitchell, Nicole; Ennis, Lisa A

2013-01-01

Librarians are using social networking sites as one means of sharing information and connecting with users from diverse groups. Usage statistics and other metrics compiled in 2011 for the library's Facebook page, representative library blogs, and the library YouTube channel were analyzed in an effort to understand how patrons use the library's social networking sites. Librarians also hoped to get a sense of these tools' effectiveness in reaching users at the point of need and engaging them in different ways.

A University-Wide Collaborative Effort to Designing a Makerspace at an Academic Health Sciences Library.

PubMed

Herron, Jennifer; Kaneshiro, Kellie

2017-01-01

This article describes the planning and development of a 3D printing makerspace at an academic health sciences library. At the start of 2015, a new library Technology Team was formed consisting of a team leader, an emerging technologies librarian, and a library systems analyst. One of the critical steps in the development of the proposal and with the planning of this project was collaborating and partnering with different departments and units outside the library. These connections helped shape the design of the makerspace.

Iris-Claw Intraocular Lens and Scleral-Fixated Posterior Chamber Intraocular Lens Implantations in Correcting Aphakia: A Meta-Analysis.

PubMed

Jing, Wu; Guanlu, Liang; Qianyin, Zheng; Shuyi, Li; Fengying, He; Jian, Liu; Wen, Xu

2017-07-01

A meta-analysis to compare iris-claw intraocular lens (IC-IOL) and scleral-fixated posterior chamber intraocular lens (SF-PCIOL) implantations in correcting aphakia without sufficient capsular support. Eligible studies were collected through PubMed, Web of Science, Embase, and the Cochrane library. The pooled relative risks (RR), pooled standardized mean difference (SMD), and their 95% confidence interval of the eligible studies were then calculated. Seven studies met our inclusion criteria, involving 232 and 158 eyes in IC-IOL and SF-PCIOL groups, respectively. The pooled SMD of the mean postoperative corrected distance visual acuity (CDVA) (logMAR) was -0.25. The pooled RR of the eyes achieving 20/40 or better postoperatively was 1.16. The pooled SMD of the surgical time was -2.97. The pooled RR of the surgical complications was 0.86. The pooled RR of IOL dislocation, retinal detachment (RD), and cystoid macular edema (CME) between the two groups were 0.22, 0.63, and 0.64. Implantation of IC-IOL has a more simple procedure and shorter learning curve than SF-PCIOL implantation in correcting aphakia without sufficient capsular support.

Internet Use in Libraries in South East Asia with Special Reference to the Role of the Universiti Sains Malaysia Library in Promoting the Use of the Internet for Teaching and Learning.

ERIC Educational Resources Information Center

Rashidah Begum; Wong, Sook Jean

This paper studies the extent of Internet connectivity and usage among Southeast Asian libraries and how many of them are using the Internet to provide electronic information resources and services through their homepages. It also presents a case study of the Universiti Sains Malaysia (USM) Library's strategy in promoting the use of the Internet…

IJ-OpenCV: Combining ImageJ and OpenCV for processing images in biomedicine.

PubMed

Domínguez, César; Heras, Jónathan; Pascual, Vico

2017-05-01

The effective processing of biomedical images usually requires the interoperability of diverse software tools that have different aims but are complementary. The goal of this work is to develop a bridge to connect two of those tools: ImageJ, a program for image analysis in life sciences, and OpenCV, a computer vision and machine learning library. Based on a thorough analysis of ImageJ and OpenCV, we detected the features of these systems that could be enhanced, and developed a library to combine both tools, taking advantage of the strengths of each system. The library was implemented on top of the SciJava converter framework. We also provide a methodology to use this library. We have developed the publicly available library IJ-OpenCV that can be employed to create applications combining features from both ImageJ and OpenCV. From the perspective of ImageJ developers, they can use IJ-OpenCV to easily create plugins that use any functionality provided by the OpenCV library and explore different alternatives. From the perspective of OpenCV developers, this library provides a link to the ImageJ graphical user interface and all its features to handle regions of interest. The IJ-OpenCV library bridges the gap between ImageJ and OpenCV, allowing the connection and the cooperation of these two systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

In vitro optimization of truncated stem-loop II variants of the hammerhead ribozyme for cleavage in low concentrations of magnesium under non-turnover conditions.

PubMed Central

Zillmann, M; Limauro, S E; Goodchild, J

1997-01-01

By truncating helix II to two base pairs in a hammerhead ribozyme having long flanking sequences (greater than 30 bases), the rate of cleavage in 1 mM magnesium can be increased roughly 100-fold. Replacing most of the nucleotides in a typical stem-loop II with 1-4 randomized nucleotides gave an RNA library that, even before selection, was more active in 1 mM magnesium than the parent ribozyme, but considerably less active than the truncated stem-loop II ribozyme. A novel, multiround selection for intermolecular cleavage was exploited to optimize this library for cleavage in low concentrations of magnesium. After three rounds of selection at sequentially lower concentrations of magnesium, the library cleaved substrate RNA 20-fold faster than the initial pool and was cloned. This pool was heavily enriched for one particular sequence (5'-CGUG-3') that represented 16 of 52 isolates (the next most common sequence was represented only six times). This sequence also represented the most active sequence, exceeding the activity of the short helix II variant under the conditions of the selection, thereby demonstrating the effectiveness of the selection technique. Analysis of the cleavage rates of RNAs made from eight isolates having different four-base insert sequences allowed assignment of highly preferred bases at each position in the insert. Analysis of pool clones having insert of differing lengths showed that, in general, activity decreased as the length of the insert decreased from 4 to 1. This supports the suggested role of stem-loop II in stabilizing the non-Watson-Crick interactions between the conserved bases of the catalytic core. PMID:9214657

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay

PubMed Central

Jin, Zhao; Di Rienzi, Sara C.; Janzon, Anders; Werner, Jeff J.; Angenent, Largus T.; Dangl, Jeffrey L.; Fowler, Douglas M.

2015-01-01

Metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. How this diversity impacts protein function can be explored through selection assays aimed to optimize function. While artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. Here, we investigate an alternative strategy, the use of soil microbial DNA as a starting point. We demonstrate this approach by optimizing the function of a widely occurring soil bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. We identified a specific ACC deaminase domain region (ACCD-DR) that, when PCR amplified from the soil, produced a variant pool that we could swap into functional plasmids carrying ACC deaminase-encoding genes. Functional clones of ACC deaminase were selected for in a competition assay based on their capacity to provide nitrogen to Escherichia coli in vitro. The most successful ACCD-DR variants were identified after multiple rounds of selection by sequence analysis. We observed that previously identified essential active-site residues were fixed in the original unselected library and that additional residues went to fixation after selection. We identified a divergent essential residue whose presence hints at the possible use of alternative substrates and a cluster of neutral residues that did not influence ACCD performance. Using an artificial ACCD-DR variant library generated by DNA oligomer synthesis, we validated the same fixation patterns. Our study demonstrates that soil metagenomes are useful starting pools of protein-coding-gene diversity that can be utilized for protein optimization and functional characterization when synthetic libraries are not appropriate. PMID:26637602

Automation Is the Answer, but What Is the Question? Progress and Prospects for Central and Eastern European Libraries.

ERIC Educational Resources Information Center

Borgman, Christine L.

1996-01-01

Reports on a survey of 70 research libraries in Croatia, Czech Republic, Hungary, Poland, Slovakia, and Slovenia. Results show that libraries are rapidly acquiring automated processing systems, CD-ROM databases, and connections to computer networks. Discusses specific data on system implementation and network services by country and by type of…

Library Outreach to Part-Time and Distance Education Instructors

ERIC Educational Resources Information Center

Shelton, Kay

2009-01-01

As community colleges rely on part-time faculty and offer more online courses, faculty teaching in those capacities may not be as connected to the college as their full-time, on-campus counterparts. They may know very little about the library; in turn their students may not learn what the library has to offer. This article provides suggestions for…

Sharing NASA's Scientific Explorations with Communities Across the Country: A Study of Public Libraries Collaborating with NASA STEM Experts

NASA Astrophysics Data System (ADS)

Dusenbery, P.; LaConte, K.; Holland, A.; Harold, J. B.; Johnson, A.; Randall, C.; Fitzhugh, G.

2017-12-01

NASA research programs are helping humanity understand the origin and evolution of galaxies, stars, and planets, how our Sun varies and impacts the heliosphere, and defining the conditions necessary to support life beyond Earth. As places that offer their services for free, public libraries have become the "public square" by providing a place where members of a community can gather for information, educational programming, and policy discussions. Libraries are also developing new ways to engage their patrons in STEM learning. The Space Science Institute's (SSI) National Center for Interactive Learning (NCIL) was funded by NASA`s Science Mission Directorate (SMD) to develop and implement a project called NASA@ My Library: A National Earth and Space Science Initiative That Connects NASA, Public Libraries and Their Communities. NCIL's STAR Library Network (STAR_Net) is providing important leverage to expand its community of practice that serves both librarians and STEM professionals. Seventy-five libraries were selected through a competitive application process to receive NASA STEM Facilitation Kits, NASA STEM Backpacks for circulation, financial resources, training, and partnership opportunities. Initial survey data from the 75 NASA@ My Library partners showed that, while they are actively providing programming, few STEM programs connected with NASA science and engineering. With the launch of the initiative - including training, resources, and STEM-related event opportunities - all 75 libraries are engaged in offering NASA-focused programs, including with NASA subject matter experts. This talk will highlight the impacts the initiative is having on both public library partners and many others across the country.

A Multi-Threaded Cryptographic Pseudorandom Number Generator Test Suite

DTIC Science & Technology

2016-09-01

bitcoin thieves, Google releases patch. (2013, Aug. 16). SiliconANGLE. [Online]. Available: http://siliconangle.com/blog/2013/ 08/16/android-crypto-prng...flaw-aided- bitcoin -thieves-google-releases-patch/ [5] M. Gondree. (2014, Sep. 28). NPS POSIX thread pool library. [Online]. Available: https

Juvenile anadromous salmonid production in upper Columbia River side channels with different levels of hydrological connection

USGS Publications Warehouse

Martens, Kyle D.; Connolly, Patrick J.

2014-01-01

We examined the contribution of three types of side channels based on their hydrologic connectivity (seasonally disconnected, partially connected, and connected) to production of juvenile anadromous salmonids. Juvenile steelhead Oncorhynchus mykiss and Chinook Salmon O. tshawytscha were found in all three of these side channel types and in each year of the study. Upon connection with the main stem at high flows, the seasonally disconnected side channels experienced an emptying out of the previous year's fish while filling with young-of-year fish during the 2- to 4-month period of hydrologic connection. There were no differences between the densities of juvenile steelhead and Chinook Salmon and the rate of smolts produced among the three types of side channels. Recently reintroduced Coho Salmon O. kisutch had sporadic presence and abundance in partially and connected side channels, but the smolt production rate was over two times that of steelhead and Chinook Salmon in seasonally disconnected side channels. Within seasonally disconnected side channels, young-of-year salmonids in deep pools (≥100 cm) had greater survival than those in shallow pools (<100 cm). Densities of juvenile steelhead in all side channel types were similar to those in tributaries and were higher than in main-stem lateral margins. Juvenile Chinook Salmon densities were higher in side channels than in both tributary and main-stem lateral margins. Our results suggest that improving quality of pool habitat within seasonally disconnected side channels can result in improved survival for juvenile anadromous salmonids during the period of disconnection. Habitat improvement in these seasonally disconnected side channels should be recognized as a worthy restoration strategy, especially when full connectivity of side channels may not be a feasible target (e.g., through lack of water availability) or when full connectivity may present too high a risk (e.g., flooding, stream capture, bank destabilization).

What Does it Really Cost? Allocating Indirect Costs.

ERIC Educational Resources Information Center

Snyder, Herbert; Davenport, Elisabeth

1997-01-01

Better managerial control in terms of decision making and understanding the costs of a system/service result from allocating indirect costs. Allocation requires a three-step process: selecting cost objectives, pooling related overhead costs, and selecting costs bases to connect the objectives to the pooled costs. Argues that activity-based costing…

Next-generation libraries for robust RNA interference-based genome-wide screens

PubMed Central

Kampmann, Martin; Horlbeck, Max A.; Chen, Yuwen; Tsai, Jordan C.; Bassik, Michael C.; Gilbert, Luke A.; Villalta, Jacqueline E.; Kwon, S. Chul; Chang, Hyeshik; Kim, V. Narry; Weissman, Jonathan S.

2015-01-01

Genetic screening based on loss-of-function phenotypes is a powerful discovery tool in biology. Although the recent development of clustered regularly interspaced short palindromic repeats (CRISPR)-based screening approaches in mammalian cell culture has enormous potential, RNA interference (RNAi)-based screening remains the method of choice in several biological contexts. We previously demonstrated that ultracomplex pooled short-hairpin RNA (shRNA) libraries can largely overcome the problem of RNAi off-target effects in genome-wide screens. Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen sample preparation for deep sequencing. We present next-generation high-complexity libraries targeting human and mouse protein-coding genes, which we grouped into 12 sublibraries based on biological function. A pilot screen suggests that our next-generation RNAi library performs comparably to current CRISPR interference (CRISPRi)-based approaches and can yield complementary results with high sensitivity and high specificity. PMID:26080438

Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.

PubMed

Yang, Fang; Lei, Yingying; Zhou, Meiling; Yao, Qili; Han, Yichao; Wu, Xiang; Zhong, Wanshun; Zhu, Chenghang; Xu, Weize; Tao, Ran; Chen, Xi; Lin, Da; Rahman, Khaista; Tyagi, Rohit; Habib, Zeshan; Xiao, Shaobo; Wang, Dang; Yu, Yang; Chen, Huanchun; Fu, Zhenfang; Cao, Gang

2018-02-16

Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.

Public Libraries and Community-Based Education: Making the Connection for Lifelong Learning. Volume 2: Commissioned Papers. A Conference Sponsored by the National Institute on Postsecondary Education, Libraries, and Lifelong Learning, Office of Educational Research and Improvement (Washington, D.C., April 12-13, 1995).

ERIC Educational Resources Information Center

National Inst. on Postsecondary Education, Libraries, and Lifelong Learning (ED/OERI), Washington, DC.

This conference explored the relationship between the public library, community-based adult education, and lifelong learning. The eight commissioned papers presented include: "Community Based Adult Jewish Learning Program: Issues and Concerns" (Paul A. Flexner); "Rural and Small Libraries: Provisions for Lifelong Learning" (Bernard Vavrek);…

Developing Social Media to Engage and Connect at the University of Liverpool Library

ERIC Educational Resources Information Center

Chatten, Zelda; Roughley, Sarah

2016-01-01

This case study presents the Liverpool experience of using social media as an academic library to enhance audience engagement and create a community of users. It looks at the development of social media in the library, focusing on the concerted effort to grow followers and develop a meaningful use of these tools. It considers the value of taking a…

Web 2.0 as Catalyst: Virtually Reaching Out to Users and Connecting Them to Library Resources and Services

ERIC Educational Resources Information Center

Xiao, Norah

2008-01-01

This article is based on services to library users in the area of chemistry at the Science and Engineering (S&E) Library of the University of Southern California (USC), to which I applied various new technologies as outreach approaches. Various Web 2.0 technologies such as a blog, tags, YouTube, RSS feeds, Instant Messaging, online…

Effect of NaFeEDTA-Fortified Soy Sauce on Anemia Prevalence in China: A Systematic Review and Meta-analysis of Randomized Controlled Trials.

PubMed

Huo, Jun Sheng; Yin, Ji Yong; Sun, Jing; Huang, Jian; Lu, Zhen Xin; Regina, Moench-Pfanner; Chen, Jun Shi; Chen, Chun Ming

2015-11-01

To assess the effect of sodium iron ethylenediaminetetraacetate (NaFeEDTA)-fortified soy sauce on anemia prevalence in the Chinese population. A systematic review was performed to identify potential studies by searching the electronic databases of PubMed, Cochrane Library, WHO Library, HighWire, CNKI, and other sources. The selection criteria included randomized controlled trials that compared the efficacy of NaFeEDTA-fortified soy sauce with that of non-fortified soy sauce. Anemia rates and hemoglobin levels were the outcomes of interest. Inclusion decisions, quality assessment, and data extraction were performed by two reviewers independently. A total of 16 studies met the inclusion criteria for anemia rate analysis, of which 12 studies met the inclusion criteria for hemoglobin analysis. All included studies assessed the effect of NaFeEDTA-fortified soy sauce on anemia rates and hemoglobin concentrations. After the intervention, the hemoglobin concentration increased and anemia rates decreased significantly as compared with the non-fortified soy sauce groups. For anemia rates, data from 16 studies could be pooled, and the pooled estimate odds ratio was 0.25 (95% CI 0.19-0.35). For hemoglobin concentrations, data from 12 studies could be pooled, and the pooled weighted mean difference was 8.81 g/L (95% CI 5.96-11.67). NaFeEDTA-fortified soy sauce has a positive effect on anemia control and prevention in the at-risk population. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Protein and Antibody Engineering by Phage Display

PubMed Central

Frei, J.C.; Lai, J.R.

2017-01-01

Phage display is an in vitro selection technique that allows for the rapid isolation of proteins with desired properties including increased affinity, specificity, stability, and new enzymatic activity. The power of phage display relies on the phenotype-to-genotype linkage of the protein of interest displayed on the phage surface with the encoding DNA packaged within the phage particle, which allows for selective enrichment of library pools and high-throughput screening of resulting clones. As an in vitro method, the conditions of the binding selection can be tightly controlled. Due to the high-throughput nature, rapidity, and ease of use, phage display is an excellent technological platform for engineering antibody or proteins with enhanced properties. Here, we describe methods for synthesis, selection, and screening of phage libraries with particular emphasis on designing humanizing antibody libraries and combinatorial scanning mutagenesis libraries. We conclude with a brief section on troubleshooting for all stages of the phage display process. PMID:27586328

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

NASA Astrophysics Data System (ADS)

Remotigue, Michael Gerard

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

IPPF Co-operative Information Service (ICIS). August 1977.

ERIC Educational Resources Information Center

International Planned Parenthood Federation, London (England).

The pooling of documentation service resources has resulted in the creation of an International Planned Parenthood Federation (IPPF) integrated bibliographic information system. The former Library Bulletin has become IPPF Cooperative Information Service (ICIS). Entries in ICIS are classified according to the following nine categories: (0) General…

IPPF Co-operative Information Service (ICIS). May 1977.

ERIC Educational Resources Information Center

International Planned Parenthood Federation, London (England).

The pooling of documentation service resources has resulted in the creation of an International Planned Parenthood Federation (IPPF) integrated bibliographic information system. Thus, the former Library Bulletin has become IPPF Cooperative Information Service (ICIS). This is the first such publication. Entries in ICIS are classified according to…

Designing Secure Library Networks.

ERIC Educational Resources Information Center

Breeding, Michael

1997-01-01

Focuses on designing a library network to maximize security. Discusses UNIX and file servers; connectivity to campus, corporate networks and the Internet; separation of staff from public servers; controlling traffic; the threat of network sniffers; hubs that eliminate eavesdropping; dividing the network into subnets; Switched Ethernet;…

Upregulated Genes In Sporadic, Idiopathic Pulmonary Arterial Hypertension

PubMed Central

Edgar, Alasdair J; Chacón, Matilde R; Bishop, Anne E; Yacoub, Magdi H; Polak, Julia M

2006-01-01

Background To elucidate further the pathogenesis of sporadic, idiopathic pulmonary arterial hypertension (IPAH) and identify potential therapeutic avenues, differential gene expression in IPAH was examined by suppression subtractive hybridisation (SSH). Methods Peripheral lung samples were obtained immediately after removal from patients undergoing lung transplant for IPAH without familial disease, and control tissues consisted of similarly sampled pieces of donor lungs not utilised during transplantation. Pools of lung mRNA from IPAH cases containing plexiform lesions and normal donor lungs were used to generate the tester and driver cDNA libraries, respectively. A subtracted IPAH cDNA library was made by SSH. Clones isolated from this subtracted library were examined for up regulated expression in IPAH using dot blot arrays of positive colony PCR products using both pooled cDNA libraries as probes. Clones verified as being upregulated were sequenced. For two genes the increase in expression was verified by northern blotting and data analysed using Student's unpaired two-tailed t-test. Results We present preliminary findings concerning candidate genes upregulated in IPAH. Twenty-seven upregulated genes were identified out of 192 clones examined. Upregulation in individual cases of IPAH was shown by northern blot for tissue inhibitor of metalloproteinase-3 and decorin (P < 0.01) compared with the housekeeping gene glyceraldehydes-3-phosphate dehydrogenase. Conclusion Four of the up regulated genes, magic roundabout, hevin, thrombomodulin and sucrose non-fermenting protein-related kinase-1 are expressed specifically by endothelial cells and one, muscleblind-1, by muscle cells, suggesting that they may be associated with plexiform lesions and hypertrophic arterial wall remodelling, respectively. PMID:16390543

Pop-up exhibits as an outreach tool: Connecting academic and public audiences with library resources

NASA Astrophysics Data System (ADS)

Powell, S.; Teplitzky, S.

2016-12-01

Subject specialty libraries like the Earth Sciences and Map Library at UC Berkeley thrive on active user communities, but promoting awareness of resources and services can be slow and time-consuming. In Fall 2014, two new librarians there introduced a series of monthly pop-up exhibits called "Maps and More" in order to help build that community. Now in their third year, the show-and-tell sessions are designed to lure visitors into the library and spark new connections among students, researchers and librarians, and renewed engagement with library collections. The librarians surveyed participants in spring 2015 and fall 2016 to assess the impact of "Maps and More" in terms of visitors' perception of the events and awareness of library services and materials. One significant finding from the spring 2015 survey is that a quarter of respondents had never been to the Earth Sciences and Map Library before the session. The exhibits draw in participants from a range of departments, including significant numbers from Seismology, Earth and Planetary Science, Geography, as well as members of the public. Sessions held on Cal Day - the university's annual public open house with 30-40,000 public visitors - were particularly good outreach experiences. Partnerships with other units have great potential for expanding the reach of these events. The Maps and More exhibits have proven to be a successful outreach tool for raising the profile of the library collections and services and helping users understand maps as research materials.

Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli.

PubMed

Oesterle, Sabine; Gerngross, Daniel; Schmitt, Steven; Roberts, Tania Michelle; Panke, Sven

2017-09-26

Multiplexed gene expression optimization via modulation of gene translation efficiency through ribosome binding site (RBS) engineering is a valuable approach for optimizing artificial properties in bacteria, ranging from genetic circuits to production pathways. Established algorithms design smart RBS-libraries based on a single partially-degenerate sequence that efficiently samples the entire space of translation initiation rates. However, the sequence space that is accessible when integrating the library by CRISPR/Cas9-based genome editing is severely restricted by DNA mismatch repair (MMR) systems. MMR efficiency depends on the type and length of the mismatch and thus effectively removes potential library members from the pool. Rather than working in MMR-deficient strains, which accumulate off-target mutations, or depending on temporary MMR inactivation, which requires additional steps, we eliminate this limitation by developing a pre-selection rule of genome-library-optimized-sequences (GLOS) that enables introducing large functional diversity into MMR-proficient strains with sequences that are no longer subject to MMR-processing. We implement several GLOS-libraries in Escherichia coli and show that GLOS-libraries indeed retain diversity during genome editing and that such libraries can be used in complex genome editing operations such as concomitant deletions. We argue that this approach allows for stable and efficient fine tuning of chromosomal functions with minimal effort.

Characterizing convective cold pools: Characterizing Convective Cold Pools

DOE PAGES

Drager, Aryeh J.; van den Heever, Susan C.

2017-05-09

Cold pools produced by convective storms play an important role in Earth's climate system. However, a common framework does not exist for objectively identifying convective cold pools in observations and models. The present study investigates convective cold pools within a simulation of tropical continental convection that uses a cloud-resolving model with a coupled land-surface model. Multiple variables are assessed for their potential in identifying convective cold pool boundaries, and a novel technique is developed and tested for identifying and tracking cold pools in numerical model simulations. This algorithm is based on surface rainfall rates and radial gradients in the densitymore » potential temperature field. The algorithm successfully identifies near-surface cold pool boundaries and is able to distinguish between connected cold pools. Once cold pools have been identified and tracked, composites of cold pool evolution are then constructed, and average cold pool properties are investigated. Wet patches are found to develop within the centers of cold pools where the ground has been soaked with rainwater. These wet patches help to maintain cool surface temperatures and reduce cold pool dissipation, which has implications for the development of subsequent convection.« less

Characterizing convective cold pools: Characterizing Convective Cold Pools

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

Drager, Aryeh J.; van den Heever, Susan C.

Cold pools produced by convective storms play an important role in Earth's climate system. However, a common framework does not exist for objectively identifying convective cold pools in observations and models. The present study investigates convective cold pools within a simulation of tropical continental convection that uses a cloud-resolving model with a coupled land-surface model. Multiple variables are assessed for their potential in identifying convective cold pool boundaries, and a novel technique is developed and tested for identifying and tracking cold pools in numerical model simulations. This algorithm is based on surface rainfall rates and radial gradients in the densitymore » potential temperature field. The algorithm successfully identifies near-surface cold pool boundaries and is able to distinguish between connected cold pools. Once cold pools have been identified and tracked, composites of cold pool evolution are then constructed, and average cold pool properties are investigated. Wet patches are found to develop within the centers of cold pools where the ground has been soaked with rainwater. These wet patches help to maintain cool surface temperatures and reduce cold pool dissipation, which has implications for the development of subsequent convection.« less

7 CFR 993.159 - Payments for services performed with respect to reserve tonnage prunes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (natural condition rate) for necessary services rendered by the handler in connection with such prunes so... year when the Committee recommends a reserve pool (except the Committee may extend this date by not... tonnage prunes. The Committee will compute the average industry cost for holding reserve pool prunes by...

7 CFR 993.159 - Payments for services performed with respect to reserve tonnage prunes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (natural condition rate) for necessary services rendered by the handler in connection with such prunes so... year when the Committee recommends a reserve pool (except the Committee may extend this date by not... tonnage prunes. The Committee will compute the average industry cost for holding reserve pool prunes by...

45 CFR 148.310 - Eligibility requirements for a grant.

Code of Federal Regulations, 2011 CFR

2011-10-01

... more coverage options through the pool. (d) The pool has in effect a mechanism reasonably designed to ensure continued funding of losses incurred by the State after the end of each fiscal year for which the State applies for Federal Funding in fiscal year (FY) 2005 through FY 2010 in connection with the...

45 CFR 148.310 - Eligibility requirements for a grant.

Code of Federal Regulations, 2012 CFR

2012-10-01

... more coverage options through the pool. (d) The pool has in effect a mechanism reasonably designed to ensure continued funding of losses incurred by the State after the end of each fiscal year for which the State applies for Federal Funding in fiscal year (FY) 2005 through FY 2010 in connection with the...

The Principles of Marketing and Relationship Management.

ERIC Educational Resources Information Center

Soules, Aline

2001-01-01

Discusses the concepts of marketing and relationship management as they apply to libraries. Topics include perceptions of the profession; environments that libraries operate in; connecting content and users through access and services; and the need for reliable and consistent collection of effective data. (Author/LRW)

Integrating the Learning of Mathematics and Science Using Interactive Teaching and Learning Strategies

NASA Astrophysics Data System (ADS)

Holmes, Mark H.

2006-10-01

To help students grasp the intimate connections that exist between mathematics and its applications in other disciplines a library of interactive learning modules was developed. This library covers the mathematical areas normally studied by undergraduate students and is used in science courses at all levels. Moreover, the library is designed not just to provide critical connections across disciplines but to also provide longitudinal subject reinforcement as students progress in their studies. In the process of developing the modules a complete editing and publishing system was constructed that is optimized for automated maintenance and upgradeability of materials. The result is a single integrated production system for web-based educational materials. Included in this is a rigorous assessment program, involving both internal and external evaluations of each module. As will be seen, the formative evaluation obtained during the development of the library resulted in the modules successfully bridging multiple disciplines and breaking down the disciplinary barriers commonly found in their math and non-math courses.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

PubMed Central

Woodruff, Lauren B. A.; Gorochowski, Thomas E.; Roehner, Nicholas; Densmore, Douglas; Gordon, D. Benjamin; Nicol, Robert

2017-01-01

Abstract Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated. PMID:28007941

Evaluation of proteases and protease inhibitors in Heterodera glycines cysts obtained from laboratory and field populations

USDA-ARS?s Scientific Manuscript database

Proteases and proteases inhibitors were evaluated in a number of preparations of Heterodera glycines cysts obtained from glasshouse cultures (GH) and field (LR) populations. Using a FRET-peptide library comprising 512 peptide substrate pools that detect 4 endoprotease types (aspartic, cysteine, meta...

Planning and Implementing Technical Services Workstations.

ERIC Educational Resources Information Center

Kaplan, Michael, Ed.

The job of the library cataloger has grown increasingly complex. Catalogers must draw from a vast pool of dynamic information as they handle traditional and new forms of media. Technical Services Workstations (TSWs) provide catalogers the network data, application programs, and standard hardware required to catalog all types of media quickly and…

Laptop Circulation at Eastern Washington University

ERIC Educational Resources Information Center

Munson, Doris; Malia, Elizabeth

2008-01-01

In 2001, Eastern Washington University's Libraries began a laptop circulation program with seventeen laptops. Today, there are 150 laptops in the circulation pool, as well as seventeen digital cameras, eleven digital handycams, and thirteen digital projectors. This article explains how the program has grown to its present size, the growing pains…

Consortia Building: A Handshake and a Smile, Island Style.

ERIC Educational Resources Information Center

Cutright, Patricia J.

2000-01-01

Discussion of library consortia focuses on the collaborative efforts in the Federated States of Micronesia that will enhance library services through staff training and educating while utilizing innovative technology. Highlights include background and socioeconomic overview; a project that addresses automation and Internet connectivity issues; and…

Lifecycle Librarianship

ERIC Educational Resources Information Center

Crowley, Bill

2008-01-01

In a time when information self-service and enhanced competition have sent libraries of all types into an oftentimes desperate search for a renewed sense of purpose, a fundamentally important question takes center stage: How can libraries connect with the deepest aspirations of their service communities? This article describes a new library…

Public Access Workstations in the Library: New Trends.

ERIC Educational Resources Information Center

Beecher, Henry

1991-01-01

Discusses the use of microcomputer-based workstations that are provided for public access in libraries. Criteria for workstations are discussed, including standard hardware, open-design software, scalable interface, and connectivity options for networking; systems that provide full-text access are described; and the need for standards is…

New Hampshire: The Automated Information System.

ERIC Educational Resources Information Center

Wiggin, Kendall F.

1996-01-01

Reviews statewide multitype library automation and connectivity initiatives in New Hampshire. Topics include an information system incorporating a union catalog, interlibrary loan, electronic mail, CD-ROM databases, and Internet access; state government information on the World Wide Web through the state library; OCLC FirstSearch access; and a…

Novel high throughput pooled shRNA screening identifies NQO1 as a potential drug target for host directed therapy for tuberculosis

PubMed Central

Li, Qing; Karim, Ahmad F.; Ding, Xuedong; Das, Biswajit; Dobrowolski, Curtis; Gibson, Richard M.; Quiñones-Mateu, Miguel E.; Karn, Jonathan; Rojas, Roxana E.

2016-01-01

Chemical regulation of macrophage function is one key strategy for developing host-directed adjuvant therapies for tuberculosis (TB). A critical step to develop these therapies is the identification and characterization of specific macrophage molecules and pathways with a high potential to serve as drug targets. Using a barcoded lentivirus-based pooled short-hairpin RNA (shRNA) library combined with next generation sequencing, we identified 205 silenced host genes highly enriched in mycobacteria-resistant macrophages. Twenty-one of these “hits” belonged to the oxidoreductase functional category. NAD(P)H:quinone oxidoreductase 1 (NQO1) was the top oxidoreductase “hit”. NQO1 expression was increased after mycobacterial infection, and NQO1 knockdown increased macrophage differentiation, NF-κB activation, and the secretion of pro-inflammatory cytokines TNF-α and IL-1β in response to infection. This suggests that mycobacteria hijacks NQO1 to down-regulate pro-inflammatory and anti-bacterial functions. The competitive inhibitor of NQO1 dicoumarol synergized with rifampin to promote intracellular killing of mycobacteria. Thus, NQO1 is a new host target in mycobacterial infection that could potentially be exploited to increase antibiotic efficacy in vivo. Our findings also suggest that pooled shRNA libraries could be valuable tools for genome-wide screening in the search for novel druggable host targets for adjunctive TB therapies. PMID:27297123

Patterns of Spinal Sensory-Motor Connectivity Prescribed by a Dorsoventral Positional Template

PubMed Central

Sürmeli, Gülşen; Akay, Turgay; Ippolito, Gregory; Tucker, Philip W; Jessell, Thomas M

2011-01-01

Summary Sensory-motor circuits in the spinal cord are constructed with a fine specificity that coordinates motor behavior, but the mechanisms that direct sensory connections with their motor neuron partners remain unclear. The dorsoventral settling position of motor pools in the spinal cord is known to match the distal-to-proximal position of their muscle targets in the limb, but the significance of invariant motor neuron positioning is unknown. An analysis of sensory-motor connectivity patterns in FoxP1 mutant mice, where motor neuron position has been scrambled, shows that the final pattern of sensory-motor connections is initiated by the projection of sensory axons to discrete dorsoventral domains of the spinal cord without regard for motor neuron subtype, or indeed, the presence of motor neurons. By implication, the clustering and dorsoventral settling position of motor neuron pools serves as a determinant of the pattern of sensory input specificity, and thus motor coordination. PMID:22036571

Connecting with health science students and faculty to facilitate the design of a mobile library website.

