Follow Your Heart: How Is Willingness to Pay Formed under Multiple Anchors?

PubMed Central

Lin, Chien-Huang; Chen, Ming

2017-01-01

In sales, a common promotional tactic is to supplement a required purchase (i.e., a focal product) by offering a free or discounted product (i.e., a supplementary product). The present research examines the contextual factors driving consumer evaluations of the supplementary product after the promotion has been terminated. Two experiments are used to demonstrate that consumers use multiple anchors to determine the value of a supplementary product. Consumers use other types of price information, such as the internal reference price (IRP), promotional price, and original price of the supplementary product, as anchors to adjust their willingness to pay. Among the multiple anchors, the consumer’s IRP is not only the crucial anchor to estimate the willingness to pay but also the criterion to determine whether other price information can serve as anchors. Price information, such as the promotional and original price of the supplementary product, which is higher (lower) than the IRP, will increase (decrease) the willingness to pay. However, these anchors are only employed when the price information is considered to be plausible. Assimilation and contrast effects occur when the IRP is used by consumers as a criterion to judge the reasonableness of other anchors. When the external price information belongs (does not belong) to consumers’ distribution of IRP, assimilation (contrast) effects occur, and consumers will regard the external reference price (ERP) to be a plausible (implausible) price. Limitations and future avenues for research are also discussed. PMID:29312098

Follow Your Heart: How Is Willingness to Pay Formed under Multiple Anchors?

PubMed

Lin, Chien-Huang; Chen, Ming

2017-01-01

In sales, a common promotional tactic is to supplement a required purchase (i.e., a focal product) by offering a free or discounted product (i.e., a supplementary product). The present research examines the contextual factors driving consumer evaluations of the supplementary product after the promotion has been terminated. Two experiments are used to demonstrate that consumers use multiple anchors to determine the value of a supplementary product. Consumers use other types of price information, such as the internal reference price (IRP), promotional price, and original price of the supplementary product, as anchors to adjust their willingness to pay. Among the multiple anchors, the consumer's IRP is not only the crucial anchor to estimate the willingness to pay but also the criterion to determine whether other price information can serve as anchors. Price information, such as the promotional and original price of the supplementary product, which is higher (lower) than the IRP, will increase (decrease) the willingness to pay. However, these anchors are only employed when the price information is considered to be plausible. Assimilation and contrast effects occur when the IRP is used by consumers as a criterion to judge the reasonableness of other anchors. When the external price information belongs (does not belong) to consumers' distribution of IRP, assimilation (contrast) effects occur, and consumers will regard the external reference price (ERP) to be a plausible (implausible) price. Limitations and future avenues for research are also discussed.

A Computer Model for Evaluating the Effects on Fighting Vehicle Crewmembers of Exposure to Carbon Monoxide Emissions.

DTIC Science & Technology

1980-01-01

SUPPLEMENTARY NOTES Is. KEY WORDS (Continue on reverse ede If neceseay id Identify by block number) Carbon Monoxide (CO) Computer Program Carboxyhemoglobin ...several researchers, which predicts the instantaneous amount of carboxyhemoglobin (COHb) in the blood of a person based upon the amount of carbon monoxide...developed from an empirical equation (derived from reference I and detailed in reference 3) which predicts the amount of carboxyhemoglobin (COHb) in

32 CFR 1907.25 - Action on appeal of initial Agency determination.

Code of Federal Regulations, 2012 CFR

2012-07-01

... written memorandum to the ES/ARP, refer such matters to the Director, Information Management Services (D... the denial to the ARP by sending the appeal and any supplementary information in support of the...

32 CFR 1907.25 - Action on appeal of initial Agency determination.

Code of Federal Regulations, 2014 CFR

2014-07-01

... written memorandum to the ES/ARP, refer such matters to the Director, Information Management Services (D... the denial to the ARP by sending the appeal and any supplementary information in support of the...

32 CFR 1907.25 - Action on appeal of initial Agency determination.

Code of Federal Regulations, 2013 CFR

2013-07-01

... written memorandum to the ES/ARP, refer such matters to the Director, Information Management Services (D... the denial to the ARP by sending the appeal and any supplementary information in support of the...

75 FR 62501 - Senior Executive Service Performance Review Board: Update

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-12

... AGENCY FOR INTERNATIONAL DEVELOPMENT Senior Executive Service Performance Review Board: Update... Development, Office of Inspector General's Senior Executive Service Performance Review Board. DATES: September... reference-- USAID OIG Senior Executive Service (SES) Performance Review Board). SUPPLEMENTARY INFORMATION: 5...

75 FR 78619 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System 48 CFR Parts 216 and 237 Defense Federal Acquisition Regulation Supplement; Technical Amendments AGENCY: Defense Acquisition Regulations... the Defense Federal Acquisition Regulation Supplement (DFARS) to set forth references to supplementary...

42 CFR 410.140 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SUPPLEMENTARY MEDICAL INSURANCE (SMI) BENEFITS Outpatient Diabetes Self-Management Training and Diabetes Outcome... for the American Diabetes Association. Approved entity means an individual, physician, or entity... furnish training, CMS refers to this entity as an “approved entity”. Diabetes means diabetes mellitus, a...

42 CFR 410.140 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SUPPLEMENTARY MEDICAL INSURANCE (SMI) BENEFITS Outpatient Diabetes Self-Management Training and Diabetes Outcome... for the American Diabetes Association. Approved entity means an individual, physician, or entity... furnish training, CMS refers to this entity as an “approved entity”. Diabetes means diabetes mellitus, a...

Welding Supplementary Units.

ERIC Educational Resources Information Center

Johnson, Don; And Others

This document contains supplemental materials for special needs high school students intended to facilitate their mainstreaming in regular welding classes. Teacher's materials precede the materials for students and include general notes for the instructor, suggestions, eight references, a class progress chart, a questionnaire on the usefulness of…

Air Conditioning and Refrigeration Supplementary Units.

ERIC Educational Resources Information Center

Winston, Del; And Others

This document contains supplemental materials for special needs high school students intended to facilitate their mainstreaming in regular air conditioning and refrigeration courses. Teacher's materials precede the materials for students and include general notes for the instructor, additional suggestions, two references, a questionnaire on the…

78 FR 21502 - Proposed Information Collection (Women Veterans Healthcare Barriers Survey)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-10

... Veterans Healthcare Barriers Survey) AGENCY: Veterans Health Administration, Department of Veterans Affairs.... 2900-NEW, Women Veterans Healthcare Barriers Survey'' in any correspondence. FOR FURTHER INFORMATION... . Please refer to ``OMB Control No. 2900-NEW, Women Veterans Healthcare Barriers Survey.'' SUPPLEMENTARY...

75 FR 26346 - Agency Information Collection (Marital Status Questionnaire) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0495] Agency Information Collection (Marital Status Questionnaire) Activity Under OMB Review AGENCY: Veterans Benefits Administration, Department of... refer to ``OMB Control No. 2900-0495.'' SUPPLEMENTARY INFORMATION: Title: Marital Status Questionnaire...

Auto Mechanics Supplementary Units.

ERIC Educational Resources Information Center

Donovan, Roger; Smith, Sam

This document contains supplemental materials for special needs high school students intended to facilitate their mainstreaming in regular auto mechanics courses. Teacher's materials precede the materials for students and include general notes for the instructor, suggestions, 18 references, a class progress chart, a questionnaire on the usefulness…

78 FR 39342 - SHINE Medical Technologies, Inc.

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-01

... NUCLEAR REGULATORY COMMISSION [Docket No. 50-608; NRC-2013-0053] SHINE Medical Technologies, Inc... Technologies, Inc., is acceptable for docketing. ADDRESSES: Please refer to Docket ID NRC-2013-0053 when...: [email protected] . SUPPLEMENTARY INFORMATION: On March 26, 2013, SHINE Medical Technologies (SHINE...

76 FR 40455 - Agency Information Collection (Veterans Mortgage Life Insurance Inquiry) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-08

... Mortgage Life Insurance Inquiry) Activity Under OMB Review AGENCY: Veterans Benefits Administration... refer to ``OMB Control No. 2900-0501.'' SUPPLEMENTARY INFORMATION: Title: Veterans Mortgage Life... approved collection. Abstract: Veterans whose mortgage is insured under Veterans Mortgage Life Insurance...

Making Meaning Out of Text.

ERIC Educational Resources Information Center

Kathpalia, Sujata S.

2001-01-01

Investigates textual coherence of popular psychology articles mediated through the theory of frames and identifies the linguistic evidence of factual frames. Inferencing is also discussed as a supplementary means to comprehension, with particular reference to the notion of bridging assumptions. Evidence for textual frames is discussed in relation…

76 FR 27381 - Agency Information Collection (Financial Statement) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-11

... (Financial Statement) Activity Under OMB Review AGENCY: Veterans Benefits Administration, Department of... . Please refer to ``OMB Control No. 2900-0047.'' SUPPLEMENTARY INFORMATION: Title: Financial Statement, VA.../assumers meet the creditworthiness requirements. The data is also used to determine a borrower's financial...

BIBLIOGRAPHY ON LEARNING PROCESS. SUPPLEMENT II.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge, MA. Graduate School of Education.

THIS SUPPLEMENTARY BIBLIOGRAPHY LISTS MATERIALS ON VARIOUS FACETS OF HUMAN LEARNING. APPROXIMATELY 60 UNANNOTATED REFERENCES ARE PROVIDED FOR DOCUMENTS DATING FROM 1954 TO 1966. JOURNAL ARTICLES, BOOKS, RESEARCH REPORTS, AND CONFERENCE PAPERS ARE LISTED. SOME SUBJECT AREAS INCLUDED ARE (1) LEARNING PARAMETERS AND ABILITY, (2) RETENTION AND…

Hoer-Sprech-Uebungen fuer Iraner (Aural-Oral Exercises for Iranians).

ERIC Educational Resources Information Center

Scharf, Kurt

1980-01-01

Exercises are presented as supplementary material for beginning classes. Many examples illustrate ways to consolidate the learned material, with particular reference to the textbook "Ich lerne Deutsch" and its pictures. Other exercises are designed to compare German and Farsi sentence structure. (IFS/WGA)

78 FR 16039 - Reports, Forms, and Record Keeping Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-13

... (OMB Control Number 2127-0629) was published on February 27, 2012. The February 2012 ``Request for... collection of information by referring to its OMB Control Number. SUPPLEMENTARY INFORMATION: [[Page 16040.... OMB Control Number: 2127-0629. Type of Request: Information Collection Renewal. Affected Public...

78 FR 19008 - Meeting of the Advisory Committee; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-28

... inclusion on future Joint Board examinations in actuarial mathematics, pension law and methodology referred... closed meeting of the Advisory Committee on Actuarial Examinations. DATES: The meeting will be held on.... SUPPLEMENTARY INFORMATION: Notice is hereby given that the Advisory Committee on Actuarial Examinations will...

QUAST: quality assessment tool for genome assemblies.

PubMed

Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay; Tesler, Glenn

2013-04-15

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

Quark enables semi-reference-based compression of RNA-seq data.

PubMed

Sarkar, Hirak; Patro, Rob

2017-11-01

The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. Although these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive. We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression. Quark is implemented in C ++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark. rob.patro@cs.stonybrook.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

76 FR 35949 - Agency Information Collection (Civil Rights Discrimination Complaint) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-20

... Rights Discrimination Complaint) Activity Under OMB Review AGENCY: Veterans Health Administration... refer to ``OMB Control No. 2900-0662.'' SUPPLEMENTARY INFORMATION: Title: Civil Rights Discrimination... collection. Abstract: Veterans and other VHA customers who believe that their civil rights were violated by...

78 FR 16825 - Approval of Air Quality Implementation Plans; Navajo Nation; Regional Haze Requirements for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-19

... Quality Implementation Plans; Navajo Nation; Regional Haze Requirements for Navajo Generating Station... source-specific federal implementation plan (FIP) requiring the Navajo Generating Station (NGS), located... . SUPPLEMENTARY INFORMATION: Throughout this document, ``we'', ``us'', and ``our'' refer to EPA. Table of Contents...

Health Care Assistant. Instructor [Guide.] Revised.

ERIC Educational Resources Information Center

Missouri Univ., Columbia. Instructional Materials Lab.

This instructor's guide contains 65 lessons designed to aid teachers in presenting a course in basic nursing procedures for students studying for careers as health care assistants. Lesson plans consist of a scope, objectives, suggested supplementary teaching and learning items; references, an introduction, a lesson outline, handouts, evaluation…

78 FR 6851 - Agency Information Collection (Dental Record Authorization and Invoice for Outpatient Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-31

... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0335] Agency Information Collection (Dental....gov . Please refer to ``OMB Control No. 2900-0335.'' SUPPLEMENTARY INFORMATION: Title: Dental Record... proper administration of VA outpatient fee dental program. The associated instructions make it possible...

76 FR 65529 - Agency Information Collection Activities: Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-21

... National Land Remote Sensing Education, Outreach and Research Activity (NLRSEORA). As required by the... Drive MS 517, Reston, VA, 20192 (mail) . SUPPLEMENTARY INFORMATION: Title: National Land Remote Sensing... Remote Sensing Program, therefore it is more appropriate to refer to this effort as an activity rather...

77 FR 59249 - Agency Information Collection (Access to Financial Records) Activities Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-26

... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0739] Agency Information Collection (Access...) of 1995 (44 U.S.C. 3501-3521), this notice announces that the Veterans Benefits Administration (VBA... . Please refer to ``OMB Control No. 2900-0739.'' SUPPLEMENTARY INFORMATION: Title: Access to Financial...

75 FR 68038 - Agency Information Collection (Veterans Mortgage Life Insurance Statement) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-04

... Mortgage Life Insurance Statement) Activity Under OMB Review AGENCY: Veterans Benefits Administration... . Please refer to ``OMB Control No. 2900- 0212.'' SUPPLEMENTARY INFORMATION: Title: Veterans Mortgage Life... currently approved collection. Abstract: Veterans complete VA Form 29-8636 to decline Veterans Mortgage Life...

77 FR 38397 - Agency Information Collection (Interest Rate Reduction Refinancing Loan Worksheet) Activities...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-27

... . Please refer to ``OMB Control No. 2900- 0386.'' SUPPLEMENTARY INFORMATION: Title: Interest Rate Reduction... guaranty on all interest rate reduction refinancing loan and provide a receipt as proof that the funding... ensure lenders computed the funding fee and the maximum permissible loan amount for interest rate...

Selective Bibliography in United States History Resources.

ERIC Educational Resources Information Center

Ramos, June E.; Crevling, Barbara

The selective bibliography identifies United States history materials for grades 7 through 12. It has been compiled to give teachers a representative sample of texts and supplementary materials, most of which have been published since 1975. Section one contains references to 16 basal curriculum materials. Information is given on title, author,…

77 FR 7242 - Agency Information Collection (Contract for Training and Employment): Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-10

... Human Resources and Housing Branch, New Executive Office Building, Room 10235, Washington, DC 20503 (202... for Training and Employment): Activity Under OMB Review AGENCY: Veterans Benefits Administration... . Please refer to ``OMB Control No. 2900-0677.'' SUPPLEMENTARY INFORMATION: Title: Contract for Training...

77 FR 68153 - Meetings of Humanities Panel

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-15

... NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES Meetings of Humanities Panel AGENCY: National... Foundation on the Arts and Humanities Act of 1965 (20 U.S.C. 951-960, as amended). DATES: See SUPPLEMENTARY... Reference Resources grant program on the subject of Music and Performing Arts, submitted to the Division of...

78 FR 57003 - Agency Information Collection (Statement of Purchaser or Owner Assuming Seller's Loans) Activity...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-16

.... 2900- 0111'' in any correspondence. FOR FURTHER INFORMATION CONTACT: Crystal Rennie, Enterprise Records...-7492 or email crystal[email protected] . Please refer to ``OMB Control No. 2900-0111.'' SUPPLEMENTARY... Average Burden Per Respondent: 15 minutes. Frequency of Response: One-time. Estimated Number of...

78 FR 46419 - Agency Information Collection (Inquiry Concerning Applicant for Employment) Activities Under OMB...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-31

... FURTHER INFORMATION OR A COPY OF THE SUBMISSION CONTACT: Crystal Rennie, Enterprise Records Service... email: crystal[email protected] . Please refer to ``OMB Control No. 2900-0117.'' SUPPLEMENTARY INFORMATION... Burden per Respondent: 15 minutes. Frequency of Response: One-time. Estimated Number of Respondents: 12...

78 FR 53507 - Agency Information Collection (Request for Details of Expenses) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-29

...- 0138'' in any correspondence. FOR FURTHER INFORMATION CONTACT: Crystal Rennie, Enterprise Records...-7492 or email crystal[email protected] . Please refer to ``OMB Control No. 2900-0138.'' SUPPLEMENTARY... Respondent: 15 minutes. Frequency of Response: One time. Estimated Number of Respondents: 22,800. Dated...

78 FR 73965 - Manufactured Home Construction and Safety Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-09

... the toll-free Federal Information Relay Service at 800-877-8339. SUPPLEMENTARY INFORMATION: I... skylight reference standards contained in the proposed rule. The commenter stated that AAMA/WDMA 100/I.S 7... standards (i.e., the restrictive and less restrictive) are not significant. HUD is also using this final...

76 FR 44090 - Agency Information Collection (Application for Extended Care Services); Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... (Application for Extended Care Services); Activity Under OMB Review AGENCY: Veterans Health Administration... . Please refer to ``OMB Control No. 2900-0629.'' SUPPLEMENTARY INFORMATION: Title: Application for Extended... from nonservice-connected veterans and their spouse when applying for extended care services and to...

76 FR 31682 - Agency Information Collection (Time Record (Work-Study Program)) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-01

... Record (Work-Study Program)) Activity Under OMB Review AGENCY: Veterans Benefits Administration... refer to ``OMB Control No. 2900-0379.'' SUPPLEMENTARY INFORMATION: Title: Time Record (Work-Study... work-study hours a claimant has completed. When a claimant elects to receive an advance payment, VA...

Environnement et elaboration de materiel pedagogique (The Environment and the Elaboration of Instructional Materials).

ERIC Educational Resources Information Center

Capelle, Marie-Jose; Archard-Bayle, Guy

1982-01-01

Describes the method and the instructional materials entitled "Contacts," which were developed specifically for Nigeria. The discussion covers the use of audiovisual supplementary material, the essentially African sociocultural reference of the text, the methodology peculiar to the Nigeria plurilingual situation, and the goals for both…

78 FR 36575 - Meeting of the Advisory Committee; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-18

... Joint Board examinations in actuarial mathematics and methodology referred to in 29 U.S.C. 1242(a)(1)(B... meeting of the Advisory Committee on Actuarial Examinations (a portion of which will be open to the public...- 2173. SUPPLEMENTARY INFORMATION: Notice is hereby given that the Advisory Committee on Actuarial...

76 FR 75912 - Meeting of the Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... Joint Board examinations in actuarial mathematics and methodology referred to in 29 U.S.C. 1242(a)(1)(B... Advisory Committee on Actuarial Examinations (portions of which will be open to the public) in Washington.... SUPPLEMENTARY INFORMATION: Notice is hereby given that the Advisory Committee on Actuarial Examinations will...

78 FR 73564 - Meeting of the Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-06

... Joint Board examinations in actuarial mathematics and methodology referred to in 29 U.S.C. 1242(a)(1)(B... Advisory Committee on Actuarial Examinations (portions of which will be open to the public) in Washington.... SUPPLEMENTARY INFORMATION: Notice is hereby given that the Advisory Committee on Actuarial Examinations will...

75 FR 67911 - Amendment of Class E Airspace; Jeannette, PA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-04

...) 305-5588. SUPPLEMENTARY INFORMATION: History The Point in Space in the legal description of the Class... reference from the legal description. The Point in Space within the legal description will continue to serve... E airspace areas extending upward from 700 feet or more above the surface of the earth...

75 FR 68217 - Acquisition Regulation: Agency Supplementary Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-05

... amending the Department of Energy Acquisition Regulation (DEAR) on DOE Management and Operating Contracts..., and update references. Today's rule does not alter substantive rights or obligations under current law... Contracts to conform it to the FAR. None of today's changes are substantive or of a nature to cause any...

76 FR 60134 - Agency Information Collection (Child Care Subsidy) Activity Under OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-28

... Care Subsidy) Activity Under OMB Review AGENCY: Human Resources and Administration, Department of....gov . Please refer to ``OMB Control No. 2900-0717.'' SUPPLEMENTARY INFORMATION: Titles a. Child Care Subsidy Application Form, VA Form 0730a. b. Child Care Provider Information (For the Child Care Subsidy...