PubMed

Grabowsky, Adelia; Wright, Melissa

2013-01-01

Observing increasing usage of smartphones by students and faculty of the University of Mississippi Medical Center, librarians at Rowland Medical Library decided to explore student and faculty interest in a mobile website for the library. Focus groups were held to examine interest in a site, essential resources to include on a site, and format of the site itself. The study found significant interest in the development of a mobile library website; additionally, participants believed it essential that the site be simple and easy to use and that only certain library resources should be included on the site.

Librarian participation in expanding the pool of potential medical students.

PubMed

Guerrieri, Rose

2012-01-01

This article reports on the results of an exploratory survey to determine if librarians actively participate in medical school student recruiting programs. It looks specifically at what librarians are doing to assist with recruitment and what biomedical career resources their libraries offer. The survey link was e-mailed to all U.S. medical school library directors, who were asked to forward it to the appropriate librarian. Out of 113 medical schools, 68 (60%) responded to most questions. Forty-three (86%) of 50 item respondents do participate in such activities, and 29 (67%) of 43 item respondents have been doing so for more than five years. Thirty-two (64%) of 50 item respondents provide resources on biomedical careers in the libraries. Copyright © Taylor & Francis Group, LLC

Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata.

PubMed

Fracassetti, Marco; Griffin, Philippa C; Willi, Yvonne

2015-01-01

Sequencing pooled DNA of multiple individuals from a population instead of sequencing individuals separately has become popular due to its cost-effectiveness and simple wet-lab protocol, although some criticism of this approach remains. Here we validated a protocol for pooled whole-genome re-sequencing (Pool-seq) of Arabidopsis lyrata libraries prepared with low amounts of DNA (1.6 ng per individual). The validation was based on comparing single nucleotide polymorphism (SNP) frequencies obtained by pooling with those obtained by individual-based Genotyping By Sequencing (GBS). Furthermore, we investigated the effect of sample number, sequencing depth per individual and variant caller on population SNP frequency estimates. For Pool-seq data, we compared frequency estimates from two SNP callers, VarScan and Snape; the former employs a frequentist SNP calling approach while the latter uses a Bayesian approach. Results revealed concordance correlation coefficients well above 0.8, confirming that Pool-seq is a valid method for acquiring population-level SNP frequency data. Higher accuracy was achieved by pooling more samples (25 compared to 14) and working with higher sequencing depth (4.1× per individual compared to 1.4× per individual), which increased the concordance correlation coefficient to 0.955. The Bayesian-based SNP caller produced somewhat higher concordance correlation coefficients, particularly at low sequencing depth. We recommend pooling at least 25 individuals combined with sequencing at a depth of 100× to produce satisfactory frequency estimates for common SNPs (minor allele frequency above 0.05).

Hydrology and landscape connectivity of vernal pools. Chapter 3.

Treesearch

Scott G. Liebowitz; Robert T. Brooks

2008-01-01

Hydrology is fundamental to wetland establishment and maintenance of wetland processes (Cole et al. 2002). Hydrology has been shown to affect, if not control, many aspects of wetland ecology, including litter decomposition and the accumulation of organic matter and sediment (Barlocher et al. 1978), the composition and productivity of pool fauna (Paton and Couch 2002),...

17 CFR 200.20b - Director of Division of Investment Management.

Code of Federal Regulations, 2011 CFR

2011-04-01

... registered under the Investment Company Act of 1940 (15 U.S.C. 80a-1 et seq.) and pooled investment funds or... registered under the Investment Company Act of 1940 and pooled investment funds or accounts in connection... Investment Management. 200.20b Section 200.20b Commodity and Securities Exchanges SECURITIES AND EXCHANGE...

CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens.

PubMed

Michlits, Georg; Hubmann, Maria; Wu, Szu-Hsien; Vainorius, Gintautas; Budusan, Elena; Zhuk, Sergei; Burkard, Thomas R; Novatchkova, Maria; Aichinger, Martin; Lu, Yiqing; Reece-Hoyes, John; Nitsch, Roberto; Schramek, Daniel; Hoepfner, Dominic; Elling, Ulrich

2017-12-01

Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.

Computer Literacy and the Library: A New Connection.

ERIC Educational Resources Information Center

Fenske, Rachel F.

1998-01-01

Describes a program at Eastern Washington University that integrates library skills as a component of the English composition program, and is part of a computer-literacy program stemming from a general-education curriculum reform. Discusses program development and design, assessment of student learning, and effectiveness of the program. (LRW)

Connecting and Reflecting: Transformative Learning in Academic Libraries

ERIC Educational Resources Information Center

Hooper, Michaela D. Willi; Scharf, Emily

2017-01-01

This literature review is intended to examine transformative learning within the context of academic libraries and its applications for librarians. Although the main audience is academic librarians who facilitate student learning, it may also be of interest to other practitioners and researchers who are interested in applying transformative…

Perspectives on Information Literacy: A Framework for Conceptual Understanding

ERIC Educational Resources Information Center

Addison, Colleen; Meyers, Eric

2013-01-01

Information literacy, 40 years since the term was coined, remains a conceptually contested aspect of library and information science research. This paper uses a review of the literature related to the concept of information literacy to identify three different perspectives, their historical origins, and connection to library and information…

Building Connections, Collections, and Communities: Increasing the Visibility and Impact of Extension through Institutional Repositories

ERIC Educational Resources Information Center

Inefuku, Harrison W.; Franz, Nancy K.

2015-01-01

Over the past 20 years, university libraries have developed and manage institutional repositories--digital libraries that provide free, public access to the research, scholarship, and publications of their university's faculty, staff, and students. Although underused by Extension professionals, institutional repositories are powerful tools that…

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…

Capital City Column.

ERIC Educational Resources Information Center

Carter, Carl

1994-01-01

Provides a suggested model for SCHOOLNET, a voice, video, and data network. Proposes that library media centers should be the site of the SCHOOLNET hub; students and teachers should be able to access the INFOhio library automation system and other information systems; and digital fiber optic hubs and trunk lines should connect school buildings…

Cura Personalis: The School Library through an Ignatian Lens

ERIC Educational Resources Information Center

Bogel, Gayle

2012-01-01

Effective school libraries provide services that are based on meeting each individual's need for information. Information needs arise from both immediate and global communities--from the school building to the "flat world" of online connections. The strategy for successfully engaging individuals as lifelong learners begins with acknowledging the…

Six Degrees of Information Seeking: Stanley Milgram and the Small World of the Library

ERIC Educational Resources Information Center

James, Kathryn

2006-01-01

Stanley Milgram's 1967 "small world" social connectivity study is used to analyze information connectivity, or patron information-seeking behavior. The "small world" study, upon examination, offers a clear example of the failure of social connectivity. This failure is used to highlight the importance of the subjectivities of patron experience of…

Production of a Human Antibody Library in the Phage-Display Vector pSEX81.

PubMed

Welschof, M; Little, M; Dörsam, H

1998-01-01

Human monoclonal antibodies (MAbs) are more suitable than MAbs of animal origin for clinical applications because of lower hypersensitivity reactions, less formation of circulating immune complexes and lower anti-immunoglobulin responses The classical production of human MAbs via the hybridoma technique or Epstein-Barr virus (EBV) transformation is limited by the instability of cell lines, low antibody production, and the problems of imununizing humans with certain antigens (1,2). A promising alternative 1s the production of human recombinant antibodies (3). Recombinant DNA technology has made it possible to clone human antibody genes in vectors and to generate antibody expression libraries (4-7). One approach has been to amplify and recombine the IgG repertoire of an "immunized" donor. This has been used to isolate several antibodies related to diseases (8,9). In order to obtain more universal antibody libraries the naive IgM repertoire of several "unimmunized" donors were pooled (10,12). The complexity of the combinatorial libraries has been further increased by creating the so-called "semisynthetic" antibody libraries (22-14).

A broad-group cross-section library based on ENDF/B-VII.0 for fast neutron dosimetry Applications

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

Alpan, F.A.

2011-07-01

A new ENDF/B-VII.0-based coupled 44-neutron, 20-gamma-ray-group cross-section library was developed to investigate the latest evaluated nuclear data file (ENDF) ,in comparison to ENDF/B-VI.3 used in BUGLE-96, as well as to generate an objective-specific library. The objectives selected for this work consisted of dosimetry calculations for in-vessel and ex-vessel reactor locations, iron atom displacement calculations for reactor internals and pressure vessel, and {sup 58}Ni(n,{gamma}) calculation that is important for gas generation in the baffle plate. The new library was generated based on the contribution and point-wise cross-section-driven (CPXSD) methodology and was applied to one of the most widely used benchmarks, themore » Oak Ridge National Laboratory Pool Critical Assembly benchmark problem. In addition to the new library, BUGLE-96 and an ENDF/B-VII.0-based coupled 47-neutron, 20-gamma-ray-group cross-section library was generated and used with both SNLRML and IRDF dosimetry cross sections to compute reaction rates. All reaction rates computed by the multigroup libraries are within {+-} 20 % of measurement data and meet the U. S. Nuclear Regulatory Commission acceptance criterion for reactor vessel neutron exposure evaluations specified in Regulatory Guide 1.190. (authors)« less

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

Connection Development: Web Lessons from Westchester.

ERIC Educational Resources Information Center

Freedman, Maurice J.

1996-01-01

Committed to utilizing information technology, the Westchester Library System (New York) made the World Wide Web publicly accessible. Describes the planning, implementation, and management process; obstacles involving financing; establishing Internet connectivity; and vendor negotiations. Westchester hired a Web manager, created Internet use…

President Clinton's Statement on the Comprehensive Nuclear Test Ban Treaty

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

Clinton, Bill

This is video footage of President Clinton delivering a statement to the press on signing the Comprehensive Nuclear Test Ban Treaty and answering press pool questions before departing Kansas City, Missouri. This footage is official public record produced by the White House Television (WHTV) crew, provided by the Clinton Presidential Library.

Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms.

PubMed

Milnthorpe, Andrew T; Soloviev, Mikhail

2011-04-15

The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries. We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selected libraries and may omit genes found within the libraries. Other errors include the incorrect estimation of the significance values and inaccurate settings for the library size cut-off values. We advocated a revised approach to finding libraries associated with tissues. In doing so, libraries from dependent or irrelevant tissues do not get included in the final library pool. We also revised the method for determining the presence or absence of a gene by searching the UniGene relational database, revised calculation of statistical significance and sorted the library cut-off filter. Our results justify re-evaluation of all previously reported results where NCBI CGAP expression data and tools were used.

Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms

PubMed Central

2011-01-01

Background The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries. Results We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selected libraries and may omit genes found within the libraries. Other errors include the incorrect estimation of the significance values and inaccurate settings for the library size cut-off values. We advocated a revised approach to finding libraries associated with tissues. In doing so, libraries from dependent or irrelevant tissues do not get included in the final library pool. We also revised the method for determining the presence or absence of a gene by searching the UniGene relational database, revised calculation of statistical significance and sorted the library cut-off filter. Conclusion Our results justify re-evaluation of all previously reported results where NCBI CGAP expression data and tools were used. PMID:21496233

E-library Implementation in Library University of Riau

NASA Astrophysics Data System (ADS)

Yuhelmi; Rismayeti

2017-12-01

This research aims to see how the e-book implementation in Library University of Riau and the obstacle in its implementation. In the Globalization era, digital libraries should be developed or else it will decrease the readers’ interest, with the recent advanced technology, digital libraries are one of the learning tools that can be used to finding an information through the internet access, hence digital libraries or commonly known as E-Library is really helping the students and academic community in finding information. The methods that used in this research is Observation, Interview, and Literature Study. The respondents in this research are the staff who involved in the process of digitization in Library University of Riau. The result of this research shows that implementation of e-library in Library University of Riau is already filled the user needs for now, although there is obstacle faced just like technical problems for example the internet connection speed and the technical problem to convert the format from Microsoft Word .doc to Adobe.pdf

NASA's Coordinated Efforts to Enhance STEM Education: Bringing NASA Science into the Library

NASA Astrophysics Data System (ADS)

Meinke, B. K.; Thomas, C.; Eyermann, S.; Mitchell, S.; LaConte, K.; Hauck, K.

2015-11-01

Libraries are community-centered, free-access venues serving learners of all ages and backgrounds. Libraries also recognize the importance of science literacy and strive to include science in their programming portfolio. Scientists and educators can partner with local libraries to advance mutual goals of connecting the public to Earth and Space Science. In this interactive Special Interest Group (SIG) discussion, representatives from the NASA Science Mission Directorate (SMD) Education and Public Outreach (EPO) community's library collaborations discussed the opportunities for partnership with public and school libraries; explored the resources, events, and programs available through libraries; explored NASA science programming and professional development opportunities available for librarians; and strategized about the types of support that librarians require to plan and implement programs that use NASA data and resources. We also shared successes, lessons learned, and future opportunities for incorporating NASA science programming into library settings.

Hydrology of the Floral City Pool of Tsala Apopka Lake, west-central Florida

USGS Publications Warehouse

Bradner, L.A.

1988-01-01

Tsala Apopka Lake, in west-central Florida, has an area of about 19,000 acres and is divided into three water-management pools, with the Floral City Pool, the most upgradient. The Floral City Pool, which has a surface area of approximately 4,750 acres, contains an extensive combination of lakes, wetlands, and connecting canals. The Pool receives inflow from the Withlacoochee River through two canals. Outflow is through one manmade canal and one natural slough. Canal flow is partially controlled by manmade structures. A cumulative deficit of 19.4 inches of rainfall from August 1984 through May 1985 reduced surface-water inflow to the Floral City Pool to about 0.5 cu ft/sec by May 1985. During May 1985, pool levels declined approximately 0.04 ft/day. By the end of May, there was no observable outflow. From June 1985 through September 1985, 39.8 inches of rainfall caused above-average inflow to the Floral City Pool and a pool-level increase of 6.2 ft. The inflow of 340 CFS nearly equaled the outflow of 338 CFS by the end of September. (USGS)

Protein and Antibody Engineering by Phage Display.

PubMed

Frei, J C; Lai, J R

2016-01-01

Phage display is an in vitro selection technique that allows for the rapid isolation of proteins with desired properties including increased affinity, specificity, stability, and new enzymatic activity. The power of phage display relies on the phenotype-to-genotype linkage of the protein of interest displayed on the phage surface with the encoding DNA packaged within the phage particle, which allows for selective enrichment of library pools and high-throughput screening of resulting clones. As an in vitro method, the conditions of the binding selection can be tightly controlled. Due to the high-throughput nature, rapidity, and ease of use, phage display is an excellent technological platform for engineering antibody or proteins with enhanced properties. Here, we describe methods for synthesis, selection, and screening of phage libraries with particular emphasis on designing humanizing antibody libraries and combinatorial scanning mutagenesis libraries. We conclude with a brief section on troubleshooting for all stages of the phage display process. © 2016 Elsevier Inc. All rights reserved.

Hierarchy and extremes in selections from pools of randomized proteins

PubMed Central

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-01-01

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different “frameworks” typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution). PMID:26969726

Hierarchy and extremes in selections from pools of randomized proteins.

PubMed

Boyer, Sébastien; Biswas, Dipanwita; Kumar Soshee, Ananda; Scaramozzino, Natale; Nizak, Clément; Rivoire, Olivier

2016-03-29

Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different "frameworks" typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution).

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

PubMed

Woodruff, Lauren B A; Gorochowski, Thomas E; Roehner, Nicholas; Mikkelsen, Tarjei S; Densmore, Douglas; Gordon, D Benjamin; Nicol, Robert; Voigt, Christopher A

2017-02-17

Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Inventory of Anchialine Pools in Hawaii's National Parks

USGS Publications Warehouse

Foote, David

2005-01-01

BACKGROUND Anchialine (?near the sea?) pools are rare and localized brackish waters along coastal lava flows that exhibit tidal fluctuations without a surface connection with the ocean (Fig. 1). In Hawai`i, these pools were frequently excavated or otherwise modified by Hawaiians to serve as sources of drinking water, baths and fish ponds. National Parks in Hawai`i possess the full spectrum of pool types, from walled fish ponds to undisturbed pools in collapsed lava tubes, cracks and caves. Pools contain relatively rare and unique fauna threatened primarily by invasive species and habitat loss. In collaboration with the National Park Service?s Inventory and Monitoring Program, the U.S. Geological Survey?s Pacific Island Ecosystems Research Center undertook inventories of these unique ecosystems in two National Parks on the island of Hawai`i: Hawai`i Volcanoes National Park and Kaloko-Honokohau National Historical Park.

The Imagination Library Program: Increasing Parental Reading through Book Distribution

ERIC Educational Resources Information Center

Ridzi, Frank; Sylvia, Monica R.; Singh, Sunita

2014-01-01

Research has established a connection between print exposure and reading skills. The authors examined the impact of book access on print exposure via a monthly book distribution program. At 10 months of implementation, 170 families enrolled in the Imagination Library Program in Syracuse, New York responded to a survey. Results indicated that…

Keeping Current. Ideas, Information, and Organization: Connecting Information Literacy and Writing

ERIC Educational Resources Information Center

Thompson, Helen M.

2005-01-01

With the current focus on writing across the curriculum and the emphasis on schoolwide writing programs, perhaps library media specialists should consider adding writing instruction to the learning that takes place in the library media center. The teaching of writing should be a natural extension of the teaching of information literacy. Both…

In the Curriculum. Health: Mental Agility and Memory; Reading/Language Arts: The Writer/Reader Connection; Science: Stars.

ERIC Educational Resources Information Center

Robinson, Alice A.

2003-01-01

Provides six library media activities that are designed for use with specific curriculum units in health, science, language arts, and social studies. Each activity identifies library media skills and curriculum objectives, grade levels, resources, instructional roles, procedures, evaluation guidelines, and follow-up activities. (AEF)

Investigating a Student-Driven Taxonomy for Library Website Design

ERIC Educational Resources Information Center

Hulseberg, Anna; Monson, Sarah

2011-01-01

Libraries spend countless hours developing websites to connect users and resources. However, how much do we really know about what website terminology and features are meaningful to our patrons? And how can we best organize websites to facilitate access to resources? This article examines these questions by presenting a case study of a…

Local Places, Global Connections: Libraries in the Digital Age. What's Going On Series.

ERIC Educational Resources Information Center

Benton Foundation, Washington, DC.

Libraries have long been pivotal community institutions--public spaces where people can come together to learn, reflect, and interact. Today, information is rapidly spreading beyond books and journals to digital government archives, business databases, electronic sound and image collections, and the flow of electronic impulses over computer…

Making Connections: Outreach to Preschoolers through Satellite Library Collections.

ERIC Educational Resources Information Center

Bagley, Norman E., IV

2000-01-01

Describes a program at the Waterford Public Library (New York) that expanded existing outreach efforts to children in local preschools and a local childcare center, while adding services to a preschool play group. Discusses costs, the creation of story kits that included picture books and related activities, and evaluation results. (Contains 16…

Using Wireless Devices to Enhance Reference and Information Services

ERIC Educational Resources Information Center

Forsyth, Ellen

2006-01-01

A growing number of libraries have installed wireless data connections as a way of providing access to the Internet for members of the public. Some libraries have used their wireless networks to enable staff to use wireless devices to increase their mobility, effectiveness and responsiveness to client need particularly in providing reference and…

From Collections to Connections: Building a Revised Platform for Library and Information Science

ERIC Educational Resources Information Center

Audunson, Ragnar; Aabo, Svanhild

2013-01-01

Introduction: The paper discusses the often-repeated assertion that digitization makes libraries and librarians redundant by giving everyone access to the information they need without having to rely upon librarians as information middlemen. Method: Relevant articles both from research literature and from discussions in the public sphere…

Learning-assisted theorem proving with millions of lemmas☆

PubMed Central

Kaliszyk, Cezary; Urban, Josef

2015-01-01

Large formal mathematical libraries consist of millions of atomic inference steps that give rise to a corresponding number of proved statements (lemmas). Analogously to the informal mathematical practice, only a tiny fraction of such statements is named and re-used in later proofs by formal mathematicians. In this work, we suggest and implement criteria defining the estimated usefulness of the HOL Light lemmas for proving further theorems. We use these criteria to mine the large inference graph of the lemmas in the HOL Light and Flyspeck libraries, adding up to millions of the best lemmas to the pool of statements that can be re-used in later proofs. We show that in combination with learning-based relevance filtering, such methods significantly strengthen automated theorem proving of new conjectures over large formal mathematical libraries such as Flyspeck. PMID:26525678

Arrayed antibody library technology for therapeutic biologic discovery.

PubMed

Bentley, Cornelia A; Bazirgan, Omar A; Graziano, James J; Holmes, Evan M; Smider, Vaughn V

2013-03-15

Traditional immunization and display antibody discovery methods rely on competitive selection amongst a pool of antibodies to identify a lead. While this approach has led to many successful therapeutic antibodies, targets have been limited to proteins which are easily purified. In addition, selection driven discovery has produced a narrow range of antibody functionalities focused on high affinity antagonism. We review the current progress in developing arrayed protein libraries for screening-based, rather than selection-based, discovery. These single molecule per microtiter well libraries have been screened in multiplex formats against both purified antigens and directly against targets expressed on the cell surface. This facilitates the discovery of antibodies against therapeutically interesting targets (GPCRs, ion channels, and other multispanning membrane proteins) and epitopes that have been considered poorly accessible to conventional discovery methods. Copyright © 2013. Published by Elsevier Inc.

Exploring system interconnection architectures with VIPACES: from direct connections to NOCs

NASA Astrophysics Data System (ADS)

Sánchez-Peña, Armando; Carballo, Pedro P.; Núñez, Antonio

2007-05-01

This paper presents a simple environment for the verification of AMBA 3 AXI systems in Verification IP (VIP) production called VIPACES (Verification Interface Primitives for the development of AXI Compliant Elements and Systems). These primitives are presented as a not compiled library written in SystemC where interfaces are the core of the library. The definition of interfaces instead of generic modules let the user construct custom modules improving the resources spent during the verification phase as well as easily adapting his modules to the AMBA 3 AXI protocol. This topic is the main discussion in the VIPACES library. The paper focuses on comparing and contrasting the main interconnection schemes for AMBA 3 AXI as modeled by VIPACES. For assessing these results we propose a validation scenario with a particular architecture belonging to the domain of MPEG4 video decoding, which is compound by an AXI bus connecting an IDCT and other processing resources.

Robot Task Commander with Extensible Programming Environment

NASA Technical Reports Server (NTRS)

Hart, Stephen W (Inventor); Wightman, Brian J (Inventor); Dinh, Duy Paul (Inventor); Yamokoski, John D. (Inventor); Gooding, Dustin R (Inventor)

2014-01-01

A system for developing distributed robot application-level software includes a robot having an associated control module which controls motion of the robot in response to a commanded task, and a robot task commander (RTC) in networked communication with the control module over a network transport layer (NTL). The RTC includes a script engine(s) and a GUI, with a processor and a centralized library of library blocks constructed from an interpretive computer programming code and having input and output connections. The GUI provides access to a Visual Programming Language (VPL) environment and a text editor. In executing a method, the VPL is opened, a task for the robot is built from the code library blocks, and data is assigned to input and output connections identifying input and output data for each block. A task sequence(s) is sent to the control module(s) over the NTL to command execution of the task.

Livestock Grazing as a Driver of Vernal Pool Ecohydrology

NASA Astrophysics Data System (ADS)

Michaels, J.; McCarten, N. F.

2017-12-01

Vernal pools are seasonal wetlands that host rare plant communities of high conservation priority. Plant community composition is largely driven by pool hydroperiod. A previous study found that vernal pools grazed by livestock had longer hydroperiods compared with pools excluded from grazing for 10 years, and suggests that livestock grazing can be used to protect plant diversity. It is important to assess whether observed differences are due to the grazing or due to water balance variables including upland discharge into or out of the pools since no a priori measurements were made of the hydrology prior to grazing. To address this question, in 2016 we compared 15 pools that have been grazed continuously and 15 pools that have been fenced off for over 40 years at a site in Sacramento County. We paired pools based on abiotic characteristics (size, shape, slope, soil type) to minimize natural variation. We sampled vegetation and water depth using Solinst level loggers. We found that plant diversity and average hydroperiod was significantly higher in the grazed pools. We are currently measuring groundwater connectivity and upland inputs in order to compare the relative strength of livestock grazing as a driver of hydroperiod to these other drivers.

Dynamic behavior of the weld pool in stationary GMAW

NASA Astrophysics Data System (ADS)

Chapuis, J.; Romero, E.; Bordreuil, C.; Soulié, F.; Fras, G.

2010-06-01

Because hump formation limits welding productivity, better understanding of the humping phenomena during the welding process is needed to access to process modifications that decrease the tendency for hump formation and then allow higher productivity welding. From a physical point of view, the mechanism identified is the Rayleigh instability initiated by strong surface tension gradient which induces a variation of kinetic flow. But the causes of the appearance of this instability are not yet well explained. Because of the phenomena complex and multi-physics, we chose in first step to conduct an analysis of the characteristic times involved in weld pool in pulsed stationary GMAW. The goal is to study the dynamic behavior of the weld pool, using our experimental multi physics approach. The experimental tool and methodology developed to understand these fast phenomena are presented first: frames acquisition with high speed digital camera and specific optical devices, numerical library. The analysis of geometric parameters of the weld pool during welding operation are presented in the last part: we observe the variations of wetting angles (or contact lines angles), the base and the height of the weld pool (macro-drop) versus weld time.

Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand.

PubMed

Hetzer, Adrian; Morgan, Hugh W; McDonald, Ian R; Daughney, Christopher J

2007-07-01

Surveys of Champagne Pool, one of New Zealand's largest terrestrial hot springs and rich in arsenic ions and compounds, have been restricted to geological and geochemical descriptions, and a few microbiological studies applying culture-independent methods. In the current investigation, a combination of culture and culture-independent approaches were chosen to determine microbial density and diversity in Champagne Pool. Recovered total DNA and adenosine 5'-triphosphate (ATP) content of spring water revealed relatively low values compared to other geothermal springs within New Zealand and are in good agreement with low cell numbers of 5.6 +/- 0.5 x 10(6) cells/ml obtained for Champagne Pool water samples by 4',6-diamidino-2-phenylindole (DAPI) staining. Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA (small-subunit ribosomal nucleic acid) gene clone library analyses of environmental DNA indicated the abundance of Sulfurihydrogenibium, Sulfolobus, and Thermofilum-like populations in Champagne Pool. From these results, media were selected to target the enrichment of hydrogen-oxidizing and sulfur-dependent microorganisms. Three isolates were successfully obtained having 16S rRNA gene sequences with similarities of approximately 98% to Thermoanaerobacter tengcongensis, 94% to Sulfurihydrogenibium azorense, and 99% to Thermococcus waiotapuensis, respectively.

BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing.

PubMed

Pang, Chao; Hendriksen, Dennis; Dijkstra, Martijn; van der Velde, K Joeri; Kuiper, Joel; Hillege, Hans L; Swertz, Morris A

2015-01-01

Pooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However, searching for desired data elements among the thousands of available elements and harmonizing differences in terminology, data collection, and structure, is arduous and time consuming. To speed up biobank data pooling we developed BiobankConnect, a system to semi-automatically match desired data elements to available elements by: (1) annotating the desired elements with ontology terms using BioPortal; (2) automatically expanding the query for these elements with synonyms and subclass information using OntoCAT; (3) automatically searching available elements for these expanded terms using Lucene lexical matching; and (4) shortlisting relevant matches sorted by matching score. We evaluated BiobankConnect using human curated matches from EU-BioSHaRE, searching for 32 desired data elements in 7461 available elements from six biobanks. We found 0.75 precision at rank 1 and 0.74 recall at rank 10 compared to a manually curated set of relevant matches. In addition, best matches chosen by BioSHaRE experts ranked first in 63.0% and in the top 10 in 98.4% of cases, indicating that our system has the potential to significantly reduce manual matching work. BiobankConnect provides an easy user interface to significantly speed up the biobank harmonization process. It may also prove useful for other forms of biomedical data integration. All the software can be downloaded as a MOLGENIS open source app from http://www.github.com/molgenis, with a demo available at http://www.biobankconnect.org. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association.

BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing

PubMed Central

Pang, Chao; Hendriksen, Dennis; Dijkstra, Martijn; van der Velde, K Joeri; Kuiper, Joel; Hillege, Hans L; Swertz, Morris A

2015-01-01

Objective Pooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However, searching for desired data elements among the thousands of available elements and harmonizing differences in terminology, data collection, and structure, is arduous and time consuming. Materials and methods To speed up biobank data pooling we developed BiobankConnect, a system to semi-automatically match desired data elements to available elements by: (1) annotating the desired elements with ontology terms using BioPortal; (2) automatically expanding the query for these elements with synonyms and subclass information using OntoCAT; (3) automatically searching available elements for these expanded terms using Lucene lexical matching; and (4) shortlisting relevant matches sorted by matching score. Results We evaluated BiobankConnect using human curated matches from EU-BioSHaRE, searching for 32 desired data elements in 7461 available elements from six biobanks. We found 0.75 precision at rank 1 and 0.74 recall at rank 10 compared to a manually curated set of relevant matches. In addition, best matches chosen by BioSHaRE experts ranked first in 63.0% and in the top 10 in 98.4% of cases, indicating that our system has the potential to significantly reduce manual matching work. Conclusions BiobankConnect provides an easy user interface to significantly speed up the biobank harmonization process. It may also prove useful for other forms of biomedical data integration. All the software can be downloaded as a MOLGENIS open source app from http://www.github.com/molgenis, with a demo available at http://www.biobankconnect.org. PMID:25361575

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands.

PubMed

Oloo, Felix; Valverde, Angel; Quiroga, María Victoria; Vikram, Surendra; Cowan, Don; Mataloni, Gabriela

2016-05-10

Bacteria play critical roles in peatland ecosystems. However, very little is known of how habitat heterogeneity affects the structure of the bacterial communities in these ecosystems. Here, we used amplicon sequencing of the 16S rRNA and nifH genes to investigate phylogenetic diversity and bacterial community composition in three different sub-Antarctic peat bog aquatic habitats: Sphagnum magellanicum interstitial water, and water from vegetated and non-vegetated pools. Total and putative nitrogen-fixing bacterial communities from Sphagnum interstitial water differed significantly from vegetated and non-vegetated pool communities (which were colonized by the same bacterial populations), probably as a result of differences in water chemistry and biotic interactions. Total bacterial communities from pools contained typically aquatic taxa, and were more dissimilar in composition and less species rich than those from Sphagnum interstitial waters (which were enriched in taxa typically from soils), probably reflecting the reduced connectivity between the former habitats. These results show that bacterial communities in peatland water habitats are highly diverse and structured by multiple concurrent factors.

Classification of upper Mississippi River pools based on contiguous aquatic/geomorphic habitats

USGS Publications Warehouse

Koel, Todd M.

2001-01-01

Navigation pools of the upper Mississippi River (UMR) vary greatly in terms of available contiguous aquatic/geomorphic habitats. These habitats are critical for the biotic diversity and overall productivity of the floodplain corridor of each pool. In this study, similarities among pools 4-26 and an open river reach (river kilometer 47-129) of the UMR were determined from multivariate analysis of eleven habitat types that were hydrologically-contiguous (non-leveed). Isolated floodplain habitats were not included in final analyses because this isolation limits their contribution to overall riverine productivity, in part due to a lack of hydrological connectivity to the main channel during the flood pulse. Cluster analysis based on simple Euclidean distance was used to produce two major pool groups and five pool subgroups. Important habitat variables in defining pool groups, as interpreted from principal components analysis (PCA) axis 1, were contiguous floodplain shallow aquatic area and contiguous impounded area. The habitat variable most important in defining pool subgroups, as interpreted from PCA axis 2, was tertiary channel. Most notably, pool 6 was more similar to pools 14-24 than other upper pools, and pools 19 and 25 were more similar to pools 4-13 than other lower pools. These results were quite different from those of two previous investigators, primarily because only areas of non-isolated aquatic habitat were considered.

Connecting the Libraries and Athletics through Instruction and Outreach.

PubMed

Sapp, Lara; Vaughan, K T L

2017-01-01

This column describes the approaches taken by librarians and staff at James Madison University (JMU) Libraries & Educational Technologies (LET) to extend library support to university athletics. The model resembles that used for outreach to academic programs and was first adapted to the semi-clinical, nonacademic Strength & Conditioning Department, then to JMU Athletics as a whole. Librarians offered targeted instructional sessions, orientations, and asynchronous learning modules embedded in the learning management system. This new relationship has provided an opportunity for broader collaboration, increasing LET's presence across campus.

Online Professional Profiles: Health Care and Library Researchers Show Off Their Work.

PubMed

Brigham, Tara J

2016-01-01

In an increasingly digital world, online profiles can help health care and library professionals showcase their research and scholarly work. By sharing information about their investigations, studies, and projects, health care and library researchers can elevate their personal brand and connect with like-minded individuals. This column explores different types of online professional profiles and addresses some of the concerns that come with using them. A list of online professional profile and platform examples is also provided.

Induction of Strain-Transcending Immunity against Plasmodium chabaudi adami Malaria with a Multiepitope DNA Vaccine

PubMed Central

Scorza, T.; Grubb, K.; Smooker, P.; Rainczuk, A.; Proll, D.; Spithill, T. W.

2005-01-01

A major goal of current malaria vaccine programs is to develop multivalent vaccines that will protect humans against the many heterologous malaria strains that circulate in endemic areas. We describe a multiepitope DNA vaccine, derived from a genomic Plasmodium chabaudi adami DS DNA expression library of 30,000 plasmids, which induces strain-transcending immunity in mice against challenge with P. c. adami DK. Segregation of this library and DNA sequence analysis identified vaccine subpools encoding open reading frames (ORFs)/peptides of >9 amino acids [aa] (the V9+ pool, 303 plasmids) and >50 aa (V50+ pool, 56 plasmids), respectively. The V9+ and V50+ plasmid vaccine subpools significantly cross-protected mice against heterologous P. c. adami DK challenge, and protection correlated with the induction of both specific gamma interferon production by splenic cells and opsonizing antibodies. Bioinformatic analysis showed that 22 of the V50+ ORFs were polypeptides conserved among three or more Plasmodium spp., 13 of which are predicted hypothetical proteins. Twenty-nine of these ORFs are orthologues of predicted Plasmodium falciparum sequences known to be expressed in the blood stage, suggesting that this vaccine pool encodes multiple blood-stage antigens. The results have implications for malaria vaccine design by providing proof-of-principle that significant strain-transcending immunity can be induced using multiepitope blood-stage DNA vaccines and suggest that both cellular responses and opsonizing antibodies are necessary for optimal protection against P. c. adami. PMID:15845504

Lawriter - OAC

Science.gov Websites

authorized by section 3709.05 of the Revised Code. (C) "Circulation system" means an arrangement of transferred and does not mean the person who formerly operated or maintained the public swimming pool. (J ://catalog.asme.org/. ASME documents are also generally available at the state library of Ohio. (c) American national

Military Librarians Workshop (19th). Intellectual Updating: Changes in the State of the Art of Librarianship, 30 September - 2 October 1975

DTIC Science & Technology

1975-01-01

Force instructor pilots two swimming pools, basketball will administer the 18 hours of this courts, squash and handball courts, program. Additional...Group Annex Fort Lee, VA 23801 Naval Weapons Station. Seal Beach Corona, CA 91720 ELDEEN J. GREENLAND Library Technician MARGARET L. GALLAGHER USA

Heterodera glycines cysts contain an extensive array of endoproteases as well as inhibitors of proteases in H. glycines and Meloidogyne incognita infective juvenile stages

USDA-ARS?s Scientific Manuscript database

Heterodera glycines cysts contain proteases, and inhibitors of protease activities in various nematode species. In this investigation, proteases in H. glycines cysts were identified using a commercially available FRET-peptide library comprising 512 peptide pools qualified to detect up to 4 endoprot...

Head First into the Patron-Driven Acquisition Pool: A Comparison of Librarian Selections versus Patron Purchases

ERIC Educational Resources Information Center

Shen, Lisa; Cassidy, Erin Dorris; Elmore, Eric; Griffin, Glenda; Manolovitz, Tyler; Martinez, Michelle; Turney, Linda M.

2011-01-01

Although many recent studies have been conducted on the implementation and results of patron-driven acquisition (PDA) initiatives at academic libraries, very few have focused on whether, or how, patrons' selections vary from selection choices librarians would have made. This study compares titles selected by patrons during a PDA pilot program…

45 CFR 148.314 - Periods during which eligible States may apply for a grant.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Operation of Qualified High Risk Pools § 148.314 Periods during which eligible States may apply for a grant... connection with the operation of its qualified high risk pool. Funding for FY 2007 through FY 2010 under the... fiscal year, a State may apply for losses incurred in a partial fiscal year if a partial year audit is...

47 CFR 54.502 - Eligible services.

Code of Federal Regulations, 2011 CFR

2011-10-01

... telecommunications can be provided in whole or in part via fiber by any entity. (3) Internet access. For purposes of...'s internal connections if such service is necessary to transport information within one or more... library system has separate administrative buildings, unless those internal connections are essential for...

Library and Information Professionals as Knowledge Engagement Specialists. Theories, Competencies and Current Educational Possibilities in Accredited Graduate Programmes

ERIC Educational Resources Information Center

Prado, Javier Calzada; Marzal, Miguel Angel

2013-01-01

Introduction: The role of library and information science professionals as knowledge facilitators is solidly grounded in the profession's theoretical foundations as much as connected with its social relevance. Knowledge science is presented in this paper as a convenient theoretical framework for this mission, and knowledge engagement…

Serving Higher Education's Highest Goals: Assessment of the Academic Library as Place

ERIC Educational Resources Information Center

Jackson, Heather Lea; Hahn, Trudi Bellardo

2011-01-01

An empirical study was conducted using methods borrowed from the psychology of religion (instead of corporate assessment techniques) to assess whether the academic library as place supports students' desire to feel connected to higher education's mission. The findings from an in-person survey of fifty-four students at three universities showed a…

Embracing a Customer Service Mindset: A Fresh Examination of Services for Distance Learners

ERIC Educational Resources Information Center

Steiner, Heidi

2013-01-01

Library literature and blogs frequently discuss customer service and user experience in physical libraries and Web sites, but little is said about this mentality toward services for distance learners specifically. This paper takes customer service best practices from well-known thinkers of the business world and makes connections to services for…

Use of Social Networking Sites by Academic Librarians in Six Selected States of Nigeria

ERIC Educational Resources Information Center

Tella, Adeyinka; Olarongbe, Shuaib Agboola; Akanbi-Ademolake, Hauwa Bolanle; Adisa, Mulikat Y.

2013-01-01

The attractiveness of social networking sites (SNSs) has extended to almost all professionals in numerous human organizations including the library. Librarians as a result of this development are now making use of these sites to connect to other libraries and librarians both within and outside their environment. However, it is observed that the…

75 FR 70260 - Notice of Public Information Collection(s) Being Reviewed by the Federal Communications...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-17

...) released a Sixth Report and Order (Sixth R&O), FCC 10-175, upgrading and modernizing the schools and... Internet access to schools and libraries across the country, and eliminating rules that no longer serve the... in the process of implementing a program to provide off-premises connectivity to students or library...

Connecting to Collections in Florida: Current Conditions and Critical Needs in Libraries, Archives, and Museums

ERIC Educational Resources Information Center

Jorgensen, Corinne; Marty, Paul F.; Braun, Kathy

2012-01-01

This article presents results from an IMLS-funded project to evaluate the current state of collections in Florida's libraries, archives, and museums, current practices to preserve and conserve these collections, and perceived needs to maintain and improve these collections for future generations. The survey, modeled after the Heritage Health Index…

Thin Client Architecture for Networking CD-ROMs in a Medium-Sized Public Library System.

ERIC Educational Resources Information Center

Turner, Anna

1997-01-01

Describes how the Tulsa City-County Library System built a 22-branch CD-ROM-based network with the emerging thin-client/server technology, and succeeded in providing patrons with the most current research tools and information resources available. Discusses costs; networking options; the Citrix WinFrame system used; equipment and connectivity.…

The Library and Human Memory Simulation Studies. Reports on File Organization Studies.

ERIC Educational Resources Information Center

Reilly, Kevin D.

This report describes digital computer simulation efforts in a study of memory systems for two important cases: that of the individual the brain; and that of society, the library. A neural system model is presented in which a complex system is produced by connecting simple hypothetical neurons whose states change under application of a…

RSS Made Easy with Engaged Patrons and Yahoo! Pipes

ERIC Educational Resources Information Center

Widner, Melissa

2010-01-01

Jasper County Public Library in Indiana had started using EngagedPatrons.org (EP) in 2007. EP is a low-cost technology solution providing online events calendars, RSS feeds, database support, and other web services to connect libraries to their users. It was created in 2006 by Glenn Peterson, who also designs the feature-rich websites for…

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

PubMed

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

2018-05-01

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

Public Library YA Program Roundup. Fantastic Fiestas in the Library: Florida Teens Connect with Their Caribbean and Hispanic Roots; Read Any Good Movies Lately? Conducting YA Book and Movie Discussions; How To Survive a Summer Book Club: A Dialogue; What Do Teens Read in One Day? A Teen Read Week Log; Reading Rocks Music Revue; BookBusters! Spring Cleaning for Books, Teens, and Senior Citizens; Intergenerational Internet; Medieval Murder in the Library.

ERIC Educational Resources Information Center

Wexler, Sydna R.; Vaillancourt, Renee J.; Gillispie, Julie; Engdale, Adam; Lane, David; Welch, Rollie; Honnold, RoseMary; Hall, Tracie; Katz, Jeff; Bartlett, Linda

2001-01-01

These eight articles describe successful public library programs for teens. Highlights include programs emphasizing immigrants' cultures; viewing film adaptations from appropriate books; summer book discussion groups; using music to promote reading; using teen and senior citizen volunteers to help restore books; teens as computer tutors for other…

Nuclide radioactive decay data uncertainties library

NASA Astrophysics Data System (ADS)

Barabanova, D. S.; Zherdev, G. M.

2017-01-01

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

Involvement of the VEP1 gene in vascular strand development in Arabidopsis thaliana.

PubMed

Jun, Ji Hyung; Ha, Chan Man; Nam, Hong Gil

2002-03-01

A dominant mutant line characterized by abnormal leaf venation pattern was isolated from a transgenic Arabidopsis plant pool that was generated with Agrobacterium culture harboring an Arabidopsis antisense cDNA library. In the mutant line, the phenotype was due to antisense suppression of a gene we named VEP1 (Vein Patterning). The predicted amino acid sequence of the gene contained a motif related to the mammalian death domain that is found in the apoptotic machinery. Reduced expression of the VEP1 gene resulted in the reduced complexity of the venation pattern of the cotyledons and foliar leaves, which was mainly due to the reduced number of the minor veins and their incomplete connection. The analysis of mutant embryos indicated that the phenotype was originated, at least in part, from a defect in the procambium patterning. In the mutant, the stem and root were thinner than those in wild type. This phenotype was associated with reduced vascular development. The promoter activity of the VEP1 gene was detected preferentially in the vascular regions. We propose that the death domain-containing protein VEP1 functions as a positive element required for vascular strand development in Arabidopsis thaliana.

Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems.

PubMed

Zhang, Hongkai; Torkamani, Ali; Jones, Teresa M; Ruiz, Diana I; Pons, Jaume; Lerner, Richard A

2011-08-16

Use of large combinatorial antibody libraries and next-generation sequencing of nucleic acids are two of the most powerful methods in modern molecular biology. The libraries are screened using the principles of evolutionary selection, albeit in real time, to enrich for members with a particular phenotype. This selective process necessarily results in the loss of information about less-fit molecules. On the other hand, sequencing of the library, by itself, gives information that is mostly unrelated to phenotype. If the two methods could be combined, the full potential of very large molecular libraries could be realized. Here we report the implementation of a phenotype-information-phenotype cycle that integrates information and gene recovery. After selection for phage-encoded antibodies that bind to targets expressed on the surface of Escherichia coli, the information content of the selected pool is obtained by pyrosequencing. Sequences that encode specific antibodies are identified by a bioinformatic analysis and recovered by a stringent affinity method that is uniquely suited for gene isolation from a highly degenerate collection of nucleic acids. This approach can be generalized for selection of antibodies against targets that are present as minor components of complex systems.

Functional genomics platform for pooled screening and mammalian genetic interaction maps

PubMed Central

Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

2014-01-01

Systematic genetic interaction maps in microorganisms are powerful tools for identifying functional relationships between genes and defining the function of uncharacterized genes. We have recently implemented this strategy in mammalian cells as a two-stage approach. First, genes of interest are robustly identified in a pooled genome-wide screen using complex shRNA libraries. Second, phenotypes for all pairwise combinations of hit genes are measured in a double-shRNA screen and used to construct a genetic interaction map. Our protocol allows for rapid pooled screening under various conditions without a requirement for robotics, in contrast to arrayed approaches. Each stage of the protocol can be implemented in ~2 weeks, with additional time for analysis and generation of reagents. We discuss considerations for screen design, and present complete experimental procedures as well as a full computational analysis suite for identification of hits in pooled screens and generation of genetic interaction maps. While the protocols outlined here were developed for our original shRNA-based approach, they can be applied more generally, including to CRISPR-based approaches. PMID:24992097

Blur and the School Library Media Specialist.

ERIC Educational Resources Information Center

Barron, Daniel D.

1999-01-01

Discusses the concept of "Blur" (described in "Blur: The Speed of Change in the Connected Economy") and what the technology-based, expanded connectivity means for K-12 educators and information specialists. Reviews online and print resources that deal with the rapid development of technology and its effects on society. (AEF)

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity.

PubMed

Chen, Hong-Ming; Armstrong, Zachary; Hallam, Steven J; Withers, Stephen G

2016-02-08

Screening of large enzyme libraries such as those derived from metagenomic sources requires sensitive substrates. Fluorogenic glycosides typically offer the best sensitivity but typically must be used in a stopped format to generate good signal. Use of fluorescent phenols of pKa < 7, such as halogenated coumarins, allows direct screening at neutral pH. The synthesis and characterisation of a set of nine different glycosides of 6-chloro-4-methylumbelliferone are described. The use of these substrates in a pooled format for screening of expressed metagenomic libraries yielded a "hit rate" of 1 in 60. Hits were then readily deconvoluted with the individual substrates in a single plate to identify specific activities within each clone. The use of such a collection of substrates greatly accelerates the screening process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of obstructive sleep apnea hypopnea syndrome on lipid profile: a meta-regression analysis.

PubMed

Nadeem, Rashid; Singh, Mukesh; Nida, Mahwish; Waheed, Irfan; Khan, Adnan; Ahmed, Saeed; Naseem, Jawed; Champeau, Daniel

2014-05-15

Obstructive sleep apnea (OSA) is associated with obesity, metabolic syndrome, and dyslipidemia, which may be related to decrease androgen levels found in OSA patients. Dyslipidemia may contribute to atherosclerosis leading to increasing risk of heart disease. Systematic review was conducted using PubMed and Cochrane library by utilizing different combinations of key words; sleep apnea, obstructive sleep apnea, serum lipids, dyslipidemia, cholesterol, total cholesterol, low density lipoprotein (LDL), high density lipoprotein (HDL), and triglyceride (TG). Inclusion criteria were: English articles, and studies with adult population in 2 groups of patients (patients with OSA and without OSA). A total 96 studies were reviewed for inclusion, with 25 studies pooled for analysis. Sixty-four studies were pooled for analysis; since some studies have more than one dataset, there were 107 datasets with 18,116 patients pooled for meta-analysis. All studies measured serum lipids. Total cholesterol pooled standardized difference in means was 0.267 (p = 0.001). LDL cholesterol pooled standardized difference in means was 0.296 (p = 0.001). HDL cholesterol pooled standardized difference in means was -0.433 (p = 0.001). Triglyceride pooled standardized difference in means was 0.603 (p = 0.001). Meta-regression for age, BMI, and AHI showed that age has significant effect for TC, LDL, and HDL. BMI had significant effect for LDL and HDL, while AHI had significant effect for LDL and TG. Patients with OSA appear to have increased dyslipidemia (high total cholesterol, LDL, TG, and low HDL).

RELAP5 Analysis of the Hybrid Loop-Pool Design for Sodium Cooled Fast Reactors

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

Hongbin Zhang; Haihua Zhao; Cliff Davis

2008-06-01

An innovative hybrid loop-pool design for sodium cooled fast reactors (SFR-Hybrid) has been recently proposed. This design takes advantage of the inherent safety of a pool design and the compactness of a loop design to improve economics and safety of SFRs. In the hybrid loop-pool design, primary loops are formed by connecting the reactor outlet plenum (hot pool), intermediate heat exchangers (IHX), primary pumps and the reactor inlet plenum with pipes. The primary loops are immersed in the cold pool (buffer pool). Passive safety systems -- modular Pool Reactor Auxiliary Cooling Systems (PRACS) – are added to transfer decay heatmore » from the primary system to the buffer pool during loss of forced circulation (LOFC) transients. The primary systems and the buffer pool are thermally coupled by the PRACS, which is composed of PRACS heat exchangers (PHX), fluidic diodes and connecting pipes. Fluidic diodes are simple, passive devices that provide large flow resistance in one direction and small flow resistance in reverse direction. Direct reactor auxiliary cooling system (DRACS) heat exchangers (DHX) are immersed in the cold pool to transfer decay heat to the environment by natural circulation. To prove the design concepts, especially how the passive safety systems behave during transients such as LOFC with scram, a RELAP5-3D model for the hybrid loop-pool design was developed. The simulations were done for both steady-state and transient conditions. This paper presents the details of RELAP5-3D analysis as well as the calculated thermal response during LOFC with scram. The 250 MW thermal power conventional pool type design of GNEP’s Advanced Burner Test Reactor (ABTR) developed by Argonne National Laboratory was used as the reference reactor core and primary loop design. The reactor inlet temperature is 355 °C and the outlet temperature is 510 °C. The core design is the same as that for ABTR. The steady state buffer pool temperature is the same as the reactor inlet temperature. The peak cladding, hot pool, cold pool and reactor inlet temperatures were calculated during LOFC. The results indicate that there are two phases during LOFC transient – the initial thermal equilibration phase and the long term decay heat removal phase. The initial thermal equilibration phase occurs over a few hundred seconds, as the system adjusts from forced circulation to natural circulation flow. Subsequently, during long-term heat removal phase all temperatures evolve very slowly due to the large thermal inertia of the primary and buffer pool systems. The results clearly show that passive safety PRACS can effectively transfer decay heat from the primary system to the buffer pool by natural circulation. The DRACS system in turn can effectively transfer the decay heat to the environment.« less

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

Schwantes, Jon M.

Kelly Fitzgerald Kelly Fitzgerald assisted with laboratory testing for an ongoing R&D project known as Electrochemically Modulated Separation (EMS) for on-line rapid preseparations of actinides prior to mass spectrometry analysis. Ryne Burgess Ryne Burgess used SCALE 5.1 ORIGEN-ARP to predict isotope libraries for the Units 1, 2 and 3 reactors and Unit 4 spent fuel pool for comparing against measurements of environmental sampled collected at the site in order to identify the source terms of the accident. Comparison of the cesium 134/137 and cesium 136/137 ratios observed in environmental samples and ORIGEN-ARP predictions indicated that the Unit 4 Spent Fuelmore » Pool did not significantly contribute to radionuclide release during the Fukushima Daiichi accident.« less

The Library in the Laboratory: Implementing an Online Library Tutorial in a Freshman Biology Lab

ERIC Educational Resources Information Center

Barkley, Meg

2018-01-01

Online tutorials are a way many librarians connect with students. The main benefit is the ability to reach more students than traditional face-to-face instruction sessions. In 2016, the Life & Health Sciences Librarian received instruction session requests for a freshman biology lab to teach students how to search for articles and use proper…

The Library's New Relevance: Fostering the First-Year Student's Acquisition, Evaluation, and Integration of Print and Electronic Materials

ERIC Educational Resources Information Center

Hlavaty, Greg; Townsend, Murphy

2010-01-01

Modern composition instructors often use and teach research methods for Internet search engines and electronic databases. It is not their intent to turn back the clock. However, if they can help students connect the world of Internet searches and the university library, they can promote information literacy in its broadest sense by developing…

Determining and Meeting Personnel Training Needs

ERIC Educational Resources Information Center

Jennings, Anita

2005-01-01

The role of the library has changed significantly during the past 2 decades. Twenty years ago, it could have been considered the norm for a small to mid-sized library to have one or two computers for patron use. Staff was fortunate to have a computer connected to a printer--a tractor-feed ink jet printer--with a basic word processing application…

QR Codes as Finding Aides: Linking Electronic and Print Library Resources

ERIC Educational Resources Information Center

Kane, Danielle; Schneidewind, Jeff

2011-01-01

As part of a focused, methodical, and evaluative approach to emerging technologies, QR codes are one of many new technologies being used by the UC Irvine Libraries. QR codes provide simple connections between print and virtual resources. In summer 2010, a small task force began to investigate how QR codes could be used to provide information and…

Is There a Standard Default Keyword Operator? A Bibliometric Analysis of Processing Options Chosen by Libraries To Execute Keyword Searches in Online Public Access Catalogs.

ERIC Educational Resources Information Center

Klein, Gary M.

1994-01-01

Online public access catalogs from 67 libraries using NOTIS software were searched using Internet connections to determine the positional operators selected as the default keyword operator on each catalog. Results indicate the lack of a processing standard for keyword searches. Five tables provide information. (Author/AEF)

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

Design of 240,000 orthogonal 25mer DNA barcode probes.

PubMed

Xu, Qikai; Schlabach, Michael R; Hannon, Gregory J; Elledge, Stephen J

2009-02-17

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

Design of 240,000 orthogonal 25mer DNA barcode probes

PubMed Central

Xu, Qikai; Schlabach, Michael R.; Hannon, Gregory J.; Elledge, Stephen J.

2009-01-01

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications. PMID:19171886

Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion

PubMed Central

Yung, Pui Yi; Burke, Catherine; Lewis, Matt; Egan, Suhelen; Kjelleberg, Staffan; Thomas, Torsten

2009-01-01

Metagenomics provides access to the uncultured majority of the microbial world. The approaches employed in this field have, however, had limited success in linking functional genes to the taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient strategy to recover environmental DNA fragments that contain phylogenetic marker genes from metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and selection of an antibiotic resistance cassette. This approach was applied to screen a library of 6500 fosmid clones derived from the microbial community associated with the sponge Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to previously unknown organisms. In addition, compositional features of these fosmid clones were used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information. PMID:19767618

Centralization vs. decentralization in medical school libraries.

PubMed

Crawford, H

1966-07-01

Does the medical school library in the United States operate more commonly under the university library or the medical school administration? University-connected medical school libraries were asked to indicate (a) the source of their budgets, whether from the central library or the medical school, and (b) the responsibility for their acquisitions and cataloging. Returns received from sixtyeight of the seventy eligible institutions showed decentralization to be much the most common: 71 percent of the libraries are funded by their medical schools; 79 percent are responsible for their own acquisitions and processing. The factor most often associated with centralization of both budget and operation is public ownership. Decentralization is associated with service to one or two rather than three or more professional schools. Location of the medical school in a different city from the university is highly favorable to autonomy. Other factors associated with these trends are discussed.

Centralization vs. Decentralization in Medical School Libraries

PubMed Central

Crawford, Helen

1966-01-01

Does the medical school library in the United States operate more commonly under the university library or the medical school administration? University-connected medical school libraries were asked to indicate (a) the source of their budgets, whether from the central library or the medical school, and (b) the responsibility for their acquisitions and cataloging. Returns received from sixtyeight of the seventy eligible institutions showed decentralization to be much the most common: 71 percent of the libraries are funded by their medical schools; 79 percent are responsible for their own acquisitions and processing. The factor most often associated with centralization of both budget and operation is public ownership. Decentralization is associated with service to one or two rather than three or more professional schools. Location of the medical school in a different city from the university is highly favorable to autonomy. Other factors associated with these trends are discussed. PMID:5945568

Engineering of ribozyme-based aminoglycoside switches of gene expression by in vivo genetic selection in Saccharomyces cerevisiae.

PubMed

Klauser, Benedikt; Rehm, Charlotte; Summerer, Daniel; Hartig, Jörg S

2015-01-01

Synthetic RNA-based switches are a growing class of genetic controllers applied in synthetic biology to engineer cellular functions. In this chapter, we detail a protocol for the selection of posttranscriptional controllers of gene expression in yeast using the Schistosoma mansoni hammerhead ribozyme as a central catalytic unit. Incorporation of a small molecule-sensing aptamer domain into the ribozyme renders its activity ligand-dependent. Aptazymes display numerous advantages over conventional protein-based transcriptional controllers, namely, the use of little genomic space for encryption, their modular architecture allowing for easy reprogramming to new inputs, the physical linkage to the message to be controlled, and the ability to function without protein cofactors. Herein, we describe the method to select ribozyme-based switches of gene expression in Saccharomyces cerevisiae that we successfully implemented to engineer neomycin- and theophylline-responsive switches. We also highlight how to adapt the protocol to screen for switches responsive to other ligands. Reprogramming of the sensor unit and incorporation into any RNA of interest enables the fulfillment of a variety of regulatory functions. However, proper functioning of the aptazyme is largely dependent on optimal connection between the aptamer and the catalytic core. We obtained functional switches from a pool of variants carrying randomized connection sequences by an in vivo selection in MaV203 yeast cells that allows screening of a large sequence space of up to 1×10(9) variants. The protocol given explains how to construct aptazyme libraries, carry out the in vivo selection and characterize novel ON- and OFF-switches. © 2015 Elsevier Inc. All rights reserved.

A graph-based approach to construct target-focused libraries for virtual screening.

PubMed

Naderi, Misagh; Alvin, Chris; Ding, Yun; Mukhopadhyay, Supratik; Brylinski, Michal

2016-01-01

Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can be used to augment existing compound libraries with novel drug-like compounds, the broad chemical space is often too large to be explored. Consequently, the trend in library design has shifted to produce screening collections specifically tailored to modulate the function of a particular target or a protein family. Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. On this account, we developed eSynth, an exhaustive graph-based search algorithm to computationally synthesize new compounds by reconnecting these building blocks following their connectivity patterns. We conducted a series of benchmarking calculations against the Directory of Useful Decoys, Enhanced database. First, in a self-benchmarking test, the correctness of the algorithm is validated with the objective to recover a molecule from its building blocks. Encouragingly, eSynth can efficiently rebuild more than 80 % of active molecules from their fragment components. Next, the capability to discover novel scaffolds is assessed in a cross-benchmarking test, where eSynth successfully reconstructed 40 % of the target molecules using fragments extracted from chemically distinct compounds. Despite an enormous chemical space to be explored, eSynth is computationally efficient; half of the molecules are rebuilt in less than a second, whereas 90 % take only about a minute to be generated. eSynth can successfully reconstruct chemically feasible molecules from molecular fragments. Furthermore, in a procedure mimicking the real application, where one expects to discover novel compounds based on a small set of already developed bioactives, eSynth is capable of generating diverse collections of molecules with the desired activity profiles. Thus, we are very optimistic that our effort will contribute to targeted drug discovery. eSynth is freely available to the academic community at www.brylinski.org/content/molecular-synthesis.Graphical abstractAssuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. Here, we developed eSynth, an automated method to synthesize new compounds by reconnecting these building blocks following the connectivity patterns via an exhaustive graph-based search algorithm. eSynth opens up a possibility to rapidly construct virtual screening libraries for targeted drug discovery.

Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

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

Hirdt, J.A.; Brown, D.A., E-mail: dbrown@bnl.gov

The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of socialmore » networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.« less

Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

NASA Astrophysics Data System (ADS)

Hirdt, J. A.; Brown, D. A.

2016-01-01

The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

Connecting to the Internet: The Challenge for Canada's County and Regional Libraries.

ERIC Educational Resources Information Center

Curry, Ann; Curtis, Alison

2000-01-01

Describes survey results that indicate Internet access and connectivity is proceeding rapidly despite the geographical, technical, and financial difficulties faced by Canadian systems with large geographical areas and members from different municipal or county jurisdictions. Discusses funding and using the World Wide Web as a reference tool.…

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands

PubMed Central

Oloo, Felix; Valverde, Angel; Quiroga, María Victoria; Vikram, Surendra; Cowan, Don; Mataloni, Gabriela

2016-01-01

Bacteria play critical roles in peatland ecosystems. However, very little is known of how habitat heterogeneity affects the structure of the bacterial communities in these ecosystems. Here, we used amplicon sequencing of the 16S rRNA and nifH genes to investigate phylogenetic diversity and bacterial community composition in three different sub-Antarctic peat bog aquatic habitats: Sphagnum magellanicum interstitial water, and water from vegetated and non-vegetated pools. Total and putative nitrogen-fixing bacterial communities from Sphagnum interstitial water differed significantly from vegetated and non-vegetated pool communities (which were colonized by the same bacterial populations), probably as a result of differences in water chemistry and biotic interactions. Total bacterial communities from pools contained typically aquatic taxa, and were more dissimilar in composition and less species rich than those from Sphagnum interstitial waters (which were enriched in taxa typically from soils), probably reflecting the reduced connectivity between the former habitats. These results show that bacterial communities in peatland water habitats are highly diverse and structured by multiple concurrent factors. PMID:27162086

Electrorefining process and apparatus for recovery of uranium and a mixture of uranium and plutonium from spent fuels

DOEpatents

Ackerman, J.P.; Miller, W.E.

1987-11-05

An electrorefining process and apparatus for the recovery of uranium and a mixture of uranium and plutonium from spent fuels is disclosed using an electrolytic cell having a lower molten cadmium pool containing spent nuclear fuel, an intermediate electrolyte pool, an anode basket containing spent fuels, two cathodes and electrical power means connected to the anode basket, cathodes and lower molten cadmium pool for providing electrical power to the cell. Using this cell, additional amounts of uranium and plutonium from the anode basket are dissolved in the lower molten cadmium pool, and then purified uranium is electrolytically transported and deposited on a first molten cadmium cathode. Subsequently, a mixture of uranium and plutonium is electrotransported and deposited on a second cathode. 3 figs.

The Health and Libraries of Public Use Retrospective Study (HeLPURS).

PubMed

Zager, Sam; Haskins, Amy; Maland, Katherine; Holt, Christina

2016-09-01

Public libraries may promote health through literacy, education and social connections. To conduct the first broad-based, quantitative exploration of health and public library patronage. Retrospective cross-sectional study. All 2925 adult patients at a general practice clinic living in a small north-eastern U.S. city were invited by mail to participate; 243 consented. Clinical variables from the medical records were combined with library usage variables from the public library patron database. The authors analysed how patient health characteristics were associated with library cardholding, average card use or recency of use. Approximately 72% of participants held a library card; 40% of these had used it within the last month. Library cardholding was not associated with patient characteristics. Higher average card use was associated with pregnancy, having youth at home and depression severity. Lack of recent library usage was associated with current smoking (P = 0.01) and drug use (P = 0.01). Among ever-smokers, moderate/high card use and card use within six months were both associated with over two times the odds of quitting smoking. Public libraries and health appear to intersect around substance abuse and depression-anxiety disorders. Moderate or higher use of public libraries is strongly associated with tobacco cessation. © 2016 Health Libraries Group.

New Title Tweets: Using Twitter and Microsoft Excel to Broadcast New Title Lists

ERIC Educational Resources Information Center

Rodzvilla, John

2010-01-01

Today's library should be part of the online social networks so it can connect with patrons and inform them of new services and opportunities. But this need to utilize new technology must be balanced against shrinking budgets and increased costs. One way libraries can juggle these demands is to spend more time on creating content, using a mix of…

Science and Technology Undergraduate Students' Use of the Internet, Cell Phones and Social Networking Sites to Access Library Information

ERIC Educational Resources Information Center

Salisbury, Lutishoor; Laincz, Jozef; Smith, Jeremy J.

2012-01-01

Many academic libraries and publishers have developed mobile-optimized versions of their web sites and catalogs. Almost all database vendors and major journal publishers have provided a way to connect to their resources via the Internet and the mobile web. In light of this pervasive use of the Internet, mobile devices and social networking, this…

Connecting Marketing and Implementation Research and Library Program Development: A Case Study of the Implementation of [U.S.] National Guidelines and Standards.