Three-Dimensional Evolution of Erupted Flux Ropes from the Sun (2-20 Solar Radii) to 1 AU

DTIC Science & Technology

2012-12-01

public release; distribution unlimited 13. SUPPLEMENTARY NOTES Preprint, Solar Phys., 2013 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY ...NASA GSFC (USA), RAL and University of Birmingham (UK), MPS(Germany), CSL (Belgium), IOTA and IAS (France). References Brueckner, G.E., Howard, R.A

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Stationary Engineers Apprenticeship. Related Training Modules. 3.1-3.4 Drawing.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of four learning modules on drawing is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a…

Millwright Apprenticeship. Related Training Modules. 17.1-17.13 Hydraulics.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 13 learning modules on hydraulics is 1 of 6 such packets developed for apprenticeship training for millwrights. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check list of…

Stationary Engineers Apprenticeship. Related Training Modules. 10.1-10.5 Machine Components.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of five learning modules on machine components is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, statement…

75 FR 80420 - Reasonable Further Progress Requirements for the 1997 8-Hour Ozone National Ambient Air Quality...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-22

... Air and Radiation Docket and Information Center is in the EPA Headquarters Library, Room Number 3334... hold a public hearing. Please refer to SUPPLEMENTARY INFORMATION for additional information on the... Information Center, Attention Docket ID No. EPA-HQ-OAR-2010-0891, Environmental Protection Agency, 1301...

Resources and Wastes. In-Service Package for Volunteer Workshop Leaders.

ERIC Educational Resources Information Center

Miiller, Marnie

Designed to be used as a supplementary teaching aid for subjects such as science, social studies, and environmental education, this packet of modules contains materials related to waste and waste management for secondary level students. Each of the eight modules consists of a teacher's page, background information, references, questions, projects,…

Stationary Engineers Apprenticeship. Related Training Modules. 8.1-8.13 Hydraulics.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 13 learning modules on hydraulics is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a…

Erratum: Correction to: Rearrangements of Open Magnetic Flux and Formation of Polar Coronal Holes in Cycle 24

NASA Astrophysics Data System (ADS)

Golubeva, E. M.; Mordvinov, A. V.

2017-12-01

Correction to: Solar Phys DOI 10.1007/s11207-017-1200-6 Due to an error during processing the Electronic Supplementary Material (ESM) supplied by the author was not included with the article. Please find in this correction document the reference to the ESM.

SEVENTH GRADE MATHEMATICS FOR THE ACADEMICALLY TALENTED, TEACHERS' GUIDE.

ERIC Educational Resources Information Center

HORN, R.A.

MATERIALS FOR BOTH ENRICHED AND ACCELERATED MATHEMATICS COURSES ARE GIVEN. THE PRESENTATION OF THE MATERIALS IS INTENDED FOR EASY ADAPTATION OF MODIFICATION TO MEET THE NEEDS OF MOST MATHEMATICS CLASSES. SUGGESTIONS AND SUPPLEMENTARY REFERENCES IN EACH UNIT ARE OFFERED AS AIDS TO THE MATHEMATICS TEACHER IN REGULAR OR ACCELERATED CLASS. UNITS…

Stationary Engineers Apprenticeship. Related Training Modules. 9.1-9.6 Refrigeration.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of six learning modules on refrigeration is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, statement of…

Stationary Engineers Apprenticeship. Related Training Modules. 5.1-5.17 Electricity/Electronics.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 17 learning modules on electricity/electronics is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators,…

Millwright Apprenticeship. Related Training Modules. 15.1-15.5 Miscellaneous.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of five learning modules on miscellaneous topics is one of six such packets developed for apprenticeship training for millwrights. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a…

Educating the Disadvantaged: School Year 1968-1969. Volume 1, Part 1; Volume 1, Part 2.

ERIC Educational Resources Information Center

Ornstein, Allan C., Ed.

This yearbook is a compilation of journal and magazine articles with an interdisciplinary approach toward the problem of educating the disadvantaged. The readings are considered as supplementary reference material designed for professors, school administrators, civil rights workers, and other interested investigators who often lack sufficient time…

77 FR 34408 - Meeting of the Advisory Committee; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-11

... examinations in actuarial mathematics and methodology referred to in 29 U.S.C. 1242(a)(1)(B) and to review the... meeting of the Advisory Committee on Actuarial Examinations (a portion of which will be open to the public.... SUPPLEMENTARY INFORMATION: Notice is hereby given that the Advisory Committee on Actuarial Examinations will...

Millwright Apprenticeship. Related Training Modules. 13.1-13.2 Air Compressors.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of two learning modules on air compressors is one of six such packets developed for apprenticeship training for millwrights. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check…

Millwright Apprenticeship. Related Training Modules. 12.1-12.3 Feedwater.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of three learning modules on feedwater is one of six such packets developed for apprenticeship training for millwrights. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check list…

75 FR 21603 - Renewal of Department of Defense Federal Advisory Committee; Missouri River (North Dakota) Task...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

...-6128. SUPPLEMENTARY INFORMATION: The Task Force is a non-discretionary Federal advisory committee and... Committee; Missouri River (North Dakota) Task Force AGENCY: Department of Defense (DoD). ACTION: Renewal of... Missouri River (North Dakota) Task Force (hereafter referred to as the Task Force). FOR FURTHER INFORMATION...

75 FR 1683 - Application and Renewal Fees Imposed on Surety Companies and Reinsuring Companies; Increase in...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-12

... and Reinsuring Companies; Increase in Fees Imposed AGENCY: Financial Management Service, Fiscal... Treasury, Financial Management Service, is increasing the fees it imposes on and collects from surety.... SUPPLEMENTARY INFORMATION: The fees imposed and collected, as referred to in 31 CFR 223.22, cover the costs...

Bibliography of Law-Related Curriculum Materials: Annotated (Second Edition). Working Notes No. 10.

ERIC Educational Resources Information Center

Davison, Susan E., Ed.

This annotated bibliography cites over 1,000 elementary- and secondary-level materials dealing with the philosophy, substance, and pedagogy of law-related education. It lists textbooks, curriculum kits and guides, journals and newsletters, and books that can serve as reference or supplementary materials. The bibliography is divided by topic into…

Stationary Engineers Apprenticeship. Related Training Modules. 4.1-4.5 Tools.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of five learning modules on tools is one of 20 such packets developed for apprenticeship training for stationary engineers. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: a lesson goal, performance indicators, study guide…

Reflecting on the structure of soil classification systems: insights from a proposal for integrating subsoil data into soil information systems

NASA Astrophysics Data System (ADS)

Dondeyne, Stefaan; Juilleret, Jérôme; Vancampenhout, Karen; Deckers, Jozef; Hissler, Christophe

2017-04-01

Classification of soils in both World Reference Base for soil resources (WRB) and Soil Taxonomy hinges on the identification of diagnostic horizons and characteristics. However as these features often occur within the first 100 cm, these classification systems convey little information on subsoil characteristics. An integrated knowledge of the soil, soil-to-substratum and deeper substratum continuum is required when dealing with environmental issues such as vegetation ecology, water quality or the Critical Zone in general. Therefore, we recently proposed a classification system of the subsolum complementing current soil classification systems. By reflecting on the structure of the subsoil classification system which is inspired by WRB, we aim at fostering a discussion on some potential future developments of WRB. For classifying the subsolum we define Regolite, Saprolite, Saprock and Bedrock as four Subsolum Reference Groups each corresponding to different weathering stages of the subsoil. Principal qualifiers can be used to categorize intergrades of these Subsoil Reference Groups while morphologic and lithologic characteristics can be presented with supplementary qualifiers. We argue that adopting a low hierarchical structure - akin to WRB and in contrast to a strong hierarchical structure as in Soil Taxonomy - offers the advantage of having an open classification system avoiding the need for a priori knowledge of all possible combinations which may be encountered in the field. Just as in WRB we also propose to use principal and supplementary qualifiers as a second level of classification. However, in contrast to WRB we propose to reserve the principal qualifiers for intergrades and to regroup the supplementary qualifiers into thematic categories (morphologic or lithologic). Structuring the qualifiers in this manner should facilitate the integration and handling of both soil and subsoil classification units into soil information systems and calls for paying attention to these structural issues in future developments of WRB.

Proteome reference maps of Medicago truncatula embryogenic cell cultures generated from single protoplasts.

PubMed

Imin, Nijat; De Jong, Femke; Mathesius, Ulrike; van Noorden, Giel; Saeed, Nasir A; Wang, Xin-Ding; Rose, Ray J; Rolfe, Barry G

2004-07-01

Using a combination of two-dimensional gel electrophoresis (2-DE) protein mapping and mass spectrometry (MS) analysis, we have established proteome reference maps of Medicago truncatula embryogenic tissue culture cells. The cultures were generated from single protoplasts, which provided a relatively homogeneous cell population. We used these to analyze protein expression at the globular stages of somatic embryogenesis, which is the earliest morphogenetic embryonic stage. Over 3000 proteins could reproducibly be resolved over a pI range of 4-11. Three hundred and twelve protein spots were extracted from colloidal Coomassie Blue-stained 2-DE gels and analyzed by matrix-assisted laser desorption/ionization-time of flight MS analysis and tandem MS sequencing. This enabled the identification of 169 protein spots representing 128 unique gene products using a publicly available expressed sequence tag database and the MASCOT search engine. These reference maps will be valuable for the investigation of the molecular events which occur during somatic embryogenesis in M. truncatula. The proteome reference maps and supplementary materials will be available and updated for public access at http://semele.anu.edu.au/.

Low Voltage Alarm Apprenticeship. Related Training Modules. 29.1-29.5 Drawing.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of five learning modules on drawing is one of eight such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check…

75 FR 55728 - Withdrawal of Proposed Rules; Discontinuing Rulemaking Efforts Listed in the Unified Agenda of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-14

... section 4 of TSCA was to support ATSDR's Substance Specific Applied Research Program, a program [email protected] . SUPPLEMENTARY INFORMATION: I. Does this Action Apply to Me? This action is directed to the... Office of Air and Radiation (OAR), along with EPA's Office of Research and Development (ORD), referred...

78 FR 9044 - Adequacy Status of the Motor Vehicle Emission Budgets for Metropolitan Washington DC Area (DC-MD...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-07

... and NO X is effective February 22, 2013. FOR FURTHER INFORMATION CONTACT: Martin Kotsch, U.S...: http://www.epa.gov/otaq/stateresources/transconf/currsips.htm . SUPPLEMENTARY INFORMATION: The word ``budgets'' refers to the motor vehicle emission budgets for VOCs and NO X . The word ``SIP'' in this...

Measurement and Classification Methods Using the ASAE S572.1 Reference Nozzles

DTIC Science & Technology

2012-01-01

Accepted: September 17, 2012 Abstract: An increasing number of spray nozzle and agrochemical manufacturers are incorporating droplet size...are incorporating droplet size measurements into both research and development of agrochemical technologies. Each laboratory has invariably...distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT An increasing number of spray nozzle and agrochemical manufacturers are incorporating droplet

Low Voltage Alarm Apprenticeship. Related Training Modules. 28.1-28.12 Human Relations.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 12 learning modules on human relations is 1 of 8 such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check…

Low Voltage Alarm Apprenticeship. Related Training Modules. 6.1-6.6 Safety.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of six learning modules on safety is one of eight such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check…

Low Voltage Alarm Apprenticeship. Related Training Modules. 27.1-27.4 Computer Usage.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of four learning modules on computer usage is one of eight such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide…

Low Voltage Alarm Apprenticeship. Related Training Modules. 0.1 History of Alarms.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of one learning module on the history of alarms is one of eight such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study…

Low Voltage Alarm Apprenticeship. Related Training Modules. 7.1-26.10 Alarm Basics.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 70 learning modules on alarm basics is 1 of 8 such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check…

Military Air Power: The CADRE Digest of Air Power Opinions and Thoughts

DTIC Science & Technology

1990-10-01

SUPPLEMENTARY NOTES 14. ABSTRACT 15. SUBJECT TERMS Air warfare; Air power; Military art and science 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...bibliographical references. 1. Air warfare. 2. Air power. 3. Military art and science . 1. Air University (US). Center for Aerospace Doctrine, Research, and...on Policy and War........................................ ........................................57 War as Art and Science

Low Voltage Alarm Apprenticeship. Related Training Modules. 2.1-5.3 Electricity/Electronics.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 29 learning modules on electricity/electronics is 1 of 8 such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide…

Certified In-lined Reference Monitoring on .NET

DTIC Science & Technology

2006-06-01

Introduction Language -based approaches to computer security have employed two major strategies for enforcing security policies over untrusted programs. • Low...automatically verify IRM’s using a static type-checker. Mobile (MOnitorable BIL with Effects) is an exten- sion of BIL (Baby Intermediate Language ) [15], a...AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES Proceedings of the 2006 Programming Languages and

Strand I - Physical Health; Dental Health for Grades 4-6. Special Edition for Evaluation and Discussion.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Curriculum Development Center.

This is a curriculum guide for teaching dental health for grades 4-6. Each topic area is outlined under the headings of: (1) reference; (2) major understandings and fundamental concepts; (3) suggested teaching aids and learning activities; and (4) supplementary information for teachers. Main topics include: (1) growth and development of teeth; (2)…

Reclamation of Synthetic Turbine Engine Lubricants.

DTIC Science & Technology

1981-08-01

test in which the comparison of lubricants is based upon differences in degradation levels produced under a fixed time/temperature condition. Referring...release; distribution unlimited 17. DISTRIBUTION STATEMENT (of the abstract entered in Block 20, II different from Report) 18 SUPPLEMENTARY NOTES 19 KEY...plant. Division in this respect was entirely fortuitous, depending only upon convenience in handling and inspecting the barrels at different delivery

BIOLOGICAL SCIENCE TEACHING TIPS FROM TST, A COMPILATION OF ARTICLES FROM SEVEN YEARS OF THE SCIENCE TEACHER, 1960-1966.

ERIC Educational Resources Information Center

PORTER, T.R.

SELECTED ARTICLES THAT APPEARED IN "THE SCIENCE TEACHER" DURING THE PERIOD 1960-1966 ARE INCLUDED IN THIS SUPPLEMENTARY REFERENCE FOR HIGH SCHOOL BIOLOGY TEACHERS. SUBDIVISIONS ARE (1) CONTENT BACKGROUND FOR TEACHERS, (2) CURRICULUM, AND (3) CLASSROOM IDEAS. CONTENT ARTICLES ARE PRIMARILY CONCERNED WITH THOSE ASPECTS OF BIOLOGY THAT ARE…

Low Voltage Alarm Apprenticeship. Related Training Modules. 1.1-1.14 Trade Math.

ERIC Educational Resources Information Center

Lane Community Coll., Eugene, OR.

This packet of 14 learning modules on trade math is 1 of 8 such packets developed for apprenticeship training for low voltage alarm. Introductory materials are a complete listing of all available modules and a supplementary reference list. Each module contains some or all of these components: goal, performance indicators, study guide (a check list…

A taxonomic review of white grubs and leaf chafers (Coleoptera: Scarabaeidae: Melolonthinae) recorded from forestry and agricultural crops in Sub-Saharan Africa.

PubMed

Harrison, J du G; Wingfield, M J

2016-04-01

Integrated pest management (IPM) is difficult to implement when one knows little about the pest complex or species causing the damage in an agricultural system. To implement IPM on Sub-Saharan African melolonthine pests access to taxon specific knowledge (their identity) and what is known (their biology) of potential pest species is a crucial step. What is known about Sub-Saharan African melolonthine white grubs and chafers has not yet been amalgamated, and this review thus synthesizes all available literature for the Region. The comprehensive nature of the review highlights pest taxon trends within African melolonthines. To facilitate the retrieval of this information for IPM purposes, all relevant taxonomic and biological information is provided for the taxa covered including an on-line supplementary annotated-checklist of taxon, crop, locality and reference(s). Based on the literature reviewed, recommendations are made to promote effective and efficient management of African melolonthine scarab pests. An on-line supplementary appendix provides a list of specialists, useful internet resources, keys, catalogues and sampling methods for the larvae and adults of melolonthine scarab beetles for subsequent morphological or molecular work.

ReadXplorer—visualization and analysis of mapped sequences

PubMed Central

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

2014-01-01

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

Effect of supplementary zinc on body mass index, pulmonary function and hospitalization in children with cystic fibrosis.

PubMed

Ataee, Pedram; Najafi, Mehri; Gharagozlou, Mohammad; Aflatounian, Majid; Mahmoudi, Maryam; Khodadad, Ahmad; Farahmand, Fatemeh; Motamed, Farzaneh; Fallahi, Glolam Hossein; Kalantari, Najmoddin; Soheili, Habib; Modarresi, Vajiheh; Modarresi, Mozhgan Sabbaghian; Rezaei, Nima

2014-01-01

Zinc deficiency, which is common in patients with cystic fibrosis (CF), can lead to several complications that may increase the number of hospital admissions in this group of patients. As supplementary zinc can prevent such complications, this study was performed to evaluate the effect of supplementary zinc on body mass index (BMI), forced expiratory volume in one second (FEV1) and number of hospitalizations in CF patients. In this study, 30 children with CF, who were referred to the Digestive Diseases Clinic of the Children's Medical Center in Tehran, were enrolled. Supplementary zinc of 2 mg/kg per day was administered to all patients. Serum level of zinc, alkaline phosphatase, and albumin as well as BMI, FEV1, and number of hospitalizations were compared before and after zinc administration. Height (p<0.001), weight (p<0.001) and BMI (p=0.001) were significantly increased after zinc, while the number of hospitalizations was significantly decreased (p=0.023). In contrast to patients with normal pulmonary function tests who received supplement therapy, BMI was not increased in those with abnormal pulmonary function after supplementary zinc. Supplementary zinc can increase BMI in CF patients, mostly in those with normal pulmonary function. While supplementary zinc may decrease the number of hospitalizations, other factors can also influence the hospitalization number.

Reference materials for the monitoring of the aquatic environment--a review with special emphasis on organic priority pollutants.

PubMed

Bercaru, Ofelia; Gawlik, Bernd Manfred; Ulberth, Franz; Vandecasteele, Carlo

2003-08-01

During recent years, the awareness of quality assurance and quality control in environmental analyses has constantly increased, especially due to the implementation of new guidelines and regulations at both the national and international level. Achieving comparable results by using certified reference materials is one of the primary concerns of the scientific community. As a result, there is a growing demand for certified reference materials to cover different matrices and pollutants. Moreover, these CRMs should be in close relationship to the determinants and target concentrations required by environmental bodies and European Directives as well. Supplementary information to this paper presents an inventory of reference materials available on the market from different suppliers against the priority pollutants listed in the Water Framework Directive. These CRMs cover matrices such as water, sediment and biota. The use of CRMs in relationship to appropriate analytical methods and relevant determinants is discussed and the need for matrix-CRMs, particularly for organic pollutants is emphasised. The use of proficiency testing schemes as an alternative for the lack of appropriate CRMs and future trends in the production of CRMs within the BCR framework are also discussed.

Enhanced ionic liquid mobility induced by confinement in 1D CNT membranes

NASA Astrophysics Data System (ADS)

Berrod, Q.; Ferdeghini, F.; Judeinstein, P.; Genevaz, N.; Ramos, R.; Fournier, A.; Dijon, J.; Ollivier, J.; Rols, S.; Yu, D.; Mole, R. A.; Zanotti, J.-M.

2016-04-01

Water confined within carbon nanotubes (CNT) exhibits tremendous enhanced transport properties. Here, we extend this result to ionic liquids (IL) confined in vertically aligned CNT membranes. Under confinement, the IL self-diffusion coefficient is increased by a factor 3 compared to its bulk reference. This could lead to high power battery separators.Water confined within carbon nanotubes (CNT) exhibits tremendous enhanced transport properties. Here, we extend this result to ionic liquids (IL) confined in vertically aligned CNT membranes. Under confinement, the IL self-diffusion coefficient is increased by a factor 3 compared to its bulk reference. This could lead to high power battery separators. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01445c

Evaluation of MALDI-TOF mass spectrometry for identification of environmental yeasts and development of supplementary database.

PubMed

Agustini, Bruna Carla; Silva, Luciano Paulino; Bloch, Carlos; Bonfim, Tania M B; da Silva, Gildo Almeida

2014-06-01

Yeast identification using traditional methods which employ morphological, physiological, and biochemical characteristics can be considered a hard task as it requires experienced microbiologists and a rigorous control in culture conditions that could implicate in different outcomes. Considering clinical or industrial applications, the fast and accurate identification of microorganisms is a crescent demand. Hence, molecular biology approaches has been extensively used and, more recently, protein profiling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved to be an even more efficient tool for taxonomic purposes. Nonetheless, concerning to mass spectrometry, data available for the differentiation of yeast species for industrial purpose is limited and reference databases commercially available comprise almost exclusively clinical microorganisms. In this context, studies focusing on environmental isolates are required to extend the existing databases. The development of a supplementary database and the assessment of a commercial database for taxonomic identifications of environmental yeast are the aims of this study. We challenge MALDI-TOF MS to create protein profiles for 845 yeast strains isolated from grape must and 67.7 % of the strains were successfully identified according to previously available manufacturer database. The remaining 32.3 % strains were not identified due to the absence of a reference spectrum. After matching the correct taxon for these strains by using molecular biology approaches, the spectra concerning the missing species were added in a supplementary database. This new library was able to accurately predict unidentified species at first instance by MALDI-TOF MS, proving it is a powerful tool for the identification of environmental yeasts.