ERIC Educational Resources Information Center

Haycock, Ken; Cavill, Pat

This case study examined: (1) what market research is required for planning for the implementation of "Information Power: Building Partnerships for Learning," the 1998 national guidelines for effective school library media programs; (2) what issues need to be addressed and what target audiences are required to effect change, as well as…

School Library 2.0: Say Good-Bye to Your Mother's School Library. The Web Is All about New Possibilities

ERIC Educational Resources Information Center

Harris, Christopher

2006-01-01

Blogs and the whole gamut of interactive, Web-based tools are redefining how we connect with people and content on the Internet. This is the widely discussed next step known as Web 2.0, a truly revolutionary concept in which pervasive interactivity, where multitudes of users online actively exchange or contribute content, will transform the very…

Benefits and Results of Learning 2.0: A Case Study of CityLibrariesLearning--Discover*Play*Connect

ERIC Educational Resources Information Center

Stephens, Michael; Cheetham, Warren

2012-01-01

Replicated across the globe, the Learning 2.0 programme--also known as "23 Things"--has been touted as a means to not only educate staff about emerging social and mobile technologies but as a means of moving the participating library forward as a learning organisation. This paper explores the results of a multi-faceted research project…

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

PubMed

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

2012-09-01

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

A Polymerase Chain Reaction-Based Method for Isolating Clones from a Complimentary DNA Library in Sheep

PubMed Central

Friis, Thor Einar; Stephenson, Sally; Xiao, Yin; Whitehead, Jon

2014-01-01

The sheep (Ovis aries) is favored by many musculoskeletal tissue engineering groups as a large animal model because of its docile temperament and ease of husbandry. The size and weight of sheep are comparable to humans, which allows for the use of implants and fixation devices used in human clinical practice. The construction of a complimentary DNA (cDNA) library can capture the expression of genes in both a tissue- and time-specific manner. cDNA libraries have been a consistent source of gene discovery ever since the technology became commonplace more than three decades ago. Here, we describe the construction of a cDNA library using cells derived from sheep bones based on the pBluescript cDNA kit. Thirty clones were picked at random and sequenced. This led to the identification of a novel gene, C12orf29, which our initial experiments indicate is involved in skeletal biology. We also describe a polymerase chain reaction-based cDNA clone isolation method that allows the isolation of genes of interest from a cDNA library pool. The techniques outlined here can be applied in-house by smaller tissue engineering groups to generate tools for biomolecular research for large preclinical animal studies and highlights the power of standard cDNA library protocols to uncover novel genes. PMID:24447069

Customized USB Flash Drives Used to Promote Library Resources and Services to First-year Medical and Dental Students

PubMed Central

Matsoukas, Konstantina; Meret, Anca; Oliver, John T.; Purcell, Michael

2011-01-01

In line with its institution’s commitment to keep new student orientation/welcome events “green,” Columbia University’s Health Sciences Library (HSL) applied for a National Network of Libraries of Medicine Middle Atlantic Region (NN/LM MAR) Small Projects Award1 in Spring/Summer 2009 to explore paperless modes of outreach. This article describes the project that resulted from this funding, whose purpose was to determine whether customized 1 GB USB flash drives are a good vehicle for distributing library promotional materials to incoming medical and dental students. This project gave HSL librarians the opportunity to connect with students in a way that had not been done before and to consider how these new students use/view the information the library produces. PMID:21534111

Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling.

PubMed

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. Copyright © 2015 the American Physiological Society.

Electronic Connection Between the Quinone and Cytochrome c Redox Pools and Its Role in Regulation of Mitochondrial Electron Transport and Redox Signaling

PubMed Central

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. PMID:25540143

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.

75 FR 50758 - Leader One Energy, LLC; Supplemental Notice of Intent To Prepare an Environmental Assessment for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-17

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Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-18

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Connecting Learning: Brain-Based Strategies for Linking Prior Knowledge in the Library Media Center

ERIC Educational Resources Information Center

Vanderbilt, Kathi L.

2005-01-01

The brain is a complex organ and learning is a complex process. While there is not complete agreement among researchers about brain-based learning and its direct connection to neuroscience, knowledge about the brain as well as the examination of cognitive psychology, anthropology, professional experience, and educational research can provide…

Connecting and Communicating with Students on Facebook

ERIC Educational Resources Information Center

Miller, Sarah Elizabeth; Jensen, Lauren A.

2007-01-01

Facebook is a social network that connects people with other people. Librarians have created Facebook Groups to share ideas and to debate how to use this resource as a potential marketing and/or reference tool. Based on conversations among these librarians, it appears that student response to library outreach on this medium is lackluster at best,…

Library workers' personal beliefs about childhood vaccination and vaccination information provision.

PubMed

Keselman, Alla; Smith, Catherine Arnott; Hundal, Savreen

2014-07-01

This is a report on the impact of library workers' personal beliefs on provision of vaccination information. Nine public librarians were interviewed about a hypothetical scenario involving a patron who is concerned about possible vaccination-autism connections. The analysis employed thematic coding. Results suggested that while most participants supported childhood vaccination, tension between their personal views and neutrality impacted their ability to conduct the interaction. The neutrality stance, though consonant with professional guidelines, curtails librarians' ability to provide accurate health information. Outreach and communication between public and health sciences libraries can help librarians provide resources to address health controversies.

Tribal connections health information outreach: results, evaluation, and challenges

PubMed Central

Wood, Fred B.; Sahali, Roy; Press, Nancy; Burroughs, Catherine; Mala, Theodore A.; Siegel, Elliot R.; Fuller, Sherrilynne S.; Rambo, Neil

2003-01-01

In 1997, the National Library of Medicine (NLM), a component of the National Institutes of Health (NIH), initiated a program of intensified outreach to Native Americans, initially focusing on the Pacific Northwest in collaboration with the Pacific Northwest Regional Medical Library (PNRML). This initiative, known as the Tribal Connections Project, emphasized the establishment or strengthening of Internet connections at select Indian reservations and Alaska Native villages and related needs assessment and training. The hope was that these efforts would improve tribal access to health information available via the Internet and the Web. Phase I included sixteen tribal sites—eight in Washington, four in Alaska, two in Montana, and one each in Oregon and Idaho. Phase I results indicate that the project was successful in assessing local needs and building awareness of the Internet, forging new partnerships with and between the participating Indian reservations and Alaska Native villages and other organizations, making real improvements in the information technology (IT) infrastructure and Internet connectivity at fifteen of sixteen sites, and conducting training sessions with several hundred tribal participants across thirteen sites. Most importantly, the project demonstrated the key role of tribal community involvement and empowerment and contributed to development of an outreach evaluation field manual and the evolving concept of community-based outreach. The knowledge gained from Tribal Connections Project Phase I is helping refine and enhance subsequent NLM-sponsored tribal connections and similar community outreach efforts. PMID:12568158

Counting on β-Diversity to Safeguard the Resilience of Estuaries

PubMed Central

de Juan, Silvia; Thrush, Simon F.; Hewitt, Judi E.

2013-01-01

Coastal ecosystems are often stressed by non-point source and cumulative effects that can lead to local-scale community homogenisation and a concomitant loss of large-scale ecological connectivity. Here we investigate the use of β-diversity as a measure of both community heterogeneity and ecological connectivity. To understand the consequences of different environmental scenarios on heterogeneity and connectivity, it is necessary to understand the scale at which different environmental factors affect β-diversity. We sampled macrofauna from intertidal sites in nine estuaries from New Zealand’s North Island that represented different degrees of stress derived from land-use. We used multiple regression models to identify relationships between β-diversity and local sediment variables, factors related to the estuarine and catchment hydrodynamics and morphology and land-based stressors. At local scales, we found higher β-diversity at sites with a relatively high total richness. At larger scales, β-diversity was positively related to γ-diversity, suggesting that a large regional species pool was linked with large-scale heterogeneity in these systems. Local environmental heterogeneity influenced β-diversity at both local and regional scales, although variables at the estuarine and catchment scales were both needed to explain large scale connectivity. The estuaries expected a priori to be the most stressed exhibited higher variance in community dissimilarity between sites and connectivity to the estuary species pool. This suggests that connectivity and heterogeneity metrics could be used to generate early warning signals of cumulative stress. PMID:23755252

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

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

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

2011-11-30

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

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

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

2011-01-01

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

From Osler's Library to the Osler Library of the History of Medicine, McGill University, Montreal: an overview.

PubMed

Lyons, Christopher

2007-01-01

The Osler Library of the History of Medicine was opened in 1929 at McGill University, Montreal, Canada. Sir William Osler (1849-1919), arguably McGill's and Canada's most famous doctor at the time, had bequeathed his magnificent library of almost 8,000 historical works in medicine and, to a lesser extent, science and literature to the university. Under the 30-year reign of its first librarian, Dr. W W. Francis, the Osler Library became famous for its rare books and for its connection with Sir William. Since the 1950s, however, the library has pursued an active collection development policy for both primary and secondary material that has taken it far beyond Osler's original gift. The library has grown in both the size and scope of its holdings and the services it offers to scholars and students of the history of medicine. These have made the Osler Library a major resource centre for studies in the history of the health sciences. This article looks at the Osler Library today in the hopes of making the range of its collections and services better known to the Canadian and international communities.

Water inventory management in condenser pool of boiling water reactor

DOEpatents

Gluntz, Douglas M.

1996-01-01

An improved system for managing the water inventory in the condenser pool of a boiling water reactor has means for raising the level of the upper surface of the condenser pool water without adding water to the isolation pool. A tank filled with water is installed in a chamber of the condenser pool. The water-filled tank contains one or more holes or openings at its lowermost periphery and is connected via piping and a passive-type valve (e.g., squib valve) to a high-pressure gas-charged pneumatic tank of appropriate volume. The valve is normally closed, but can be opened at an appropriate time following a loss-of-coolant accident. When the valve opens, high-pressure gas inside the pneumatic tank is released to flow passively through the piping to pressurize the interior of the water-filled tank. In so doing, the initial water contents of the tank are expelled through the openings, causing the water level in the condenser pool to rise. This increases the volume of water available to be boiled off by heat conducted from the passive containment cooling heat exchangers. 4 figs.

Water inventory management in condenser pool of boiling water reactor

DOEpatents

Gluntz, D.M.

1996-03-12

An improved system for managing the water inventory in the condenser pool of a boiling water reactor has means for raising the level of the upper surface of the condenser pool water without adding water to the isolation pool. A tank filled with water is installed in a chamber of the condenser pool. The water-filled tank contains one or more holes or openings at its lowermost periphery and is connected via piping and a passive-type valve (e.g., squib valve) to a high-pressure gas-charged pneumatic tank of appropriate volume. The valve is normally closed, but can be opened at an appropriate time following a loss-of-coolant accident. When the valve opens, high-pressure gas inside the pneumatic tank is released to flow passively through the piping to pressurize the interior of the water-filled tank. In so doing, the initial water contents of the tank are expelled through the openings, causing the water level in the condenser pool to rise. This increases the volume of water available to be boiled off by heat conducted from the passive containment cooling heat exchangers. 4 figs.

CMS Connect

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Gardner, R., Jr.; Hurtado Anampa, K.; Jayatilaka, B.; Aftab Khan, F.; Lannon, K.; Larson, K.; Letts, J.; Marra Da Silva, J.; Mascheroni, M.; Mason, D.; Perez-Calero Yzquierdo, A.; Tiradani, A.

2017-10-01

The CMS experiment collects and analyzes large amounts of data coming from high energy particle collisions produced by the Large Hadron Collider (LHC) at CERN. This involves a huge amount of real and simulated data processing that needs to be handled in batch-oriented platforms. The CMS Global Pool of computing resources provide +100K dedicated CPU cores and another 50K to 100K CPU cores from opportunistic resources for these kind of tasks and even though production and event processing analysis workflows are already managed by existing tools, there is still a lack of support to submit final stage condor-like analysis jobs familiar to Tier-3 or local Computing Facilities users into these distributed resources in an integrated (with other CMS services) and friendly way. CMS Connect is a set of computing tools and services designed to augment existing services in the CMS Physics community focusing on these kind of condor analysis jobs. It is based on the CI-Connect platform developed by the Open Science Grid and uses the CMS GlideInWMS infrastructure to transparently plug CMS global grid resources into a virtual pool accessed via a single submission machine. This paper describes the specific developments and deployment of CMS Connect beyond the CI-Connect platform in order to integrate the service with CMS specific needs, including specific Site submission, accounting of jobs and automated reporting to standard CMS monitoring resources in an effortless way to their users.

Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View.

PubMed

Yuen, Lik Hang; Franzini, Raphael M

2017-05-04

DNA-encoded chemical libraries (DECLs) are pools of DNA-tagged small molecules that enable facile screening and identification of bio-macromolecule binders. The successful development of DECLs has led to their increasingly important role in drug development, and screening hits have entered clinical trials. In this review, we summarize the development and currently active research areas of DECLs with a focus on contributions from groups at academic institutes. We further look at opportunities and future directions of DECL research in medicinal chemistry and chemical biology based on the symbiotic relationship between academia and industry. Challenges associated with the application of DECLs in academic drug discovery are further discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Incorporating incorporating economic models into seasonal pool conservation planning

USGS Publications Warehouse

Freeman, Robert C.; Bell, Kathleen P.; Calhoun, Aram J.K.; Loftin, Cyndy

2012-01-01

Massachusetts, New Jersey, Connecticut, and Maine have adopted regulatory zones around seasonal (vernal) pools to conserve terrestrial habitat for pool-breeding amphibians. Most amphibians require access to distinct seasonal habitats in both terrestrial and aquatic ecosystems because of their complex life histories. These habitat requirements make them particularly vulnerable to land uses that destroy habitat or limit connectivity (or permeability) among habitats. Regulatory efforts focusing on breeding pools without consideration of terrestrial habitat needs will not ensure the persistence of pool-breeding amphibians. We used GIS to combine a discrete-choice, parcel-scale economic model of land conversion with a landscape permeability model based on known habitat requirements of wood frogs (Lithobates sylvaticus) in Maine (USA) to examine permeability among habitat elements for alternative future scenarios. The economic model predicts future landscapes under different subdivision open space and vernal pool regulatory requirements. Our model showed that even “no build” permit zones extending 76 m (250 ft) outward from the pool edge were insufficient to assure permeability among required habitat elements. Furthermore, effectiveness of permit zones may be inconsistent due to interactions with other growth management policies, highlighting the need for local and state planning for the long-term persistence of pool-breeding amphibians in developing landscapes.

45 CFR 1602.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Corporation in connection with the transaction of the Corporation's business and preserved by the Corporation... include, inter alia, books, magazines, or other materials acquired solely for library purposes. (h...

45 CFR 1602.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Corporation in connection with the transaction of the Corporation's business and preserved by the Corporation... include, inter alia, books, magazines, or other materials acquired solely for library purposes. (h...

Marketing Trends to Watch

ERIC Educational Resources Information Center

Circle, Alison

2009-01-01

This article identifies 13 cultural trends that libraries can turn into opportunites to reach patrons. These trends include: Twitter, online reputation management, value added content, mobile marketing, and emotional connection.

Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening

PubMed Central

Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Platt, Randall J.; Brigham, Mark D.; Sanjana, Neville E.; Zhang, Feng

2017-01-01

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified from the screen, we further describe strategies for confirming the screening phenotype as well as genetic perturbation through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9–15 weeks followed by 4–5 weeks of validation. PMID:28333914

Highly multiplexed targeted DNA sequencing from single nuclei.

PubMed

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.

PubMed

Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S; Abudayyeh, Omar O; Platt, Randall J; Brigham, Mark D; Sanjana, Neville E; Zhang, Feng

2017-04-01

Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified by the screen, we further describe strategies for confirming the screening phenotype, as well as genetic perturbation, through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9-15 weeks, followed by 4-5 weeks of validation.

Unlocking Index Animalium: From paper slips to bytes and bits

PubMed Central

Pilsk, Suzanne C.; Kalfatovic, Martin R.; Richard, Joel M.

2016-01-01

Abstract In 1996 Smithsonian Libraries (SIL) embarked on the digitization of its collections. By 1999, a full-scale digitization center was in place and rare volumes from the natural history collections, often of high illustrative value, were the focus for the first years of the program. The resulting beautiful books made available for online display were successful to a certain extent, but it soon became clear that the data locked within the texts needed to be converted to more usable and re-purposable form via digitization methods that went beyond simple page imaging and included text conversion elements. Library staff met with researchers from the taxonomic community to understand their path to the literature and identified tools (indexes and bibliographies) used to connect to the library holdings. The traditional library metadata describing the titles, which made them easily retrievable from the shelves of libraries, was not meeting the needs of the researcher looking for more detailed and granular data within the texts. The result was to identify proper print tools that could potential assist researchers in digital form. This paper outlines the project undertaken to convert Charles Davies Sherborn’s Index Animalium into a tool to connect researchers to the library holdings: from a print index to a database to eventually a dataset. Sherborn’s microcitation of a species name and his bibliographies help bridge the gap between taxonomist and literature holdings of libraries. In 2004, SIL received funding from the Smithsonian’s Atherton Seidell Endowment to create an online version of Sherborn’s Index Animalium. The initial project was to digitize the page images and re-key the data into a simple data structure. As the project evolved, a more complex database was developed which enabled quality field searching to retrieve species names and to search the bibliography. Problems with inconsistent abbreviations and styling of his bibliographies made the parsing of the data difficult. Coinciding with the development of the Biodiversity Heritage Library (BHL) in 2005, it became obvious there was a need to integrate the database converted Index Animalium, BHL’s scanned taxonomic literature, and taxonomic intelligence (the algorithmic identification of binomial, Latinate name-strings). The challenges of working with legacy taxonomic citation, computer matching algorithms, and making connections have brought us to today’s goal of making Sherborn available and linked to other datasets. Partnering with others to allow machine-to-machine communications the data is being examined for possible transformation into RDF markup and meeting the standards of Linked Open Data. SIL staff have partnered with Thomson Reuters and the Global Names Initiative to further enhance the Index Animalium data set. Thomson Reuters’ staff is now working on integrating the species microcitation and species name in the ION: Index to Organism Names project; Richard Pyle (The Bishop Museum) is also working on further parsing of the text. The Index Animalium collaborative project’s ultimate goal is to successful have researchers go seamlessly from the species name in either ION or the scanned pages of Index Animalium to the digitized original description in BHL - connecting taxonomic researchers to original authored species descriptions with just a click. PMID:26877657

Unlocking Index Animalium: From paper slips to bytes and bits.

PubMed

Pilsk, Suzanne C; Kalfatovic, Martin R; Richard, Joel M

2016-01-01

In 1996 Smithsonian Libraries (SIL) embarked on the digitization of its collections. By 1999, a full-scale digitization center was in place and rare volumes from the natural history collections, often of high illustrative value, were the focus for the first years of the program. The resulting beautiful books made available for online display were successful to a certain extent, but it soon became clear that the data locked within the texts needed to be converted to more usable and re-purposable form via digitization methods that went beyond simple page imaging and included text conversion elements. Library staff met with researchers from the taxonomic community to understand their path to the literature and identified tools (indexes and bibliographies) used to connect to the library holdings. The traditional library metadata describing the titles, which made them easily retrievable from the shelves of libraries, was not meeting the needs of the researcher looking for more detailed and granular data within the texts. The result was to identify proper print tools that could potential assist researchers in digital form. This paper outlines the project undertaken to convert Charles Davies Sherborn's Index Animalium into a tool to connect researchers to the library holdings: from a print index to a database to eventually a dataset. Sherborn's microcitation of a species name and his bibliographies help bridge the gap between taxonomist and literature holdings of libraries. In 2004, SIL received funding from the Smithsonian's Atherton Seidell Endowment to create an online version of Sherborn's Index Animalium. The initial project was to digitize the page images and re-key the data into a simple data structure. As the project evolved, a more complex database was developed which enabled quality field searching to retrieve species names and to search the bibliography. Problems with inconsistent abbreviations and styling of his bibliographies made the parsing of the data difficult. Coinciding with the development of the Biodiversity Heritage Library (BHL) in 2005, it became obvious there was a need to integrate the database converted Index Animalium, BHL's scanned taxonomic literature, and taxonomic intelligence (the algorithmic identification of binomial, Latinate name-strings). The challenges of working with legacy taxonomic citation, computer matching algorithms, and making connections have brought us to today's goal of making Sherborn available and linked to other datasets. Partnering with others to allow machine-to-machine communications the data is being examined for possible transformation into RDF markup and meeting the standards of Linked Open Data. SIL staff have partnered with Thomson Reuters and the Global Names Initiative to further enhance the Index Animalium data set. Thomson Reuters' staff is now working on integrating the species microcitation and species name in the ION: Index to Organism Names project; Richard Pyle (The Bishop Museum) is also working on further parsing of the text. The Index Animalium collaborative project's ultimate goal is to successful have researchers go seamlessly from the species name in either ION or the scanned pages of Index Animalium to the digitized original description in BHL - connecting taxonomic researchers to original authored species descriptions with just a click.

The Connectivity Map: a new tool for biomedical research.

PubMed

Lamb, Justin

2007-01-01

The ultimate objective of biomedical research is to connect human diseases with the genes that underlie them and drugs that treat them. But this remains a daunting task, and even the most inspired researchers still have to resort to laborious screens of genetic or chemical libraries. What if at least some parts of this screening process could be systematized and centralized? And hits found and hypotheses generated with something resembling an internet search engine? These are the questions the Connectivity Map project set out to answer.

Abstracting data warehousing issues in scientific research.

PubMed

Tews, Cody; Bracio, Boris R

2002-01-01

This paper presents the design and implementation of the Idaho Biomedical Data Management System (IBDMS). This system preprocesses biomedical data from the IMPROVE (Improving Control of Patient Status in Critical Care) library via an Open Database Connectivity (ODBC) connection. The ODBC connection allows for local and remote simulations to access filtered, joined, and sorted data using the Structured Query Language (SQL). The tool is capable of providing an overview of available data in addition to user defined data subset for verification of models of the human respiratory system.

Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates.

PubMed

Shi, Handuo; Colavin, Alexandre; Lee, Timothy K; Huang, Kerwyn Casey

2017-02-01

Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but it suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), which is a high-throughput, automated microscopy workflow for large strain collections that requires minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multiwell plates onto large agar pads using inexpensive replicator pins and automatically imaging the resulting single cells. The acquired images are subsequently reviewed and analyzed by custom MATLAB scripts that segment single-cell contours and extract quantitative metrics. SLIP yields rich data sets on cell morphology and gene expression that illustrate the function of certain genes and the connections among strains in a library. For a library arrayed on 96-well plates, image acquisition can be completed within 4 min per plate.

Reductive dechlorination in recalcitrant sources of chloroethenes in the transition zone between aquifers and aquitards.

PubMed

Puigserver, Diana; Herrero, Jofre; Torres, Mònica; Cortés, Amparo; Nijenhuis, Ivonne; Kuntze, Kevin; Parker, Beth L; Carmona, José M

2016-09-01

In the transition zone between aquifers and basal aquitards, the perchloroethene pools at an early time in their evolution are more recalcitrant than those elsewhere in the aquifer. The aim of this study is to demonstrate that the biodegradation of chloroethenes from aged pools (i.e., pools after decades of continuous groundwater flushing and dissolution) of perchloroethene is favored in the transition zone. A field site was selected where an aged pool exists at the bottom of a transition zone. Two boreholes were drilled to obtain sediment and groundwater samples to perform chemical, isotopic, molecular, and clone library analyses and microcosm experiments. The main results were as follows: (i) the transition zone is characterized by a high microbial richness; (ii) reductively dechlorinating microorganisms are present and partial reductive dechlorination coexists with denitrification, Fe and Mn reduction, and sulfate reduction; (iii) reductively dechlorinating microorganisms were also present in the zone of the aged pool; (v) the high concentrations of perchloroethene in this zone resulted in a decrease in microbial richness; (vi) however, the presence of fermenting microorganisms supplying electrons for the reductively dechlorinating microorganisms prevented the reductive dechlorination to be inhibited. These findings suggest that biostimulation and/or bioaugmentation could be applied to promote complete reductive dechlorination and to enhance the dissolution of more nonaqueous phase liquids (DNAPL).

[The effect of corticosteroids on the prevention of fat embolism syndrome after long bone fracture of the lower limbs: a systematic review and meta-analysis].

PubMed

Cavallazzi, Rodrigo; Cavallazzi, Antonio César

2008-01-01

To analyze the available evidence regarding the effect that corticosteroids have on the prevention of fat embolism syndrome after long bone fracture of the lower limbs or pelvic fracture. In March of 2007, we performed a search of various electronic databases, including Medline, the Excerpta Medica database, the Cochrane Library, the Latin American and Caribbean Health Sciences Literature database and the Scientific Electronic Library Online. We selected randomized controlled trials that compared the effect of corticosteroids with that of placebo (or standard care) on the prevention of fat embolism syndrome after long bone fracture of the lower limbs or pelvic fracture. References from the studies included were also reviewed. Six studies were included. The pooled relative risk for developing fat embolism syndrome was 0.16 (95% CI: 0.08-0.35) in the corticosteroid group as compared with the control group. The pooled relative risk for developing hypoxemia was 0.34 (95% CI: 0.19-0.59) in the corticosteroid group as compared with the control group. The analysis of evidence showed that corticosteroids decrease the risk of developing fat embolism syndrome and hypoxemia after long bone fracture of the lower limbs.

Genetic screens in human cells using the CRISPR-Cas9 system.

PubMed

Wang, Tim; Wei, Jenny J; Sabatini, David M; Lander, Eric S

2014-01-03

The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into the genome, which enabled a complex mutant pool to be tracked by massively parallel sequencing. We used a library containing 73,000 sgRNAs to generate knockout collections and performed screens in two human cell lines. A screen for resistance to the nucleotide analog 6-thioguanine identified all expected members of the DNA mismatch repair pathway, whereas another for the DNA topoisomerase II (TOP2A) poison etoposide identified TOP2A, as expected, and also cyclin-dependent kinase 6, CDK6. A negative selection screen for essential genes identified numerous gene sets corresponding to fundamental processes. Last, we show that sgRNA efficiency is associated with specific sequence motifs, enabling the prediction of more effective sgRNAs. Collectively, these results establish Cas9/sgRNA screens as a powerful tool for systematic genetic analysis in mammalian cells.

Evaluation of the Pool Critical Assembly Benchmark with Explicitly-Modeled Geometry using MCNP6

DOE PAGES

Kulesza, Joel A.; Martz, Roger Lee

2017-03-01

Despite being one of the most widely used benchmarks for qualifying light water reactor (LWR) radiation transport methods and data, no benchmark calculation of the Oak Ridge National Laboratory (ORNL) Pool Critical Assembly (PCA) pressure vessel wall benchmark facility (PVWBF) using MCNP6 with explicitly modeled core geometry exists. As such, this paper provides results for such an analysis. First, a criticality calculation is used to construct the fixed source term. Next, ADVANTG-generated variance reduction parameters are used within the final MCNP6 fixed source calculations. These calculations provide unadjusted dosimetry results using three sets of dosimetry reaction cross sections of varyingmore » ages (those packaged with MCNP6, from the IRDF-2002 multi-group library, and from the ACE-formatted IRDFF v1.05 library). These results are then compared to two different sets of measured reaction rates. The comparison agrees in an overall sense within 2% and on a specific reaction- and dosimetry location-basis within 5%. Except for the neptunium dosimetry, the individual foil raw calculation-to-experiment comparisons usually agree within 10% but is typically greater than unity. Finally, in the course of developing these calculations, geometry that has previously not been completely specified is provided herein for the convenience of future analysts.« less

STS-45 MS Foale dons EMU with technicians' help in JSC's WETF Bldg 29

NASA Technical Reports Server (NTRS)

1991-01-01

STS-45 Atlantis, Orbiter Vehicle (OV) 104, Mission Specialist (MS) C. Michael Foale stands on a platform as technicians help him don his extravehicular mobility unit (EMU). The technicians are preparing to connect the EMU upper and lower torsos at the waist ring. When fully suited, Foale will be lowered into a nearby 25 ft deep pool for an underwater simulation of contingency extravehicular activity (EVA) procedures. The pool is located in JSC's Weightless Environment Training Facility (WETF) Bldg 29.

Internet as a Tool for Reference Work Experiences from the IFLA/Danida Trial Project in Ghana.

ERIC Educational Resources Information Center

Kondrup, Ruth

The basic ideas of the project described in this paper are to establish Internet connections to libraries in developing countries, to give access to information and to organize training of staff. Technical solutions with radio and microwave Internet connections have been established. Access to on-line journals has been established by the PERI…

Using Adobe Connect to Deliver Online Library Instruction to the RN to BSN Program

ERIC Educational Resources Information Center

Carlson, Kathleen

2011-01-01

This paper takes a look at how one academic health sciences librarian brought mediated literature searching to the distance RN to BSN nursing students. It takes a look at why Adobe Connect was the webinar software that was selected to deliver online instruction to the students. The article explains how students participated in a pre-class survey…

PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus

PubMed Central

Brinkmann, Ulrich; Vasmatzis, George; Lee, Byungkook; Yerushalmi, Noga; Essand, Magnus; Pastan, Ira

1998-01-01

We have used a combination of computerized database mining and experimental expression analyses to identify a gene that is preferentially expressed in normal male and female reproductive tissues, prostate, testis, fallopian tube, uterus, and placenta, as well as in prostate cancer, testicular cancer, and uterine cancer. This gene is located on the human X chromosome, and it is homologous to a family of genes encoding GAGE-like proteins. GAGE proteins are expressed in a variety of tumors and in testis. We designate the novel gene PAGE-1 because the expression pattern in the Cancer Genome Anatomy Project libraries indicates that it is predominantly expressed in normal and neoplastic prostate. Further database analysis indicates the presence of other genes with high homology to PAGE-1, which were found in cDNA libraries derived from testis, pooled libraries (with testis), and in a germ cell tumor library. The expression of PAGE-1 in normal and malignant prostate, testicular, and uterine tissues makes it a possible target for the diagnosis and possibly for the vaccine-based therapy of neoplasms of prostate, testis, and uterus. PMID:9724777

PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus.

PubMed

Brinkmann, U; Vasmatzis, G; Lee, B; Yerushalmi, N; Essand, M; Pastan, I

1998-09-01

We have used a combination of computerized database mining and experimental expression analyses to identify a gene that is preferentially expressed in normal male and female reproductive tissues, prostate, testis, fallopian tube, uterus, and placenta, as well as in prostate cancer, testicular cancer, and uterine cancer. This gene is located on the human X chromosome, and it is homologous to a family of genes encoding GAGE-like proteins. GAGE proteins are expressed in a variety of tumors and in testis. We designate the novel gene PAGE-1 because the expression pattern in the Cancer Genome Anatomy Project libraries indicates that it is predominantly expressed in normal and neoplastic prostate. Further database analysis indicates the presence of other genes with high homology to PAGE-1, which were found in cDNA libraries derived from testis, pooled libraries (with testis), and in a germ cell tumor library. The expression of PAGE-1 in normal and malignant prostate, testicular, and uterine tissues makes it a possible target for the diagnosis and possibly for the vaccine-based therapy of neoplasms of prostate, testis, and uterus.

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

Culbert, A.A.; Wallis, G.A.; Kadler, K.E.

The brittleness of bone in people with lethal (type II) osteogenesis imperfecta, a heritable disorder caused by mutations in the type I collagen genes, arises from the deposition of abnormal collagen in the bone matrix. The inability of the abnormal collagen to participate in mineralization may be caused by its failure to interact with other bone proteins. Here, we have designed a strategy to isolate the genes important for mineralization of collagen during bone formation. Cells isolated from 16-day embryonic chick calvaria and seeded post-confluence in culture deposited a mineralized matrix over a period of 2 weeks. Chick skin fibroblastsmore » seeded and cultured under the same conditions did not mineralize. Using RT-PCR, we prepared short cDNAs ({approximately}300 bp) corresponding to the 3{prime} ends of mRNA from fibroblasts and separately from the mineralizing calvarial cells. Subtractive cDNA hybridization generated a pool of cDNAs that were specific to mineralizing calvarial cells but not to fibroblasts. Screening of 100,000 plaques of a chick bone ZAP Express cDNA library with this pool of mineralizing-specific cDNAs identified ten clones which comprised full-length cDNAs for the bone proteins osteopontin (eight of the ten positives), bone sialoprotein II (one of the ten positives), and cystatin (one of the ten positives). cDNAs for type I collagen, fibronectin, alkaline phosphatase, house-keeping genes, and other genes expressed in fibroblasts were not identified in this preliminary screen. The pool of short cDNAs is likely to comprise cDNAs for further bone-specific genes and will be used to screen the entire bone cDNA library of 4.2 million clones. 30 refs., 4 figs.« less

Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

PubMed Central

Legault, Boris A; Lopez-Lopez, Arantxa; Alba-Casado, Jose Carlos; Doolittle, W Ford; Bolhuis, Henk; Rodriguez-Valera, Francisco; Papke, R Thane

2006-01-01

Background Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present. Results The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions. Conclusion These results point to a large pan-genome (total gene repertoire of the genus/species) even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities. PMID:16820057

Highly efficient spatial data filtering in parallel using the opensource library CPPPO

NASA Astrophysics Data System (ADS)

Municchi, Federico; Goniva, Christoph; Radl, Stefan

2016-10-01

CPPPO is a compilation of parallel data processing routines developed with the aim to create a library for "scale bridging" (i.e. connecting different scales by mean of closure models) in a multi-scale approach. CPPPO features a number of parallel filtering algorithms designed for use with structured and unstructured Eulerian meshes, as well as Lagrangian data sets. In addition, data can be processed on the fly, allowing the collection of relevant statistics without saving individual snapshots of the simulation state. Our library is provided with an interface to the widely-used CFD solver OpenFOAM®, and can be easily connected to any other software package via interface modules. Also, we introduce a novel, extremely efficient approach to parallel data filtering, and show that our algorithms scale super-linearly on multi-core clusters. Furthermore, we provide a guideline for choosing the optimal Eulerian cell selection algorithm depending on the number of CPU cores used. Finally, we demonstrate the accuracy and the parallel scalability of CPPPO in a showcase focusing on heat and mass transfer from a dense bed of particles.