Just Watch What I'm Saying: A Television Teaching Course for the Deaf and the Hard of Hearing.

ERIC Educational Resources Information Center

Wermer, F. E.

1969-01-01

The Netherlands Television Academy Foundation prepared a weekly television series intended to teach lip reading to the deaf and to the hard of hearing. This article outlines the scope of this project, referring to the format of the 18 half-hour lessons, to the supplementary written materials employed, to the nature of the criticism received, and…

Moeglichkeiten eines gegenwartsorientierten Landeskundeunterrichts. Unter besonderer Beruecksichtigung der Haupt- und Realschuloberstufe (Possibilities of Present-Oriented Area-Study Teaching, with Special Reference to the Upper Grade of High Schools)

ERIC Educational Resources Information Center

Hermes, Liesel

1975-01-01

Area study materials should be factual, contemporary, objective, and designed with regard to the student's level. Content should be limited to material contrasting with, or supplementary to, the students' knowledge. Penguin's series "Connexions" is better than available German texts. (Text is in German.) (IFS/WGA)

General Loss Function Applied to Satellite Scheduling Optimization

DTIC Science & Technology

2014-09-01

radio frequency communication with ground stations. The demand for satellite images is vast, spanning the industries of meteorology, oceanography...oscillators with the common frequency : / 2h  . 58 THIS PAGE INTENTIONALLY LEFT BLANK 59 LIST OF REFERENCES Apollo Mapping. 2014. “High...WA 98345-7610 10. SPONSORING/MONITORING AGENCY REPORT NUMBER 11 . SUPPLEMENTARY NOTES The views expressed in this thesis are those of the author and

Final report on EURAMET.QM-S10/1274: supplementary comparison of preparative capabilities for automotive gas mixtures

NASA Astrophysics Data System (ADS)

Val'ková, M.; Ďurišová, Z.; Szilágyi, Z. N.; Büki, T.; Fükű, J.

2016-01-01

This bilateral supplementary preparative comparison involves standard gas mixtures of automotive gas containing carbon monoxide, carbon dioxide and propane in nitrogen. Two laboratories (SMU, Slovakia and MKEH, Hungary) participated in this supplementary comparison. SMU was the coordinating laboratory, responsible for collecting and reporting measurement results. The participants have established facilities for automotive gas gravimetric preparation and analysis. The agreement of the results in this supplementary comparison is good. All the results with their reported uncertainties are in agreement with the reference values for the participants. SMU participated and obtained good results in the previous preparative comparison organised within EURAMET in this field. Both laboratories have existing claims for their Calibration and Measurement Capabilities (CMCs) for automotive gas mixtures. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Activity measurements of a suite of radionuclides (241Am, 239,240Pu, 238Pu, 238U, 234U, 235U, 232Th, 230Th, 228Th, 228Ra, 137Cs, 210Pb, 90Sr and 40K) in biota reference material (Ocean Shellfish): CCRI(II)-S3

NASA Astrophysics Data System (ADS)

Nour, S.; Karam, L. R.; Inn, K. G. W.

2012-01-01

In 2005, the CCRI decided that a comparison undertaken from 2002 to 2008 by the NIST (under the auspices of the Inter-America Metrology System [SIM]) in the development of a new biota (Ocean Shellfish) standard reference material (SRM) was sufficiently well constructed that it could be converted into a supplementary comparison under CCRI(II), with comparison identifier CCRI(II)-S3. This would enable the comparison to be used to support calibration and measurement capability (CMC) claims for radionuclide measurements in reference materials (specifically, animal-based organic materials). Previous comparisons of radionuclides have been of single or multiple nuclides in non-complex matrices and results of such could not be extended to support capabilities to measure the same nuclides in reference materials. The results of this comparison have been used to determine the certified reference value of the SRM. The key comparison working group (KCWG) of the CCRI(II) has approved this approach as a mechanism to link all the results to certified 'reference values' in lieu of the key comparison reference value (KCRV) of these specified radionuclides in this type of matrix (shellfish) so as to support CMCs of similar materials submitted by the present participants. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Developing the Clarity and Openness in Reporting: E3-based (CORE) Reference user manual for creation of clinical study reports in the era of clinical trial transparency.

PubMed

Hamilton, Samina; Bernstein, Aaron B; Blakey, Graham; Fagan, Vivien; Farrow, Tracy; Jordan, Debbie; Seiler, Walther; Shannon, Anna; Gertel, Art

2016-01-01

Interventional clinical studies conducted in the regulated drug research environment are reported using International Council for Harmonisation (ICH) regulatory guidance documents: ICH E3 on the structure and content of clinical study reports (CSRs) published in 1995 and ICH E3 supplementary Questions & Answers (Q & A) published in 2012.Since the ICH guidance documents were published, there has been heightened awareness of the importance of disclosure of clinical study results. The use of the CSR as a key source document to fulfil emerging obligations has resulted in a re-examination of how ICH guidelines are applied in CSR preparation. The dynamic regulatory and modern drug development environments create emerging reporting challenges. Regulatory medical writing and statistical professionals developed Clarity and Openness in Reporting: E3-based (CORE) Reference over a 2-year period. Stakeholders contributing expertise included a global industry association, regulatory agency, patient advocate, academic and Principal Investigator representatives. CORE Reference should help authors navigate relevant guidelines as they create CSR content relevant for today's studies. It offers practical suggestions for developing CSRs that will require minimum redaction and modification prior to public disclosure.CORE Reference comprises a Preface, followed by the actual resource. The Preface clarifies intended use and underlying principles that inform resource utility. The Preface lists references contributing to development of the resource, which broadly fall into 'regulatory' and 'public disclosure' categories. The resource includes ICH E3 guidance text, ICH E3 Q & A 2012-derived guidance text and CORE Reference text, distinguished from one another through the use of shading. Rationale comments are used throughout for clarification purposes.A separate mapping tool comparing ICH E3 sectional structure and CORE Reference sectional structure is also provided.Together, CORE Reference and the mapping tool constitute the user manual. This publication is intended to enhance the use, understanding and dissemination of CORE Reference.The CORE Reference user manual and the associated website (http://www.core-reference.org) should improve the reporting of interventional clinical studies.Periodic updates of CORE Reference are planned to maintain its relevance. CORE Reference was registered with http://www.equator-network.org on 23 March 2015.

iDoComp: a compression scheme for assembled genomes

PubMed Central

Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy

2015-01-01

Motivation: With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000. Thus we are approaching a milestone in the sequencing history, known as the $1000 genome era, where the sequencing of individuals is affordable, opening the doors to effective personalized medicine. Massive generation of genomic data, including assembled genomes, is expected in the following years. There is crucial need for compression of genomes guaranteed of performing well simultaneously on different species, from simple bacteria to humans, which will ease their transmission, dissemination and analysis. Further, most of the new genomes to be compressed will correspond to individuals of a species from which a reference already exists on the database. Thus, it is natural to propose compression schemes that assume and exploit the availability of such references. Results: We propose iDoComp, a compressor of assembled genomes presented in FASTA format that compresses an individual genome using a reference genome for both the compression and the decompression. In terms of compression efficiency, iDoComp outperforms previously proposed algorithms in most of the studied cases, with comparable or better running time. For example, we observe compression gains of up to 60% in several cases, including H.sapiens data, when comparing with the best compression performance among the previously proposed algorithms. Availability: iDoComp is written in C and can be downloaded from: http://www.stanford.edu/~iochoa/iDoComp.html (We also provide a full explanation on how to run the program and an example with all the necessary files to run it.). Contact: iochoa@stanford.edu Supplementary information: Supplementary Data are available at Bioinformatics online. PMID:25344501

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

PubMed Central

Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Zaitlen, Noah; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Chen, Gary K.; Le Marchand, Loic; Henderson, Brian; Reich, David; Haiman, Christopher A.; Gonzàlez Burchard, Esteban; Halperin, Eran

2013-01-01

Motivation: Local ancestry analysis of genotype data from recently admixed populations (e.g. Latinos, African Americans) provides key insights into population history and disease genetics. Although methods for local ancestry inference have been extensively validated in simulations (under many unrealistic assumptions), no empirical study of local ancestry accuracy in Latinos exists to date. Hence, interpreting findings that rely on local ancestry in Latinos is challenging. Results: Here, we use 489 nuclear families from the mainland USA, Puerto Rico and Mexico in conjunction with 3204 unrelated Latinos from the Multiethnic Cohort study to provide the first empirical characterization of local ancestry inference accuracy in Latinos. Our approach for identifying errors does not rely on simulations but on the observation that local ancestry in families follows Mendelian inheritance. We measure the rate of local ancestry assignments that lead to Mendelian inconsistencies in local ancestry in trios (MILANC), which provides a lower bound on errors in the local ancestry estimates. We show that MILANC rates observed in simulations underestimate the rate observed in real data, and that MILANC varies substantially across the genome. Second, across a wide range of methods, we observe that loci with large deviations in local ancestry also show enrichment in MILANC rates. Therefore, local ancestry estimates at such loci should be interpreted with caution. Finally, we reconstruct ancestral haplotype panels to be used as reference panels in local ancestry inference and show that ancestry inference is significantly improved by incoroprating these reference panels. Availability and implementation: We provide the reconstructed reference panels together with the maps of MILANC rates as a public resource for researchers analyzing local ancestry in Latinos at http://bogdanlab.pathology.ucla.edu. Contact: bpasaniuc@mednet.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23572411

Magnetohydrodynamics (MHD) Engineering Test Facility (ETF) 200 MWe power plant. Conceptual Design Engineering Report (CDER). Volume 4: Supplementary engineering data

NASA Astrophysics Data System (ADS)

1981-09-01

The reference conceptual design of the Magnetohydrodynamic Engineering Test Facility (ETF), a prototype 200 MWe coal-fired electric generating plant designed to demonstrate the commercial feasibility of open cycle MHD is summarized. Main elements of the design are identified and explained, and the rationale behind them is reviewed. Major systems and plant facilities are listed and discussed. Construction cost and schedule estimates, and identification of engineering issues that should be reexamined are also given. The latest (1980-1981) information from the MHD technology program are integrated with the elements of a conventional steam power electric generating plant. Supplementary Engineering Data (Issues, Background, Performance Assurance Plan, Design Details, System Design Descriptions and Related Drawings) is presented.

Magnetohydrodynamics (MHD) Engineering Test Facility (ETF) 200 MWe power plant. Conceptual Design Engineering Report (CDER). Volume 4: Supplementary engineering data

NASA Technical Reports Server (NTRS)

1981-01-01

The reference conceptual design of the Magnetohydrodynamic Engineering Test Facility (ETF), a prototype 200 MWe coal-fired electric generating plant designed to demonstrate the commercial feasibility of open cycle MHD is summarized. Main elements of the design are identified and explained, and the rationale behind them is reviewed. Major systems and plant facilities are listed and discussed. Construction cost and schedule estimates, and identification of engineering issues that should be reexamined are also given. The latest (1980-1981) information from the MHD technology program are integrated with the elements of a conventional steam power electric generating plant. Supplementary Engineering Data (Issues, Background, Performance Assurance Plan, Design Details, System Design Descriptions and Related Drawings) is presented.

Assessment of Chiropractic Treatment for Low Back Pain, Military Readiness and Smoking Cessation in Military Active Duty Personnel

DTIC Science & Technology

2014-03-01

AD_________________ Award Number: W81XWH-11-2-0107 TITLE: Assessment of Chiropractic Treatment for...Annual 3. DATES COVERED 15 February 2013 – 14 February 2014 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Assessment of Chiropractic Treatment for...SUPPLEMENTARY NOTES 14. ABSTRACT This study is comprised of three trials, referred to as the Assessment of Chiropractic Treatment (ACT). The

Identification of Novel Genes and Candidate Targets in CML Stem Cells

DTIC Science & Technology

2008-07-01

myeloblastosis viral oncogene homolog (avian) 6q22–q23 12 GATCCTGTGTTTGCAAC 1 FLI1 NM_002017 Friend leukemia virus integration 1 11q24.1–q24.3 3...AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Chronic myeloid leukemia (CML) is...Conclusion 6 References 6 Supporting Data 8 Appendices 16 4 INTRODUCTION: Chronic myeloid leukemia (CML) is a blood

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

PubMed Central

2007-01-01

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol−1. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol−1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol−1. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta6Cl12]2+ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0233-4) contains supplementary material, which is available to authorized users. PMID:17828561

WHO expert committee on specifications for pharmaceutical preparations. Fortieth report.

PubMed

2006-01-01

This report presents the recommendations of an international group of experts convened by the World Health Organization to consider matters concerning the quality assurance of pharmaceuticals and specifications for drug substances and dosage forms. The report is complemented by a number of annexes. These include: a list of available International Chemical Reference Substances and International Infrared Spectra; supplementary guidelines on good manufacturing practices for heating, ventilation and air-conditioning systems for non-sterile pharmaceutical dosage forms; updated supplementary guidelines on good manufacturing practices for the manufacture of herbal medicines; supplementary guidelines on good manufacturing practices for validation; good distribution practices for pharmaceutical products; a model quality assurance system for procurement agencies (recommendations for quality assurance systems focusing on prequalification of products and manufacturers, purchasing, storage and distribution of pharmaceutical products); multisource (generic) pharmaceutical products: guidelines on registration requirements to establish interchangeability; a proposal to waive in vivo bioequivalence requirements for WHO Model List of Essential Medicines immediate-release, solid oral dosage forms; and additional guidance for organizations performing in vivo bioequivalence studies.

Grassroots Environmentalism in Vietnam: How Communities Can Initiate Change

DTIC Science & Technology

2013-11-01

5d. PROJECT NUMBER Boll, Christian D., CDR, USN 5e. TASK NUMBER Paper Advisor: Prof. William McDonald 5f. WORK UNIT NUMBER 7...number of IGO environmental funds that are administered by the World Bank . The Climate Investment Fund, for example, sponsors a number of projects in...Distribution is unlimited. Reference: DOD Directive 5230.24 13. SUPPLEMENTARY NOTES A paper submitted to the Naval War College faculty in partial

Magnetic Anomaly Detection by Remote Means

DTIC Science & Technology

2016-09-21

REFERENCES 1. W. Happer, "Laser Remote Sensing of Magnetic Fields in the Atmosphere by Two-Photon Optical Pumping of Xe 129,” , NADC Report N62269-78-M...by Remote Means 5b. GRANT NUMBER NOOO 14-13-1-0282 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Miles , Richard and Dogariu...unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT Research on the possibility of detecting magnetic anomalies remotely using laser excitation of a

Mendel-GPU: haplotyping and genotype imputation on graphics processing units

PubMed Central

Chen, Gary K.; Wang, Kai; Stram, Alex H.; Sobel, Eric M.; Lange, Kenneth

2012-01-01

Motivation: In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data. Results: Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand. Availability: Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/. Contact: gary.k.chen@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22954633

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies.

PubMed

Bushmanova, Elena; Antipov, Dmitry; Lapidus, Alla; Suvorov, Vladimir; Prjibelski, Andrey D

2016-07-15

Ability to generate large RNA-Seq datasets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for RNA-Seq assemblies. We present rnaQUAST-a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report. rnaQUAST is implemented in Python and is freely available at http://bioinf.spbau.ru/en/rnaquast ap@bioinf.spbau.ru Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SUPPLEMENTARY COMPARISON: Final report on supplementary comparison APMP-T-S3-03 of industrial platinum resistance and liquid in glass thermometers from -40 °C to 250 °C

NASA Astrophysics Data System (ADS)

Norranim, Uthai; Nguyen, Mong Kim; Ballico, Mark J.

2007-01-01

Industrial thermometers such as industrial platinum resistance thermometers (iprts) and liquid-in-glass thermometers (LIGTs) are widely used in industry. Because Key Comparisons are limited to direct realizations of ITS-90, and not all APMP NMIs have participated in them, the national metrology institutes (NMIs) of Thailand and Australia (NIMT and NIMA) organized an APMP supplementary comparison to support the approval of CMCs (calibration and measurement capabilities) for these laboratories. The comparison, performed in 2003, covered the range from -40.0 °C to 250.0 °C, using IPRTs (Hart Scientific 5626-12-S), total immersion (ASTM 62C, 120C) and partial immersion (ASTM 40C) LIGTs. Ten NMIs from the APMP: KIM-LIPI (Indonesia), ITDI (Philippines), MSL (New Zealand), NBSM (Nepal), NMIA (Australia), NIMT (Thailand), SCL (Hong Kong), SIRIM (Malaysia), SPRING (Singapore) and VMI (Vietnam) were divided into two loops to shorten the circulation time, and these were linked by the two pilot laboratories. This report describes details of the artifacts, the circulation schedule, the measurement procedures, the results submitted by participants, uncertainties and the analysis of the results. Reference values calculated using simple mean, median and weighted mean were consistent with each other, but as the Birge criterion was satisfied, the weighted mean with its lower uncertainty was adopted. The artifacts were found to be stable over the comparison and the results of the loop linking labs consistent, allowing an uncertainty of 2 mK to 4 mK to be achieved for the IPRT reference value and 10 mK to 20 mK for the LIGT reference values. These uncertainties allowed the comparison data to be used to adequately test the uncertainties of all the participant laboratories, and hence to directly support their CMC claims. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the APMP, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

Cluster Beam Deposition Technology for Optical Coatings. Phase 1

DTIC Science & Technology

1987-05-01

Particles 55 5.4.3 Growth of Ultrafine Particles or 61 Clusters by Gas Quenching 6.0 REFERENCES 67 APPENDIX: SUPPLEMENTARY INFORMATION 69 COP TR-407/5-87...approach, based on growth and transport of ultrafine particles or clusters in a quenching gas, appears more promising in our view and has been proposed for... Ultrafine Particles or Clusters by Gas quenching The apparent difficulty of making metal clusters with a Takagi-type source led us to explore other

Plastic Deformation and Fracture of Steel under Dynamic Loading.

DTIC Science & Technology

1980-05-01

distribution unlimited. 17. DISTRIBUTION STATEMENT (of thme abstract antered ins Black 20, it dii ioreui how. Reprt) r NA I *. SUPPLEMENTARY NOTES The view...under the previous ARO grant has been completed and accepted for publication. I References [1] Wilson, M. L., Hawley, R . H. and Duffy, J., "Strain...of Fracture in a Mild, Rate-Sensitive Steel," Journal of Engineering Materials and Technology, July, 1979 , pp. 258-264. [4] Wilson, M. L., Hawley, R

Comparing Rising Powers: The Case of Pre-World War II Japanese Nationalism and Contemporary Chinese Nationalism

DTIC Science & Technology

2018-03-01

S) AND ADDRESS(ES) N/A 10. SPONSORING / MONITORING AGENCY REPORT NUMBER 11. SUPPLEMENTARY NOTES The views expressed in this thesis are those of...military force, economy, and religion, to name only a few, are frequently referred to by scholars as sources for uniting people under the banner...main drivers of Japanese nationalism before 1945, and are these same factors driving Chinese nationalism today? After comparing similarities between

C3I Analysis Tools for Development Planning. Volume 1

DTIC Science & Technology

1985-09-27

otherwise as in any manner licensing the holder or any other person or conveying any rights or permission to manufacture, use, or sell any patented... PERSONAL AUTHOR(S) ».A. Vail, G.H. Weissman, J.G. Wohl TYPE OF REPORT ?inal 13b. TIME COVERED FROM SUPPLEMENTARY NOTATION Refer to ESD-TR-86...support for decisions about the relative value of acquisition programs. 5. The software tool developed on a personal computer demonstrates that

Final report on COOMET.AUV.A-S1: Technical report on supplementary comparison 'Comparison of national standards of the sound pressure unit in air through calibration of working reference microphones'

NASA Astrophysics Data System (ADS)

Pozdeeva, Valentina; Chalyy, Vladimir

2014-01-01

The supplementary comparison COOMET.AUV.A-S1 for secondary calibration methods using WS1 and WS2 measurement microphones was carried out from 2009 to 2010. The results were submitted to and approved by CCAUV in April 2014. Four National Metrology Institutes took part in this comparison and are as follows: BelGIM (Belarus), VNIIFTRI (Russia), SMU (Slovakia) and DP NDI 'Sistema' (Ukraine). Three of the above NMIs (VNIIFTRI, SMU and DP NDI 'Sistema') had earlier participated in COOMET key comparisons and one NMI (VNIIFTRI) had also participated in CCAUV key comparisons. The Comparison Reference Values were calculated as the weighted mean values from results obtained by three institutes. The comparison results show agreement for all participants in the frequency range from 20 Hz to 12.5 kHz for WS1 microphones, and in the frequency range from 20 Hz to 16 kHz for WS2 microphones. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

SUPPLEMENTARY COMPARISON: APMP.PR-S1 comparison of irradiance responsivity of UVA detectors

NASA Astrophysics Data System (ADS)

Xu, Gan; Huang, Xuebo; Liu, Yuanjie

2007-01-01

APMP.PR-S1, a supplementary comparison of irradiance responsivity of UVA detectors, was carried out among seven national metrology institutes piloted by SPRING Singapore from 2003 to 2005. Two quantities, the narrow band UV (365 nm ± 5 nm) irradiance responsivity and the broad band UVA (315 nm-400 nm) irradiance responsivity of the transfer detectors, have been compared. Commercial UV source (medium pressure mercury short arc lamp) and UVA detectors were used as transfer standards in the comparison. Measurement results from participants were reported and their uncertainties associated with the comparison were analysed in this report. The method of weighted mean with cut-off was used to calculate the comparison reference values. The results from most participating labs lie within ±5% against the comparison reference values with a few exceptions. The degree of agreement of the comparison depends not only on the base scales of spectral responsivity and spectral irradiance of a laboratory, but also equally importantly on the method used for the measurement. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the APMP, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

X-MATE: a flexible system for mapping short read data

PubMed Central

Pearson, John V.; Cloonan, Nicole; Grimmond, Sean M.

2011-01-01

Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software. Availability: Executables, source code, junction libraries, test data and results and the user manual are available from http://grimmond.imb.uq.edu.au/X-MATE/. Contact: n.cloonan@uq.edu.au; s.grimmond@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics Online. PMID:21216778

Bibliography of Aeronautics: 1928

NASA Technical Reports Server (NTRS)

Brockett, Paul

1928-01-01

This Bibliography of Aeronautics for 1928 covers the aeronautical literature published from January 1 to December 31, 1928. The first Bibliography of Aeronautics was published by the Smithsonian Institution as volume 55 of the Smithsonian Miscellaneous Collections and covered the material published prior to June 30, 1909. Supplementary volumes of the Bibliography of Aeronautics for the subsequent years have been published by the National Advisory Committee for Aeronautics. The last preceding volume was for the calendar year 1927. As in the previous volumes, citations of the publications of all nations are included in the languages in which these publications originally appeared. The arrangement is in dictionary form with author and subject entry, and one alphabetical arrangement. Detail in the matter of subject reference has been omitted on account of the cost of presentation, but an attempt has been made to give sufficient cross reference for research in special lines.

Bibliography of Aeronautics: 1926

NASA Technical Reports Server (NTRS)

Brockett, Paul

1928-01-01

This Bibliography of Aeronautics for 1926 covers the aeronautical literature published from January 1 to December 31, 1926. The first Bibliography of Aeronautics was published by the Smithsonian Institution as volume 55 of the Smithsonian Miscellaneous Collections and covered the material published prior to June 30, 1909. Supplementary volumes of the Bibliography of Aeronautics for the subsequent years have been published by the National Advisory Committee for Aeronautics. The last preceding volume was for the calendar year 1925. As in the previous volumes, citations of the publications of all nations are included in the languages in which these publications originally appeared. The arrangement is dictionary form with author find subject entry, and one alphabetical arrangement. Detail in the matter of subject reference has been omitted on aCC01.mt of the cost of presentation, but an attempt has been made to give sufficient cross reference for research in special lines.

Bibliography of Aeronautics, 1929

NASA Technical Reports Server (NTRS)

Brockett, Paul

1930-01-01

This Bibliography of Aeronautics for 1929 covers the aeronautical literature published from January 1 to December 31, 1929. The first Bibliography of Aeronautics was published by the Smithsonian Institution as Volume 55 of the Smithsonian Miscellaneous Collections and covered the material published prior to June 30, 1909. Supplementary volumes of the Bibliography of Aeronautics for the subsequent years have been published by the National Advisory Committee for Aeronautics. The last preceding volume was for the calendar year 1928. As in the previous volumes, citations of the pUblications of all nations are included in th.e languages in which. these publications originally appeared. The arrangement is in dictionary form with author and subject entry, and one alphabetical arrangement. Detail in the matter of subject reference has been omitted on account of the cost of presentation, but an attempt has been made to give sufficient cross reference for research in special lines.

Bibliography of Aeronautics: 1932

NASA Technical Reports Server (NTRS)

1935-01-01

This Bibliography of Aeronautics for 1932 covers the aeronautical literature published from January 1 to December 31, 1932. The first Bibliography of Aeronautics was published by the Smithsonian Institution as volume 55 of the Smithsonian Miscellaneous Collections and covered the material published prior to June 30, 1909. Supplementary volumes of the Bibliography of Aeronautics for the subsequent years have been published by the National Advisory Committee for Aeronautics. The last preceding volume was for the calendar year 1931. As in the previous volumes, citations of the publications of all nations are included in the languages in which these publications originally appeared. The arrangement is in dictionary form with author and subject entry and one alphabetical arrangement. Detail in the matter of subject reference has been omitted on account of the cost of presentation, but an attempt has been made to give sufficient cross-reference for research in special lines.

MetaQUAST: evaluation of metagenome assemblies.

PubMed

Mikheenko, Alla; Saveliev, Vladislav; Gurevich, Alexey

2016-04-01

During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets. http://bioinf.spbau.ru/metaquast aleksey.gurevich@spbu.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.

PubMed

Westbrook, John D; Shao, Chenghua; Feng, Zukang; Zhuravleva, Marina; Velankar, Sameer; Young, Jasmine

2015-04-15

The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described. The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and can be accessed from http://wwpdb.org. jwest@rcsb.rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An AERONET-Based Aerosol Classification Using the Mahalanobis Distance

NASA Technical Reports Server (NTRS)

Hamill, Patrick; Giordano, Marco; Ward, Carolyne; Giles, David; Holben, Brent

2016-01-01

We present an aerosol classification based on AERONET aerosol data from 1993 to 2012. We used the AERONET Level 2.0 almucantar aerosol retrieval products to define several reference aerosol clusters which are characteristic of the following general aerosol types: Urban-Industrial, Biomass Burning, Mixed Aerosol, Dust, and Maritime. The classification of a particular aerosol observation as one of these aerosol types is determined by its five-dimensional Mahalanobis distance to each reference cluster. We have calculated the fractional aerosol type distribution at 190 AERONET sites, as well as the monthly variation in aerosol type at those locations. The results are presented on a global map and individually in the supplementary material. Our aerosol typing is based on recognizing that different geographic regions exhibit characteristic aerosol types. To generate reference clusters we only keep data points that lie within a Mahalanobis distance of 2 from the centroid. Our aerosol characterization is based on the AERONET retrieved quantities, therefore it does not include low optical depth values. The analysis is based on point sources (the AERONET sites) rather than globally distributed values. The classifications obtained will be useful in interpreting aerosol retrievals from satellite borne instruments.

Anthropometric Cockpit Compatibility Assessment of US Army Aircraft for Large and Small Personnel Wearing a Training, Warm-Weather Clothing Configuration

DTIC Science & Technology

1984-07-01

SUPPLEMENTARY NOTES 19. KEY WORDS (Continue on rover&* side If necessary and Identify by block number) Anthropometry , Cockpit Compatibility, Aircraft...report is one of a series of reports on anthropometry in US Army Aviation produced by the US Army Aeromedical Research Laboratory (USAARL...and stick (OV-1D). 4 , 26 *w. I.. REFERENCES Churchill, E., Churchill, T., McConville, J.T., and White, R.M. 1977. Anthropometry of women of the U.S

Computation of the Hydrodynamic Forces and Moments on a Body of Revolution with and without Appendages

DTIC Science & Technology

1991-08-01

SUPPLEMENTARY NOTATION 1 COSA. CODES 18 SUBJECT TERMS (,ontnuo 0 ner of necessary Atdi, block n" mbr ) FIELD GROUP SUB.GROUP Submarine ’hyoroaynamic ’~ aDS...hydrodynamic forces and moments developed on the hull and appendages of a submerged vehicle is required for determining its stability, control, and...an approximate method has been developed to compute the hydrodynamic forces and moments for a submerged vehicle. As discussed in Reference 1, the

Experience with Health Coach-Mediated Physician Referral in an Employed Insured Population

PubMed Central

Rao, Sowmya R.; Rogers, Robert S.; Mailhot, Johanna R.; Galvin, Robert

2010-01-01

BACKGROUND Given increasing interest in helping consumers choose high-performing (higher quality, lower cost) physicians, one approach chosen by several large employers is to provide assistance in the form of a telephonic “health coach” — a registered nurse who assists with identifying appropriate and available providers. OBJECTIVE To evaluate the health coach’s influence on provider choice and the quality of the user experience in the early introduction of this service. DESIGN Cross-sectional survey of 3490 employees and covered dependents of a large national firm that offered health coach services to all employees and covered dependents. The survey began in September 2007 with proportionate stratified sampling of 1750 employees and covered dependents who used the services between October 2007 and February 2008, and 1740 non-users. PARTICIPANTS Insured adults (ages 21–64) employed by a large national firm or covered dependents of employees. MEASUREMENTS Awareness of the service, reason for using service, visits to providers recommended by service, use of health advice provided by service, user satisfaction. MAIN RESULTS The primary reason for using the service was to obtain provider referrals (73%). Fifty-two percent of users sought a specialist referral, 33% a PCP referral and 9% a hospital referral. Eighty-nine percent of users seeking a provider referral were referred in-network; 81% of those referred visited the referred provider. Measures of satisfaction with both the service and the care delivered by recommended providers were over 70%. CONCLUSIONS Customers largely follow the provider recommendation of the health coach. Users express general satisfaction with existing health coach services, but differences in performance between vendors highlight the need for the services to be well implemented. Electronic supplementary material The online version of this article (doi:10.1007/s11606-010-1428-4) contains supplementary material, which is available to authorized users. PMID:20556533

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

PubMed Central

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

PubMed

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

Joint Transform Correlation for face tracking: elderly fall detection application

NASA Astrophysics Data System (ADS)

Katz, Philippe; Aron, Michael; Alfalou, Ayman

2013-03-01

In this paper, an iterative tracking algorithm based on a non-linear JTC (Joint Transform Correlator) architecture and enhanced by a digital image processing method is proposed and validated. This algorithm is based on the computation of a correlation plane where the reference image is updated at each frame. For that purpose, we use the JTC technique in real time to track a patient (target image) in a room fitted with a video camera. The correlation plane is used to localize the target image in the current video frame (frame i). Then, the reference image to be exploited in the next frame (frame i+1) is updated according to the previous one (frame i). In an effort to validate our algorithm, our work is divided into two parts: (i) a large study based on different sequences with several situations and different JTC parameters is achieved in order to quantify their effects on the tracking performances (decimation, non-linearity coefficient, size of the correlation plane, size of the region of interest...). (ii) the tracking algorithm is integrated into an application of elderly fall detection. The first reference image is a face detected by means of Haar descriptors, and then localized into the new video image thanks to our tracking method. In order to avoid a bad update of the reference frame, a method based on a comparison of image intensity histograms is proposed and integrated in our algorithm. This step ensures a robust tracking of the reference frame. This article focuses on face tracking step optimisation and evalutation. A supplementary step of fall detection, based on vertical acceleration and position, will be added and studied in further work.

Final report on COOMET.QM-S1 (COOMET project no 483/RU/09): Supplementary comparison of primary standard gas mixtures: Nitrogen monoxide in nitrogen (50 µmol/mol)

NASA Astrophysics Data System (ADS)

Konopelko, L. A.; Kustikov, Y. A.; Kolobova, A. V.; Shor, N. B.; Efremova, O. V.; Rozhnov, M. S.; Melnyk, D. M.; Kozia, V. G.; Shpilnyi, S. A.; Petryshyn, P. V.; Iakubov, S. E.; Kluchits, A. S.; Ananyin, V. N.; Mironchik, A. M.; Mokhnach, M. V.; Valkova, M.; Stovcik, V.; Walden, J.; Augusto, C. R.; Fioravante, A. L.; Ribeiro, C. C.; Sobrinho, D. C. G.; Oudwater, R. J.; da Cunha, V. S.

2014-01-01

Nitrogen monoxide is one of the main contaminants present in the atmospheric air due to emissions of vehicles and power stations. Taking into account the positive experience of VNIIM in the pilot study CCQM-P73 (Nitrogen monoxide gas standards, 30 µmol/mol to 70 µmol/mol), a COOMET project (No 483/RU/09) on the subject was decided and registered in the KCDB as supplementary comparison COOMET.QM-S1. This involved six National Metrology Institutes, aiming to consolidate or support their Calibration and Measurement Capabilities in this field. It was found that most of the results were consistent with the reference (gravimetric) values, with observed differences not exceeding ±1.3% and not exceeding either the appropriate assigned expanded uncertainties. There was, however, one exception: the INMETRO difference from the reference value is slightly higher than the expended uncertainty. The mixtures prepared for this exercise were found to be stable during about one year within the uncertainty of the measurements. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by COOMET, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

JADOPPT: java based AutoDock preparing and processing tool.

PubMed

García-Pérez, Carlos; Peláez, Rafael; Therón, Roberto; Luis López-Pérez, José

2017-02-15

AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results. JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http://visualanalytics.land/cgarcia/JADOPPT.html. carlosgarcia@usal.es or pelaez@usal.es. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Icarus: visualizer for de novo assembly evaluation.

PubMed

Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey

2016-11-01

: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Alternatives for managing wastes from reactors and post-fission operations in the LWR fuel cycle. Volume 5. Appendices

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

Not Available

1976-05-01

Volume V of the five-volume report consists of appendices, which provide supplementary information, with emphasis on characteristics of geologic formations that might be used for final storage or disposal. Appendix titles are: selected glossary; conversion factors; geologic isolation, including, (a) site selection factors for repositories of wastes in geologic media, (b) rock types--geologic occurrence, (c) glossary of geohydrologic terms, and (d) 217 references; the ocean floor; and, government regulations pertaining to the management of radioactive materials. (JGB)

[The regulatory regime and the health insurance industry in Brazil].

PubMed

Costa, Nilson do Rosário

2008-01-01

This paper analyzes the regulatory regime for health insurance and prepayment schemes in Brazil. It describes the ideas that have influenced the creation of the Agência Nacional de Saúde Suplementar-ANS (National Agency of Supplementary Health) in 2000, showing that the independent agency model was a direct result of the privatization process and of the induction of new competition mechanisms in a natural state monopoly. The paper concludes that the prepayment firms in Brazil are facing a new institutional environment as refers to their market entry or exit conditions.

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C

2017-03-15

LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Scattering Theory for the Acoustic Wave Equation in an Arbitrary Exterior Domain

DTIC Science & Technology

1976-08-30

65) will be further studied in the follow-up article. REFERENCES 1. C.H. Wilcox, Scattering Theory for the d - Alembert Equation in Exterior Domains...Exterior Domain Naval Research Lab Washington D C 30 Aug 76 254060 NRL Report 8030 Scattering Theory for the Acoustic Wave SEquation in an Arbitrary...STATEMENT (of the .b.Ia te ntere., d in loc k 10. If diferegn from R pr)A. 16 SUPPLEMENTARY NOTES IS KEY WORDS (Co.n.v onl r*eers Od*e ifftoneemy and

Bibliography on Tidal Hydraulics. Report 2. Supplement 9. Supplementary Material Compiled from June 1980 to June 1983. Tidal Flows in Rivers and Harbors,

DTIC Science & Technology

1985-06-01

plicated in that the Ilow may vary between Peru Coast. JOURNAL OF PHYSICAL OCEANOG-RAPHY, 8(6):1025-1041, November 1978. well-mixed and stratified...coast of Peru . The fects. References (29 items). observations were made near 150 S, a region of particularly strong and persistent coastal Bowden, K.F...as well as the semi-w,,v ,,r lump iclompanied by instabilities up diurnal shallow-water tides in the Amazon es- iii_) m highll A further, unexpected

[The effective evaluation on the supplementary immunization activities among the migrant pre-school children in Chaoyang District of Beijing].

PubMed

Luo, Feng-ji; Liu, Fang; Zhang, Jing

2009-06-01

To evaluate the effect of Supplementary Immunization Activities (SIAs) among the migrant preschool children in Chaoyang district of Beijing since 2005 to 2007, and to provide reference for formulating the strategies for Expanded Program on Immunization (EPI). The descriptive epidemiology was used to analyze the data of SIAs among the migrant preschool children in Chaoyang district since 2005 to 2007. The SIAs data demonstrated an increasing number of the floating preschool children in Chaoyang district from 2005 to 2007, and the increase rate of year-on-year in 2006 to 2007 was 12.67% and 4.60% respectively. The registration rates of immunization card and identification among the floating preschool children increased by years from 2005 to 2007. The zero-dose rates of Oral Polio Vaccine (OPV), Measles Vaccine (MV), Diphtheria-Pertus-sis-Tetaus vaccine (DPT), Meningococcal Polysaccharide Vaccine (MPV) and Japanese Encephalitis Vaccine (JEV) showed a decrease trends since 2005 to 2007. The age special incidence rate and proportion of vaccine-preventable diseases for the people who were 1- 4-years-old decreased. It is an effective management pattern that the government plays a dominated role in Supplementary Immunization Activities (SIAs).

Practical automated glass selection and the design of apochromats with large field of view.

PubMed

Siew, Ronian

2016-11-10

This paper presents an automated approach to the selection of optical glasses for the design of an apochromatic lens with large field of view, based on a design originally provided by Yang et al. [Appl. Opt.55, 5977 (2016)APOPAI0003-693510.1364/AO.55.005977]. Following from this reference's preliminary optimized structure, it is shown that the effort of glass selection is significantly reduced by using the global optimization feature in the Zemax optical design program. The glass selection process is very fast, complete within minutes, and the key lies in automating the substitution of glasses found from the global search without the need to simultaneously optimize any other lens parameter during the glass search. The result is an alternate optimized version of the lens from the above reference possessing zero axial secondary color within the visible spectrum and a large field of view. Supplementary material is provided in the form of Zemax and text files, before and after final optimization.

A dose response randomised controlled trial of docosahexaenoic acid (DHA) in preterm infants.

PubMed

Collins, C T; Sullivan, T R; McPhee, A J; Stark, M J; Makrides, M; Gibson, R A

2015-08-01

Thirty one infants born less than 30 weeks׳ gestational age were randomised to receive either 40 (n=11), 80 (n=9) or 120 (n=11) mg/kg/day of docosahexaenoic acid (DHA) respectively as an emulsion, via the feeding tube, commenced within 4 days of the first enteral feed. Twenty three infants were enroled in non-randomised reference groups; n=11 who had no supplementary DHA and n=12 who had maternal DHA supplementation. All levels of DHA in the emulsion were well tolerated with no effect on number of days of interrupted feeds or days to full enteral feeds. DHA levels in diets were directly related to blood DHA levels but were unrelated to arachidonic acid (AA) levels. All randomised groups and the maternal supplementation reference group prevented the drop in DHA levels at study end that was evident in infants not receiving supplementation. Australian New Zealand Clinical Trials Registry: ACTRN12610000382077. Copyright © 2015 Elsevier Ltd. All rights reserved.

Analysis of on-line clinical laboratory manuals and practical recommendations.

PubMed

Beckwith, Bruce; Schwartz, Robert; Pantanowitz, Liron

2004-04-01

On-line clinical laboratory manuals are a valuable resource for medical professionals. To our knowledge, no recommendations currently exist for their content or design. To analyze publicly accessible on-line clinical laboratory manuals and to propose guidelines for their content. We conducted an Internet search for clinical laboratory manuals written in English with individual test listings. Four individual test listings in each manual were evaluated for 16 data elements, including sample requirements, test methodology, units of measure, reference range, and critical values. Web sites were also evaluated for supplementary information and search functions. We identified 48 on-line laboratory manuals, including 24 academic or community hospital laboratories and 24 commercial or reference laboratories. All manuals had search engines and/or test indices. No single manual contained all 16 data elements evaluated. An average of 8.9 (56%) elements were present (range, 4-14). Basic sample requirements (specimen and volume needed) were the elements most commonly present (98% of manuals). The frequency of the remaining data elements varied from 10% to 90%. On-line clinical laboratory manuals originate from both hospital and commercial laboratories. While most manuals were user-friendly and contained adequate specimen-collection information, other important elements, such as reference ranges, were frequently absent. To ensure that clinical laboratory manuals are of maximal utility, we propose the following 13 data elements be included in individual test listings: test name, synonyms, test description, test methodology, sample requirements, volume requirements, collection guidelines, transport guidelines, units of measure, reference range, critical values, test availability, and date of latest revision.

DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts.

PubMed

Lee, Donghyung; Bigdeli, T Bernard; Williamson, Vernell S; Vladimirov, Vladimir I; Riley, Brien P; Fanous, Ayman H; Bacanu, Silviu-Alin

2015-10-01

To increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts. To decrease computational and access requirements for the analysis of cosmopolitan cohorts, we propose DISTMIX, which extends DIST capabilities to the analysis of mixed ethnicity cohorts. The method uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistics at measured SNPs and estimated/user-specified ethnic proportions. Simulations show that the proposed method adequately controls the Type I error rates. The 1000 Genomes panel imputation of summary statistics from the ethnically diverse Psychiatric Genetic Consortium Schizophrenia Phase 2 suggests that, when compared to genotype imputation methods, DISTMIX offers comparable imputation accuracy for only a fraction of computational resources. DISTMIX software, its reference population data, and usage examples are publicly available at http://code.google.com/p/distmix. dlee4@vcu.edu Supplementary Data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

PubMed Central

Veal, Colin D.; Xu, Hang; Reekie, Katherine; Free, Robert; Hardwick, Robert J.; McVey, David; Brookes, Anthony J.; Hollox, Edward J.; Talbot, Christopher J.