Let's Get This Party Started: Pump up the Volume. Streaming Music Is a Great Way to Connect with Older Kids

ERIC Educational Resources Information Center

Pritchard, Kate

2010-01-01

It's not always easy to get teens talking. But when the author became a young adult specialist at the Wilbraham (Massachusetts) Public Library four years ago, that's exactly what she had to do. Her main mission was to bring in as many high schoolers as possible. She needed to find out exactly what they wanted from the library. when she asked them…

A survey of computer search service costs in the academic health sciences library.

PubMed Central

Shirley, S

1978-01-01

The Norris Medical Library, University of Southern California, has recently completed an extensive survey of costs involved in the provision of computer search services beyond vendor charges for connect time and printing. In this survey costs for such items as terminal depreciation, repair contract, personnel time, and supplies are analyzed. Implications of this cost survey are discussed in relation to planning and price setting for computer search services. PMID:708953

Investigation on the Mechanism and Failure Mode of Laser Transmission Spot Welding Using PMMA Material for the Automotive Industry

PubMed Central

Wang, Xiao; Liu, Baoguang; Liu, Wei; Zhong, Xuejiao; Jiang, Yingjie; Liu, Huixia

2017-01-01

To satisfy the need of polymer connection in lightweight automobiles, a study on laser transmission spot welding using polymethyl methacrylate (PMMA) is conducted by using an Nd:YAG pulse laser. The influence of three variables, namely peak voltages, defocusing distances and the welding type (type I (pulse frequency and the duration is 25 Hz, 0.6 s) and type II (pulse frequency and the duration is 5 Hz, 3 s)) to the welding quality was investigated. The result showed that, in the case of the same peak voltages and defocusing distances, the number of bubbles for type I was obviously more than type II. The failure mode of type I was the base plate fracture along the solder joint, and the connection strength of type I was greater than type II. The weld pool diameter:depth ratio for type I was significantly greater than type II. It could be seen that there was a certain relationship between the weld pool diameter:depth ratio and the welding strength. By the finite element simulation, the weld pool for type I was more slender than type II, which was approximately the same as the experimental results. PMID:28772383

Investigation on the Mechanism and Failure Mode of Laser Transmission Spot Welding Using PMMA Material for the Automotive Industry.

PubMed

Wang, Xiao; Liu, Baoguang; Liu, Wei; Zhong, Xuejiao; Jiang, Yingjie; Liu, Huixia

2017-01-01

To satisfy the need of polymer connection in lightweight automobiles, a study on laser transmission spot welding using polymethyl methacrylate (PMMA) is conducted by using an Nd:YAG pulse laser. The influence of three variables, namely peak voltages, defocusing distances and the welding type (type I (pulse frequency and the duration is 25 Hz, 0.6 s) and type II (pulse frequency and the duration is 5 Hz, 3 s)) to the welding quality was investigated. The result showed that, in the case of the same peak voltages and defocusing distances, the number of bubbles for type I was obviously more than type II. The failure mode of type I was the base plate fracture along the solder joint, and the connection strength of type I was greater than type II. The weld pool diameter:depth ratio for type I was significantly greater than type II. It could be seen that there was a certain relationship between the weld pool diameter:depth ratio and the welding strength. By the finite element simulation, the weld pool for type I was more slender than type II, which was approximately the same as the experimental results.

De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products.

PubMed

Han, R; Rai, A; Nakamura, M; Suzuki, H; Takahashi, H; Yamazaki, M; Saito, K

2016-01-01

Study on transcriptome, the entire pool of transcripts in an organism or single cells at certain physiological or pathological stage, is indispensable in unraveling the connection and regulation between DNA and protein. Before the advent of deep sequencing, microarray was the main approach to handle transcripts. Despite obvious shortcomings, including limited dynamic range and difficulties to compare the results from distinct experiments, microarray was widely applied. During the past decade, next-generation sequencing (NGS) has revolutionized our understanding of genomics in a fast, high-throughput, cost-effective, and tractable manner. By adopting NGS, efficiency and fruitful outcomes concerning the efforts to elucidate genes responsible for producing active compounds in medicinal plants were profoundly enhanced. The whole process involves steps, from the plant material sampling, to cDNA library preparation, to deep sequencing, and then bioinformatics takes over to assemble enormous-yet fragmentary-data from which to comb and extract information. The unprecedentedly rapid development of such technologies provides so many choices to facilitate the task, which can cause confusion when choosing the suitable methodology for specific purposes. Here, we review the general approaches for deep transcriptome analysis and then focus on their application in discovering biosynthetic pathways of medicinal plants that produce important secondary metabolites. © 2016 Elsevier Inc. All rights reserved.

An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.

PubMed

Bansal, Vikas

2018-01-01

The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut. vibansal@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

PubMed

Yang, Cheng-Hong; Chuang, Li-Yeh; Shih, Tsung-Mu; Chang, Hsueh-Wei

2010-12-17

SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers. To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are not in "inclusion", the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM) and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries. The hSAGEing tool provides a combination of friendly cross-tissue analysis and an interface for comparing SAGE libraries for the first time. Some up- or down-regulated genes with tissue-specific or common tumor markers and suppressors are identified computationally. The tool is useful and convenient for in silico cancer transcriptomic studies and is freely available at http://bio.kuas.edu.tw/hSAGEing.

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

NONE

The Library Services Alliance is a unique multi-type library consortium committed to resource sharing. As a voluntary association of university and governmental laboratory libraries supporting scientific research, the Alliance has become a leader in New Mexico in using cooperative ventures to cost-effectively expand resources supporting their scientific and technical communities. During 1994, the alliance continued to expand on their strategic planning foundation to enhance access to research information for the scientific and technical communities. Significant progress was made in facilitating easy access to the on-line catalogs of member libraries via connections through the Internet. Access to Alliance resources is nowmore » available via the World Wide Web and Gopher, as well as links to other databases and electronic information. This report highlights the accomplishments of the Alliance during calendar year 1994.« less

Library workers' personal beliefs about childhood vaccination and vaccination information provision*

PubMed Central

Keselman, Alla; Smith, Catherine Arnott; Hundal, Savreen

2014-01-01

This is a report on the impact of library workers' personal beliefs on provision of vaccination information. Nine public librarians were interviewed about a hypothetical scenario involving a patron who is concerned about possible vaccination-autism connections. The analysis employed thematic coding. Results suggested that while most participants supported childhood vaccination, tension between their personal views and neutrality impacted their ability to conduct the interaction. The neutrality stance, though consonant with professional guidelines, curtails librarians' ability to provide accurate health information. Outreach and communication between public and health sciences libraries can help librarians provide resources to address health controversies. PMID:25031563

Meibomianitis

MedlinePlus

... less oil being made for the normal tear film. These people often have symptoms of dry eye. ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes.

PubMed

Popovic, Ana; Tchigvintsev, Anatoly; Tran, Hai; Chernikova, Tatyana N; Golyshina, Olga V; Yakimov, Michail M; Golyshin, Peter N; Yakunin, Alexander F

2015-01-01

This chapter discusses metagenomics and its application for enzyme discovery, with a focus on hydrolytic enzymes from marine metagenomic libraries. With less than one percent of culturable microorganisms in the environment, metagenomics, or the collective study of community genetics, has opened up a rich pool of uncharacterized metabolic pathways, enzymes, and adaptations. This great untapped pool of genes provides the particularly exciting potential to mine for new biochemical activities or novel enzymes with activities tailored to peculiar sets of environmental conditions. Metagenomes also represent a huge reservoir of novel enzymes for applications in biocatalysis, biofuels, and bioremediation. Here we present the results of enzyme discovery for four enzyme activities, of particular industrial or environmental interest, including esterase/lipase, glycosyl hydrolase, protease and dehalogenase.

2011 Summary: Coastal wetland restoration research

USGS Publications Warehouse

Kowalski, Kurt P.; Wiley, Michael J.; Wilcox, Douglas A.; Carlson Mazur, Martha L.; Czayka, Alex; Dominguez, Andrea; Doty, Susan; Eggleston, Mike; Green, Sean; Sweetman, Amanda

2014-01-01

The Great Lakes Restoration Initiative (GLRI) projects currently taking place in Great Lakes coastal wetlands provide a unique opportunity to study ecosystem response to management actions as practitioners strive to improve wetland function and increase ecosystem services. Through a partnership between the U.S. Geological Survey – Great Lakes Science Center (GLSC), U.S. Fish and Wildlife Service (USFWS), and Ducks Unlimited, a GLRI-funded project has reestablished the hydrologic connection between an intensively managed impounded wetland (Pool 2B) and Crane Creek, a small Lake Erie tributary, by building a water-control structure that was opened in the spring of 2011. The study site is located within the USFWS Ottawa National Wildlife Refuge (ONWR) and lies within the boundaries of the U.S. Environmental Protection Agency (EPA)-designated Maumee River Area of Concern. The broad objective of the project is to evaluate how hydrologically reconnecting a previously diked wetland impacts fish, mollusks, and other biota and affects nutrient transport, nutrient cycling, water quality, flood storage, and many other abiotic conditions. The results from this project suggest large system-wide benefits from sustainable reestablishment of lake-driven hydrology in this and other similar systems. We comprehensively sampled water chemistry, fish, birds, plants, and invertebrates in Crane Creek coastal wetlands, Pool 2A (a reference diked wetland), and Pool 2B (the reconnected wetland) in 2010 and 2011 to: 1) Characterize spatial and seasonal patterns for these parameters. 2) Examine ecosystem response to the opening of a water-control structure that allows fish passage Our sampling efforts have yielded data that reveal striking changes in water quality, hydrology, and fish assemblages in our experimental unit (2B). Prior to the reconnection, the water chemistry in pools 2A and 2B were very similar. Afterwards, we found that the water chemistry in reconnected Pool 2B was more similar to Crane Creek (e.g., greater turbidity, higher concentration of nitrogen). Sites closest to the structure showed the most creek influence with that influence decreasing with distance from the structure, suggesting that input water from Crane Creek is not mixing fully with the pool water. We also found that water level fluctuations were much greater in the reconnected wetland due to the influence of seiches in Lake Erie. We measured the nutrient concentrations of water flowing into and out of Pool 2B during seiche events and found that the phosphorous and nitrogen concentrations generally were drastically reduced after pulsing through the reconnected wetland. Fish response to the reconnection was equally striking. High-resolution sonar revealed extensive bidirectional movement of fish through the structure on a daily and seasonal basis. There also were significant increases in both the catch per unit effort (CPUE) and the species richness of all sites in Pool 2B from 2010 to 2011. Reconnecting the diked pool to the larger Crane Creek wetland complex, and therefore Lake Erie, has opened up rich new habitat for many fish species. Thirteen species of fish not previously found in the pool entered through the structure and actively used the reconnected wetland. We also found that the wetland functions as a productive spawning ground and nursery area with notable shifts in the predominant age-class of several species of fish, especially northern pike. We observed no negative effects of reconnection on the avian or vegetative communities. All sites within the connected pool had increases in diversity and abundance in the avian community and decreases in the species richness and Floristic Quality Assessment Index values for vegetative communities. After one year of study, data suggest that maintaining a hydrologic connection between diked and coastal wetlands in Lake Erie allows fishes to use vegetated habitats regularly, reduces the concentration of nutrients in coastal waters, and maintains productive habitats for birds and other biota.  It will be important to continue to monitor the status of the reconnected wetland to determine the effect of long-term connection to Crane Creek and Lake Erie.  If conditions degrade, periodic management actions involving hydrologic isolation of the rehabilitated coastal wetland could be used to mimic intermediate levels of disturbance and maintain wetland vegetation.

22 CFR 303.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Peace Corps in connection with the transaction of Peace Corps' business and preserved by the Peace Corps... include, inter alia, books, magazines, or other materials acquired solely for library purpose, or that are...

22 CFR 303.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Peace Corps in connection with the transaction of Peace Corps' business and preserved by the Peace Corps... include, inter alia, books, magazines, or other materials acquired solely for library purpose, or that are...

22 CFR 303.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Peace Corps in connection with the transaction of Peace Corps' business and preserved by the Peace Corps... include, inter alia, books, magazines, or other materials acquired solely for library purpose, or that are...

X-ray

MedlinePlus

... The images are recorded on a computer or film. Structures that are dense (such as bone) will ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Retrograde cystography

MedlinePlus

... of computed tomography, magnetic resonance imaging, and plain film. In: Wein AJ, Kavoussi LR, Partin AW, Peters ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Venogram - leg

MedlinePlus

... through the body to form an image on film. Structures that are dense (such as bone) will ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

American Nephrology Nurses' Association

MedlinePlus

... Contact National Office ANNA Election Center Member Spotlight Leadership Board of Directors ANNA Chapter Support Team Chapter ... Opportunities Members Only ANNA Connected ANNA Open Forum Leadership Library Membership Card Member Directory Social Media Post ...

Assessment of Customer Service in Academic Health Care Libraries (ACSAHL): an instrument for measuring customer service*†

PubMed Central

Crossno, Jon E.; Berkins, Brenda; Gotcher, Nancy; Hill, Judith L.; McConoughey, Michelle; Walters, Mitchel

2001-01-01

Objectives: In a pilot study, the library had good results using SERVQUAL, a respected and often-used instrument for measuring customer satisfaction. The SERVQUAL instrument itself, however, received some serious and well-founded criticism from the respondents to our survey. The purpose of this study was to test the comparability of the results of SERVQUAL with a revised and shortened instrument modeled on SERVQUAL. The revised instrument, the Assessment of Customer Service in Academic Health Care Libraries (ACSAHL), was designed to better assess customer service in academic health care libraries. Methods: Surveys were sent to clients who had used the document delivery services at three academic medical libraries in Texas over the previous twelve to eighteen months. ACSAHL surveys were sent exclusively to clients at University of Texas (UT) Southwestern, while the client pools at the two other institutions were randomly divided and provided either SERVQUAL or ACSAHL surveys. Results: Results indicated that more respondents preferred the shorter ACSAHL instrument to the longer and more complex SERVQUAL instrument. Also, comparing the scores from both surveys indicated that ACSAHL elicited comparable results. Conclusions: ACSAHL appears to measure the same type of data in similar settings, but additional testing is recommended both to confirm the survey's results through data replication and to investigate whether the instrument applies to different service areas. PMID:11337948

Single Cell Transcriptomics of Hypothalamic Warm Sensitive Neurons that Control Core Body Temperature and Fever Response

PubMed Central

Eberwine, James; Bartfai, Tamas

2011-01-01

We report on an ‘unbiased’ molecular characterization of individual, adult neurons, active in a central, anterior hypothalamic neuronal circuit, by establishing cDNA libraries from each individual, electrophysiologically identified warm sensitive neuron (WSN). The cDNA libraries were analyzed by Affymetrix microarray. The presence and frequency of cDNAs was confirmed and enhanced with Illumina sequencing of each single cell cDNA library. cDNAs encoding the GABA biosynthetic enzyme. GAD1 and of adrenomedullin, galanin, prodynorphin, somatostatin, and tachykinin were found in the WSNs. The functional cellular and in vivo studies on dozens of the more than 500 neurotransmitter -, hormone- receptors and ion channels, whose cDNA was identified and sequence confirmed, suggest little or no discrepancy between the transcriptional and functional data in WSNs; whenever agonists were available for a receptor whose cDNA was identified, a functional response was found.. Sequencing single neuron libraries permitted identification of rarely expressed receptors like the insulin receptor, adiponectin receptor2 and of receptor heterodimers; information that is lost when pooling cells leads to dilution of signals and mixing signals. Despite the common electrophysiological phenotype and uniform GAD1 expression, WSN- transcriptomes show heterogenity, suggesting strong epigenetic influence on the transcriptome. Our study suggests that it is well-worth interrogating the cDNA libraries of single neurons by sequencing and chipping. PMID:20970451

"Be Informed, Stay Connected, Community Transformation!" Selected Papers from the PIALA Conference 2014, Pacific Islands Association of Libraries, Archives, and Museums Annual Conference (24th, Koror, Republic of Palau, Nov 10-15, 2014)

ERIC Educational Resources Information Center

Drake, Paul Burton

2015-01-01

This publication follows the tradition of publishing selected papers from the Pacific Islands Association of Libraries, Archives and Museums (PIALA) annual conferences. This 24th annual conference was held in Koror, Republic of Palau, November 10-15, 2014. This volume includes a listing of the PIALA 2014 Organizing Committee and PIALA Officers and…

USAF Expeditionary Security Operations 2040:A Technology Vision For Deployed Air Base Defense Capabilities

DTIC Science & Technology

2014-04-09

development is the ability to connect to language translation service providers, exemplified by the hand-held Enabling Language Service Anywhere ( ELSA ...device. Designed primarily for use by first responders, ELSA connects via cellular signal to a company employing interpreters for over 180 languages...69 ELSA provides a possible model for military emulation where a pool of linguists is available on-call for use in a tactical environment

High air volume to low liquid volume aerosol collector

DOEpatents

Masquelier, Donald A.; Milanovich, Fred P.; Willeke, Klaus

2003-01-01

A high air volume to low liquid volume aerosol collector. A high volume flow of aerosol particles is drawn into an annular, centripetal slot in a collector which directs the aerosol flow into a small volume of liquid pool contained is a lower center section of the collector. The annular jet of air impinges into the liquid, imbedding initially airborne particles in the liquid. The liquid in the pool continuously circulates in the lower section of the collector by moving to the center line, then upwardly, and through assistance by a rotating deflector plate passes back into the liquid at the outer area adjacent the impinging air jet which passes upwardly through the liquid pool and through a hollow center of the collector, and is discharged via a side outlet opening. Any liquid droplets escaping with the effluent air are captured by a rotating mist eliminator and moved back toward the liquid pool. The collector includes a sensor assembly for determining, controlling, and maintaining the level of the liquid pool, and includes a lower centrally located valve assembly connected to a liquid reservoir and to an analyzer for analyzing the particles which are impinged into the liquid pool.

Cold weather effects on Dresden Unit 1

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

Anagnostopoulos, H.

1995-03-01

Dresden Unit 1 is in the final stages of a decommissioning effort directed at preparing the unit to enter a SAFSTOR status. Following an extended sub-zero cold wave, about 55,000 gallons of water were discovered in the lowest elevation of the spherical reactor enclosure. Cold weather had caused the freezing and breaking of several service water lines that had not been completely isolated. Two days later, at a regularly scheduled decommissioning meeting, the event was communicated to the decommissioning team, who quickly recognized the potential for freezing of a 42 inches diameter Fuel Transfer Tube that connects the sphere tomore » the Spent Fuel Pool. The team directed that the pool gates between the adjacent Spent Fuel Pool and the Fuel Transfer Pool be installed, and a portable source of heat was installed on the Fuel Transfer Tube. It was later determined that, with the fuel pool gates removed, and with a worst case freeze break at the 502 elevation on the Fuel Transfer Tube (in the Sphere), the fuel in the Spent Fuel Pool could be uncovered to a level 3 below the top of active fuel.« less

Blocked tear duct

MedlinePlus

... may be closed or covered by a thin film, which causes a partial blockage. In adults, the ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Extremity x-ray

MedlinePlus

... through the body to form an image on film. Structures that are dense (such as bone) will ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Abdominal x-ray

MedlinePlus

... are, or may be, pregnant. Alternative Names Abdominal film; X-ray - abdomen; Flat plate; KUB x-ray ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

X-ray - skeleton

MedlinePlus

... pass through the body. A computer or special film records the images. Structures that are dense (such ... Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, ...

Thumb sucking

MedlinePlus

... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated: 04 June 2018

Suprapubic catheter care

MedlinePlus

... going back into your bladder. Try not to disconnect the catheter more than you need to. Keeping ... Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for EHRs For Developers U.S. National Library of ...

NASA and Public Libraries: Enhancing STEM Literacy in Underserved Communities

NASA Astrophysics Data System (ADS)

Dusenbery, P.; LaConte, K.; Harold, J. B.; Randall, C.

2016-12-01

NASA research programs are helping humanity understand the origin and evolution of galaxies, stars, and planets, and defining the conditions necessary to support life beyond Earth. The Space Science Institute's (SSI) National Center for Interactive Learning (NCIL) was recently funded by NASA`s Science Mission Directorate (SMD) to develop and implement a project called NASA@ My Library: A National Earth and Space Science Initiative That Connects NASA, Public Libraries and Their Communities. As places that offer their services for free, public libraries have become the "public square" by providing a place where members of a community can gather for information, educational programming, and policy discussions. Libraries are developing new ways to engage their patrons in STEM learning, and NCIL's STAR Library Education Network (STAR_Net) has been supporting their efforts for the last eight years, including through a vibrant community of practice that serves both librarians and STEM professionals. Project stakeholders include public library staff, state libraries, the earth and space science education community at NASA, subject matter experts, and informal science educators. The project will leverage high-impact SMD and library events to catalyze partnerships through dissemination of SMD assets and professional development. It will also develop frameworks for public libraries to increase STEM interest pathways in their communities (with supports for reaching underserved audiences). This presentation will summarize the key activities and expected outcomes of the 5-year project.

Diagnostic value of secreted frizzled-related protein 2 gene promoter hypermethylation in stool for colorectal cancer: A meta-analysis.

PubMed

Zhou, Zhiran; Zhang, Huitian; Lei, Yunxia

2016-10-01

To evaluate the diagnostic value of secreted frizzled-related protein 2 (SFRP2) gene promoter hypermethylation in stool for colorectal cancer (CRC). Open published diagnostic study of SFRP2 gene promoter hypermethylation in stool for CRC detection was electronic searched in the databases of PubMed, EMBASE, Cochrane Library, Web of Science, and China National Knowledge Infrastructure. The data of true positive, false positive false negative, and true negative identified by stool SFRP2 gene hypermethylation was extracted and pooled for diagnostic sensitivity, specificity, and summary receiver operating characteristic (SROC) curve. According to the inclusion and exclusion criteria, we finally included nine publications with 792 cases in the meta-analysis. Thus, the diagnostic sensitivity was aggregated through random effect model. The pooled sensitivity was 0.82 with the corresponding 95% confidence interval (95% CI) of 0.79-0.85; the pooled specificity and its corresponding 95% CI were 0.47 and 0.40-0.53 by the random effect model; we pooled the SROC curve by sensitivity versus specificity according to data published in the nine studies. The area under the SROC curve was 0.70 (95% CI: 0.65-0.73). SFRP2 gene promoter hypermethylation in stool can was a potential biomarker for CRC diagnosis with relative high sensitivity.

Concomitant fibromyalgia complicating chronic inflammatory arthritis: a systematic review and meta-analysis.

PubMed

Duffield, Stephen J; Miller, Natasha; Zhao, Sizheng; Goodson, Nicola J

2018-05-16

This systematic review and meta-analysis will describe the prevalence of concomitant FM in adults with inflammatory arthritis and quantify the impact of FM on DAS. Cochrane library, MEDLINE, Psychinfo, PubMed, Scopus and Web of Science were searched using key terms and predefined exclusion criteria. As appropriate, proportional and pairwise meta-analysis methods were used to pool results. Forty articles were identified. In RA the prevalence of FM ranged from 4.9 to 52.4% (21% pooled). In axSpA the range was 4.11-25.2% (13% pooled in AS only). In PsA the range was 9.6-27.2% (18% pooled). The presence of concomitant FM was related to higher DAS in patients with RA and AS (DAS28 mean difference 1.24, 95% CI: 1.10, 1.37 in RA; BASDAI mean difference 2.22, 95% CI: 1.86, 2.58 in AS). Concomitant FM was also associated with higher DAS in existing PsA studies. Self-reported, rather than objective, components of DAS appear to be raised in the presence of FM (e.g. tender joint count and Visual Analogue Scale (VAS) pain scores). FM is common in RA, AxSpA and PsA. Comorbid FM appears to amplify DAS and could therefore influence management of these rheumatic conditions.

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

PubMed

Canver, Matthew C; Haeussler, Maximilian; Bauer, Daniel E; Orkin, Stuart H; Sanjana, Neville E; Shalem, Ophir; Yuan, Guo-Cheng; Zhang, Feng; Concordet, Jean-Paul; Pinello, Luca

2018-05-01

CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments. Here, we present a protocol that describes in detail both the computational and benchtop implementation of an arrayed and/or pooled CRISPR genome-editing experiment. This protocol provides instructions for sgRNA design with CRISPOR (computational tool for the design, evaluation, and cloning of sgRNA sequences), experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso (computational tool for analysis of genome-editing outcomes from deep-sequencing data). This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts, as well as computational data analysis that can be performed in 1-2 d by both computational and noncomputational biologists alike using web-based and/or command-line versions.

Local structuring factors of invertebrate communities in ephemeral freshwater rock pools and the influence of more permanent water bodies in the region

USGS Publications Warehouse

Jocque, M.; Graham, T.; Brendonck, L.

2007-01-01

We used three isolated clusters of small ephemeral rock pools on a sandstone flat in Utah to test the importance of local structuring processes on aquatic invertebrate communities. In the three clusters we characterized all ephemeral rock pools (total: 27) for their morphometry, and monitored their water quality, hydrology and community assemblage during a full hydrocycle. In each cluster we also sampled a set of more permanent interconnected freshwater systems positioned in a wash, draining the water from each cluster of rock pools. This design allowed additional testing for the potential role of more permanent water bodies in the region as source populations for the active dispersers and the effect on the community structure in the rock pools. Species richness and community composition in the rock pools correlated with level of permanence and the ammonia concentration. The length of the rock pool inundation cycle shaped community structure, most probably by inhibiting colonization by some taxa (e.g. tadpoles and insect larvae) through developmental constraints. The gradient in ammonia concentrations probably reflects differences in primary production. The more permanent water bodies in each wash differed both environmentally and in community composition from the connected set of rock pools. A limited set of active dispersers was observed in the rock pools. Our findings indicate that aquatic invertebrate communities in the ephemeral rock pools are mainly structured through habitat permanence, possibly linked with biotic interactions and primary production. ?? 2007 Springer Science+Business Media B.V.

77 FR 56093 - Consolidation of Seizure and Forfeiture Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-12

... search engine. Given the current state of technology, the Department believes that this practice is far... Study 2010-2011 (Libraries Connect Communities), at 3, available at http://viewer.zmags.com/publication...

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

Snepvangers, J.J.M.

Equipment and results are described connected with irradiation studies of UO/sub 2/ fuels, fuel element testing in pressurized water loops, graphite irradiation, and steel irradiations with and without temperature control. The apparatus described is associated with a 20-Mw pool-type research reactor. (T.F.H.)

[Paternal exposure to occupational electromagnetic radiation and sex ratio of the offspring: a meta-analysis].

PubMed

Tong, Shu-Hui; Liu, Yi-Ting; Liu, Yang

2013-02-01

To investigate the association between paternal exposure to occupational electromagnetic radiation and the sex ratio of the offspring. We searched various databases, including PubMed, Embase, Cochrane Library, OVID, Bioscience Information Service (BIOSIS), China National Knowledge Infrastructure, VIP Database for Chinese Technical Periodicals and Wanfang Database, for the literature relevant to the association of paternal exposure to occupational electromagnetic radiation with the sex ratio of the offspring. We conducted a meta-analysis on their correlation using Stata 11.0. There was no statistically significant difference in the sex ratio between the offspring with paternal exposure to occupational electromagnetic radiation and those without (pooled OR = 1.00 [95% CI: 0.95 -1.05], P = 0.875). Subgroup analysis of both case-control and cohort studies revealed no significant difference (pooled OR = 1.03 [95% CI: 0.99 -1.08], P = 0.104 and pooled OR = 0.98 [95% CI: 0.99 -1.08], P = 0.186, respectively). Paternal exposure to occupational electromagnetic radiation is not correlated with the sex ratio of the offspring.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

PubMed

Litichevskiy, Lev; Peckner, Ryan; Abelin, Jennifer G; Asiedu, Jacob K; Creech, Amanda L; Davis, John F; Davison, Desiree; Dunning, Caitlin M; Egertson, Jarrett D; Egri, Shawn; Gould, Joshua; Ko, Tak; Johnson, Sarah A; Lahr, David L; Lam, Daniel; Liu, Zihan; Lyons, Nicholas J; Lu, Xiaodong; MacLean, Brendan X; Mungenast, Alison E; Officer, Adam; Natoli, Ted E; Papanastasiou, Malvina; Patel, Jinal; Sharma, Vagisha; Toder, Courtney; Tubelli, Andrew A; Young, Jennie Z; Carr, Steven A; Golub, Todd R; Subramanian, Aravind; MacCoss, Michael J; Tsai, Li-Huei; Jaffe, Jacob D

2018-04-25

Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP). A majority of these drugs elicited reproducible signatures, but notable cell line- and assay-specific differences were observed. Using the "connectivity" framework, we compared signatures across cell types and integrated data across assays, including a transcriptional assay (L1000). Consistent connectivity among cell types revealed cellular responses that transcended lineage, and consistent connectivity among assays revealed unexpected associations between drugs. We further leveraged the resource against public data to formulate hypotheses for treatment of multiple myeloma and acute lymphocytic leukemia. This resource is publicly available at https://clue.io/proteomics. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Topographic heterogeneity influences fish use of an experimentally restored tidal marsh.

PubMed

Larkin, Daniel J; Madon, Sharook P; West, Janelle M; Zedler, Joy B

2008-03-01

Ecological theory predicts that incorporating habitat heterogeneity into restoration sites should enhance diversity and key functions, yet research is limited on how topographic heterogeneity affects higher trophic levels. Our large (8-ha) southern California restoration experiment tested effects of tidal creek networks and pools on trophic structure of salt marsh habitat and high-tide use by two regionally dominant fish species, California killifish (Fundulus parvipinnis) and longjaw mudsucker (Gillichthys mirabilis). We expected tidal creeks to function as "conduits" that would enhance connectivity between subtidal and intertidal habitat and pools to serve as microhabitat "oases" for fishes. Pools did provide abundant invertebrate prey and were a preferred microhabitat for F. parvipinnis, even when the entire marsh was inundated (catch rates were 61% higher in pools). However, G. mirabilis showed no preference for pools. At a larger scale, effects of tidal creek networks were also mixed. Areas containing creeks had 12% higher catch rates of G. mirabilis, but lower catch rates and feeding rates of F. parvipinnis. Collectively, the results indicate that restoring multiple forms of heterogeneity is required to provide opportunities for multiple target consumers.

Active smoking and risk of metabolic syndrome: a meta-analysis of prospective studies.

PubMed

Sun, Kan; Liu, Jianmin; Ning, Guang

2012-01-01

Epidemiological evidence suggests that smoking has been associated with emergence of metabolic syndrome. However, data on this issue are inconsistent and controversial. We therefore conducted a meta-analysis to examine the association between smoking and metabolic syndrome. We searched the Medline, Embase and the Cochrane Library database up to March 2012 to identify prospective cohort studies related to smoking and metabolic syndrome. Reference lists of retrieved articles were also reviewed. Summary effect estimates were derived using a random-effects model and stratified by gender, smoking dose, follow-up duration and geographical area. Primary analysis of 13 studies involving 56,691 participants and 8,688 cases detected a significant positive association between active smoking and risk of metabolic syndrome (pooled relative risk [RR] 1.26, 95% CI: 1.10-1.44). Estimates of effects were substantially consistent in the stratified analyses. In the dose-response analysis, risk of metabolic syndrome was stronger for active male smokers (pooled RR 1.34, 95% CI: 1.20-1.50) than it was for former male smokers (pooled RR 1.19, 95% CI: 1.00-1.42), and greater for heavy smokers (pooled RR 1.42, 95% CI: 1.27-1.59) compared with light smokers (pooled RR 1.10, 95% CI: 0.90-1.35). No evidence of statistical publication bias was found (Egger' s test P=0.227, Begg' s test P=0.113). Active smoking is associated with development of metabolic syndrome. Smoking cessation appears to reduce the risk of metabolic syndrome.