2013-01-01

Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact: cjt14@le.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23742985

Geomorphology and depositional subenvironments of Gulf Islands National Seashore, Perdido Key and Santa Rosa Island, Florida

USGS Publications Warehouse

Morton, Robert A.; Montgomery, Marilyn C.

2010-01-01

The primary mapping procedures were supervised functions within a Geographic Information System (GIS) that were applied to delineate and classify depositional subenvironments and features, collectively referred to as map units. The delineated boundaries of the map units were exported to create one shapefile, and are differentiated by the field "Type" in the associated attribute table. Map units were delineated and classified based on differences in tonal patterns of features in contrast to adjacent features observed on orthophotography. Land elevations from recent lidar surveys served as supplementary data to assist in delineating the map unit boundaries.

The gravity apple tree

NASA Astrophysics Data System (ADS)

Espinosa Aldama, Mariana

2015-04-01

The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion.

Use of X-ray diffraction to quantify amorphous supplementary cementitious materials in anhydrous and hydrated blended cements

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

Snellings, R., E-mail: ruben.snellings@epfl.ch; Salze, A.; Scrivener, K.L., E-mail: karen.scrivener@epfl.ch

2014-10-15

The content of individual amorphous supplementary cementitious materials (SCMs) in anhydrous and hydrated blended cements was quantified by the PONKCS [1] X-ray diffraction (XRD) method. The analytical precision and accuracy of the method were assessed through comparison to a series of mixes of known phase composition and of increasing complexity. A 2σ precision smaller than 2–3 wt.% and an accuracy better than 2 wt.% were achieved for SCMs in mixes with quartz, anhydrous Portland cement, and hydrated Portland cement. The extent of reaction of SCMs in hydrating binders measured by XRD was 1) internally consistent as confirmed through the standardmore » addition method and 2) showed a linear correlation to the cumulative heat release as measured independently by isothermal conduction calorimetry. The advantages, limitations and applicability of the method are discussed with reference to existing methods that measure the degree of reaction of SCMs in blended cements.« less

Automated Fault Interpretation and Extraction using Improved Supplementary Seismic Datasets

NASA Astrophysics Data System (ADS)

Bollmann, T. A.; Shank, R.

2017-12-01

During the interpretation of seismic volumes, it is necessary to interpret faults along with horizons of interest. With the improvement of technology, the interpretation of faults can be expedited with the aid of different algorithms that create supplementary seismic attributes, such as semblance and coherency. These products highlight discontinuities, but still need a large amount of human interaction to interpret faults and are plagued by noise and stratigraphic discontinuities. Hale (2013) presents a method to improve on these datasets by creating what is referred to as a Fault Likelihood volume. In general, these volumes contain less noise and do not emphasize stratigraphic features. Instead, planar features within a specified strike and dip range are highlighted. Once a satisfactory Fault Likelihood Volume is created, extraction of fault surfaces is much easier. The extracted fault surfaces are then exported to interpretation software for QC. Numerous software packages have implemented this methodology with varying results. After investigating these platforms, we developed a preferred Automated Fault Interpretation workflow.

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

The role of the supplementary motor area for speech and language processing.

PubMed

Hertrich, Ingo; Dietrich, Susanne; Ackermann, Hermann

2016-09-01

Apart from its function in speech motor control, the supplementary motor area (SMA) has largely been neglected in models of speech and language processing in the brain. The aim of this review paper is to summarize more recent work, suggesting that the SMA has various superordinate control functions during speech communication and language reception, which is particularly relevant in case of increased task demands. The SMA is subdivided into a posterior region serving predominantly motor-related functions (SMA proper) whereas the anterior part (pre-SMA) is involved in higher-order cognitive control mechanisms. In analogy to motor triggering functions of the SMA proper, the pre-SMA seems to manage procedural aspects of cognitive processing. These latter functions, among others, comprise attentional switching, ambiguity resolution, context integration, and coordination between procedural and declarative memory structures. Regarding language processing, this refers, for example, to the use of inner speech mechanisms during language encoding, but also to lexical disambiguation, syntax and prosody integration, and context-tracking. Copyright © 2016 Elsevier Ltd. All rights reserved.

SUPPLEMENTARY COMPARISON: Final report on APMP.PR-S1.1: Bilateral comparison of irradiance responsivity of UVA detectors

NASA Astrophysics Data System (ADS)

Huang, Xuebo

2009-01-01

In order to assess the performance of the standards and techniques used for calibration and measurement of UVA irradiance responsivity of photodetectors in NMISA, South Africa, a new comparison was decided as a follow-up to comparison APMP.PR-S1. It is registered in the Key Comparison Data Base (KCDB) of BIPM as a bilateral supplementary comparison, with the identifier APMP.PR-S1.1. The comparison was carried out following the same technical protocol as that of supplementary comparison APMP PR-S1. The principle, organization and method of the comparison, as well as the preliminary measurements at the pilot laboratory NMC-A*STAR Singapore, were described in the Final Report of the APMP.PR-S1 comparison. The results of this bilateral comparison show that the NMISA's results lie within ±2% against the comparison reference values of APMP.PR-S1, which is a great improvement. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the APMP, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

Final report on the regional supplementary comparison APMP.AUV.A-S1

NASA Astrophysics Data System (ADS)

Plangsangmas, Virat; Leeudomwong, Surat; Scott, Andrew; Zhong, Bo; Huang, Yuchung

2014-01-01

A regional supplementary comparison APMP.AUV.A-S1 has been carried out for the measurement of sound pressure level, frequency and total distortion of a multi-frequency sound calibrator. The role of the Pilot laboratory was undertaken by the National Institute of Metrology (Thailand) (NIMT). The multi-frequency sound calibrator was circulated through thirteen National Metrology Institutes (NMIs). Two NMIs were added to the original time schedule after starting the circulation. The measurements took place between September 2008 and July 2010. This report includes the measurement results from all the participants. Supplementary Comparison Reference Values (SCRVs) have been determined from the results. Deviations from the SCRVs are mostly within declared expanded uncertainties. It has been found that a term for the inherent instability in this type of device needs to be included in any uncertainty budget, and a recommended minimum value of this has been given. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

PAs and NPs in an emergency room-linked acute care clinic.

PubMed

Currey, C J

1984-12-01

The use of hospital emergency rooms for nonurgent care during evenings hours often strains medical resources and may affect the quality of emergency care. One facility's effective use of an after-hours acute care clinic staffed by PAs and NPs to divert nonurgent problems away from its emergency room is outlined. PAs and NPs work during peak demand hours (evenings and weekends) under the supervision of an emergency room physician, and receive supplementary support from other emergency room personnel. Incoming patients are referred to the emergency room or acute care clinic, depending on the nature of their problems. Acute care clinic patients are then treated by the PA or NP and either released or referred to an emergency room physician, if their conditions warrant additional treatment. As a result, use of the acute care clinic has greatly reduced the amount of non-urgent medical treatment in the emergency room and has provided other advantages to both patients and staff as well. These advantages and the encouraging statistics following six months of the clinic's operation are discussed.

VizieR Online Data Catalog: Revised source list for the Rees 38-MHz survey (Hales+ 1995)

NASA Astrophysics Data System (ADS)

Hales, S. E. G.; Waldram, E. M.; Rees, N.; Warner, P. J.

1994-11-01

We present a revised machine-readable source list for the Rees 38-MHz (or '8C') survey with improved positions and no redundancy. The Rees 38-MHz survey covers an area of about 1 sr north of declination +60 degrees. The angular resolution is 4.5 x 4.5cosec(Dec) arcmin**2 and the limiting flux density over much of the survey area is about 1 Jy. Both of these figures are an improvement by nearly an order of magnitude on previous surveys at this frequency. Users of these data should consult and cite the original survey paper by Rees as primary reference (1990MNRAS.244..233R) with the present publication (1995MNRAS.274..447H) as a supplementary revision. The recommended style of reference is thus : "The revised Rees 38-MHz survey (Rees 1990, catalogue revised Hales et. al 1995)." Note that for interest the source list includes data on some sources at declinations lower than +60 degrees, but that the right ascension coverage is not complete below +60 degrees. (1 data file).

mHealth to revolutionize information retrieval in low and middle income countries: introduction and proposed solutions using Botswana as reference point.

PubMed

Littman-Quinn, Ryan; Luberti, Anthony A; Kovarik, Carrie

2013-01-01

Information retrieval (IR) practice is invaluable in health care, where the growth of medical knowledge has long surpassed human memory capabilities, and health care workers often have unmet information needs. While the information and communications technology (ICT) revolution is improving, IR in the Western world, the global digital divide has never been wider. Low and Middle Income Countries (LMICs) have the least advanced ICT infrastructure and service provision, and are also burdened with the majority of the world's health issues and severe shortages of health care workers. Initiatives utilizing mobile technology in healthcare and public health (mHealth) have shown potential at addressing these inequalities and challenges. Using Botswana as a reference point, this paper aims to broadly describe the healthcare and ICT challenges facing LMICs, the promise of mHealth as a field in health informatics, and then propose health informatics solutions that specifically address IR content and needs. One solution proposes utilizing Unstructured Supplementary Service Data (USSD) for accessing treatment guidelines, and the other solution outlines applications of smart devices for IR.

ORCAN-a web-based meta-server for real-time detection and functional annotation of orthologs.

PubMed

Zielezinski, Andrzej; Dziubek, Michal; Sliski, Jan; Karlowski, Wojciech M

2017-04-15

ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points. The service is available for free at http://www.combio.pl/orcan/ . wmk@amu.edu.pl. 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

Convergence of Legendre Expansion of Doppler-Broadened Double Differential Elastic Scattering Cross Section

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

Arbanas, Goran; Dunn, Michael E; Larson, Nancy M

2012-01-01

Convergence properties of Legendre expansion of a Doppler-broadened double-differential elastic neutron scattering cross section of {sup 238}U near the 6.67 eV resonance at temperature 10{sup 3} K are studied. A variance of Legendre expansion from a reference Monte Carlo computation is used as a measure of convergence and is computed for as many as 15 terms in the Legendre expansion. When the outgoing energy equals the incoming energy, it is found that the Legendre expansion converges very slowly. Therefore, a supplementary method of computing many higher-order terms is suggested and employed for this special case.

The effect of various pozzolanic additives on the concrete strength index

NASA Astrophysics Data System (ADS)

Vitola, L.; Sahmenko, G.; Erdmane, D.; Bumanis, G.; Bajare, D.

2017-10-01

The concrete industry is searching continuously for new effective mineral additives to improve the concrete properties. Replacing cement with the pozzolanic additives in most cases has resulted not only in positive impact on the environment but also has improved strength and durability of the concrete. Effective pozzolanic additives can be obtained from natural resources such as volcanic ashes, kaolin and other sediments as well as from different production industries that create various by-products with high pozzolanic reactivity. Current research deals with effectiveness evaluation of various mineral additives/wastes, such as coal combustion bottom ash, barley bottom ash, waste glass and metakaolin containing waste as well as calcined illite clays as supplementary cementitious materials, to be used in concrete production as partial cement replacement. Most of the examined materials are used as waste stream materials with potential reactive effect on the concrete. Milling time and fineness of the tested supplementary material has been evaluated and effectiveness was detected. Results indicate that fineness of the tested materials has crucial effect on the concrete compressive strength index. Not in all cases the prolonged milling time can increase fineness and reactivity of the supplementary materials; however the optimal milling time and fineness of the pozolanic additives increased the strength index of concrete up to 1.16 comparing to reference, even in cases when cement was substituted by 20 w%.

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.

PubMed

Lemieux Perreault, Louis-Philippe; Legault, Marc-André; Asselin, Géraldine; Dubé, Marie-Pierre

2016-12-01

Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic epidemiology (Sequence Kernel Association Test, Cox proportional hazards for survival analysis, and linear mixed models for repeated measurements in longitudinal studies). The genipe package is an open source Python software and is freely available for non-commercial use (CC BY-NC 4.0) at https://github.com/pgxcentre/genipe Documentation and tutorials are available at http://pgxcentre.github.io/genipe CONTACT: louis-philippe.lemieux.perreault@statgen.org or marie-pierre.dube@statgen.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Textual data compression in computational biology: a synopsis.

PubMed

Giancarlo, Raffaele; Scaturro, Davide; Utro, Filippo

2009-07-01

Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been used. When possible, a unifying organization of the main ideas and techniques is also provided. It goes without saying that most of the research results reviewed here offer software prototypes to the bioinformatics community. The Supplementary Material provides pointers to software and benchmark datasets for a range of applications of broad interest. In addition to provide reference to software, the Supplementary Material also gives a brief presentation of some fundamental results and techniques related to this paper. It is at: http://www.math.unipa.it/ approximately raffaele/suppMaterial/compReview/

Load and dynamic assessment of B-52B-008 carrier aircraft for finned configuration 1 space shuttle solid rocket booster decelerator subsystem drop test vehicle. Volume 2: Airplane flutter and load analysis results

NASA Technical Reports Server (NTRS)

Quade, D. A.

1978-01-01

The airplane flutter and maneuver-gust load analysis results obtained during B-52B drop test vehicle configuration (with fins) evaluation are presented. These data are presented as supplementary data to that given in Volume 1 of this document. A brief mathematical description of airspeed notation and gust load factor criteria are provided as a help to the user. References are defined which provide mathematical description of the airplane flutter and load analysis techniques. Air-speed-load factor diagrams are provided for the airplane weight configurations reanalyzed for finned drop test vehicle configuration.

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

PubMed

Mapleson, Daniel; Garcia Accinelli, Gonzalo; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo J

2017-02-15

De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . bernardo.clavijo@earlham.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Supplementary comparisons of COOMET in the field of measurements of liquids kinematical viscosity COOMET.M.V-S1

NASA Astrophysics Data System (ADS)

Demyanov, A. A.; Tsurko, A. A.

2017-01-01

In the comparisons three Newtonian liquid samples were used with nominal values of 20 mm2/s 100 mm2/s and 1000 mm2/s ('20', '100' and '1000' respectively) at 20 °C. Each NMI presented results of measurements values kinematic viscosity samples, uncertainty and uncertainty budget. The purpose of these comparisons was confirmation of measurement and calibration capabilities (CMC) of the relevant NMI. As a reference the values of kinematic viscosity reference samples were taken as average values of measurement results obtained in the research laboratory of the national standards and research in the field of measurements of viscosity and density of the D I Mendeleev Institute for Metrology (VNIIM, RF), as a participant in international comparisons CCM.V-K1, BIPM. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Supplementary comparisons of COOMET in the field of measurements of liquids kinematical viscosity COOMET.M.V-S2

NASA Astrophysics Data System (ADS)

Demyanov, A. A.; Tsurko, A. A.

2017-01-01

In the comparisons three Newtonian liquid samples were used with nominal values of 20 mm2/s 100 mm2/s and 1000 mm2/s ('20', '100' and '1000', respectively) at 20 °C. Each NMI presented results of measurements values kinematic viscosity samples, uncertainty and uncertainty budget. The purpose of these comparisons was confirmation of measurement and calibration capabilities (CMC) of the relevant NMI. As a reference the values of kinematic viscosity reference samples were taken as average values of measurement results obtained in the research laboratory of the national standards and research in the field of measurements of viscosity and density of the D I Mendeleev Institute for Metrology (VNIIM, RF), as a participant in international comparisons CCM.V-K1, BIPM. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Electrical safety Q&A. A reference guide for the clinical engineer.

PubMed

2005-02-01

This guide, which ECRI developed to answer the electrical safety questions most frequently asked by member hospitals, features practical advice for addressing electrical safety concerns in the healthcare environment. Questions addressed include: STANDARDS AND APPROVALS: What electrical safety standards apply? How do NFPA 99 and IEC 60601-1 differ? What organizations approve medical devices? LEAKAGE CURRENT LIMITS AND TESTING: How are leakage current limits established? What limits apply to equipment used in the hospital? And how should the limits be applied in special cases, such as the use of PCs in the patient care area or equipment used in the clinical laboratory? ISOLATED POWER: What are its advantages and disadvantages, and is isolated power needed in the operating room? Other topics addressed include double insulation, ground-fault circuit interrupters (GFCIs), and requirements for medical devices used in the home. Supplementary articles discuss acceptable alternatives to UL listing, the use of Hospital Grade plugs, the limitations of leakage current testing of devices connected to isolated power systems, and the debate about whether to designate ORs as wet locations. Experienced clinical engineers should find this guide to be a handy reference, while those new to the field should find it to be a helpful educational resource.

Bias estimates used in lieu of validation of fission products and minor actinides in MCNP K eff calculations for PWR burnup credit casks

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

Mueller, Don E.; Marshall, William J.; Wagner, John C.

The U.S. Nuclear Regulatory Commission (NRC) Division of Spent Fuel Storage and Transportation recently issued Interim Staff Guidance (ISG) 8, Revision 3. This ISG provides guidance for burnup credit (BUC) analyses supporting transport and storage of PWR pressurized water reactor (PWR) fuel in casks. Revision 3 includes guidance for addressing validation of criticality (k eff) calculations crediting the presence of a limited set of fission products and minor actinides (FP&MA). Based on previous work documented in NUREG/CR-7109, recommendation 4 of ISG-8, Rev. 3, includes a recommendation to use 1.5 or 3% of the FP&MA worth to conservatively cover the biasmore » due to the specified FP&MAs. This bias is supplementary to the bias and bias uncertainty resulting from validation of k eff calculations for the major actinides in SNF and does not address extension to actinides and fission products beyond those identified herein. The work described in this report involves comparison of FP&MA worths calculated using SCALE and MCNP with ENDF/B-V, -VI, and -VII based nuclear data and supports use of the 1.5% FP&MA worth bias when either SCALE or MCNP codes are used for criticality calculations, provided the other conditions of the recommendation 4 are met. The method used in this report may also be applied to demonstrate the applicability of the 1.5% FP&MA worth bias to other codes using ENDF/B V, VI or VII based nuclear data. The method involves use of the applicant s computational method to generate FP&MA worths for a reference SNF cask model using specified spent fuel compositions. The applicant s FP&MA worths are then compared to reference values provided in this report. The applicants FP&MA worths should not exceed the reference results by more than 1.5% of the reference FP&MA worths.« less

Accuracy and readability of cardiovascular entries on Wikipedia: are they reliable learning resources for medical students?

PubMed Central

Azer, Samy A; AlSwaidan, Nourah M; Alshwairikh, Lama A; AlShammari, Jumana M

2015-01-01

Objective To evaluate accuracy of content and readability level of English Wikipedia articles on cardiovascular diseases, using quality and readability tools. Methods Wikipedia was searched on the 6 October 2013 for articles on cardiovascular diseases. Using a modified DISCERN (DISCERN is an instrument widely used in assessing online resources), articles were independently scored by three assessors. The readability was calculated using Flesch-Kincaid Grade Level. The inter-rater agreement between evaluators was calculated using the Fleiss κ scale. Results This study was based on 47 English Wikipedia entries on cardiovascular diseases. The DISCERN scores had a median=33 (IQR=6). Four articles (8.5%) were of good quality (DISCERN score 40–50), 39 (83%) moderate (DISCERN 30–39) and 4 (8.5%) were poor (DISCERN 10–29). Although the entries covered the aetiology and the clinical picture, there were deficiencies in the pathophysiology of diseases, signs and symptoms, diagnostic approaches and treatment. The number of references varied from 1 to 127 references; 25.9±29.4 (mean±SD). Several problems were identified in the list of references and citations made in the articles. The readability of articles was 14.3±1.7 (mean±SD); consistent with the readability level for college students. In comparison, Harrison’s Principles of Internal Medicine 18th edition had more tables, less references and no significant difference in number of graphs, images, illustrations or readability level. The overall agreement between the evaluators was good (Fleiss κ 0.718 (95% CI 0.57 to 0.83). Conclusions The Wikipedia entries are not aimed at a medical audience and should not be used as a substitute to recommended medical resources. Course designers and students should be aware that Wikipedia entries on cardiovascular diseases lack accuracy, predominantly due to errors of omission. Further improvement of the Wikipedia content of cardiovascular entries would be needed before they could be considered a supplementary resource. PMID:26443650

Mortality in a cohort of Danish firefighters; 1970-2014.