Association between dioxin and cancer incidence and mortality: a meta-analysis

NASA Astrophysics Data System (ADS)

Xu, Jinming; Ye, Yao; Huang, Fang; Chen, Hanwen; Wu, Han; Huang, Jian; Hu, Jian; Xia, Dajing; Wu, Yihua

2016-11-01

The objective of the present study was to systematically assess the association between dioxin/2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and cancer incidence and mortality. Systematic literature searches were conducted until July 2015 in Pubmed, Embase and Cochrane library to identify relevant studies. A random-effects model was applied to estimate the pooled odds ratio (OR), risk ratio (RR), standard incidence ratio (SIR) or standard mortality ratio (SMR) for cancer incidence or mortality. In addition, dose-response, meta-regression, subgroup, and publication bias analyses were conducted. Thirty-one studies involving 29,605 cancer cases and 3,478,748 participants were included. Higher external exposure level of TCDD was significantly associated with all cancer mortality (pooled SMR = 1.09, 95% CI: 1.01-1.19, p = 0.04), but not all cancer incidence (pooled RR = 1.01, 95% CI: 0.97-1.06, p = 0.49). Higher blood level of TCDD was both significantly associated with all cancer incidence (pooled RR = 1.57, 95% CI: 1.21-2.04, p = 0.001) and all cancer mortality (pooled SMR = 1.45, 95% CI: 1.25-1.69, p < 0.001). Subgroup analysis suggested that higher external exposure and blood level of TCDD were both significantly associated with the mortality caused by non-Hodgkin’s lymphoma. In conclusion, external exposure and blood level of TCDD were both significantly associated with all cancer mortality, especially for non-Hodgkin’s lymphoma.

The relationship between heart rate and mortality of patients with acute coronary syndromes in the coronary intervention era: Meta-analysis.

PubMed

Xu, Tan; Zhan, Youqin; Xiong, Jianping; Lu, Nan; He, Zhuoqiao; Su, Xi; Tan, Xuerui

2016-11-01

Most of acute coronary syndromes (ACS) were receiving intervention treatment a high overall rate of coronary angiography in the modern medical practice.Consequently, we conduct a review to determine the heart rate (HR) on the prognosis of ACS in the coronary intervention era. PubMed, EMBASE, MEDLINE, and the Cochrane Library was systematically searched up to May 2016 using the search terms "heart rate," "acute coronary syndrome," "acute myocardial infarction," "ST elevation myocardial infarction," "non-ST-segment elevation." The outcome of interest was all-cause mortality. All analyses were performed using Review Manager. Database searches retrieved 2324 citations. Eleven studies enrolling 156,374 patients were included. In-hospital mortality was significantly higher in the elevated HR group compared to the lower HR group (pooled RR 2.04, 95%CI 1.80-2.30, P < 0.0001). Individuals with elevated admission HR had increased risk of long-term mortality (Pooled RR = 1.63, 95%CI 1.27-2.10, P = 0.008) compared to lower admission HR. The pooled results showed elevated discharge and resting HR were related to increased mortality of patients with ACS (pooled RR 1.88, 95% CI 1.02-3.47, P = 0.04; pooled RR 2.14, 95%CI 1.37-3.33, P < 0.0001, respectively). Elevated HR may increase the mortality of ACS patients in the percutaneous coronary intervention era.

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.

Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway.

PubMed

Zhang, Ping; Kratz, Anne Sophie; Salama, Mohammed; Elabd, Seham; Heinrich, Thorsten; Wittbrodt, Joachim; Blattner, Christine; Davidson, Gary

2015-10-08

The p53 tumor suppressor protein is mainly regulated by alterations in the half-life of the protein, resulting in significant differences in p53 protein levels in cells. The major regulator of this process is Mdm2, which ubiquitinates p53 and targets it for proteasomal degradation. This process can be enhanced or reduced by proteins that associate with p53 or Mdm2 and several proteins have been identified with such an activity. Furthermore, additional ubiquitin ligases for p53 have been identified in recent years. Nevertheless, our understanding of how p53 abundance and Mdm2 activity are regulated remains incomplete. Here we describe a cell culture based overexpression screen to identify evolutionarily conserved regulators of the p53/Mdm2 circuit. The results from this large-scale screening method will contribute to a better understanding of the regulation of these important proteins. Expression screening was based on co-transfection of H1299 cells with pools of cDNA's from a Medaka library together with p53, Mdm2 and, as internal control, Ror2. After cell lysis, SDS-PAGE/WB analysis was used to detect alterations in these proteins. More than one hundred hits that altered the abundance of either p53, Mdm2, or both were identified in the primary screen. Subscreening of the library pools that were identified in the primary screen identified several potential novel regulators of p53 and/or Mdm2. We also tested whether the human orthologues of the Medaka genes regulate p53 and/or Mdm2 abundance. All human orthologues regulated p53 and/or Mdm2 abundance in the same manner as the proteins from Medaka, which underscores the suitability of this screening methodology for the identification of new modifiers of p53 and Mdm2. Despite enormous efforts in the last two decades, many unknown regulators for p53 and Mdm2 abundance are predicted to exist. This cross-species approach to identify evolutionarily conserved regulators demonstrates that our Medaka unigene cDNA library represents a powerful tool to screen for these novel regulators of the p53/Mdm2 pathway.

An Author in Every Classroom: Kids Connecting with Authors via Skype. It's the next Best Thing to Being There

ERIC Educational Resources Information Center

Messner, Kate

2010-01-01

This article discusses how Skype and other video-conferencing software have become a staple for teachers, librarians, and authors who want to get kids excited about reading. The past year has brought a huge increase in the number of schools and libraries using Skype to connect classrooms and bring in experts to talk with kids. And with cuts in…

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

PubMed

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22-48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.

Combining yeast display and competitive FACS to select rare hapten-specific clones from recombinant antibody libraries

DOE PAGES

Sun, Yue; Ban, Bhupal; Bradbury, Andrew; ...

2016-08-29

The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 10 6 ) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used firstmore » to enrich the library between 20- and 100- fold for clones that bound to phenanthrene-protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. Furthermore, this selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies.« less

Combining yeast display and competitive FACS to select rare hapten-specific clones from recombinant antibody libraries

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

Sun, Yue; Ban, Bhupal; Bradbury, Andrew

The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 10 6 ) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used firstmore » to enrich the library between 20- and 100- fold for clones that bound to phenanthrene-protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. Furthermore, this selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies.« less

High-throughput, image-based screening of pooled genetic variant libraries

PubMed Central

Emanuel, George; Moffitt, Jeffrey R.; Zhuang, Xiaowei

2018-01-01

Image-based, high-throughput screening of genetic perturbations will advance both biology and biotechnology. We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in numerous individual cells. We achieve genotyping by introducing barcoded genetic variants into cells and using massively multiplexed FISH to measure the barcodes. We demonstrated this method by screening mutants of the fluorescent protein YFAST, yielding brighter and more photostable YFAST variants. PMID:29083401

The 2017 Solar Eclipse Community Impacts through Public Library Engagement

NASA Astrophysics Data System (ADS)

Dusenbery, P.; Holland, A.; LaConte, K.; Mosshammer, G.; Harold, J. B.; Fraknoi, A.; Schatz, D.; Duncan, D. K.

2017-12-01

More than two million pairs of eclipse glasses were distributed free through public libraries in the U.S. for the solar eclipse of the Sun taking place on August 21, 2017. About 7,000 organizations, including public library branches, bookmobiles, tribal libraries, library consortia, and state libraries took part in the celestial event of the century. Many organizations received a package of free safe-viewing glasses, plus a 24-page information booklet about eclipse viewing and suggested program ideas. An educational video was also produced on how best to do public outreach programs about the eclipse. The project was supported, in part, by the Gordon and Betty Moore Foundation, with additional help from Google, NASA, the Research Corporation, and the National Science Foundation (NSF). The program was managed through the Space Science Institute's National Center for Interactive Learning as part of its STAR Library Network (STAR_Net). Resources developed by STAR_Net for this event included an Eclipse Resource Center; a newsletter for participating libraries to learn about eclipses and how to implement an effective and safe eclipse program; eclipse program activities on its STEM Activity Clearinghouse; webinars; and connections to subject matter experts from NASA's and the American Astronomical Society's volunteer networks. This presentation will provide an overview of the extensive collaboration that made this program possible as well as highlight the national impact that public libraries made in their communities.

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.

Multiplexed microsatellite recovery using massively parallel sequencing

USGS Publications Warehouse

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Gene-targeted Random Mutagenesis to Select Heterochromatin-destabilizing Proteasome Mutants in Fission Yeast.

PubMed

Seo, Hogyu David; Lee, Daeyoup

2018-05-15

Random mutagenesis of a target gene is commonly used to identify mutations that yield the desired phenotype. Of the methods that may be used to achieve random mutagenesis, error-prone PCR is a convenient and efficient strategy for generating a diverse pool of mutants (i.e., a mutant library). Error-prone PCR is the method of choice when a researcher seeks to mutate a pre-defined region, such as the coding region of a gene while leaving other genomic regions unaffected. After the mutant library is amplified by error-prone PCR, it must be cloned into a suitable plasmid. The size of the library generated by error-prone PCR is constrained by the efficiency of the cloning step. However, in the fission yeast, Schizosaccharomyces pombe, the cloning step can be replaced by the use of a highly efficient one-step fusion PCR to generate constructs for transformation. Mutants of desired phenotypes may then be selected using appropriate reporters. Here, we describe this strategy in detail, taking as an example, a reporter inserted at centromeric heterochromatin.

Fragment-Based Phenotypic Lead Discovery: Cell-Based Assay to Target Leishmaniasis.

PubMed

Ayotte, Yann; Bilodeau, François; Descoteaux, Albert; LaPlante, Steven R

2018-05-02

A rapid and practical approach for the discovery of new chemical matter for targeting pathogens and diseases is described. Fragment-based phenotypic lead discovery (FPLD) combines aspects of traditional fragment-based lead discovery (FBLD), which involves the screening of small-molecule fragment libraries to target specific proteins, with phenotypic lead discovery (PLD), which typically involves the screening of drug-like compounds in cell-based assays. To enable FPLD, a diverse library of fragments was first designed, assembled, and curated. This library of soluble, low-molecular-weight compounds was then pooled to expedite screening. Axenic cultures of Leishmania promastigotes were screened, and single hits were then tested for leishmanicidal activity against intracellular amastigote forms in infected murine bone-marrow-derived macrophages without evidence of toxicity toward mammalian cells. These studies demonstrate that FPLD can be a rapid and effective means to discover hits that can serve as leads for further medicinal chemistry purposes or as tool compounds for identifying known or novel targets. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment.

PubMed

Minovski, Nikola; Perdih, Andrej; Solmajer, Tom

2012-05-01

The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial 6-FQs were assessed using an in-house developed drug-likeness filter integrating the Lipinski/Veber rule-sets. The compounds recognized as drug-like were used as an external set for prediction of the biological activity values using a neural-networks (NN) model based on an experimentally-determined set of active 6-FQs. Furthermore, a subset of compounds was extracted from the pool of drug-like 6-FQs, with predicted biological activity, and subsequently used in virtual screening (VS) campaign combining pharmacophore modeling and molecular docking studies. This complex scheme, a powerful combination of chemometric and molecular modeling approaches provided novel QSAR guidelines that could aid in the further lead development of 6-FQs agents.

Unilateral vocal fold paralysis after congenital cardiothoracic surgery: a meta-analysis.

PubMed

Strychowsky, Julie E; Rukholm, Gavin; Gupta, Michael K; Reid, Diane

2014-06-01

There is variation in the literature in regard to the occurrence of unilateral vocal fold paralysis (UVFP) after congenital cardiothoracic surgery. The objective of this study was to identify and appraise the evidence for the occurrence of UVFP after congenital cardiothoracic surgery in a meta-analysis. A comprehensive search strategy in Medline, Embase, and the Cochrane Library was conducted, limited to English publications. Two independent reviewers screened studies for eligibility criteria. Of the 162 identified studies, 32 (20%) met the inclusion criteria. Using the Oxford Centre for Evidence-Based Medicine guidelines, 2 reviewers appraised the level of evidence, extracted data, and resolved discrepancies by consensus. Weighted pooled proportion and 95% confidence intervals (CIs) are reported. Thirty-two studies (n = 5625 patients) were included. Levels of evidence varied from level 3 to 4. Among all studies, the weighted pooled proportion of UVFP was 9.3% (95% CI, 6.6% to 12.5%), and among 11 studies (n = 584 patients) that postoperatively evaluated patients with flexible nasopharyngolaryngoscopy to document presence of UVFP, the weighted pooled proportion of UVFP was 29.8% (95% CI, 18.5% to 42.5%). Twenty-one studies (n = 2748 patients) evaluated patients undergoing patent ductus arteriosus ligation surgery, and the weighted pooled proportion of UVFP was 8.7% (95% CI, 5.4% to 12.6%). Six of these (n = 274 patients) assessed all patients postoperatively, and the weighted pooled proportion of UVFP was 39% (95% CI, 18% to 63%). Pooled analyses of risk factors and comorbidities are reported. Heterogeneity and publication bias were detected. UVFP is a demonstrated risk of congenital cardiothoracic surgery. Routine postoperative nasopharyngolaryngoscopy for vocal fold assessment by an otolaryngologist is suggested. Copyright © 2014 by the American Academy of Pediatrics.

Endoscopic needle-knife treatment for symptomatic esophageal Zenker's diverticulum: A meta-analysis and systematic review.

PubMed

Li, Lian Yong; Yang, Yong Tao; Qu, Chang Min; Liang, Shu Wen; Zhong, Chang Qing; Wang, Xiao Ying; Chen, Yan; Spandorfer, Robert M; Christofaro, Sarah; Cai, Qiang

2018-04-01

The aim of this study was to assess the efficacy and safety following endoscopic management of Zenker's diverticulum (ZD) using a needle-knife technique. A systematic search of PubMed, Embase and Cochrane library databases was performed. All original studies reporting efficacy and safety of needle-knife technique for treatment of ZD were included. Pooled event rates across studies were expressed with summative statistics. Main outcomes, such as rates of immediate symptomatic response (ISR), adverse events and recurrence, were extracted, pooled and analyzed. Heterogeneity among studies was assessed using the R statistic. The random effects model was used and results were expressed with forest plots and summative statistics. Thirteen studies included 589 patients were enrolled. Pooled event rates for ISR, overall complication, bleeding and perforation were 88% (95% confidence interval [CI] 79-94%), 13% (95% CI 8-22%), 5% (95% CI 3-10%) and 7% (95% CI 4-12%), respectively. The pooled data demonstrated an overall recurrence rate of 14% (95% CI 9-21%). Diverticulum size of at least 4 cm and less than 4 cm demonstrated pooled adverse event rates of 17% (95% CI 10-27%) and 7% (95% CI 2-18%), respectively. When using diverticuloscope as an accessory, pooled ISR and adverse events rates were 84% (95% CI 58-95%) and 10% (95% CI 3-26%), respectively. Flexible endoscopic procedures using needle-knife offers a relatively safe and effective treatment of symptomatic ZD, especially for ZD of <4 cm in diameter. © 2018 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.

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

Calculations of the skyshine gamma-ray dose rates from independent spent fuel storage installations (ISFSI) under worst case accident conditions

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

Pace, J.V. III; Cramer, S.N.; Knight, J.R.

1980-09-01

Calculations of the skyshine gamma-ray dose rates from three spent fuel storage pools under worst case accident conditions have been made using the discrete ordinates code DOT-IV and the Monte Carlo code MORSE and have been compared to those of two previous methods. The DNA 37N-21G group cross-section library was utilized in the calculations, together with the Claiborne-Trubey gamma-ray dose factors taken from the same library. Plots of all results are presented. It was found that the dose was a strong function of the iron thickness over the fuel assemblies, the initial angular distribution of the emitted radiation, and themore » photon source near the top of the assemblies. 16 refs., 11 figs., 7 tabs.« less

GABAergic neurons in ferret visual cortex participate in functionally specific networks

PubMed Central

Wilson, Daniel E.; Smith, Gordon B.; Jacob, Amanda; Walker, Theo; Dimidschstein, Jordane; Fishell, Gord J.; Fitzpatrick, David

2017-01-01

Summary Functional circuits in the visual cortex require the coordinated activity of excitatory and inhibitory neurons. Molecular genetic approaches in the mouse have led to the ‘local nonspecific pooling principle’ of inhibitory connectivity, in which inhibitory neurons are untuned for stimulus features due to the random pooling of local inputs. However, it remains unclear whether this principle generalizes to species with a columnar organization of feature selectivity such as carnivores, primates, and humans. Here we use virally-mediated GABAergic-specific GCaMP6f expression to demonstrate that inhibitory neurons in ferret visual cortex respond robustly and selectively to oriented stimuli. We find that the tuning of inhibitory neurons is inconsistent with the local non-specific pooling of excitatory inputs, and that inhibitory neurons exhibit orientation-specific noise correlations with local and distant excitatory neurons. These findings challenge the generality of the non-specific pooling principle for inhibitory neurons, suggesting different rules for functional excitatory-inhibitory interactions in non-murine species. PMID:28279352

MedlinePlus FAQ: Disease or Condition Information

MedlinePlus

... on the Health Topics button on the MedlinePlus homepage. You can also find the Health Topics button ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

Into the Curriculum.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1986

1986-01-01

Provides fully-developed library media activities designed to be used in connection with specific curriculum units in mathematics (consumer education); reading and language arts ("Foolish People in Folk Tales"); science (dinosaurs); and social studies (Roman cities and Third World countries). (Author/EM)

Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy.

PubMed

Eberwine, James; Bartfai, Tamas

2011-03-01

We report on an 'unbiased' molecular characterization of individual, adult neurons, active in a central, anterior hypothalamic neuronal circuit, by establishing cDNA libraries from each individual, electrophysiologically identified warm sensitive neuron (WSN). The cDNA libraries were analyzed by Affymetrix microarray. The presence and frequency of cDNAs were confirmed and enhanced with Illumina sequencing of each single cell cDNA library. cDNAs encoding the GABA biosynthetic enzyme Gad1 and of adrenomedullin, galanin, prodynorphin, somatostatin, and tachykinin were found in the WSNs. The functional cellular and in vivo studies on dozens of the more than 500 neurotransmitters, hormone receptors and ion channels, whose cDNA was identified and sequence confirmed, suggest little or no discrepancy between the transcriptional and functional data in WSNs; whenever agonists were available for a receptor whose cDNA was identified, a functional response was found. Sequencing single neuron libraries permitted identification of rarely expressed receptors like the insulin receptor, adiponectin receptor 2 and of receptor heterodimers; information that is lost when pooling cells leads to dilution of signals and mixing signals. Despite the common electrophysiological phenotype and uniform Gad1 expression, WSN transcriptomes show heterogeneity, suggesting strong epigenetic influence on the transcriptome. Our study suggests that it is well-worth interrogating the cDNA libraries of single neurons by sequencing and chipping. Copyright © 2010 Elsevier Inc. All rights reserved.

Preparation and screening of an arrayed human genomic library generated with the P1 cloning system.

PubMed Central

Shepherd, N S; Pfrogner, B D; Coulby, J N; Ackerman, S L; Vaidyanathan, G; Sauer, R H; Balkenhol, T C; Sternberg, N

1994-01-01

We describe here the construction and initial characterization of a 3-fold coverage genomic library of the human haploid genome that was prepared using the bacteriophage P1 cloning system. The cloned DNA inserts were produced by size fractionation of a Sau3AI partial digest of high molecular weight genomic DNA isolated from primary cells of human foreskin fibroblasts. The inserts were cloned into the pAd10sacBII vector and packaged in vitro into P1 phage. These were used to generate recombinant bacterial clones, each of which was picked robotically from an agar plate into a well of a 96-well microtiter dish, grown overnight, and stored at -70 degrees C. The resulting library, designated DMPC-HFF#1 series A, consists of approximately 130,000-140,000 recombinant clones that were stored in 1500 microtiter dishes. To screen the library, clones were combined in a pooling strategy and specific loci were identified by PCR analysis. On average, the library contains two or three different clones for each locus screened. To date we have identified a total of 17 clones containing the hypoxanthine-guanine phosphoribosyltransferase, human serum albumin-human alpha-fetoprotein, p53, cyclooxygenase I, human apurinic endonuclease, beta-polymerase, and DNA ligase I genes. The cloned inserts average 80 kb in size and range from 70 to 95 kb, with one 49-kb insert and one 62-kb insert. Images PMID:8146166

Database Entity Persistence with Hibernate for the Network Connectivity Analysis Model

DTIC Science & Technology

2014-04-01

time savings in the Java coding development process. Appendices A and B describe address setup procedures for installing the MySQL database...development environment is required: • The open source MySQL Database Management System (DBMS) from Oracle, which is a Java Database Connectivity (JDBC...compliant DBMS • MySQL JDBC Driver library that comes as a plug-in with the Netbeans distribution • The latest Java Development Kit with the latest

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

7 CFR 1710.252 - Construction work plans-power supply borrowers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... operating systems of supporting power pools and to connect with adjacent power suppliers; (4) Improvements..., new substations and substation improvements and replacements, and Systems Control and Data Acquisition... include studies of load flows, voltage regulation, and stability characteristics to demonstrate system...

WAIS Searching of the Current Contents Database

NASA Astrophysics Data System (ADS)

Banholzer, P.; Grabenstein, M. E.

The Homer E. Newell Memorial Library of NASA's Goddard Space Flight Center is developing capabilities to permit Goddard personnel to access electronic resources of the Library via the Internet. The Library's support services contractor, Maxima Corporation, and their subcontractor, SANAD Support Technologies have recently developed a World Wide Web Home Page (http://www-library.gsfc.nasa.gov) to provide the primary means of access. The first searchable database to be made available through the HomePage to Goddard employees is Current Contents, from the Institute for Scientific Information (ISI). The initial implementation includes coverage of articles from the last few months of 1992 to present. These records are augmented with abstracts and references, and often are more robust than equivalent records in bibliographic databases that currently serve the astronomical community. Maxima/SANAD selected Wais Incorporated's WAIS product with which to build the interface to Current Contents. This system allows access from Macintosh, IBM PC, and Unix hosts, which is an important feature for Goddard's multiplatform environment. The forms interface is structured to allow both fielded (author, article title, journal name, id number, keyword, subject term, and citation) and unfielded WAIS searches. The system allows a user to: Retrieve individual journal article records. Retrieve Table of Contents of specific issues of journals. Connect to articles with similar subject terms or keywords. Connect to other issues of the same journal in the same year. Browse journal issues from an alphabetical list of indexed journal names.

Making connections: Listening to visitor conversations at different styles of sea jelly exhibits

NASA Astrophysics Data System (ADS)

Galvan, Tamara M.

This study sought to determine what types of connections to prior experiences and knowledge were being made at two different styles of exhibits focusing on sea jellies. Family groups, consisting of one or two adults with one or two children aged 6-11, were audio recorded and tracked as they visited a view-only or touch pool sea jelly exhibit. A short interview was given after their visit to the sea jelly exhibit. The discourse from the exhibit and survey were coded for types of learning talk. Coding was also done to determine the inspiration for the connection and the subject of the connection (structural or behavioral). Visitors made connections regardless of the seajelly.exhibit design and results showed no differences in the type or frequency of the connections made. However, visitors were more likely to make connections on the subject of the sea jelly structure at the view only exhibit. Many of the connections, regardless of subject or inspiration, were metaphoric connections, demonstrating the importance of metaphors for making prior experience connections. Findings provide useful information for future aquarium practice.

Genome-Wide Mutagenesis in Borrelia burgdorferi.

PubMed

Lin, Tao; Gao, Lihui

2018-01-01

Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector. STM procedure combined with Luminex Flex ® Map™ technology and next-generation sequencing (e.g., Tn-seq) are the powerful high-throughput tools for the determination of Borrelia burgdorferi virulence determinants. The assessment of multiple tissue sites and two DNA resources at two different time points using Luminex Flex ® Map™ technology provides a robust data set. B. burgdorferi transposon mutant screening indicates that a high proportion of genes are the novel virulence determinants that are required for mouse and tick infection. In this protocol, an effective signature-tagged Himar1-based transposon suicide vector was developed and used to generate a sequence-defined library of nearly 4800 mutants in the infectious B. burgdorferi B31 clone. In STM, signature-tagged suicide vectors are constructed by inserting unique DNA sequences (tags) into the transposable elements. The signature-tagged transposon mutants are generated when transposon suicide vectors are transformed into an infectious B. burgdorferi clone, and the transposable element is transposed into the 5'-TA-3' sequence in the B. burgdorferi genome with the signature tag. The transposon library is created and consists of many sub-libraries, each sub-library has several hundreds of mutants with same tags. A group of mice or ticks are infected with a mixed population of mutants with different tags, after recovered from different tissues of infected mice and ticks, mutants from output pool and input pool are detected using high-throughput, semi-quantitative Luminex ® FLEXMAP™ or next-generation sequencing (Tn-seq) technologies. Thus far, we have created a high-density, sequence-defined transposon library of over 6600 STM mutants for the efficient genome-wide investigation of genes and gene products required for wild-type pathogenesis, host-pathogen interactions, in vitro growth, in vivo survival, physiology, morphology, chemotaxis, motility, structure, metabolism, gene regulation, plasmid maintenance and replication, etc. The insertion sites of 4480 transposon mutants have been determined. About 800 predicted protein-encoding genes in the genome were disrupted in the STM transposon library. The infectivity and some functions of 800 mutants in 500 genes have been determined. Analysis of these transposon mutants has yielded valuable information regarding the genes and gene products important in the pathogenesis and biology of B. burgdorferi and its tick vectors.

Influence of intermittent stream connectivity on water quality and salmonid survivorship.

NASA Astrophysics Data System (ADS)

Hildebrand, J.; Woelfle-Erskine, C. A.; Larsen, L.

2014-12-01

Anthropogenic stress and climate change are causing an increasing number of California streams to become intermittent and are driving earlier and more severe summertime drying. The extent to which emerging water conservation alternatives impact flows or habitat quality (e.g. temperature, DO) for salmonids remains poorly understood. Here, we investigate the proximal drivers of salmonid mortality over a range of connectivity conditions during summertime intermittency in Salmon Creek watershed, Sonoma County, CA. Through extensive sampling in paired subwatersheds over a period of two years, we tested the hypothesis that accumulation of readily bioavailable DOC in poorly flushed pools drives DO decline associated with loss of salmonids. We then traced the origin and flow pathways of DOC throughout the watershed using Parallel Factor Analysis (PARAFAC). We obtained samples for DOC and stable isotope analyses at monthly intervals from 20 piezometers and surface water in the study reaches and from private wells and springs distributed throughout the watersheds. We also obtained in situ DO, conductivity and pH readings within stream study reaches. We determined DOC quality by SUVA (specific UV absorbance) and fluorescence index. We calculated stream metabolism rates using the single station method. In pools instrumented with DO sensors, we compared changing DOC quality during the summer months to changes in DO concentrations and stream metabolism. Our results show that the duration of complete disconnection of pools during the summer months and stream metabolic rates are positively correlated with salmonid mortality. Furthermore, our results indicate that salmonid mortality is greatest in disconnected pools with low DOC fluorescence indices and high SUVA values, indicative of terrestrially derived DOC and little or no groundwater inflow. Conversely low salmonid mortality was found in disconnected pools with high fluorescence index and low SUVA, indicative of microbially derived DOC. These pools showed clear signs of hyporheic inflow during summertime drying despite complete surficial disconnection. PARAFAC analysis pinpointed groundwater sources of hyporheic flow in the watershed, suggesting that targeted aquifer recharge may contribute to salmonid recovery by augmenting flow in summer refugia.

Mapping internal connectivity through human migration in malaria endemic countries.

PubMed

Sorichetta, Alessandro; Bird, Tom J; Ruktanonchai, Nick W; Zu Erbach-Schoenberg, Elisabeth; Pezzulo, Carla; Tejedor, Natalia; Waldock, Ian C; Sadler, Jason D; Garcia, Andres J; Sedda, Luigi; Tatem, Andrew J

2016-08-16

Human mobility continues to increase in terms of volumes and reach, producing growing global connectivity. This connectivity hampers efforts to eliminate infectious diseases such as malaria through reintroductions of pathogens, and thus accounting for it becomes important in designing global, continental, regional, and national strategies. Recent works have shown that census-derived migration data provides a good proxy for internal connectivity, in terms of relative strengths of movement between administrative units, across temporal scales. To support global malaria eradication strategy efforts, here we describe the construction of an open access archive of estimated internal migration flows in endemic countries built through pooling of census microdata. These connectivity datasets, described here along with the approaches and methods used to create and validate them, are available both through the WorldPop website and the WorldPop Dataverse Repository.

Mapping internal connectivity through human migration in malaria endemic countries

PubMed Central

Sorichetta, Alessandro; Bird, Tom J.; Ruktanonchai, Nick W.; zu Erbach-Schoenberg, Elisabeth; Pezzulo, Carla; Tejedor, Natalia; Waldock, Ian C.; Sadler, Jason D.; Garcia, Andres J.; Sedda, Luigi; Tatem, Andrew J.

2016-01-01

Human mobility continues to increase in terms of volumes and reach, producing growing global connectivity. This connectivity hampers efforts to eliminate infectious diseases such as malaria through reintroductions of pathogens, and thus accounting for it becomes important in designing global, continental, regional, and national strategies. Recent works have shown that census-derived migration data provides a good proxy for internal connectivity, in terms of relative strengths of movement between administrative units, across temporal scales. To support global malaria eradication strategy efforts, here we describe the construction of an open access archive of estimated internal migration flows in endemic countries built through pooling of census microdata. These connectivity datasets, described here along with the approaches and methods used to create and validate them, are available both through the WorldPop website and the WorldPop Dataverse Repository. PMID:27529469

Biogenic silicon pools in terrestrial biogeosystems and their significance for silicon cycling

NASA Astrophysics Data System (ADS)

Puppe, Daniel; Höhn, Axel; Kaczorek, Danuta; Ehrmann, Otto; Wanner, Manfred; Sommer, Michael

2017-04-01

On a global scale the biogeochemical cycles of silicon (Si) and carbon are connected by weathering processes and fluxes of dissolved Si from terrestrial to aquatic ecosystems. Various pro- and eukaryotic organisms are evolutionarily adapted to synthesize amorphous siliceous structures (biosilicification). In soils these siliceous structures can accumulate and form biogenic Si (BSi) pools, whereat it can be differentiated between phytogenic (BSi synthesized by plants), zoogenic (BSi synthesized by sponges), microbial (BSi synthesized by bacteria and fungi) and protistic (BSi synthesized by unicellular organisms) pools. Accumulation and recycling of BSi in terrestrial biogeosystems influence fluxes of dissolved Si from the continents to the oceans, thus act as a filter in the global Si cycle. As research has primarily been focused on the role of phytogenic Si pools until now there is only little information available on the other BSi pools in soils. In order to fill this knowledge gap we examined different BSi pools in soils of initial and forested terrestrial biogeosystems using modern microscopical methods (laser scanning and scanning electron microscopy). In forested biogeosystems we further analyzed abiotic (e.g. soil pH) and biotic (earthworm biomasses) influencing factors on BSi pool size, while samples of initial biogeosystems were used to analyze spatiotemporal BSi pool dynamics. We found that especially biotic interactions are important factors for protistic BSi pools (represented by testate amoebae) and that phytogenic Si pools are about several 100-times bigger than protistic (testate amoebae) Si pools (0.2-4.7 kg Si ha-1). However, annual biosilicification rates of testate amoebae (up to 80 kg Si ha-1) are comparable to or even can exceed annual silicon uptake by trees. Our studies of initial biogeosystems revealed that BSi pool sizes increased markedly within a relatively short time span (<10 years) of ecosystem development. Differences in quantities, dynamics and resistibility against dissolution of various BSi pools indicated their possibility to influence biogeochemical Si cycling relatively rapid (protistic Si pools) or slow (zoogenic Si pools). In conclusion, our results are crucial for a detailed understanding and a more precise modeling of Si fluxes from terrestrial to aquatic ecosystems.

Spatial variation in fish species richness of the upper Mississippi River system

USGS Publications Warehouse

Koel, T.M.

2004-01-01

Important natural environmental gradients, including the connectivity of off-channel aquatic habitats to the main-stem river, have been lost in many reaches of the upper Mississippi River system, and an understanding of the consequences of this isolation is lacking in regard to native fish communities. The objectives of this study were to describe patterns of fish species richness, evenness, and diversity among representative habitats and river reaches and to examine the relationship between fish species richness and habitat diversity. Each year (1994-1999) fish communities of main-channel borders (MCB), side channel borders (SCB), and contiguous backwater shorelines (BWS) were sampled using boat-mounted electrofishing, mini-fyke-nets, tyke nets, hoop nets, and seines at a standardized number of sites. A total of 0.65 million fish were collected, representing 106 species from upper Mississippi River Pools 4, 8, 13, and 26; the open (unimpounded) river reach; and the La Grange Reach of the Illinois River. Within pools, species richness based on rarefaction differed significantly among habitats and was highest in BWS and lowest in MCB (P < 0.0001). At the reach scale, Pools 4, 8, and 13 consistently had the highest species richness and Pool 26, the open-river reach, and the La Grange Reach were significantly lower (P < 0.0001). Species evenness and diversity indices showed similar trends. The relationship between native fish species richness and habitat diversity was highly significant (r(2) = 0.85; P = 0.0091). These results support efforts aimed at the conservation and enhancement of connected side channels and backwaters. Although constrained by dams, pools with high native species richness could serve as a relative reference. The remnants of natural riverine dynamics that remain in these reaches should be preserved and enhanced; conditions could be used to guide restoration activities in more degraded reaches.