PubMed

Petersen, Kajsa Ugelvig; Pedersen, Julie Elbæk; Bonde, Jens Peter; Ebbehøj, Niels Erik; Hansen, Johnni

2018-05-28

Occupational exposure of firefighters involves a complex range of potential health threats from toxic chemicals, shift work, extreme heat, physical and emotional strain. The aim of this study is to examine overall and disease-specific mortality among Danish firefighters. Through systematic collection of personnel and membership records from employers and trade unions, past and present male Danish firefighters were identified (n = 11,775). Using the unique Danish personal identification number, information on additional employment, vital status and cause of death was linked to each member of the cohort from the Supplementary Pension Fund Register, the Danish Civil Registration System and the Danish Register of Causes of Death. Standardized mortality ratios (SMRs) were calculated for specific causes of death using rates for two reference groups, a random sample of the male working population (n = 262,168) and the military (n = 396,739), respectively. Overall mortality was significantly reduced among the firefighters compared to both the sample of the working population and the military (SMR 0.74, 95% CI 0.69-0.78 and SMR 0.88, 95% CI 0.83-0.93). Further, the SMRs for endocrine diseases, mental disorders, non-traffic related accidents and other external causes were significantly lower against both reference groups. Death from stomach cancer was significantly increased among the full time firefighters, while part time/volunteer workers shared a significant increase in prostate cancer death compared to both references. Despite potential exposure to several occupational hazards, male Danish firefighters have a lower mortality than both the Danish working population in general and Danish military employees.

Randomized trial of supplementary interviewing techniques to enhance recall of sexual partners in contact interviews.

PubMed

Brewer, Devon D; Potterat, John J; Muth, Stephen Q; Malone, Patricia Z; Montoya, Pamela; Green, David L; Rogers, Helen L; Cox, Patricia A

2005-03-01

People with multiple sex partners tend to forget a significant proportion when recalling them. Randomized trial of supplementary interviewing techniques during routine partner notification contact interviews for chlamydia, gonorrhea, and syphilis in Colorado Springs, CO. Cases with multiple sex partners in the last 3 months (n = 123) participated. Interviewers prompted nonspecifically and read back the list of elicited partners after cases recalled partners on their own. We then randomly assigned cases to receive 1 of 3 sets of recall cues: (1) an experimental set of cues consisting of locations where people meet partners, role relationships, network ties, and first letters of names; (2) another experimental set including common first names; and (3) control cues referring to individual characteristics (e.g., physical appearance). Nonspecific prompting and reading back the list each increased the number of additional partners elicited and located by 3% to 5% on average. On average, the combined location/role/letter/network cues elicited more additional partners (0.57) than did the first-name (0.29) and individual characteristics (0.28) cues. The location and first-name cues were the most effective in eliciting located partners. The supplementary techniques increased the number of new cases found by 12% and, importantly, identified branches of the sexual network that would not otherwise have been discovered. Elicitation of sex partners can be enhanced in contact interviews with simple interviewing techniques, resulting in improved network ascertainment and sexually transmitted disease case finding.

Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade

PubMed Central

Collins, Rupert A.; Armstrong, Karen F.; Meier, Rudolf; Yi, Youguang; Brown, Samuel D. J.; Cruickshank, Robert H.; Keeling, Suzanne; Johnston, Colin

2012-01-01

Background Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species. Methodology/Principal Findings We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90–99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii. Conclusions/Significance We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade. PMID:22276096

Clinical effectiveness and cost-effectiveness of parenting interventions for children with severe attachment problems: a systematic review and meta-analysis.

PubMed

Wright, Barry; Barry, Melissa; Hughes, Ellen; Trépel, Dominic; Ali, Shehzad; Allgar, Victoria; Cottrill, Lucy; Duffy, Steven; Fell, Jenny; Glanville, Julie; Glaser, Danya; Hackney, Lisa; Manea, Laura; McMillan, Dean; Palmer, Stephen; Prior, Vivien; Whitton, Clare; Perry, Amanda; Gilbody, Simon

2015-07-01

Services have variable practices for identifying and providing interventions for 'severe attachment problems' (disorganised attachment patterns and attachment disorders). Several government reports have highlighted the need for better parenting interventions in at-risk groups. This report was commissioned to evaluate the clinical effectiveness and cost-effectiveness of parenting interventions for children with severe attachment problems (the main review). One supplementary review explored the evaluation of assessment tools and a second reviewed 10-year outcome data to better inform health economic aspects of the main review. A total of 29 electronic databases were searched with additional mechanisms for identifying a wide pool of references using the Cochrane methodology. Examples of databases searched include PsycINFO (1806 to January week 1, 2012), MEDLINE and MEDLINE In-Process & Other Non-Indexed Citations (1946 to December week 4, 2011) and EMBASE (1974 to week 1, 2012). Searches were carried out between 6 and 12 January 2012. Papers identified were screened and data were extracted by two independent reviewers, with disagreements arbitrated by a third independent reviewer. Quality assessment tools were used, including quality assessment of diagnostic accuracy studies - version 2 and the Cochrane risk of bias tool. Meta-analysis of randomised controlled trials (RCTs) of parenting interventions was undertaken. A health economics analysis was conducted. The initial search returned 10,167 citations. This yielded 29 RCTs in the main review of parenting interventions to improve attachment patterns, and one involving children with reactive attachment disorder. A meta-analysis of eight studies seeking to improve outcome in at-risk populations showed statistically significant improvement in disorganised attachment. The interventions saw less disorganised attachment at outcome than the control (odds ratio 0.47, 95% confidence interval 0.34 to 0.65; p < 0.00001). Much of this focused around interventions improving maternal sensitivity, with or without video feedback. In our first supplementary review, 35 papers evaluated an attachment assessment tool demonstrating validity or psychometric data. Only five reported test-retest data. Twenty-six studies reported inter-rater reliability, with 24 reporting a level of 0.7 or above. Cronbach's alphas were reported in 12 studies for the comparative tests (11 with α > 0.7) and four studies for the reference tests (four with α > 0.7). Three carried out concurrent validity comparing the Strange Situation Procedure (SSP) with another assessment tool. These had good sensitivity but poor specificity. The Disturbances of Attachment Interview had good sensitivity and specificity with the research diagnostic criteria (RDC) for attachment disorders. In our supplementary review of 10-year outcomes in cohorts using a baseline reference standard, two studies were found with disorganised attachment at baseline, with one finding raised psychopathology in adolescence. Budget impact analysis of costs was estimated because a decision model could not be justifiably populated. This, alongside other findings, informed research priorities. There are relatively few UK-based clinical trials. A 10-year follow-up, while necessary for our health economists for long-term sequelae, yielded a limited number of papers. Maternal sensitivity interventions show good outcomes in at-risk populations, but require further research with complex children. The SSP and RDC for attachment disorders remain the reference standards for identification until more concurrent and predictive validity research is conducted. A birth cohort with sequential attachment measures and outcomes across different domains is recommended with further, methodologically sound randomised controlled intervention trials. The main area identified for future work was a need for good-quality RCTs in at-risk groups such as those entering foster care or adoption. This study is registered as PROSPERO CRD42011001395. The National Institute for Health Research Health Technology Assessment programme.

Biologically inspired EM image alignment and neural reconstruction.

PubMed

Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

2011-08-15

Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

PubMed Central

Green, Kevin T.; Dutilh, Bas E.; Edwards, Robert A.

2016-01-01

Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. Contact: redwards@mail.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26454280

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.

PubMed

González-Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil

2016-12-15

MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively. Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Modeling genome coverage in single-cell sequencing

PubMed Central

Daley, Timothy; Smith, Andrew D.

2014-01-01

Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. Results: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. Availability and implementation: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online. PMID:25107873

APMP supplementary comparison report of absorbed dose rate in tissue for beta radiation (BIPM KCDB: APMP.RI(I)-S2)

NASA Astrophysics Data System (ADS)

Kato, M.; Kurosawa, T.; Saito, N.; Kadni, T. B.; Kim, I. J.; Kim, B. C.; Yi, C.-Y.; Pungkun, V.; Chu, C.-H.

2017-01-01

The supplementary comparison of absorbed dose rate in tissue for beta radiation (APMP.RI(I)-S2) was performed with five national metrology institutes in 2013 and 2014. Two commercial thin window ionization chambers were used as transfer instruments and circulated among the participants. Two of the NMIs measured the calibration coefficients of the chambers in reference fields produced from Pm-147, Kr-85 and Sr-90/Y-90, while the other three measured those only in Sr-90/Y-90 beta-particle field. The degree of equivalence for the participants was determined and this comparison verifies the calibration capabilities of the participating laboratories. In addition, most of the results of this comparison are consistent with another international comparison (EUROMET.RI(I)-S2) reported before this work. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Cognition and medial frontal cortex in health and disease

PubMed Central

Nachev, Parashkev

2009-01-01

Purpose of review Recent work on the role of medial frontal cortex in cognition and its involvement in neurological disorders is critically reviewed. Recent findings The highly influential notion of conflict monitoring by the anterior cingulate has been called into question by monkey single-cell neurophysiology and lesion studies in monkeys and humans. An alternative role for this region in adapting behaviour in response to changing demands over time is gaining support. By contrast, the more dorsally placed pre-supplementary motor area and supplementary eye field have been implicated in direct executive control in situations of response conflict. Although more rostral medial areas have been linked to complex cognitive operations involving references to the self, conceptual obstacles make the evidence difficult to interpret. The role of orbitofrontal cortex in guiding action based on value has been reinforced. Summary This area continues to generate both interest and controversy. A few striking discrepancies between data from functional imaging and interventional techniques illustrate the hazards of drawing strong conclusions from merely correlative evidence. More broadly, a case can be made for tempering the empirical enthusiasm here with a little more theoretical restraint. PMID:17102698

Super resolution terahertz imaging by subpixel estimation: application to hyperspectral beam profiling

NASA Astrophysics Data System (ADS)

Logofătu, Petre C.; Damian, Victor

2018-05-01

A super-resolution terahertz imaging technique based on subpixel estimation was applied to hyperspectral beam profiling. The topic of hyperspectral beam profiling was chosen because the beam profile and its dependence on wavelength are not well known and are important for imaging applications. Super-resolution is required here to avoid diffraction effects and to provide a stronger signal. Super-resolution usually adds supplementary information to the measurement, but in this case, it is a prerequisite for it. We report that the beam profile is almost Gaussian for many frequencies; the waist of the Gaussian profile increases with frequency while the center wobbles slightly. Knowledge of the beam profile may subsequently be used as reference for imaging.

ProbOnto: ontology and knowledge base of probability distributions.

PubMed

Swat, Maciej J; Grenon, Pierre; Wimalaratne, Sarala

2016-09-01

Probability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of probability distributions. Although some resources exist, no suitably detailed and complex ontology exists nor any database allowing programmatic access. ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 80 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. http://probonto.org mjswat@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Final report on APMP.QM-S5: Essential and toxic elements in seafood

NASA Astrophysics Data System (ADS)

Valiente, Liliana; Bennett, John W.; Caciano de Sena, Rodrigo; Kotzeva, Boriana; Massiff, Gabriela; Chao, Jingbo; Wang, Jun; Nasr, Randa; Labarraque, Guillaume; Kakoulidis, Elias; Lampi, Eugenia; Wai-mei Sin, Della; Mok, Chuen-shing; Wong, Siu-kay; Yip, Yiu-chung; Gopala Aggarwal, Shankar; Gupta, Prabhat K.; Zhu, Yanbei; Miyashita, Shin-ichi; Yim, Yong-Hyeon; Zakaria, Osman; Manzano, Judith Velina Lara; Shin, Richard; Horvat, Milena; Yafa, Charun

2013-01-01

The supplementary comparison APMP.QM-S5 was undertaken to demonstrate the capability of participating national metrology institutes (NMIs) and designated institutes (DIs) in measuring the contents of the incurred essential elements (iron and zinc) and toxic elements (total arsenic and cadmium) at µg/g levels in a test sample of dried shrimp by various analytical techniques. At the APMP TCQM Meeting held in Pattaya, Thailand in November 2010, Government Laboratory of the Government of the Hong Kong Special Administrative Region (GLHK) proposed this APMP supplementary comparison. The proposal was further discussed and agreed upon at the CCQM Inorganic Analysis Working Group Meeting held in Paris in April 2011. GLHK was the coordinating laboratory for the supplementary comparison. For enhancing the collaboration amongst specialized regional bodies in Asia-Pacific and to help build the laboratory capacity of NMIs/DIs from developing economies, the reference values of the supplementary comparison are used for evaluation of performance of participants of an APMP proficiency testing programme (APMP PT 11-01), an Asia-Pacific Laboratory Accreditation Cooperation proficiency testing programme (APLAC T082) and an Asia-Pacific Economic Co-operation proficiency testing programme (APEC PT), which were concurrently run using the same testing material as in APMP.QM-S5. The supplementary comparison serves to facilitate claims by participants on the Calibration and Measurement Capabilities (CMCs) as listed in Appendix C of the Key Comparison Database (KCDB) under the Mutual Recognition Arrangement of the International Committee for Weights and Measures (CIPM MRA). A total of 18 institutes registered for the supplementary comparison and all of them submitted their results. Most of the participants used microwave acid digestion methods for sample dissolution. For the instrumental determination, a variety of techniques like ICP-MS, ICP-OES, INAA and AAS were employed by the participants. For this supplementary comparison, inorganic core capabilities have been demonstrated by concerned participants with respect to methods including ICP-MS (without isotope dilution), ID-ICP-MS, ICP-OES, INAA and AAS on the determination of total arsenic, cadmium, iron and zinc in a matrix of seafood. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the APMP, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Anomalous Cases of Astronaut Helmet Detection

NASA Technical Reports Server (NTRS)

Dolph, Chester; Moore, Andrew J.; Schubert, Matthew; Woodell, Glenn

2015-01-01

An astronaut's helmet is an invariant, rigid image element that is well suited for identification and tracking using current machine vision technology. Future space exploration will benefit from the development of astronaut detection software for search and rescue missions based on EVA helmet identification. However, helmets are solid white, except for metal brackets to attach accessories such as supplementary lights. We compared the performance of a widely used machine vision pipeline on a standard-issue NASA helmet with and without affixed experimental feature-rich patterns. Performance on the patterned helmet was far more robust. We found that four different feature-rich patterns are sufficient to identify a helmet and determine orientation as it is rotated about the yaw, pitch, and roll axes. During helmet rotation the field of view changes to frames containing parts of two or more feature-rich patterns. We took reference images in these locations to fill in detection gaps. These multiple feature-rich patterns references added substantial benefit to detection, however, they generated the majority of the anomalous cases. In these few instances, our algorithm keys in on one feature-rich pattern of the multiple feature-rich pattern reference and makes an incorrect prediction of the location of the other feature-rich patterns. We describe and make recommendations on ways to mitigate anomalous cases in which detection of one or more feature-rich patterns fails. While the number of cases is only a small percentage of the tested helmet orientations, they illustrate important design considerations for future spacesuits. In addition to our four successful feature-rich patterns, we present unsuccessful patterns and discuss the cause of their poor performance from a machine vision perspective. Future helmets designed with these considerations will enable automated astronaut detection and thereby enhance mission operations and extraterrestrial search and rescue.

A validated non-linear Kelvin-Helmholtz benchmark for numerical hydrodynamics

NASA Astrophysics Data System (ADS)

Lecoanet, D.; McCourt, M.; Quataert, E.; Burns, K. J.; Vasil, G. M.; Oishi, J. S.; Brown, B. P.; Stone, J. M.; O'Leary, R. M.

2016-02-01

The non-linear evolution of the Kelvin-Helmholtz instability is a popular test for code verification. To date, most Kelvin-Helmholtz problems discussed in the literature are ill-posed: they do not converge to any single solution with increasing resolution. This precludes comparisons among different codes and severely limits the utility of the Kelvin-Helmholtz instability as a test problem. The lack of a reference solution has led various authors to assert the accuracy of their simulations based on ad hoc proxies, e.g. the existence of small-scale structures. This paper proposes well-posed two-dimensional Kelvin-Helmholtz problems with smooth initial conditions and explicit diffusion. We show that in many cases numerical errors/noise can seed spurious small-scale structure in Kelvin-Helmholtz problems. We demonstrate convergence to a reference solution using both ATHENA, a Godunov code, and DEDALUS, a pseudo-spectral code. Problems with constant initial density throughout the domain are relatively straightforward for both codes. However, problems with an initial density jump (which are the norm in astrophysical systems) exhibit rich behaviour and are more computationally challenging. In the latter case, ATHENA simulations are prone to an instability of the inner rolled-up vortex; this instability is seeded by grid-scale errors introduced by the algorithm, and disappears as resolution increases. Both ATHENA and DEDALUS exhibit late-time chaos. Inviscid simulations are riddled with extremely vigorous secondary instabilities which induce more mixing than simulations with explicit diffusion. Our results highlight the importance of running well-posed test problems with demonstrated convergence to a reference solution. To facilitate future comparisons, we include as supplementary material the resolved, converged solutions to the Kelvin-Helmholtz problems in this paper in machine-readable form.

Final report on APMP.RF-S21.F

NASA Astrophysics Data System (ADS)

Ishii, Masanori; Kim, Jeong Hwan; Ji, Yu; Cho, Chi Hyun; Zhang, Tim

2018-01-01

The supplementary comparison report APMP.RF-S21.F describes the comparison of loop antennas, which was conducted between April 2013 and January 2014. The two comparison artefacts were well-characterised active loop antennas of diameter 30 cm and 60 cm respectively, which typically operate in a frequency range from 9 kHz to 30 MHz. These antennas represent the main groups of antennas which are used around the world for EMC measurements in the frequency range below 30 MHz. There are several well-known methods for calibrating the antenna factor of these devices. The calibration systems used in this comparison for the loop antennas employed the standard magnetic field method or the three-antenna method. Despite the limitations of the algorithm, which we used to derive the reference value for each case (particularly for small samples), the actual calculated reference values seem to be reasonable. As a result, the agreement between each participant was very good in all cases. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

EURAMET.M.P-S9 / EURAMET 1170, LOOP2. Comparison in the negative gauge pressure range -950 to 0 hPa

NASA Astrophysics Data System (ADS)

Otal, P.; Boineau, F.; Medina, N.; Pražák, D.; Wüthrich, C.; Saxholm, S.; Sabuga, W.; Kocas, I.; Durgut, Y.

2017-01-01

This report gives the results of a comparison of pressure standards of seven European National Metrology institutes in the range of negative gauge pressure from -950 hPa to 0 hPa. This comparison was piloted by LNE and was carried out from January 2011 to March 2012. This work is a part of the EURAMET project 1170 and is registered as a supplementary comparison EURAMET.M.P-S9. The transfer standard used was a pressure monitor RPM4 A160Ks manufactured by DH Instruments Inc., with a resolution of 0.1 Pa. The reference values have been determined from the weighted mean of the deviations reported by the participants for each specified pressure. Seventy-three of the seventy-seven values (96%) reported by the laboratories agree with the reference values within the expanded uncertainties with a coverage factor k = 2. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Integration of gene normalization stages and co-reference resolution using a Markov logic network.

PubMed

Dai, Hong-Jie; Chang, Yen-Ching; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2011-09-15

Gene normalization (GN) is the task of normalizing a textual gene mention to a unique gene database ID. Traditional top performing GN systems usually need to consider several constraints to make decisions in the normalization process, including filtering out false positives, or disambiguating an ambiguous gene mention, to improve system performance. However, these constraints are usually executed in several separate stages and cannot use each other's input/output interactively. In this article, we propose a novel approach that employs a Markov logic network (MLN) to model the constraints used in the GN task. Firstly, we show how various constraints can be formulated and combined in an MLN. Secondly, we are the first to apply the two main concepts of co-reference resolution-discourse salience in centering theory and transitivity-to GN models. Furthermore, to make our results more relevant to developers of information extraction applications, we adopt the instance-based precision/recall/F-measure (PRF) in addition to the article-wide PRF to assess system performance. Experimental results show that our system outperforms baseline and state-of-the-art systems under two evaluation schemes. Through further analysis, we have found several unexplored challenges in the GN task. hongjie@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

The influence of contrast media on kidney function in patients with stable coronary artery disease.

PubMed

Reuter, Simon Bertram; Harutyunyan, Marina; Mygind, Naja Dam; Jørgensen, Erik; Kastrup, Jens

2014-08-01

To investigate the incidence of contrast media-induced nephropathy (CIN) in patients with stable coronary artery disease (CAD) referred for elective coronary intervention following hydration routines. The reversibility of CIN was followed in a 6 month-period. A total of 447 patients referred for elective coronary intervention due to suspected CAD were included. Blood samples were collected before and 24 h after intervention and medical records were obtained. Patients had no drinking fluid restrictions and were routinely treated with a 1000 ml saline infusion. All patients were invited to a 6-month examination and collection of blood samples. A total of 19 patients (4.3%) developed CIN. CIN patients had a pre-investigation higher estimated glomerular filtration rate (eGRF), lower level of kidney failure and lower creatinine level than non-CIN patients. Kidney function was not normalized in CIN patients 6 months after the intervention. Two patients still met the definition of CIN. With no restriction in fluid intake and supplementary infusion of saline, only a few patients with stable CAD developed early indications of CIN during elective coronary interventions. Kidney function and the amount of contrast media used was not a predictor of CIN development. The induced CIN was not completely normalized in a 6-month follow-up period.

mirPub: a database for searching microRNA publications.