Can Imaging Parameters Provide Information Regarding Histopathology in Head and Neck Squamous Cell Carcinoma? A Meta-Analysis.

PubMed

Surov, Alexey; Meyer, Hans Jonas; Wienke, Andreas

2018-04-01

Our purpose was to provide data regarding relationships between different imaging and histopathological parameters in HNSCC. MEDLINE library was screened for associations between different imaging parameters and histopathological features in HNSCC up to December 2017. Only papers containing correlation coefficients between different imaging parameters and histopathological findings were acquired for the analysis. Associations between 18 F-FDG positron emission tomography (PET) and KI 67 were reported in 8 studies (236 patients). The pooled correlation coefficient was 0.20 (95% CI = [-0.04; 0.44]). Furthermore, in 4 studies (64 patients), associations between 18 F-fluorothymidine PET and KI 67 were analyzed. The pooled correlation coefficient between SUV max and KI 67 was 0.28 (95% CI = [-0.06; 0.94]). In 2 studies (23 patients), relationships between KI 67 and dynamic contrast-enhanced magnetic resonance imaging were reported. The pooled correlation coefficient between K trans and KI 67 was -0.68 (95% CI = [-0.91; -0.44]). Two studies (31 patients) investigated correlation between apparent diffusion coefficient (ADC) and KI 67. The pooled correlation coefficient was -0.61 (95% CI = [-0.84; -0.38]). In 2 studies (117 patients), relationships between 18 F-FDG PET and p53 were analyzed. The pooled correlation coefficient was 0.0 (95% CI = [-0.87; 0.88]). There were 3 studies (48 patients) that investigated associations between ADC and tumor cell count in HNSCC. The pooled correlation coefficient was -0.53 (95% CI = [-0.74; -0.32]). Associations between 18 F-FDG PET and HIF-1α were investigated in 3 studies (72 patients). The pooled correlation coefficient was 0.44 (95% CI = [-0.20; 1.08]). ADC may predict cell count and proliferation activity, and SUV max may predict expression of HIF-1α in HNSCC. SUV max cannot be used as surrogate marker for expression of KI 67 and p53. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Effects of Pilates-based exercises on pain and disability in individuals with persistent nonspecific low back pain: a systematic review with meta-analysis.

PubMed

Lim, Edwin Choon Wyn; Poh, Ruby Li Choo; Low, Ai Ying; Wong, Wai Pong

2011-02-01

A systematic review with meta-analysis. To compare pain and disability in individuals with persistent nonspecific low back pain who were treated with Pilates exercises compared to minimal or other interventions. Searches of Medline, CINAHL, Embase, Cochrane library, PEDro, and ProQuest Dissertations and Thesis databases were conducted. Randomized controlled trials (RCTs) were selected and reviewed if they compared pain and disability in individuals with persistent nonspecific low back pain who were treated with Pilates exercises compared to other treatment approaches. Quality of the trials was evaluated. Data for pain and disability scores were extracted. Narrative synthesis plus meta-analyses were performed, with either a fixed-effects or random-effects model, standardized mean differences (SMDs), and tests for heterogeneity. Seven RCTs were identified and included in the meta-analyses. Data pooling was performed using RevMan 5. When compared to minimal intervention, Pilates-based exercise provided superior pain relief (pooled SMD, -2.72; 95% CI: -5.33, -0.11; P = .04) but the pooled disability scores were not significantly different (pooled SMD, -0.74; 95% CI: -1.81, 0.33;P = .17). No significant differences were found when comparing Pilates-based exercise to other forms of exercise for pain (pooled SMD, 0.03; 95% CI: -0.52, 0.58; P = .92) or disability scores (pooled SMD, -0.41; 95% CI: -0.96, 0.14; P = .14). Pilates-based exercises are superior to minimal intervention for pain relief. Existing evidence does not establish superiority of Pilates-based exercise to other forms of exercise to reduce pain and disability for patients with persistent nonspecific low back pain. However, the relatively low quality of existing studies and the heterogeneity of pooled studies in this systematic review combine to suggest that these results should be interpreted with caution. Therapy, level 1a.

Performance of prenatal screening using maternal serum and ultrasound markers for Down syndrome in Chinese women: a systematic review and meta-analysis.

PubMed

Tu, S; Rosenthal, M; Wang, D; Huang, J; Chen, Y

2016-09-01

Controversies about the performance of conventional prenatal screening using maternal serum and ultrasound markers (PSMSUM) in detecting Down syndrome (DS) have been raised as a result of a recently available noninvasive prenatal test based on cell-free fetal DNA sequencing. To evaluate the screening performance of PSMSUM in detecting DS in Chinese women. An exhaustive literature search of MEDLINE, Embase, the Cochrane Library, ISI Web of Science and China BioMedical Disc. Primary studies, published from January 2004 to November 2014, which examined the screening accuracy of PSMSUM in pregnant Chinese women, compared with a reference standard, either chromosomal verification or inspection of the newborn. Data were extracted as screening positive/negative results for Down and non-Down syndrome pregnancies, allowing estimation of sensitivities and specificities. Risks of bias within and across studies were assessed. Screening accuracy measures were pooled using a bivariate random effects regression model. Seventy-eight studies, involving six categories of PSMSUM, were included. Second-trimester double serum [pooled sensitivity (SEN) = 0.80, pooled specificity (SPE) = 0.95] and triple-serum (pooled SEN = 0.79, pooled SPE = 0.96) screening were the predominant PSMSUM methods. The screening performances of these methods achieved the national standard but varied enormously across studies. First-trimester combined screening (pooled SEN = 0.92, pooled SPE = 0.93) and second-trimester quadruple serum screening (median SEN = 0.86, median SPE = 0.96) performed better, but were rarely used. Second-trimester maternal serum screening has the potential to achieve satisfactory screening performance in middle- and low-income countries. The reported enormous range in screening performance of second-trimester PSMSUM calls for urgent implementation of methods for performance optimization. Meta-analysis results show good accuracy of maternal serum and ultrasound screening for trisomy 21 in Chinese women. © 2016 Royal College of Obstetricians and Gynaecologists.

The virtual library: Coming of age

NASA Technical Reports Server (NTRS)

Hunter, Judy F.; Cotter, Gladys A.

1994-01-01

With the high speed networking capabilities, multiple media options, and massive amounts of information that exist in electronic format today, the concept of a 'virtual' library or 'library without walls' is becoming viable. In virtual library environment, the information processed goes beyond the traditional definition of documents to include the results of scientific and technical research and development (reports, software, data) recorded in any format or media: electronic, audio, video, or scanned images. Network access to information must include tools to help locate information sources and navigate the networks to connect to the sources, as well as methods to extract the relevant information. Graphical User Interfaces (GUI's) that are intuitive and navigational tools such as Intelligent Gateway Processors (IGP) will provide users with seamless and transparent use of high speed networks to access, organize, and manage information. Traditional libraries will become points of electronic access to information on multiple medias. The emphasis will be towards unique collections of information at each library rather than entire collections at every library. It is no longer a question of whether there is enough information available; it is more a question of how to manage the vast volumes of information. The future equation will involve being able to organize knowledge, manage information, and provide access at the point of origin.

75 FR 42432 - Northern Natural Gas Company, Southern Natural Gas Company, Florida Gas Transmission Company, LLC...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-21

... instructions on connecting to eLibrary, refer to the last page of this notice. Land Requirements for.... However, there would be some ground disturbance associated with offshore disconnects within federal waters...

Using Pool-seq to Search for Genomic Regions Affected by Hybrid Inviability in the copepod T. californicus.

PubMed

Lima, Thiago G; Willett, Christopher S

2018-05-11

The formation of reproductive barriers between allopatric populations involves the accumulation of incompatibilities that lead to intrinsic postzygotic isolation. The evolution of these incompatibilities is usually explained by the Dobzhansky-Muller model, where epistatic interactions that arise within the diverging populations, lead to deleterious interactions when they come together in a hybrid genome. These incompatibilities can lead to hybrid inviability, killing individuals with certain genotypic combinations, and causing the population's allele frequency to deviate from Mendelian expectations. Traditionally, hybrid inviability loci have been detected by genotyping individuals at different loci across the genome. However, this method becomes time consuming and expensive as the number of markers or individuals increases. Here, we test if a Pool-seq method can be used to scan the genome of F2 hybrids to detect genomic regions that are affected by hybrid inviability. We survey the genome of hybrids between 2 populations of the copepod Tigriopus californicus, and show that this method has enough power to detect even small changes in allele frequency caused by hybrid inviability. We show that allele frequency estimates in Pool-seq can be affected by the sampling of alleles from the pool of DNA during the library preparation and sequencing steps and that special considerations must be taken when aligning hybrid reads to a reference when the populations/species are divergent.

The Road to Pathways

ERIC Educational Resources Information Center

Cooper, Sandi

2013-01-01

Frequently drawn from elite corporate backgrounds and, for public institutions, from pools of politically connected people, trustees usually have to be educated about shared governance. Corporate or political ties are scarcely reliable indices of the wisdom necessary to oversee institutions of higher learning, and some trustees, sadly, prove…

The Long-Term Effects of Large Wood Placement on Salmonid Habitat in East Fork Mill Creek, Redwood National and State Park, California

NASA Astrophysics Data System (ADS)

Rodriguez, D. L.; Stubblefield, A. P.

2017-12-01

The conservation and recovery of anadromous salmonids (Oncorhynchus sp.) depend on stream restoration and protection of freshwater habitats. Instream large wood dictates channel morphology, increase retention of terrestrial inputs such as organic matter, nutrients and sediment, and enhances the quality of fish habitat. Historic land use/land cover changes have resulted in aquatic systems devoid of this component. Restoration by placement of large wood jams is intended to restore physical and biological processes. An important question for scientists and managers, in addition to the initial effectiveness of restoration, is the persistence and fate of this type of project. In this study we compare channel change and large wood attributes on the East Fork of Mill Creek, a tributary of the Smith River in northern California, eight years after a major instream wood placement effort took place. Our results are compared with previously published data from before and one year after the restoration. Preliminary results suggest the dramatic increase in spawning gravel abundance and large wood accumulation observed in the earlier study have persisted. From 2008 to 2016 a reduction in median sediment size, ranging from 103-136 percent, has been observed in a majority of the sites. The sites have continued to grow in size and influence by racking floating wood from upstream and destabilizing proximate banks of riparian alder, increasing both instream large wood volume (5-196 %) and floodplain connectivity. Preliminary results also show a decrease in residual pool depth and an increase in pool length which may be attributed to floodplain connectivity. Changes to the following attributes are evaluated: 1) wood loading (total site wood volume, total wood volume in active channel, and wood piece count); 2) percent pool cover by large wood; 3) residual pool depth; 4) upstream sediment aggradation; 5) floodplain connectivity; and 6) mean sediment size directly above and below large wood. We present on these results and statistical comparisons of total site wood volume with response factors.

Supporting the library and information needs of UWE health and social care students on placement.

PubMed

Plaice, Caroline; Lloyd, Jon; Shaw, Pauline

2017-03-01

The aim of this research was to explore the library and information needs of health and social care students whilst on placement. Both desk and primary research were conducted and included an online questionnaire to students and semi-structured interviews. The questionnaire was completed by 252 students from a variety of programmes, equivalent to a 10% response rate. The results indicate a wide range of factors impacting on the library and information experiences of students. Whilst differences in the availability of a physical library in hospital or community locations still exist, these are mitigated by technology and a preference for home study. A significant result is that 77% (n = 193) of students on placement study at home, using a variety of Internet-connected devices. This highlights a marked change in practice and underlines the need for mobile-compliant e-resources and accessible at-a-distance services. As a result of this research, practical recommendations on how library support can be improved were developed including enhanced collaboration and learning with NHS colleagues, and knowledge sharing with other departments within the University who support our students. © 2017 Health Libraries Group.

Meeting at the crossroads: collaboration between information technology departments and health sciences libraries

PubMed Central

King, Samuel; Cataldi-Roberts, Erica; Wentz, Erin

2017-01-01

Objective The purposes of this survey were to determine the nature and extent of collaboration between health sciences libraries and their information technology (IT) departments, to identify strengths and issues connected to this relationship, and to provide examples demonstrating exceptional collaborative success. Methods A fourteen-question survey was sent to a broad selection of health care and academic libraries through a variety of email discussion lists and was limited to one response per institution. Convenience sampling was used to collect the responses. Results An overwhelming majority of libraries described the relationship with their IT departments as good or excellent, and there were a variety of creative joint initiatives underway. Opportunities exist for continued and expanded library/IT collaboration. Conclusions Good quality relationships between libraries and their IT departments are essential due to the interconnected nature of their services, and fortunately, this appears to be the norm at a variety of institutions. Mutual respect, open communication, realization of each department’s mission, and responsiveness to each other’s needs are part of what makes these relationships successful, which in turn leads to successful collaborative ventures that bode well for the future of both services. PMID:28096743

Meeting at the crossroads: collaboration between information technology departments and health sciences libraries.

PubMed

King, Samuel; Cataldi-Roberts, Erica; Wentz, Erin

2017-01-01

The purposes of this survey were to determine the nature and extent of collaboration between health sciences libraries and their information technology (IT) departments, to identify strengths and issues connected to this relationship, and to provide examples demonstrating exceptional collaborative success. A fourteen-question survey was sent to a broad selection of health care and academic libraries through a variety of email discussion lists and was limited to one response per institution. Convenience sampling was used to collect the responses. An overwhelming majority of libraries described the relationship with their IT departments as good or excellent, and there were a variety of creative joint initiatives underway. Opportunities exist for continued and expanded library/IT collaboration. Good quality relationships between libraries and their IT departments are essential due to the interconnected nature of their services, and fortunately, this appears to be the norm at a variety of institutions. Mutual respect, open communication, realization of each department's mission, and responsiveness to each other's needs are part of what makes these relationships successful, which in turn leads to successful collaborative ventures that bode well for the future of both services.

DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences.

PubMed

Kunig, Verena; Potowski, Marco; Gohla, Anne; Brunschweiger, Andreas

2018-06-27

DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

Colonic lesion characterization in inflammatory bowel disease: A systematic review and meta-analysis

PubMed Central

Lord, Richard; Burr, Nicholas E; Mohammed, Noor; Subramanian, Venkataraman

2018-01-01

AIM To perform a systematic review and meta-analysis for the diagnostic accuracy of in vivo lesion characterization in colonic inflammatory bowel disease (IBD), using optical imaging techniques, including virtual chromoendoscopy (VCE), dye-based chromoendoscopy (DBC), magnification endoscopy and confocal laser endomicroscopy (CLE). METHODS We searched Medline, Embase and the Cochrane library. We performed a bivariate meta-analysis to calculate the pooled estimate sensitivities, specificities, positive and negative likelihood ratios (+LHR, -LHR), diagnostic odds ratios (DOR), and area under the SROC curve (AUSROC) for each technology group. A subgroup analysis was performed to investigate differences in real-time non-magnified Kudo pit patterns (with VCE and DBC) and real-time CLE. RESULTS We included 22 studies [1491 patients; 4674 polyps, of which 539 (11.5%) were neoplastic]. Real-time CLE had a pooled sensitivity of 91% (95%CI: 66%-98%), specificity of 97% (95%CI: 94%-98%), and an AUSROC of 0.98 (95%CI: 0.97-0.99). Magnification endoscopy had a pooled sensitivity of 90% (95%CI: 77%-96%) and specificity of 87% (95%CI: 81%-91%). VCE had a pooled sensitivity of 86% (95%CI: 62%-95%) and specificity of 87% (95%CI: 72%-95%). DBC had a pooled sensitivity of 67% (95%CI: 44%-84%) and specificity of 86% (95%CI: 72%-94%). CONCLUSION Real-time CLE is a highly accurate technology for differentiating neoplastic from non-neoplastic lesions in patients with colonic IBD. However, most CLE studies were performed by single expert users within tertiary centres, potentially confounding these results. PMID:29563760

Partial characterization of normal and Haemophilus influenzae-infected mucosal complementary DNA libraries in chinchilla middle ear mucosa.

PubMed

Kerschner, Joseph E; Erdos, Geza; Hu, Fen Ze; Burrows, Amy; Cioffi, Joseph; Khampang, Pawjai; Dahlgren, Margaret; Hayes, Jay; Keefe, Randy; Janto, Benjamin; Post, J Christopher; Ehrlich, Garth D

2010-04-01

We sought to construct and partially characterize complementary DNA (cDNA) libraries prepared from the middle ear mucosa (MEM) of chinchillas to better understand pathogenic aspects of infection and inflammation, particularly with respect to leukotriene biogenesis and response. Chinchilla MEM was harvested from controls and after middle ear inoculation with nontypeable Haemophilus influenzae. RNA was extracted to generate cDNA libraries. Randomly selected clones were subjected to sequence analysis to characterize the libraries and to provide DNA sequence for phylogenetic analyses. Reverse transcription-polymerase chain reaction of the RNA pools was used to generate cDNA sequences corresponding to genes associated with leukotriene biosynthesis and metabolism. Sequence analysis of 921 randomly selected clones from the uninfected MEM cDNA library produced approximately 250,000 nucleotides of almost entirely novel sequence data. Searches of the GenBank database with the Basic Local Alignment Search Tool provided for identification of 515 unique genes expressed in the MEM and not previously described in chinchillas. In almost all cases, the chinchilla cDNA sequences displayed much greater homology to human or other primate genes than with rodent species. Genes associated with leukotriene metabolism were present in both normal and infected MEM. Based on both phylogenetic comparisons and gene expression similarities with humans, chinchilla MEM appears to be an excellent model for the study of middle ear inflammation and infection. The higher degree of sequence similarity between chinchillas and humans compared to chinchillas and rodents was unexpected. The cDNA libraries from normal and infected chinchilla MEM will serve as useful molecular tools in the study of otitis media and should yield important information with respect to middle ear pathogenesis.

Partial Characterization of Normal and Haemophilus influenzae–Infected Mucosal Complementary DNA Libraries in Chinchilla Middle Ear Mucosa

PubMed Central

Kerschner, Joseph E.; Erdos, Geza; Hu, Fen Ze; Burrows, Amy; Cioffi, Joseph; Khampang, Pawjai; Dahlgren, Margaret; Hayes, Jay; Keefe, Randy; Janto, Benjamin; Post, J. Christopher; Ehrlich, Garth D.

2010-01-01

Objectives We sought to construct and partially characterize complementary DNA (cDNA) libraries prepared from the middle ear mucosa (MEM) of chinchillas to better understand pathogenic aspects of infection and inflammation, particularly with respect to leukotriene biogenesis and response. Methods Chinchilla MEM was harvested from controls and after middle ear inoculation with nontypeable Haemophilus influenzae. RNA was extracted to generate cDNA libraries. Randomly selected clones were subjected to sequence analysis to characterize the libraries and to provide DNA sequence for phylogenetic analyses. Reverse transcription–polymerase chain reaction of the RNA pools was used to generate cDNA sequences corresponding to genes associated with leukotriene biosynthesis and metabolism. Results Sequence analysis of 921 randomly selected clones from the uninfected MEM cDNA library produced approximately 250,000 nucleotides of almost entirely novel sequence data. Searches of the GenBank database with the Basic Local Alignment Search Tool provided for identification of 515 unique genes expressed in the MEM and not previously described in chinchillas. In almost all cases, the chinchilla cDNA sequences displayed much greater homology to human or other primate genes than with rodent species. Genes associated with leukotriene metabolism were present in both normal and infected MEM. Conclusions Based on both phylogenetic comparisons and gene expression similarities with humans, chinchilla MEM appears to be an excellent model for the study of middle ear inflammation and infection. The higher degree of sequence similarity between chinchillas and humans compared to chinchillas and rodents was unexpected. The cDNA libraries from normal and infected chinchilla MEM will serve as useful molecular tools in the study of otitis media and should yield important information with respect to middle ear pathogenesis. PMID:20433028

Combinatorial synthesis of bimetallic complexes with three halogeno bridges.

PubMed

Gauthier, Sébastien; Quebatte, Laurent; Scopelliti, Rosario; Severin, Kay

2004-06-07

Methods for the synthesis of bimetallic complexes in which two different metal fragments are connected by three chloro or bromo bridges are reported. The reactions are general, fast, and give rise to structurally defined products in quantitative yields. Therefore, they are ideally suited for generating a library of homo- and heterobimetallic complexes in a combinatorial fashion. This is of special interest for applications in homogeneous catalysis. Selected members of this library were synthesized and comprehensively characterized; single-crystal X-ray analyses were performed for 15 new bimetallic compounds.

Community phylogenetic diversity of cyanobacterial mats associated with geothermal springs along a tropical intertidal gradient.

PubMed

Jing, Hongmei; Lacap, Donnabella C; Lau, Chui Yim; Pointing, Stephen B

2006-04-01

The 16S rRNA gene-defined bacterial diversity of tropical intertidal geothermal vents subject to varying degrees of seawater inundation was investigated. Shannon-Weaver diversity estimates of clone library-derived sequences revealed that the hottest pools located above the mean high-water mark that did not experience seawater inundation were most diverse, followed by those that were permanently submerged below the mean low-water mark. Pools located in the intertidal were the least biodiverse, and this is attributed to the fluctuating conditions caused by periodic seawater inundation rather than physicochemical conditions per se. Phylogenetic analysis revealed that a ubiquitous Oscillatoria-like phylotype accounted for 83% of clones. Synechococcus-like phylotypes were also encountered at each location, whilst others belonging to the Chroococcales, Oscillatoriales, and other non-phototrophic bacteria occurred only at specific locations along the gradient. All cyanobacterial phylotypes displayed highest phylogenetic affinity to terrestrial thermophilic counterparts rather than marine taxa.

Adhesion formation after previous caesarean section-a meta-analysis and systematic review.

PubMed

Shi, Z; Ma, L; Yang, Y; Wang, H; Schreiber, A; Li, X; Tai, S; Zhao, X; Teng, J; Zhang, L; Lu, W; An, Y; Alla, N R; Cui, T

2011-03-01

The optimal technique for performing caesarean section with respect to minimising postoperative adhesions has not been determined. To evaluate adhesion formation for three common caesarean section techniques in women undergoing repeat caesarean section surgeries. A database was constructed from Medline, EMBASE, Cochrane Library, National Science Digital Library, China Biological Medicine Database and through contact with experts in this field from January 1990 to May 2010. Studies were included if they examined adhesion formation in repeat caesarean sections as a primary objective, delineated a clear study design, specified an adhesion scoring system, and had sufficient patient exclusion criteria. We abstracted data regarding adhesion formation. The Mantel-Haenszel random-effects model was employed for all analyses using odds ratio or inverse variance, along with 95% CI. Thirty-three qualified studies including 4423 women were analysed. There were 406 adhesions among 571 women and 238 adhesions among 596 women in the Stark's caesarean section (also known as Misgav-Ladach method) group and modified Stark's caesarean section group, respectively, with pooled OR 4.69 (95% CI 3.32-6.62; P < 0.01, 12 studies); 1173 adhesions among 1555 women and 1179 adhesions among 1625 women in Stark's caesarean section group and classic lower-segment caesarean section group, respectively, with pooled odds ratio 1.28 (95% CI 0.97-1.68; P = 0.08, 21 studies); and 29 adhesions from 102 women and 115 adhesions from 193 women in modified Stark's caesarean section group and classic lower-segment caesarean section group, respectively, with pooled odds ratio 0.28 (95% CI 0.10-0.82; P = 0.02, two studies). Closure of the peritoneum in modified Stark's caesarean section resulted in less adhesion formation and should be recommended. © 2010 The Authors Journal compilation © RCOG 2010 BJOG An International Journal of Obstetrics and Gynaecology.

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

PubMed Central

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

2013-01-01

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

Combinatorial pooling enables selective sequencing of the barley gene space.

PubMed

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

2013-04-01

For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

PubMed

Karthikeyan, Muthukumarasamy; Pandit, Deepak; Vyas, Renu

2015-01-01

In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.

Job Accommodation Network

MedlinePlus

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Into the Curriculum.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1991

1991-01-01

Provides fully developed library media activities that are designed to be used in connection with specific curriculum units, including foreign language (Spanish); reading and language arts (expository writing and use of a thesaurus); science and social studies (land biomes, state birds, and country's flags). (LRW)

MedlinePlus - Health Information from the National Library of Medicine

MedlinePlus

... MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español ... Connect for EHRs About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

17 CFR 5.22 - Registered futures association membership.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., because the person solicits or accepts orders for retail forex transactions; (2) A commodity pool operator... that engages in retail forex transactions; or (3) A commodity trading advisor because the person... trading authority over, an account in connection with retail forex transactions, must become and remain a...

17 CFR 5.22 - Registered futures association membership.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., because the person solicits or accepts orders for retail forex transactions; (2) A commodity pool operator... that engages in retail forex transactions; or (3) A commodity trading advisor because the person... trading authority over, an account in connection with retail forex transactions, must become and remain a...

17 CFR 5.22 - Registered futures association membership.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., because the person solicits or accepts orders for retail forex transactions; (2) A commodity pool operator... that engages in retail forex transactions; or (3) A commodity trading advisor because the person... trading authority over, an account in connection with retail forex transactions, must become and remain a...

Sample size determination in combinatorial chemistry.

PubMed Central

Zhao, P L; Zambias, R; Bolognese, J A; Boulton, D; Chapman, K

1995-01-01

Combinatorial chemistry is gaining wide appeal as a technique for generating molecular diversity. Among the many combinatorial protocols, the split/recombine method is quite popular and particularly efficient at generating large libraries of compounds. In this process, polymer beads are equally divided into a series of pools and each pool is treated with a unique fragment; then the beads are recombined, mixed to uniformity, and redivided equally into a new series of pools for the subsequent couplings. The deviation from the ideal equimolar distribution of the final products is assessed by a special overall relative error, which is shown to be related to the Pearson statistic. Although the split/recombine sampling scheme is quite different from those used in analysis of categorical data, the Pearson statistic is shown to still follow a chi2 distribution. This result allows us to derive the required number of beads such that, with 99% confidence, the overall relative error is controlled to be less than a pregiven tolerable limit L1. In this paper, we also discuss another criterion, which determines the required number of beads so that, with 99% confidence, all individual relative errors are controlled to be less than a pregiven tolerable limit L2 (0 < L2 < 1). PMID:11607586

Cool pool development. Quarterly technical report No. 1, April-June 1979

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

Crowther, K.

1979-10-15

The Cool Pool is a passive cooling system consisting of a shaded, evaporating roof pond which thermosiphons cool water into water-filled, metal columns (culvert pipes) located within the building living space. The water in the roof pond is cooled by evaporation, convection and radiation. Because the water in the pool and downcomer is colder and denser than the water in the column a pressure difference is created and the cold water flows from the pool, through the downcomer and into the bottom of the column. The warm column water rises and flows through a connecting pipe into the pool. Itmore » is then cooled and the cycle repeats itself. The system requires no pumps. The water column absorbs heat from the building interior primarily by convection and radiation. Since the column is radiating at a significantly lower temperature than the interior walls it plays a double role in human comfort. Not only does it cool the air by convection but it provides a heat sink to which people can radiate. Since thermal radiation is important to the cooling of people, the cold water column contributes substantially to their feelings of comfort. Research on the Cool Pool system includes the following major tasks: control of biological organisms and debris in the roof pond and water cylinders; development of a heat exchanger; experimental investigation of the system's thermal performance; and development of a predictive computer simulation of the Cool Pool. Progress in these tasks is reported.« less

Spatio-temporal development of vegetation die-off in a submerging coastal marsh

USGS Publications Warehouse

Schepers, Lennert; Kirwan, Matthew; Guntenspergen, Glenn R.; Temmerman, Stijn

2017-01-01

In several places around the world, coastal marsh vegetation is converting to open water through the formation of pools. This is concerning, as vegetation die-off is expected to reduce the marshes' capacity to adapt to sea level rise by vegetation-induced sediment accretion. Quantitative analyses of the spatial and temporal development of marsh vegetation die-off are scarce, although these are needed to understand the bio-geomorphic feedback effects of vegetation die-off on flow, erosion, and sedimentation. In this study, we quantified the spatial and temporal development of marsh vegetation die-off with aerial images from 1938 to 2010 in a submerging coastal marsh along the Blackwater River (Maryland, U.S.A). Our results indicate that die-off begins with conversion of marsh vegetation into bare open water pools that are relatively far (> 75 m) from tidal channels. As vegetation die-off continues, pools expand, and new pools emerge at shorter and shorter distances from channels. Consequently larger pools are found at larger distances from the channels. Our results suggest that the size of the pools and possibly the connection of pools with the tidal channel system have important bio-geomorphic implications and aggravate marsh deterioration. Moreover, we found that the temporal development of vegetation die-off in moderately degraded marshes is similar as the spatial die-off development along a present-day gradient, which indicates that the contemporary die-off gradient might be considered a chronosequence that offers a unique opportunity to study vegetation die-off processes.

Simplified Interface to Complex Memory Hierarchies 1.x

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

Lang, Michael; Ionkov, Latchesar; Williams, Sean

2017-02-21

Memory systems are expected to get evermore complicated in the coming years, and it isn't clear exactly what form that complexity will take. On the software side, a simple, flexible way of identifying and working with memory pools is needed. Additionally, most developers seek code portability and do not want to learn the intricacies of complex memory. Hence, we believe that a library for interacting with complex memory systems should expose two kinds of abstraction: First, a low-level, mechanism-based interface designed for the runtime or advanced user that wants complete control, with its focus on simplified representation but with allmore » decisions left to the caller. Second, a high-level, policy-based interface designed for ease of use for the application developer, in which we aim for best-practice decisions based on application intent. We have developed such a library, called SICM: Simplified Interface to Complex Memory.« less

Synthesis and screening of one-bead-one-compound cyclic peptide libraries.

PubMed

Qian, Ziqing; Upadhyaya, Punit; Pei, Dehua

2015-01-01

Cyclic peptides have been a rich source of biologically active molecules. Herein we present a method for the combinatorial synthesis and screening of large one-bead-one-compound (OBOC) libraries of cyclic peptides against biological targets such as proteins. Up to ten million different cyclic peptides are rapidly synthesized on TentaGel microbeads by the split-and-pool synthesis method and subjected to a multistage screening protocol which includes magnetic sorting, on-bead enzyme-linked and fluorescence-based assays, and in-solution binding analysis of cyclic peptides selectively released from single beads by fluorescence anisotropy. Finally, the most active hit(s) is identified by the partial Edman degradation-mass spectrometry (PED-MS) method. This method allows a single researcher to synthesize and screen up to ten million cyclic peptides and identify the most active ligand(s) in ~1 month, without the time-consuming and expensive hit resynthesis or the use of any special equipment.

Understanding sources of uncertainty and bias error in models of human response to low amplitude sonic booms

NASA Astrophysics Data System (ADS)

Collmar, M.; Cook, B. G.; Cowart, R.; Freund, D.; Gavin, J.

2015-10-01

A pool of 240 subjects was exposed to a library of waveforms consisting of example signatures of low boom aircraft. The signature library included intentional variations in both loudness and spectral content, and were auralized using the Gulfstream SASS-II sonic boom simulator. Post-processing was used to quantify the impacts of test design decisions on the "quality" of the resultant database. Specific lessons learned from this study include insight regarding potential for bias error due to variations in loudness or peak over-pressure, sources of uncertainty and their relative importance on objective measurements and robustness of individual metrics to wide variations in spectral content. Results provide clear guidance for design of future large scale community surveys, where one must optimize the complex tradeoffs between the size of the surveyed population, spatial footprint of those participants, and the fidelity/density of objective measurements.

Sarcopenia as a predictor of all-cause mortality among community-dwelling older people: A systematic review and meta-analysis.