PubMed

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.

PubMed

Nelson, Chase W; Moncla, Louise H; Hughes, Austin L

2015-11-15

New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population. SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie. nelsoncw@email.sc.edu or austin@biol.sc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High-Speed Monitoring of Multiple Grid-Connected Photovoltaic Array Configurations and Supplementary Weather Station.

PubMed

Boyd, Matthew T

2017-06-01

Three grid-connected monocrystalline silicon photovoltaic arrays have been instrumented with research-grade sensors on the Gaithersburg, MD campus of the National Institute of Standards and Technology (NIST). These arrays range from 73 kW to 271 kW and have different tilts, orientations, and configurations. Irradiance, temperature, wind, and electrical measurements at the arrays are recorded, and images are taken of the arrays to monitor shading and capture any anomalies. A weather station has also been constructed that includes research-grade instrumentation to measure all standard meteorological quantities plus additional solar irradiance spectral bands, full spectrum curves, and directional components using multiple irradiance sensor technologies. Reference photovoltaic (PV) modules are also monitored to provide comprehensive baseline measurements for the PV arrays. Images of the whole sky are captured, along with images of the instrumentation and reference modules to document any obstructions or anomalies. Nearly, all measurements at the arrays and weather station are sampled and saved every 1s, with monitoring having started on Aug. 1, 2014. This report describes the instrumentation approach used to monitor the performance of these photovoltaic systems, measure the meteorological quantities, and acquire the images for use in PV performance and weather monitoring and computer model validation.

High-Speed Monitoring of Multiple Grid-Connected Photovoltaic Array Configurations and Supplementary Weather Station

PubMed Central

Boyd, Matthew T.

2017-01-01

Three grid-connected monocrystalline silicon photovoltaic arrays have been instrumented with research-grade sensors on the Gaithersburg, MD campus of the National Institute of Standards and Technology (NIST). These arrays range from 73 kW to 271 kW and have different tilts, orientations, and configurations. Irradiance, temperature, wind, and electrical measurements at the arrays are recorded, and images are taken of the arrays to monitor shading and capture any anomalies. A weather station has also been constructed that includes research-grade instrumentation to measure all standard meteorological quantities plus additional solar irradiance spectral bands, full spectrum curves, and directional components using multiple irradiance sensor technologies. Reference photovoltaic (PV) modules are also monitored to provide comprehensive baseline measurements for the PV arrays. Images of the whole sky are captured, along with images of the instrumentation and reference modules to document any obstructions or anomalies. Nearly, all measurements at the arrays and weather station are sampled and saved every 1s, with monitoring having started on Aug. 1, 2014. This report describes the instrumentation approach used to monitor the performance of these photovoltaic systems, measure the meteorological quantities, and acquire the images for use in PV performance and weather monitoring and computer model validation. PMID:28670044

Usefulness and accuracy of MALDI-TOF mass spectrometry as a supplementary tool to identify mosquito vector species and to invest in development of international database.

PubMed

Raharimalala, F N; Andrianinarivomanana, T M; Rakotondrasoa, A; Collard, J M; Boyer, S

2017-09-01

Arthropod-borne diseases are important causes of morbidity and mortality. The identification of vector species relies mainly on morphological features and/or molecular biology tools. The first method requires specific technical skills and may result in misidentifications, and the second method is time-consuming and expensive. The aim of the present study is to assess the usefulness and accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a supplementary tool with which to identify mosquito vector species and to invest in the creation of an international database. A total of 89 specimens belonging to 10 mosquito species were selected for the extraction of proteins from legs and for the establishment of a reference database. A blind test with 123 mosquitoes was performed to validate the MS method. Results showed that: (a) the spectra obtained in the study with a given species differed from the spectra of the same species collected in another country, which highlights the need for an international database; (b) MALDI-TOF MS is an accurate method for the rapid identification of mosquito species that are referenced in a database; (c) MALDI-TOF MS allows the separation of groups or complex species, and (d) laboratory specimens undergo a loss of proteins compared with those isolated in the field. In conclusion, MALDI-TOF MS is a useful supplementary tool for mosquito identification and can help inform vector control. © 2017 The Royal Entomological Society.

Accuracy and readability of cardiovascular entries on Wikipedia: are they reliable learning resources for medical students?

PubMed

Azer, Samy A; AlSwaidan, Nourah M; Alshwairikh, Lama A; AlShammari, Jumana M

2015-10-06

To evaluate accuracy of content and readability level of English Wikipedia articles on cardiovascular diseases, using quality and readability tools. Wikipedia was searched on the 6 October 2013 for articles on cardiovascular diseases. Using a modified DISCERN (DISCERN is an instrument widely used in assessing online resources), articles were independently scored by three assessors. The readability was calculated using Flesch-Kincaid Grade Level. The inter-rater agreement between evaluators was calculated using the Fleiss κ scale. This study was based on 47 English Wikipedia entries on cardiovascular diseases. The DISCERN scores had a median=33 (IQR=6). Four articles (8.5%) were of good quality (DISCERN score 40-50), 39 (83%) moderate (DISCERN 30-39) and 4 (8.5%) were poor (DISCERN 10-29). Although the entries covered the aetiology and the clinical picture, there were deficiencies in the pathophysiology of diseases, signs and symptoms, diagnostic approaches and treatment. The number of references varied from 1 to 127 references; 25.9±29.4 (mean±SD). Several problems were identified in the list of references and citations made in the articles. The readability of articles was 14.3±1.7 (mean±SD); consistent with the readability level for college students. In comparison, Harrison's Principles of Internal Medicine 18th edition had more tables, less references and no significant difference in number of graphs, images, illustrations or readability level. The overall agreement between the evaluators was good (Fleiss κ 0.718 (95% CI 0.57 to 0.83). The Wikipedia entries are not aimed at a medical audience and should not be used as a substitute to recommended medical resources. Course designers and students should be aware that Wikipedia entries on cardiovascular diseases lack accuracy, predominantly due to errors of omission. Further improvement of the Wikipedia content of cardiovascular entries would be needed before they could be considered a supplementary resource. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

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

Wolery, Thomas J.; Jove Colon, Carlos F.

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

DOE PAGES

Wolery, Thomas J.; Jove Colon, Carlos F.

2016-09-26

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

Contrasting styles of post-caldera volcanism along the Main Ethiopian Rift: Implications for contemporary volcanic hazards

NASA Astrophysics Data System (ADS)

Fontijn, Karen; McNamara, Keri; Zafu Tadesse, Amdemichael; Pyle, David M.; Dessalegn, Firawalin; Hutchison, William; Mather, Tamsin A.; Yirgu, Gezahegn

2018-05-01

The Main Ethiopian Rift (MER, 7-9°N) is the type example of a magma-assisted continental rift. The rift axis is populated with regularly spaced silicic caldera complexes and central stratovolcanoes, interspersed with large fields of small mafic scoria cones. The recent (latest Pleistocene to Holocene) history of volcanism in the MER is poorly known, and no eruptions have occurred in the living memory of the local population. Assessment of contemporary volcanic hazards and associated risk is primarily based on the study of the most recent eruptive products, typically those emplaced within the last 10-20 ky. We integrate new and published field observations and geochemical data on tephra deposits from the main Late Quaternary volcanic centres in the central MER to assess contemporary volcanic hazards. Most central volcanoes in the MER host large mid-Pleistocene calderas, with typical diameters of 5-15 km, and associated ignimbrites of trachyte and peralkaline rhyolite composition. In contrast, post-caldera activity at most centres comprises eruptions of peralkaline rhyolitic magmas as obsidian flows, domes and pumice cones. The frequency and magnitude of events varies between individual volcanoes. Some volcanoes have predominantly erupted obsidian lava flows in their most recent post-caldera stage (Fentale), whereas other have had up to 3 moderate-scale (VEI 3-4) explosive eruptions per millennium (Aluto). At some volcanoes we find evidence for multiple large explosive eruptions (Corbetti, Bora-Baricha, Boset-Bericha) which have deposited several centimetres to metres of pumice and ash in currently densely populated regions. This new overview has important implications when assessing the present-day volcanic hazard in this rapidly developing region. Supplementary Table 2 Main Ethiopian Rift outcrop localities with brief description of geology. All coordinates in Latitude - Longitude, WGS84 datum. Sample names (as listed in Supplementary Table 3a) follow outcrop name followed by a letter (e.g. A, B, etc.). Supplementary Table S3a. EMP data for all samples analysed in this study. Outcrop coordinates for terrestrial outcrops (names starting with "MER") are listed in Supplementary Table S2. Points refer to individual analysis spots, each on an individual patch of glass, avoiding visible crystals. Analyses suggesting an influence of (hidden) crystals have been omitted. Samples are grouped by volcano (South to North, Fig 1) and units are identified where possible. Only the most widely distributed units are given a unique name. Other units are identified as "NA" followed by the unit number of their corresponding section (in stratigraphic order, #1 being the youngest). Run refers to date analyses were acquired; corresponding secondary standard analyses and analytical conditions for all runs, ordered by date, are listed in Supplementary Table S3b. Analyses are normalised to volatile-free composition. Cl was also omitted from normalisation because it was not analysed for all samples. Supplementary Table S3b EMP analyses of secondary glass standards (non-normalised) run together with samples. All analyses were run at 15 kV accelerating voltage, 6 (or 4) nA beam current, and 10 (or 5) μm beam width. Standards were run at the start, regularly during and at the end of each run to monitor data quality. Error bars, also reported with the samples, are calculated as 2 x relative standard deviation on the standard analyses and hence represent precision of the data. Data accuracy is colour-coded on the average for each standard analysis during each run: green values are within 1s of the preferred values, orange within 2s, and red out of the 2s range. Standards used are ATHO-G (rhyolite), NIST-612 (synthetic glass), StHs6/80-G (andesite/dacite) and ML3B-G (basalt), and cover the range of expected values in our sample set. Preferred values, after Jochum et al. (2006, 2011), can also be consulted on GeoREM (http://georem.mpch-mainz.gwdg.de/).

Force supplementary comparison at SIM (SIM.M.F-S5), compression testing machines calibration, up to 200 kN

NASA Astrophysics Data System (ADS)

Cárdenas Moctezuma, A.; Torres Guzmán, J. C.

2016-01-01

CENAM, through the Force and Pressure Division, organized a comparison on testing machines calibration, in compression mode. The participating laboratories were SIM National Institutes of Metrology from Colombia, Peru and Costa Rica, where CENAM, Mexico was the pilot and reference laboratory. The results obtained by the laboratories are presented in this paper as well as the analysis of compatibility. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Progress in the development of peroxide-based anti-parasitic agents.

PubMed

Muraleedharan, K M; Avery, Mitchell A

2009-08-01

Progress made in the past decade pertaining to the development of anti-parasitic agents based on artemisinin is presented. Apart from discussions on important derivatives obtained through functionalization at the C-3, C-9, C-10 and O-11 positions of artemisinin, an outline on its seco analogs and artemisinin bundles are given for a broader perspective on structure-activity relationships. Success with synthetic peroxides, drug-hybrid approaches, broad-spectrum anti-infective properties of peroxide compounds and a survey on peroxide-containing natural products other than artemisinin with available biological data are included to highlight recent trends and avenues for future research. A supplementary material with details on the biological properties of a larger collection of molecules belonging to the above structural classes is also given for reference.

Distant supervision for neural relation extraction integrated with word attention and property features.

PubMed

Qu, Jianfeng; Ouyang, Dantong; Hua, Wen; Ye, Yuxin; Li, Ximing

2018-04-01

Distant supervision for neural relation extraction is an efficient approach to extracting massive relations with reference to plain texts. However, the existing neural methods fail to capture the critical words in sentence encoding and meanwhile lack useful sentence information for some positive training instances. To address the above issues, we propose a novel neural relation extraction model. First, we develop a word-level attention mechanism to distinguish the importance of each individual word in a sentence, increasing the attention weights for those critical words. Second, we investigate the semantic information from word embeddings of target entities, which can be developed as a supplementary feature for the extractor. Experimental results show that our model outperforms previous state-of-the-art baselines. Copyright © 2018 Elsevier Ltd. All rights reserved.

Results of the supplementary comparison SIM.M.FF-S12 for volume of liquids at 20 L

NASA Astrophysics Data System (ADS)

Maldonado, M.; Castillo, E.; Rodríguez, L. D.

2018-01-01

A supplementary comparison was performed in order to compare national measurement systems to determine volume of liquids, particularly at fixed volume of 20 L. The participants were CENAM (Mexico), LACOMET (Costa Rica) and RECOPE (Costa Rica). The measurements were carried out from October 2016 to June 2017. The chosen value of volume (20 L) is representative of the Calibration and Measurement Capabilities (CMCs) declared by the three participants. The transfer standard (TS) was a stainless steel pipette for volume at 20 L. Prior to the beginning of the comparison, the TS was tested by CENAM. The results of the test phase showed excellent values for both repeatability and reproducibility. During the SIM.M.FF-S12, the results of the laboratories showed good agreement with the reference values. The best estimation of the measurands, as reported by the participants, showed a +/- 0.0022 % as the largest difference among the laboratories. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Analyzing large scale genomic data on the cloud with Sparkhit

PubMed Central

Huang, Liren; Krüger, Jan

2018-01-01

Abstract Motivation The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics. Existing tools use different distributed computational platforms to scale-out bioinformatics workloads. However, the scalability of these tools is not efficient. Moreover, they have heavy run time overheads when pre-processing large amounts of data. To address these limitations, we have developed Sparkhit: a distributed bioinformatics framework built on top of the Apache Spark platform. Results Sparkhit integrates a variety of analytical methods. It is implemented in the Spark extended MapReduce model. It runs 92–157 times faster than MetaSpark on metagenomic fragment recruitment and 18–32 times faster than Crossbow on data pre-processing. We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading. Furthermore, our application on the entire Human Microbiome Project shotgun sequencing data was completed in 2 h, presenting an approach to easily associate large amounts of public datasets with reference data. Availability and implementation Sparkhit is freely available at: https://rhinempi.github.io/sparkhit/. Contact asczyrba@cebitec.uni-bielefeld.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:29253074

Final report on regional supplementary comparison SIM.M.FF-S5: Volume of liquids at 50 mL

NASA Astrophysics Data System (ADS)

Morales, Abed; Malta, Dalni; Kornblit, Fernando; Ramírez, Ruben R.; Arias, Roberto; Trujillo, Sonia

2012-01-01

A regional supplementary comparison for the volume of liquid at 50 mL was conducted during October 2009 to June 2010 between the SIM members CENAM, INTI, INMETRO, INDECOPI and INTN. The transfer standard consisted of two 50 mL glass pycnometers, of the Gay Lussac type. CENAM acted as the pilot, collected the measurement results, analyzed the data and produced the comparison report. The median of all participants' results was used to calculate the regional comparison reference value because the result for one of the two pycnometers in one laboratory failed the chi-squared test at the 0.05 probability level. The measurements reported by the participants show an excellent overlap in four out of the five NMIs (-34×10-6 < Di < 29×10-6). The degree of equivalence obtained herein will be taken into account for the preparation of calibration and measurement capabilities claims from the participants. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the SIM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Structural and functional cerebral correlates of hypnotic suggestibility.

PubMed

Huber, Alexa; Lui, Fausta; Duzzi, Davide; Pagnoni, Giuseppe; Porro, Carlo Adolfo

2014-01-01

Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

Final report on EURAMET.M.P-K4.2010: Key and supplementary comparison of national pressure standards in the range 1 Pa to 15 kPa of absolute and gauge pressure

NASA Astrophysics Data System (ADS)

Krajíček, Zdeněk; Bergoglio, Mercede; Jousten, Karl; Otal, Pierre; Sabuga, Wladimir; Saxholm, Sari; Pražák, Dominik; Vičar, Martin

2014-01-01

This report describes a EURAMET comparison of five European National Metrology Institutes in low gauge and absolute pressure in gas (nitrogen), denoted as EURAMET.M.P-K4.2010. Its main intention is to state equivalence of the pressure standards, in particular those based on the technology of force-balanced piston gauges such as e.g. FRS by Furness Controls, UK and FPG8601 by DHI-Fluke, USA. It covers the range from 1 Pa to 15 kPa, both gauge and absolute. The comparison in absolute mode serves as a EURAMET Key Comparison which can be linked to CCM.P-K4 and CCM.P-K2 via PTB. The comparison in gauge mode is a supplementary comparison. The comparison was carried out from September 2008 till October 2012. The participating laboratories were the following: CMI, INRIM, LNE, MIKES, PTB-Berlin (absolute pressure 1 kPa and below) and PTB-Braunschweig (absolute pressure 1 kPa and above and gauge pressure). CMI was the pilot laboratory and provided a transfer standard for the comparison. This transfer standard was also the laboratory standard of CMI at the same time, which resulted in a unique and logistically difficult star comparison. Both in gauge and absolute pressures all the participating institutes successfully proved their equivalence with respect to the reference value and all also proved mutual bilateral equivalences in all the points. All the participating laboratories are also equivalent with the reference values of CCM.P-K4 and CCM.P-K2 in the relevant points. The comparison also proved the ability of FPG8601 to serve as a transfer standard. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

In quest of a systematic framework for unifying and defining nanoscience

PubMed Central

2009-01-01

This article proposes a systematic framework for unifying and defining nanoscience based on historic first principles and step logic that led to a “central paradigm” (i.e., unifying framework) for traditional elemental/small-molecule chemistry. As such, a Nanomaterials classification roadmap is proposed, which divides all nanomatter into Category I: discrete, well-defined and Category II: statistical, undefined nanoparticles. We consider only Category I, well-defined nanoparticles which are >90% monodisperse as a function of Critical Nanoscale Design Parameters (CNDPs) defined according to: (a) size, (b) shape, (c) surface chemistry, (d) flexibility, and (e) elemental composition. Classified as either hard (H) (i.e., inorganic-based) or soft (S) (i.e., organic-based) categories, these nanoparticles were found to manifest pervasive atom mimicry features that included: (1) a dominance of zero-dimensional (0D) core–shell nanoarchitectures, (2) the ability to self-assemble or chemically bond as discrete, quantized nanounits, and (3) exhibited well-defined nanoscale valencies and stoichiometries reminiscent of atom-based elements. These discrete nanoparticle categories are referred to as hard or soft particle nanoelements. Many examples describing chemical bonding/assembly of these nanoelements have been reported in the literature. We refer to these hard:hard (H-n:H-n), soft:soft (S-n:S-n), or hard:soft (H-n:S-n) nanoelement combinations as nanocompounds. Due to their quantized features, many nanoelement and nanocompound categories are reported to exhibit well-defined nanoperiodic property patterns. These periodic property patterns are dependent on their quantized nanofeatures (CNDPs) and dramatically influence intrinsic physicochemical properties (i.e., melting points, reactivity/self-assembly, sterics, and nanoencapsulation), as well as important functional/performance properties (i.e., magnetic, photonic, electronic, and toxicologic properties). We propose this perspective as a modest first step toward more clearly defining synthetic nanochemistry as well as providing a systematic framework for unifying nanoscience. With further progress, one should anticipate the evolution of future nanoperiodic table(s) suitable for predicting important risk/benefit boundaries in the field of nanoscience. Electronic supplementary material The online version of this article (doi:10.1007/s11051-009-9632-z) contains supplementary material, which is available to authorized users. PMID:21170133

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment

PubMed Central

Pasaniuc, Bogdan; Zaitlen, Noah; Shi, Huwenbo; Bhatia, Gaurav; Gusev, Alexander; Pickrell, Joseph; Hirschhorn, Joel; Strachan, David P.; Patterson, Nick; Price, Alkes L.

2014-01-01

Motivation: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. Results: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1–5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case–control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of χ2 association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses. Availability and implementation: Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/. Contact: bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu Supplementary information: Supplementary materials are available at Bioinformatics online. PMID:24990607

Framing effects in choices between multioutcome life-expectancy lotteries.

PubMed

Bernstein, L M; Chapman, G B; Elstein, A S

1999-01-01

To explore framing or editing effects and a method to debias framing in a clinical context. Clinical scenarios using multioutcome life-expectancy lotteries of equal value required choices between two supplementary drugs that either prolonged or shortened life from the 20-year beneficial effect of a baseline drug. The effects of these supplementary drugs were presented in two conditions, using a between-subjects design. In segregated editing (n = 116) the effects were presented separately from the effects of the baseline drug. In integrated editing (n = 100), effects of supplementary and baseline drugs were combined in the lottery presentation. Each subject responded to 30 problems. To explore one method of debiasing, another 100 subjects made choices after viewing both segregated and integrated editings of 20 problems (dual framing). Statistically significant preference reversals between segregated and integrated editing of pure lotteries occurred only when one framing placed outcomes in the gain domain, and the other framing placed them in the loss domain. When both editings resulted in gain-domain outcomes only, there was no framing effect. There was a related relationship of framing-effect shifts from losses to gains in mixed-lottery-choice problems. Responses to the dual framing condition did not consistently coincide with responses to either single framing. In some situations, dual framing eliminated or lessened framing effects. The results support two components of prospect theory, coding outcomes as gains or losses from a reference point, and an s-shaped utility function (concave in gain, convex in loss domains). Presenting both alternative editings of a complex situation prior to choice more fully informs the decision maker and may help to reduce framing effects. Given the extent to which preferences shift in response to alternative presentations, it is unclear which choice represents the subject's "true preferences."