PubMed

Liu, Ping; Hao, Qiukui; Hai, Shan; Wang, Hui; Cao, Li; Dong, Birong

2017-09-01

The aim of this systematic review and meta-analysis was to examine the association between sarcopenia and all-cause mortality among community-dwelling older people. A systematic review was performed using three electronic databases (EMBASE, MEDLINE and the Cochrane Library) to identify prospective cohort studies from January 2009 to February 2017 examining sarcopenia as a predictor of all-cause mortality among community-dwelling older people. We conducted a pooled analysis of mortality associated with sarcopenia, and subgroup analyses based on measurements of muscle mass and length of follow-up by employing a random-effects model. Sensitivity analyses were performed evaluate the cause of high heterogeneity. In addition, methodological quality, heterogeneity and publication bias were evaluated. Of 1703 studies identified, 6 studies incorporating 7367 individuals were included in the meta-analysis for all-cause mortality. The pooled hazard ratios (HRs) of all-cause mortality from the combination of included studies suggested participants with sarcopenia had a significantly higher rate of mortality (pooled HR 1.60, 95%CI 1.24-2.06, I 2 =27.8%, p=0.216) than participants without sarcopenia. The subgroup analysis for length of follow-up suggested studies with a follow-up period of less than 5 years found a higher risk of all-cause mortality (pooled HR 2.09, 95%CI 1.21-3.60) than studies with a follow-up period of 5 years or more (pooled HR 1.52, 95%CI 1.14-2.01). A subgroup of anthropometric measures was found to identify higher mortality risks (pooled HR 2.26, 95%CI 1.30-3.92) than a subgroup of dual-energy x-ray (DXA) absorptiometry (pooled HR 1.82, 95%CI 1.04-3.18) factors or a subgroup of bioelectrical impedance analysis (BIA) factors (pooled HR 1.31, 95%CI 1.15-1.49). Sarcopenia is a predictor of all-cause mortality among community-dwelling older people. Therefore, it is important to diagnose sarcopenia and to intervene, in order to reduce mortality rates in the elderly. Copyright © 2017. Published by Elsevier B.V.

cDNA Cloning, expression and characterization of an allergenic 60s ribosomal protein of almond (prunus dulcis).

PubMed

Abolhassani, Mohsen; Roux, Kenneth H

2009-06-01

Tree nuts, including almond (prunus dulcis) are a source of food allergens often associated with life-threatening allergic reactions in susceptible individuals. Although the proteins in almonds have been biochemically characterized, relatively little has been reported regarding the identity of the allergens involved in almond sensitivity. The present study was undertaken to identify the allergens of the almond by cDNA library approach. cDNA library of almond seeds was constructed in Uni-Zap XR lamda vector and expressed in E. coli XL-1 blue. Plaques were immunoscreened with pooled sera of allergic patients. The cDNA clone reacting significantly with specific IgE antibodies was selected and subcloned and subsequently expressed in E. coli. The amino acids deducted from PCR product of clone showed homology to 60s acidic ribosomal protein of almond. The expressed protein was 11,450 Dalton without leader sequence. Immunoreactivity of the recombinant 60s ribosomal protein (r60sRP) was evaluated with dot blot analysis using pooled and individual sera of allergic patients. The data showed that r60sRP and almond extract (as positive control) possess the ability to bind the IgE antibodies. The results showed that expressed protein is an almond allergen.Whether this r60sRP represents a major allergen of almond needs to be further studied which requires a large number of sera from the almond atopic patients and also need to determine the IgE-reactive frequencies of each individual allergen.

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Rabbit seminal plasma proteome: The importance of the genetic origin.

PubMed

Casares-Crespo, Lucía; Fernández-Serrano, Paula; Vicente, José S; Marco-Jiménez, Francisco; Viudes-de-Castro, María Pilar

2018-02-01

The present study was conducted to characterise rabbit seminal plasma proteins (SP proteins) focusing on the influence of the genetic origin and seasonality. In addition, β-NGF protein quantity in SP was determined. Semen samples were recovered from January to December 2014 using 6 males belonging to genotype A and six from genotype R. For each genotype, one pooled sample at the beginning, middle and end of each season was selected to develop the experiment. A total of 24 pools (3 for each season and genetic line) were analysed. SP proteins of the two experimental groups were recovered and subjected to in-solution digestion nano LC-MS/MS and bioinformatics analysis. The resulting library included 402 identified proteins validated with ≥95% Confidence (unused Score ≥ 1.3). These data are available via ProteomeXchange with identifier PXD006308. Only 6 proteins were specifically implicated in reproductive processes according to Gene Ontology annotation. Twenty-three proteins were differentially expressed between genotypes, 11 over-expressed in genotype A and 12 in genotype R. Regarding the effect of season on rabbit SP proteome, results showed that there is no clear pattern of protein variation throughout the year. Similar β-NGF relative quantity was observed between seasons and genotypes. In conclusion, this study generates the largest library of SP proteins reported to date in rabbits and provides evidence that genotype is related to a specific abundance of SP proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

Library preparation and data analysis packages for rapid genome sequencing.

PubMed

Pomraning, Kyle R; Smith, Kristina M; Bredeweg, Erin L; Connolly, Lanelle R; Phatale, Pallavi A; Freitag, Michael

2012-01-01

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.

Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi.

PubMed

Pärtel, Meelis; Öpik, Maarja; Moora, Mari; Tedersoo, Leho; Szava-Kovats, Robert; Rosendahl, Søren; Rillig, Matthias C; Lekberg, Ylva; Kreft, Holger; Helgason, Thorunn; Eriksson, Ove; Davison, John; de Bello, Francesco; Caruso, Tancredi; Zobel, Martin

2017-10-01

The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

PubMed

Džunková, Mária; D'Auria, Giuseppe; Pérez-Villarroya, David; Moya, Andrés

2012-01-01

Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

Construction of a large-scale Burkholderia cenocepacia J2315 transposon mutant library

NASA Astrophysics Data System (ADS)

Wong, Yee-Chin; Pain, Arnab; Nathan, Sheila

2014-09-01

Burkholderia cenocepacia, a pathogenic member of the Burkholderia cepacia complex (Bcc), has emerged as a significant threat towards cystic fibrosis patients, where infection often leads to the fatal clinical manifestation known as cepacia syndrome. Many studies have investigated the pathogenicity of B. cenocepacia as well as its ability to become highly resistant towards many of the antibiotics currently in use. In addition, studies have also been undertaken to understand the pathogen's capacity to adapt and survive in a broad range of environments. Transposon based mutagenesis has been widely used in creating insertional knock-out mutants and coupled with recent advances in sequencing technology, robust tools to study gene function in a genome-wide manner have been developed based on the assembly of saturated transposon mutant libraries. In this study, we describe the construction of a large-scale library of B. cenocepacia transposon mutants. To create transposon mutants of B. cenocepacia strain J2315, electrocompetent bacteria were electrotransformed with the EZ-Tn5 transposome. Tetracyline resistant colonies were harvested off selective agar and pooled. Mutants were generated in multiple batches with each batch consisting of ˜20,000 to 40,000 mutants. Transposon insertion was validated by PCR amplification of the transposon region. In conclusion, a saturated B. cenocepacia J2315 transposon mutant library with an estimated total number of 500,000 mutants was successfully constructed. This mutant library can now be further exploited as a genetic tool to assess the function of every gene in the genome, facilitating the discovery of genes important for bacterial survival and adaptation, as well as virulence.

Defining the ABC of gene essentiality in streptococci.

PubMed

Charbonneau, Amelia R L; Forman, Oliver P; Cain, Amy K; Newland, Graham; Robinson, Carl; Boursnell, Mike; Parkhill, Julian; Leigh, James A; Maskell, Duncan J; Waller, Andrew S

2017-05-31

Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.

Into the Curriculum.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1992

1992-01-01

Provides fully developed library media activities for elementary and middle school students, most of which are designed to be used in connection with specific curriculum units. Topics covered include art; reading/language arts, including fiction, point of view, storytelling, and dictionary skills; science; and social studies. (LRW)

Testing, Testing...Managing Electronic Access in Disparate Times.

ERIC Educational Resources Information Center

Carrington, Bessie M.

1996-01-01

Duke University's Perkins Library (North Carolina) tests electronic resources and services for remote accessibility by examining capabilities on various platforms, operating systems, communications software, and World Wide Web browsers. Problems occur in establishing connections, screen display, navigation or retrieval, keyboard variations, and in…

Into the Curriculum.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 1986

1986-01-01

Provides six library media activities designed for use in connection with specific curriculum units in art, science, and social studies. The activities focus on appreciating Georgia O'Keefe, sound travel, rock identification, Thanksgiving customs, state road maps, and world religions. The descriptions include objectives, grade levels,…

Gaining Access to the Internet.

ERIC Educational Resources Information Center

Notess, Greg R.

1992-01-01

Discusses Internet services and protocols (i.e., electronic mail, file transfer, and remote login) and provides instructions for retrieving guides and directories of the Internet. Services providing access to the Internet are described, including bulletin board systems, regional networks, nationwide connections, and library organizations; and a…

Book a Book Fair Today! It's a Celebration!

ERIC Educational Resources Information Center

Brodie, Carolyn S.

2001-01-01

Discusses the value of book fairs to encourage reading and offers suggestions for planning them. Considers sponsorship, location and timing, sources to get books from, how to select books, marketing, library programs connected with the fair, volunteers, and who receives the profits. (LRW)

Customizing the Connectivity Map Approach for Functional Evaluation in Toxicogenomics Studies (SOT)

EPA Science Inventory

Evaluating effects on the transcriptome can provide insight on putative chemical-specific mechanisms of action (MOAs). With whole genome transcriptomics technologies becoming more amenable to high-throughput screening, libraries of chemicals can be evaluated in vitro to produce l...

A new age in functional genomics using CRISPR/Cas9 in arrayed library screening.

PubMed

Agrotis, Alexander; Ketteler, Robin

2015-01-01

CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. What makes CRISPR/Cas9 so revolutionary is the ability to target a protein (Cas9) to an exact genomic locus, through designing a specific short complementary nucleotide sequence, that together with a common scaffold sequence, constitute the guide RNA bridging the protein and the DNA. Wild-type Cas9 cleaves both DNA strands at its target sequence, but this protein can also be modified to exert many other functions. For instance, by attaching an activation domain to catalytically inactive Cas9 and targeting a promoter region, it is possible to stimulate the expression of a specific endogenous gene. In principle, any genomic region can be targeted, and recent efforts have successfully generated pooled guide RNA libraries for coding and regulatory regions of human, mouse and Drosophila genomes with high coverage, thus facilitating functional phenotypic screening. In this review, we will highlight recent developments in the area of CRISPR-based functional genomics and discuss potential future directions, with a special focus on mammalian cell systems and arrayed library screening.

Micropreparative capillary gel electrophoresis of DNA: rapid expressed sequence tag library construction.

PubMed

Shi, Liang; Khandurina, Julia; Ronai, Zsolt; Li, Bi-Yu; Kwan, Wai King; Wang, Xun; Guttman, András

2003-01-01

A capillary gel electrophoresis based automated DNA fraction collection technique was developed to support a novel DNA fragment-pooling strategy for expressed sequence tag (EST) library construction. The cDNA population is first cleaved by BsaJ I and EcoR I restriction enzymes, and then subpooled by selective ligation with specific adapters followed by polymerase chain reaction (PCR) amplification and labeling. Combination of this cDNA fingerprinting method with high-resolution capillary gel electrophoresis separation and precise fractionation of individual cDNA transcript representatives avoids redundant fragment selection and concomitant repetitive sequencing of abundant transcripts. Using a computer-controlled capillary electrophoresis device the transcript representatives were separated by their size and fractions were automatically collected in every 30 s into 96-well plates. The high resolving power of the sieving matrix ensured sequencing grade separation of the DNA fragments (i.e., single-base resolution) and successful fraction collection. Performance and precision of the fraction collection procedure was validated by PCR amplification of the collected DNA fragments followed by capillary electrophoresis analysis for size and purity verification. The collected and PCR-amplified transcript representatives, ranging up to several hundred base pairs, were then sequenced to create an EST library.

Preparation of highly multiplexed small RNA sequencing libraries.

PubMed

Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

2017-08-01

MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

PubMed

Huemer, Peter; Mutanen, Marko; Sefc, Kristina M; Hebert, Paul D N

2014-01-01

This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

Activity Regulates the Incidence of Heteronymous Sensory-Motor Connections

PubMed Central

Mendelsohn, Alana I.; Simon, Christian M.; Abbott, L. F.; Mentis, George Z.; Jessell, Thomas M.

2015-01-01

Summary The construction of spinal sensory-motor circuits involves the selection of appropriate synaptic partners and the allocation of precise synaptic input densities. Many aspects of spinal sensory-motor selectivity appear to be preserved when peripheral sensory activation is blocked, which has led to a view that sensory-motor circuits are assembled in an activity-independent manner. Yet it remains unclear whether activity-dependent refinement has a role in the establishment of connections between sensory afferents and those motor pools that have synergistic biomechanical functions. We show here that genetically abolishing central sensory-motor neurotransmission leads to a selective enhancement in the number and density of such “heteronymous” connections, whereas other aspects of sensory-motor connectivity are preserved. Spike-timing dependent synaptic refinement represents one possible mechanism for the changes in connectivity observed after activity blockade. Our findings therefore reveal that sensory activity does have a limited and selective role in the establishment of patterned monosynaptic sensory-motor connections. PMID:26094608

Interactive Exhibits Foster Partnership and Engage Diverse Learners at Their Local Libraries

NASA Astrophysics Data System (ADS)

LaConte, K.; Dusenbery, P.; Fitzhugh, G.; Harold, J. B.; Holland, A.

2016-12-01

Learners frequently need to access increasingly complex information to help them understand our changing world. More and more libraries are transforming themselves into places where learners not only access STEM information, but interact with professionals and undertake hands-on learning. Libraries are beginning to position themselves as part of learning ecosystems that contribute to a collective impact on the community. Traveling STEM exhibits are catalyzing these partnerships and engaging students, families, and adults in repeat visits through an accessible venue: their public library. The impact of the STAR Library Education Network's (STAR_Net) Discover Earth: A Century of Change exhibit on partnerships, the circulation of STEM resources, and the engagement of learners was studied by an external evaluation team. The STAR_Net project's summative evaluation utilized mixed methods to investigate project implementation and its outcomes. Methods included pre- and post-exhibit surveys administered to staff from each library that hosted the exhibits; interviews with staff from host libraries; patron surveys; exhibit-related circulation records; web metrics regarding the online STAR_Net community of practice; and site visits. A subset of host libraries recruited professionals, who delivered programming that connected Earth systems science, weather, climate, and conservation themes from the exhibit to local issues. Library patrons improved their knowledge about STEM topics presented in the exhibits and associated programming, and patrons viewing the exhibit reflected the demographics of their communities. In a follow-up survey, patrons reported spending an average of 60 minutes looking at the exhibit over their cumulative visits to the library. In contrast, visitors might visit a museum only once to look at a comparably-sized traveling exhibit due to barriers such as cost and distance. Exhibit host libraries reported an increase in the circulation of Earth science materials of 27% while the exhibit was at their library. The summative evaluation results, as well as tips for working with your local library, will be shared.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-09-01

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

From vision to reality--managing change in the provision of library and information services to nurses, midwives, health visitors and PAMs: (professions allied to medicine) a case study of the North Thames experience with the Inner London Consortium.

PubMed

Godbolt, S; Williamson, J; Wilson, A

1997-06-01

One of the North Thames' pioneering consortia, the Inner London Consortium (ILC) is a complex body which includes NHS Trusts with teaching hospital university connections, community-based Trusts and general hospital acute Trusts. Within the consortium there are 12,000 trained nurses, midwives, health visitors and other professional staff working in the professions allied to medicine (PAMs), all of whom require access to and provision of appropriate library information services. In 1994, taking into account experiences elsewhere in the Region and nationally, it became clear that library issues were complex and would become acute with the move of nursing libraries from ILC Trust sites over a very short timescale. A report on the issues commissioned by the Consortium recommended that a library project, which built on existing NHS Trust PGMDE funded library resources and moved these to a multidisciplinary base to serve the consortium membership, be implemented. The objective of providing access to library information services for nurses and PAMs was achieved. Successes that emerged from the implementation included: The registration in Trust libraries of almost 12 000 new members within the initial 6-month monitoring period. The development of service level agreements and standards for the delivery of services to these new user groups. This paper describes the processes behind these significant and complex changes.

Modular design of synthetic gene circuits with biological parts and pools.

PubMed

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

PMIX_Ring patch for SLURM

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

Moody, A. T.

2014-04-20

This code adds an implementation of PMIX_Ring to the existing PM12 Library in the SLURM open source software package (Simple Linux Utility for Resource Management). PMIX_Ring executes a particular communication pattern that is used to bootstrap connections between MPI processes in a parallel job.

A Labyrinth of the Wide World.

ERIC Educational Resources Information Center

Plater, William M.

1995-01-01

Discusses the design of the University Library at Indiana University, Purdue University Indianapolis. Topics include storage capacity; workstations; the user-friendly multimedia network information system; on- and off-campus connections to the system; the Center on Teaching and Learning; librarians' collaboration with faculty; and the Copyright…

37 CFR 253.2 - Definition of public broadcasting entity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... broadcasting entity. 253.2 Section 253.2 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF... CONNECTION WITH NONCOMMERCIAL EDUCATIONAL BROADCASTING § 253.2 Definition of public broadcasting entity. As used in this part, the term public broadcasting entity means a noncommercial educational broadcast...

37 CFR 253.2 - Definition of public broadcasting entity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... broadcasting entity. 253.2 Section 253.2 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF... CONNECTION WITH NONCOMMERCIAL EDUCATIONAL BROADCASTING § 253.2 Definition of public broadcasting entity. As used in this part, the term public broadcasting entity means a noncommercial educational broadcast...

47 CFR 54.508 - Technology plans.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Technology plans. 54.508 Section 54.508... SERVICE Universal Service Support for Schools and Libraries § 54.508 Technology plans. (a) Applicants must develop a technology plan when requesting discounts for internal connections and basic maintenance for...

37 CFR 302.2 - Fees.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Fees. 302.2 Section 302.2 Patents, Trademarks, and Copyrights COPYRIGHT ROYALTY BOARD, LIBRARY OF CONGRESS GENERAL PROVISIONS PUBLIC ACCESS TO RECORDS § 302.2 Fees. For services rendered in connection with document location, reproduction...

The Wireless Student & the Library.

ERIC Educational Resources Information Center

Drew, Bill

2002-01-01

Describes a program at the State University of New York College of Agriculture and Technology at Morrisville (SUNY-Morrisville) developed with IBM called ThinkPad University that integrates computers into the teaching and learning environment. Explains a partnership with Raytheon that provides wireless connectivity; and discusses changes in…

Jockeying for Supremacy in a Networked World.

ERIC Educational Resources Information Center

Barry, Jeff; And Others

1996-01-01

Provides an overview of the 1995 automated system marketplace, compiled by analysis of data gathered from 27 vendors. Topics include sales data; dominant vendors in different library sectors; company restructuring and consolidation; plans for technological upgrades, especially Internet connectivity, and improved customer support, service, and…

Creating Partnerships: Forging a Chain of Service Quality.

ERIC Educational Resources Information Center

Lynch, Richard; And Others

1993-01-01

Advocates the need for libraries to identify, nurture, and sustain new partnerships given rapid technological advancements and trends in information economics. Principles of partnerships are described, including Total Quality Management (TQM), negotiation, seamless connectivity, performance data, trust, patience, and perseverance; and steps in the…

NELS 2.0 - A general system for enterprise wide information management

NASA Technical Reports Server (NTRS)

Smith, Stephanie L.

1993-01-01

NELS, the NASA Electronic Library System, is an information management tool for creating distributed repositories of documents, drawings, and code for use and reuse by the aerospace community. The NELS retrieval engine can load metadata and source files of full text objects, perform natural language queries to retrieve ranked objects, and create links to connect user interfaces. For flexibility, the NELS architecture has layered interfaces between the application program and the stored library information. The session manager provides the interface functions for development of NELS applications. The data manager is an interface between session manager and the structured data system. The center of the structured data system is the Wide Area Information Server. This system architecture provides access to information across heterogeneous platforms in a distributed environment. There are presently three user interfaces that connect to the NELS engine; an X-Windows interface, and ASCII interface and the Spatial Data Management System. This paper describes the design and operation of NELS as an information management tool and repository.

Contrast-Enhanced Ultrasonography in Differential Diagnosis of Benign and Malignant Ovarian Tumors

PubMed Central

Qiao, Jing-Jing; Yu, Jing; Yu, Zhe; Li, Na; Song, Chen; Li, Man

2015-01-01

Objective To evaluate the accuracy of contrast-enhanced ultrasonography (CEUS) in differential diagnosis of benign and malignant ovarian tumors. Methods The scientific literature databases PubMed, Cochrane Library and CNKI were comprehensively searched for studies relevant to the use of CEUS technique for differential diagnosis of benign and malignant ovarian cancer. Pooled summary statistics for specificity (Spe), sensitivity (Sen), positive and negative likelihood ratios (LR+/LR−), and diagnostic odds ratio (DOR) and their 95%CIs were calculated. Software for statistical analysis included STATA version 12.0 (Stata Corp, College Station, TX, USA) and Meta-Disc version 1.4 (Universidad Complutense, Madrid, Spain). Results Following a stringent selection process, seven high quality clinical trials were found suitable for inclusion in the present meta-analysis. The 7 studies contained a combined total of 375 ovarian cancer patients (198 malignant and 177 benign). Statistical analysis revealed that CEUS was associated with the following performance measures in differential diagnosis of ovarian tumors: pooled Sen was 0.96 (95%CI = 0.92∼0.98); the summary Spe was 0.91 (95%CI = 0.86∼0.94); the pooled LR+ was 10.63 (95%CI = 6.59∼17.17); the pooled LR− was 0.04 (95%CI = 0.02∼0.09); and the pooled DOR was 241.04 (95% CI = 92.61∼627.37). The area under the SROC curve was 0.98 (95% CI = 0.20∼1.00). Lastly, publication bias was not detected (t = −0.52, P = 0.626) in the meta-analysis. Conclusions Our results revealed the high clinical value of CEUS in differential diagnosis of benign and malignant ovarian tumors. Further, CEUS may also prove to be useful in differential diagnosis at early stages of this disease. PMID:25764442

The Effect of Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) on Erectile Function: A Systematic Review and Meta-Analysis.

PubMed

Chen, Xiang; Zhou, ZhiRui; Qiu, XiaoChun; Wang, Bin; Dai, JiCan

2015-01-01

High prevalence of erectile dysfunction (ED) has been observed in patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). However, whether or not CP/CPPS is a risk factor of ED remains unknown and controversial. Therefore, we conducted this systematic review and meta-analysis to evaluate the relationship between CP/CPPS and ED. PubMed, Embase, Web of Science, and The Cochrane Library were searched up to November 11, 2014 to identify studies reporting the association between CP/CPPS and ED. Case-control, cohort and cross-sectional studies were included. Quality of the included studies was assessed. The odds ratio of ED and the mean difference of five-item International Index of Erectile Function (IIEF-5) score were pooled using a random effects model. Subgroup analysis and sensitivity analyses were performed. Three cross-sectional studies, two case-control studies, and four retrospective studies with 31,956 participants were included to calculate the pooled odds ratio of ED, and two studies with 1499 participants were included to calculate the pooled mean difference of IIEF-5 scores. A strong correlation was found between CP/CPPS and ED (pooled odds ratio: 3.02, 95% CI: 2.18-4.17, P < 0.01), with heterogeneity across studies (I2 = 65%; P < 0.01). A significant decrease in the IIFE-5 score was observed in the CP/CPPS group (pooled mean difference: -4.54, 95% CI: -5.11--3.98; P < 0.01). Our study indicates that patients with CP/CPPS have an increased risk of suffering from ED. Assessment of erectile function is necessary for the therapy of patients with CP/CPPS. Further evidence is necessary to confirm the relationship between CP/CPPS and ED.

Virtual reality for spherical images

NASA Astrophysics Data System (ADS)

Pilarczyk, Rafal; Skarbek, Władysław

2017-08-01

Paper presents virtual reality application framework and application concept for mobile devices. Framework uses Google Cardboard library for Android operating system. Framework allows to create virtual reality 360 video player using standard OpenGL ES rendering methods. Framework provides network methods in order to connect to web server as application resource provider. Resources are delivered using JSON response as result of HTTP requests. Web server also uses Socket.IO library for synchronous communication between application and server. Framework implements methods to create event driven process of rendering additional content based on video timestamp and virtual reality head point of view.

Accuracy of Percutaneous Core Biopsy in the Diagnosis of Small Renal Masses (≤ 4.0 cm): A Meta-analysis.

PubMed

He, Qiqi; Wang, Hanzhang; Kenyon, Jonathan; Liu, Guiming; Yang, Li; Tian, Junqiang; Yue, Zhongjin; Wang, Zhiping

2015-01-01

To use meta-analysis to determine the accuracy of percutaneous core needle biopsy in the diagnosis of small renal masses (SMRs ≤ 4.0 cm). Studies were identified by searching PubMed, Embase, and the Cochrane Library database up to March 2013. Two of the authors independently assessed the study quality using QUADAS-2 tool and extracted data that met the inclusion criteria. The sensitivity, specificity, likelihood ratios, diagnostic odds ratio (DOR) and also summary receiver operating characteristic (SROC) curve were investigated and draw. Deek's funnel plot was used to evaluate the publication bias. A total of 9 studies with 788 patients (803 biopsies) were included. Failed biopsies without repeated or aborted from follow-up/surgery result were excluded (232 patients and 353 biopsies). For all cases, the pooled sensitivity was 94.0% (95% CI: 91.0%, 95.0%), the pooled positive likelihood was 22.57 (95 % CI: 9.20-55.34), the pooled negative likelihood was 0.09 (95 % CI: 0.06-0.13), the pooled DOR was 296.52(95 % CI: 99. 42-884.38). The area under the curve of SROC analysis was 0.959 ± 0.0254. Imaging-guided percutaneous core needle biopsy of small renal masses (SMRs ≤ 4.0 cm) is highly accurate to malignant tumor diagnosis with unknown metastatic status and could be offered to some patients after clinic judgment prior to surgical intervention consideration.

Estimating the prevalence of heterozygous familial hypercholesterolaemia: a systematic review and meta-analysis

PubMed Central

Akioyamen, Leo E; Genest, Jacques; Shan, Shubham D; Reel, Rachel L; Albaum, Jordan M; Chu, Anna; Tu, Jack V

2017-01-01

Objectives Heterozygous familial hypercholesterolaemia (FH) confers a significant risk for premature cardiovascular disease (CVD). However, the estimated prevalence of FH varies substantially among studies. We aimed to provide a summary estimate of FH prevalence in the general population and assess variations in frequency across different sociodemographic characteristics. Setting, participants and outcome measures We searched MEDLINE, EMBASE, Global Health, the Cochrane Library, PsycINFO and PubMed for peer-reviewed literature using validated strategies. Results were limited to studies published in English between January 1990 and January 2017. Studies were eligible if they determined FH prevalence using clinical criteria or DNA-based analyses. We determined a pooled point prevalence of FH in adults and children and assessed the variation of the pooled frequency by age, sex, geographical location, diagnostic method, study quality and year of publication. Estimates were pooled using random-effects meta-analysis. Differences by study-level characteristics were investigated through subgroups, meta-regression and sensitivity analyses. Results The pooled prevalence of FH from 19 studies including 2 458 456 unique individuals was 0.40% (95% CI 0.29% to 0.52%) which corresponds to a frequency of 1 in 250 individuals. FH prevalence was found to vary by age and geographical location but not by any other covariates. Results were consistent in sensitivity analyses. Conclusions Our systematic review suggests that FH is a common disorder, affecting 1 in 250 individuals. These findings underscore the need for early detection and management to decrease CVD risk. PMID:28864697

Accuracy of combined dynamic contrast-enhanced magnetic resonance imaging and diffusion-weighted imaging for breast cancer detection: a meta-analysis.

PubMed

Zhang, Li; Tang, Min; Min, Zhiqian; Lu, Jun; Lei, Xiaoyan; Zhang, Xiaoling

2016-06-01

Magnetic resonance imaging (MRI) is increasingly being used to examine patients with suspected breast cancer. To determine the diagnostic performance of combined dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted imaging (DWI) for breast cancer detection. A comprehensive search of the PUBMED, EMBASE, Web of Science, and Cochrane Library databases was performed up to September 2014. Statistical analysis included pooling of sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and diagnostic accuracy using the summary receiver operating characteristic (SROC). All analyses were conducted using STATA (version 12.0), RevMan (version 5.2), and Meta-Disc 1.4 software programs. Fourteen studies were analyzed, which included a total of 1140 patients with 1276 breast lesions. The pooled sensitivity and specificity of combined DCE-MRI and DWI were 91.6% and 85.5%, respectively. The pooled sensitivity and specificity of DWI-MRI were 86.0% and 75.6%, respectively. The pooled sensitivity and specificity of DCE-MRI were 93.2% and 71.1%. The area under the SROC curve (AUC-SROC) of combined DCE-MRI and DWI was 0.94, the DCE-MRI of 0.85. Deeks testing confirmed no significant publication bias in all studies. Combined DCE-MRI and DWI had superior diagnostic accuracy than either DCE-MRI or DWI alone for the diagnosis of breast cancer. © The Foundation Acta Radiologica 2015.

Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.

PubMed

Medjahed, Djamel; Luke, Brian T; Tontesh, Tawady S; Smythers, Gary W; Munroe, David J; Lemkin, Peter F

2003-08-01

By mining publicly accessible databases, we have developed a collection of tissue-specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.

A comprehensive study of the genomic differentiation between temperate Dent and Flint maize.

PubMed

Unterseer, Sandra; Pophaly, Saurabh D; Peis, Regina; Westermeier, Peter; Mayer, Manfred; Seidel, Michael A; Haberer, Georg; Mayer, Klaus F X; Ordas, Bernardo; Pausch, Hubert; Tellier, Aurélien; Bauer, Eva; Schön, Chris-Carolin

2016-07-08

Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far. Understanding the genomic differences between germplasm pools may contribute to a better understanding of the complementarity in heterotic patterns exploited in hybrid breeding and of mechanisms involved in adaptation to different environments. We perform whole-genome screens for signatures of selection specific to temperate Dent and Flint maize by comparing high-density genotyping data of 70 American and European Dent and 66 European Flint inbred lines. We find 2.2 % and 1.4 % of the genes are under selective pressure, respectively, and identify candidate genes associated with agronomic traits known to differ between the two pools. Taking flowering time as an example for the differentiation between Dent and Flint, we investigate candidate genes involved in the flowering network by phenotypic analyses in a Dent-Flint introgression library and find that the Flint haplotypes of the candidates promote earlier flowering. Within the flowering network, the majority of Flint candidates are associated with endogenous pathways in contrast to Dent candidate genes, which are mainly involved in response to environmental factors like light and photoperiod. The diversity patterns of the candidates in a unique panel of more than 900 individuals from 38 European landraces indicate a major contribution of landraces from France, Germany, and Spain to the candidate gene diversity of the Flint elite lines. In this study, we report the investigation of pool-specific differences between temperate Dent and Flint on a genome-wide scale. The identified candidate genes represent a promising source for the functional investigation of pool-specific haplotypes in different genetic backgrounds and for the evaluation of their potential for future crop improvement like the adaptation to specific environments.

[The French National Compound Library: advances and future prospects].

PubMed

Mahuteau-Betzer, Florence

2015-04-01

The French National Compound Library (Chimiothèque Nationale) has been created in 2003 and is the federation of local collections. It contains more than 56 000 small molecules and natural compounds synthesised or isolated in different laboratories over the past years. This explains the diversity of the collection. The strength of this initiative is the ability to connect chemists and biologists for the development of hits. This development involves the synthesis of analogues or/and chemical tools to find new targets. These collaborations lead to the identification of new chemical probes. These probes able to modulate a biological function are essential to study biological pathways. They can also be useful for therapeutic applications. This article will describe the major achievements and perspectives of the French Chemical Library. © 2015 médecine/sciences – Inserm.

Free Web-based personal health records: an analysis of functionality.

PubMed

Fernández-Alemán, José Luis; Seva-Llor, Carlos Luis; Toval, Ambrosio; Ouhbi, Sofia; Fernández-Luque, Luis

2013-12-01

This paper analyzes and assesses the functionality of free Web-based PHRs as regards health information, user actions and connection with other tools. A systematic literature review in Medline, ACM Digital Library, IEEE Digital Library and ScienceDirect was used to select 19 free Web-based PHRs from the 47 PHRs identified. The results show that none of the PHRs selected met 100% of the 28 functions presented in this paper. Two free Web-based PHRs target a particular public. Around 90 % of the PHRs identified allow users throughout the world to create their own profiles without any geographical restrictions. Only half of the PHRs selected provide physicians with user actions. Few PHRs can connect with other tools. There was considerable variability in the types of data included in free Web-based PHRs. Functionality may have implications for PHR use and adoption, particularly as regards patients with chronic illnesses or disabilities. Support for standard medical document formats and protocols are required to enable data to be exchanged with other stakeholders in the health care domain. The results of our study may assist users in selecting the PHR that best fits their needs, since no significant connection exists between the number of functions of the PHRs identified and their popularity.