WHIDE—a web tool for visual data mining colocation patterns in multivariate bioimages

PubMed Central

Kölling, Jan; Langenkämper, Daniel; Abouna, Sylvie; Khan, Michael; Nattkemper, Tim W.

2012-01-01

Motivation: Bioimaging techniques rapidly develop toward higher resolution and dimension. The increase in dimension is achieved by different techniques such as multitag fluorescence imaging, Matrix Assisted Laser Desorption / Ionization (MALDI) imaging or Raman imaging, which record for each pixel an N-dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBIs) calls for new approaches to support users in the analysis of both feature domains: space (i.e. sample morphology) and molecular colocation or interaction. In this article, we present our approach WHIDE (Web-based Hyperbolic Image Data Explorer) that combines principles from computational learning, dimension reduction and visualization in a free web application. Results: We applied WHIDE to a set of MBI recorded using the multitag fluorescence imaging Toponome Imaging System. The MBI show field of view in tissue sections from a colon cancer study and we compare tissue from normal/healthy colon with tissue classified as tumor. Our results show, that WHIDE efficiently reduces the complexity of the data by mapping each of the pixels to a cluster, referred to as Molecular Co-Expression Phenotypes and provides a structural basis for a sophisticated multimodal visualization, which combines topology preserving pseudocoloring with information visualization. The wide range of WHIDE's applicability is demonstrated with examples from toponome imaging, high content screens and MALDI imaging (shown in the Supplementary Material). Availability and implementation: The WHIDE tool can be accessed via the BioIMAX website http://ani.cebitec.uni-bielefeld.de/BioIMAX/; Login: whidetestuser; Password: whidetest. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: tim.nattkemper@uni-bielefeld.de PMID:22390938

Malnourished children and supplementary feeding during the war emergency in Guinea-Bissau in 1998-1999.

PubMed

Nielsen, Jens; Valentiner-Branth, Palle; Martins, Cesario; Cabral, Fernando; Aaby, Peter

2004-10-01

Supplementary feeding programs (SFPs) are intended to mitigate the deterioration of nutritional status and the increase in mortality among malnourished children. We investigated the effect of an SFP on malnourished children in Guinea-Bissau who were returning to their homes after having been displaced within the country because of war in 1998-1999. The effect of the war on the nutritional status of children aged 6-59 mo who were present in Bissau sometime from September 1998 to June 1999 was evaluated by comparing the mortality and the prevalence of malnutrition with the values expected had the war not occurred and by comparing the severity of malnutrition in malnourished children before and during the war. The quality of the SFP was also evaluated. Children with midupper arm circumference < 130 mm were provided weekly medical consultations and supplementary feeding until recovery. The degree of malnutrition did not increase during the war. The prevalence of malnutrition increased with the start of the war but then decreased. The mortality of malnourished children did not increase during the war. Seventy-four percent of the referred children received treatment; of those, 1% died, 67% recovered, and 32% abandoned treatment. Compliance was 89%. The recovery rate was 13.1. 1000(-1). d(-1), and the median time to recovery was 48 d. Better compliance was associated with shorter time to recovery. Our findings may be biased by changes in the cultural and socioeconomic background of the malnourished children. However, 3 different analyses indicated a beneficial effect of the SFP. Thus, the home-based SFP probably prevented nutritional deterioration during the war in Guinea-Bissau.

Effects of supplementary private health insurance on physician visits in Korea.

PubMed

Kang, Sungwook; You, Chang Hoon; Kwon, Young Dae; Oh, Eun-Hwan

2009-12-01

The coverage of social health insurance has remained limited, despite it being compulsory in Korea. Accordingly, Koreans have come to rely upon supplementary private health insurance (PHI) to cover their medical costs. We examined the effects of supplementary PHI on physician visits in Korea. This study used individual data from 11,043 respondents who participated in the Korean Labor and Income Panel Survey in 2001. We conducted a single probit model to identify the relationship between PHI and physician visits, with adjustment for the following covariates: demographic characteristics, socioeconomic status, health status, and health-related behavior. Finally, we performed a bivariate probit model to examine the true effect of PHI on physician visits, with adjustment for the above covariates plus unobservable covariates that might affect not only physician visit, but also the purchase of PHI. We found that about 38% of all respondents had one or more private health plans. Forty-five percent of all respondents visited one or more physicians, and 49% of those who were privately insured had physician visits compared with 42% of the uninsured. The single probit model showed that those with PHI were about 14 percentage points more likely to visit physicians than those who do not have PHI. However, this distinction disappears in the bivariate probit model. This result might have been a consequence of the nature of private health plans in Korea. Private insurance companies pay a fixed amount directly to their enrollees in case of illness/injury, and the individuals are responsible subsequently for purchasing their own healthcare services. This study demonstrated the potential of Korean PHI to address the problem of moral hazard. These results serve as a reference for policy makers when considering how to finance healthcare services, as well as to contain healthcare expenditure.

Reuse of de-inking sludge from wastepaper recycling in cement mortar products.

PubMed

Yan, Shiqin; Sagoe-Crentsil, Kwesi; Shapiro, Gretta

2011-08-01

This paper presents results of an investigation into the use of de-inking sludge from a paper recycling mill as feedstock material in the manufacture of cement mortar products, including masonry blocks and mortar renders. Both physical and mechanical properties of mortar specimens containing various amounts of de-inking sludge were investigated. It was observed that the addition of de-inking sludge to cement mortar at a fixed water-to-cement ratio significantly reduced flow properties and increased setting time. Water absorption and volume of permeable voids of cement mortar increased with increased dosage of de-inking sludge, with a corresponding reduction of bulk density. The 91-day compressive strength of mortar samples with 2.5 wt% and 20 wt% de-inking sludge loadings retained 83% and 62% respectively of the reference mortar strength. The corresponding drying shrinkage increased by up to 160% compared to reference samples. However, a de-inking sludge loading of up to 2.5 wt% did not significantly alter measured physical and mechanical properties. The results demonstrate that despite the high moisture absorbance of de-inking sludge due to its organic matter and residual cellulose fibre content, it serves as a potential supplementary additive and its cellulosic content proving to be an active set retardant to cementitious masonry products. Copyright © 2011 Elsevier Ltd. All rights reserved.

Levels of selected carcinogens and toxicants in vapour from electronic cigarettes.

PubMed

Goniewicz, Maciej Lukasz; Knysak, Jakub; Gawron, Michal; Kosmider, Leon; Sobczak, Andrzej; Kurek, Jolanta; Prokopowicz, Adam; Jablonska-Czapla, Magdalena; Rosik-Dulewska, Czeslawa; Havel, Christopher; Jacob, Peyton; Benowitz, Neal

2014-03-01

Electronic cigarettes, also known as e-cigarettes, are devices designed to imitate regular cigarettes and deliver nicotine via inhalation without combusting tobacco. They are purported to deliver nicotine without other toxicants and to be a safer alternative to regular cigarettes. However, little toxicity testing has been performed to evaluate the chemical nature of vapour generated from e-cigarettes. The aim of this study was to screen e-cigarette vapours for content of four groups of potentially toxic and carcinogenic compounds: carbonyls, volatile organic compounds, nitrosamines and heavy metals. Vapours were generated from 12 brands of e-cigarettes and the reference product, the medicinal nicotine inhaler, in controlled conditions using a modified smoking machine. The selected toxic compounds were extracted from vapours into a solid or liquid phase and analysed with chromatographic and spectroscopy methods. We found that the e-cigarette vapours contained some toxic substances. The levels of the toxicants were 9-450 times lower than in cigarette smoke and were, in many cases, comparable with trace amounts found in the reference product. Our findings are consistent with the idea that substituting tobacco cigarettes with e-cigarettes may substantially reduce exposure to selected tobacco-specific toxicants. E-cigarettes as a harm reduction strategy among smokers unwilling to quit, warrants further study. (To view this abstract in Polish and German, please see the supplementary files online.).

[Somatic disorders in outpatient psychiatry: the added value of a standard physical examination during the intake of outpatients].

PubMed

van den Berg, K E M; Rijnders, C A Th; van Dam, A; van de Ven, A L M; van der Feltz-Cornelis, C M; Graafsma, S J

2014-01-01

It is well-known that psychiatric patients often suffer from severe somatic problems, such as diabetes mellitus and cardiovascular disease. Up till now, research has concentrated almost exclusively on the inpatient setting, but there is strong evidence that the correlation also exists in psychiatric patients who are outpatients. In the Netherlands there are, as yet, no clear recommendations regarding a standard form of somatic screening for the outpatient population. A pilot study performed by GGz Breburg has shown that somatic screening (without a physical examination) gave substantial additional value to treatment planning. To investigate the added value that a physical examination can provide when new psychiatric patients are screened for aspects of somatic concern (ASC). Newly referred outpatients (n = 70) were screened somatically by means of a questionnaire and supplementary medical interview, and by laboratory tests and physical examination. If a somatic problem was found which had not been detected previously, the patient was referred back to to the general practitioner. At least one ASC was found in 81,4% of all patients. In 45,7% of all patients the asc had not been detected. 12% of all the newly discovered somatic problems were found exclusively via the physical examination. A physical examination provides substantial information and adds value to the somatic screening of psychiatric outpatients.

Author Correction: Low frequency transcranial electrical stimulation does not entrain sleep rhythms measured by human intracranial recordings.

PubMed

Lafon, Belen; Henin, Simon; Huang, Yu; Friedman, Daniel; Melloni, Lucia; Thesen, Thomas; Doyle, Werner; Buzsáki, György; Devinsky, Orrin; Parra, Lucas C; Liu, Anli

2018-02-28

It has come to our attention that we did not specify whether the stimulation magnitudes we report in this Article are peak amplitudes or peak-to-peak. All references to intensity given in mA in the manuscript refer to peak-to-peak amplitudes, except in Fig. 2, where the model is calibrated to 1 mA peak amplitude, as stated. In the original version of the paper we incorrectly calibrated the computational models to 1 mA peak-to-peak, rather than 1 mA peak amplitude. This means that we divided by a value twice as large as we should have. The correct estimated fields are therefore twice as large as shown in the original Fig. 2 and Supplementary Figure 11. The corrected figures are now properly calibrated to 1 mA peak amplitude. Furthermore, the sentence in the first paragraph of the Results section 'Intensity ranged from 0.5 to 2.5 mA (current density 0.125-0.625 mA mA/cm 2 ), which is stronger than in previous reports', should have read 'Intensity ranged from 0.5 to 2.5 mA peak to peak (peak current density 0.0625-0.3125 mA/cm 2 ), which is stronger than in previous reports.' These errors do not affect any of the Article's conclusions.

Behavioural aspects of terrorism.

PubMed

Leistedt, Samuel J

2013-05-10

Behavioural and social sciences are useful in collecting and analysing intelligence data, understanding terrorism, and developing strategies to combat terrorism. This article aims to examine the psychopathological concepts of terrorism and discusses the developing roles for behavioural scientists. A systematic review was conducted of studies investigating behavioural aspects of terrorism. These studies were identified by a systematic search of databases, textbooks, and a supplementary manual search of references. Several fundamental concepts were identified that continue to influence the motives and the majority of the behaviours of those who support or engage in this kind of specific violence. Regardless of the psychological aspects and new roles for psychiatrists, the behavioural sciences will continue to be called upon to assist in developing better methods to gather and analyse intelligence, to understand terrorism, and perhaps to stem the radicalisation process. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Flavitrack: an annotated database of flavivirus sequences

PubMed Central

Misra, Milind

2009-01-01

Motivation Properly annotated sequence data for flaviviruses, which cause diseases, such as tick-borne encephalitis (TBE), dengue fever (DF), West Nile (WN) and yellow fever (YF), can aid in the design of antiviral drugs and vaccines to prevent their spread. Flavitrack was designed to help identify conserved sequence motifs, interpret mutational and structural data and track evolution of phenotypic properties. Summary Flavitrack contains over 590 complete flavivirus genome/protein sequences and information on known mutations and literature references. Each sequence has been manually annotated according to its date and place of isolation, phenotype and lethality. Internal tools are provided to rapidly determine relationships between viruses in Flavitrack and sequences provided by the user. Availability http://carnot.utmb.edu/flavitrack Contact chschein@utmb.edu Supplementary information http://carnot.utmb.edu/flavitrack/B1S1.html PMID:17660525

A Strategy for Origins of Life Research.

PubMed

Scharf, Caleb; Virgo, Nathaniel; Cleaves, H James; Aono, Masashi; Aubert-Kato, Nathanael; Aydinoglu, Arsev; Barahona, Ana; Barge, Laura M; Benner, Steven A; Biehl, Martin; Brasser, Ramon; Butch, Christopher J; Chandru, Kuhan; Cronin, Leroy; Danielache, Sebastian; Fischer, Jakob; Hernlund, John; Hut, Piet; Ikegami, Takashi; Kimura, Jun; Kobayashi, Kensei; Mariscal, Carlos; McGlynn, Shawn; Menard, Brice; Packard, Norman; Pascal, Robert; Pereto, Juli; Rajamani, Sudha; Sinapayen, Lana; Smith, Eric; Switzer, Christopher; Takai, Ken; Tian, Feng; Ueno, Yuichiro; Voytek, Mary; Witkowski, Olaf; Yabuta, Hikaru

2015-12-01

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes-key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap   Appendix I   Appendix II   Supplementary Materials  References.

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

PubMed

Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

2017-11-01

High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

High-speed and high-ratio referential genome compression.

PubMed

Liu, Yuansheng; Peng, Hui; Wong, Limsoon; Li, Jinyan

2017-11-01

The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio. We present a high-performance referential genome compression algorithm named HiRGC. It is based on a 2-bit encoding scheme and an advanced greedy-matching search on a hash table. We compare the performance of HiRGC with four state-of-the-art compression methods on a benchmark dataset of eight human genomes. HiRGC takes <30 min to compress about 21 gigabytes of each set of the seven target genomes into 96-260 megabytes, achieving compression ratios of 217 to 82 times. This performance is at least 1.9 times better than the best competing algorithm on its best case. Our compression speed is also at least 2.9 times faster. HiRGC is stable and robust to deal with different reference genomes. In contrast, the competing methods' performance varies widely on different reference genomes. More experiments on 100 human genomes from the 1000 Genome Project and on genomes of several other species again demonstrate that HiRGC's performance is consistently excellent. The C ++ and Java source codes of our algorithm are freely available for academic and non-commercial use. They can be downloaded from https://github.com/yuansliu/HiRGC. jinyan.li@uts.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

EURRECA-Estimating vitamin D requirements for deriving dietary reference values.

PubMed

Cashman, Kevin D; Kiely, Mairead

2013-01-01

The time course of the EURRECA from 2008 to 2012, overlapped considerably with the timeframe of the process undertaken by the North American Institute of Medicine (IOM) to revise dietary reference intakes for vitamin D and calcium (published November 2010). Therefore the aims of the vitamin D-related activities in EURRECA were formulated to address knowledge requirements that would complement the activities undertaken by the IOM and provide additional resources for risk assessors and risk management agencies charged with the task of setting dietary reference values for vitamin D. A total of three systematic reviews were carried out. The first, which pre-dated the IOM review process, identified and evaluated existing and novel biomarkers of vitamin D status and confirmed that circulating 25-hydroxyvitamin D (25(OH)D) concentrations is a robust and reliable marker of vitamin D status. The second systematic review conducted a meta-analysis of the dose-response of serum 25(OH)D to vitamin D intake from randomized controlled trials (RCT) among adults to explore the most appropriate model of the vitamin D intake-serum 25(OH)D) relationship to estimate requirements. The third review also carried out a meta-analysis to evaluate evidence of efficacy from RCT using foods fortified with vitamin D, and found they increased circulating 25(OH)D concentrations in a dose-dependent manner but identified a need for stronger data on the efficacy of vitamin D-fortified food on deficiency prevention and potential health outcomes, including adverse effects. Finally, narrative reviews provided estimates of the prevalence of inadequate intakes of vitamin D in adults and children from international dietary surveys, as well as a compilation of research requirements for vitamin D to inform current and future assessments of vitamin D requirements. [Supplementary materials are available for this article. Go to the publisher's onilne edition of Critical Reviews in Food Science and Nutrion for the following free supplemental files: Additional text, tables, and figures.].

Structural and Functional Cerebral Correlates of Hypnotic Suggestibility

PubMed Central

Huber, Alexa; Lui, Fausta; Duzzi, Davide; Pagnoni, Giuseppe; Porro, Carlo Adolfo

2014-01-01

Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity. PMID:24671130

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level.

PubMed

Arslan, Ahmed; van Noort, Vera

2017-01-15

The recent outbreak of Ebola virus disease (EVD) resulted in a large number of human deaths. Due to this devastation, the Ebola virus has attracted renewed interest as model for virus evolution. Recent literature on Ebola virus (EBOV) has contributed substantially to our understanding of the underlying genetics and its scope with reference to the 2014 outbreak. But no study yet, has focused on the conservation patterns of EBOV proteins. We analyzed the evolution of functional regions of EBOV and highlight the function of conserved residues in protein activities. We apply an array of computational tools to dissect the functions of EBOV proteins in detail: (i) protein sequence conservation, (ii) protein-protein interactome analysis, (iii) structural modeling and (iv) kinase prediction. Our results suggest the presence of novel post-translational modifications in EBOV proteins and their role in the modulation of protein functions and protein interactions. Moreover, on the basis of the presence of ATM recognition motifs in all EBOV proteins we postulate a role of DNA damage response pathways and ATM kinase in EVD. The ATM kinase is put forward, for further evaluation, as novel potential therapeutic target. http://www.biw.kuleuven.be/CSB/EBOV-PTMs CONTACT: vera.vannoort@biw.kuleuven.beSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

TopHat: discovering splice junctions with RNA-Seq

PubMed Central

Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.

2009-01-01

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu Contact: cole@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19289445

A 76-year-old woman with anaemia and cardiomegaly.

PubMed

Oh, Jin Kyung; Park, Jae-Hyeong

2017-12-01

A 76-year-old woman was referred to our hospital due to further evaluation of anaemia. During the past 3 years, she had been treated for multiple spinal compression fractures with vertebroplasty. Her blood pressure was 90/50 mm Hg, heart rate 75 beats/min, body temperature 37.7°C and respiratory rate 20/min at admission.On blood sampling, her haemoglobin level was 5.2 g/dL and white cell count and platelet count 3.7 and 22×10 3 / µL, respectively. She was diagnosed with multiple myeloma after serial diagnostic workups. Because her chest radiography showed cardiomegaly and left-sided pleural effusion with small atelectasis, transthoracic echocardiography and contrast enhanced chest CT were performed (figure 1, see online supplementary video). DC1SP110.1136/heartjnl-2017-312087.supp1Supplementary video heartjnl;103/24/2009/F1F1F1Figure 1(A) Apical four-chamber view by transthoracic echocardiography and (B) the coronal image of contrast-enhanced  chest CT. Which of the following is the most likely diagnosis of the cystic lesion?AscitesPericardial cystPericardial effusionBronchogenic cystPleural effusion. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Microsurgical and Tractographic Anatomy of the Supplementary Motor Area Complex in Humans.

PubMed

Bozkurt, Baran; Yagmurlu, Kaan; Middlebrooks, Erik H; Karadag, Ali; Ovalioglu, Talat Cem; Jagadeesan, Bharathi; Sandhu, Gauravjot; Tanriover, Necmettin; Grande, Andrew W

2016-11-01

To evaluate the microsurgical anatomy of the fiber tract connections of the supplementary motor area (SMA) and pre-SMA, and examine its potential functional role with reference to clinical trials in the literature. Ten postmortem formalin-fixed human brains (20 sides) and 1 cadaveric head were prepared following Klingler's method. The fiber dissection was performed in a stepwise fashion, from lateral to medial and also from medial to lateral, under an operating microscope, with 3D images captured at each stage. Our findings were supported by in vivo magnetic resonance imaging tractography in 2 healthy subjects. The connections of the SMA complex, composed of the pre-SMA and the SMA proper, are composed of short "U" association fibers and the superior longitudinal fasciculus I, cingulum, claustrocortical fibers, callosal fibers, corticospinal tract, frontal aslant tract, and frontostriatal tract. The claustrocortical fibers may play an important role in the integration of motor, language, and limbic functions of the SMA complex. The frontostriatal tract connects the pre-SMA to the putamen and caudate nucleus, and also forms parts of both the internal capsule and the dorsal external capsule. The SMA complex has numerous connections throughout the cerebrum. An understanding of these connections is important for presurgical planning for lesions in the frontal lobe and helps explain symptoms related to SMA injury. Copyright © 2016 Elsevier Inc. All rights reserved.

Intake of macro- and micronutrients in Danish vegans.

PubMed

Kristensen, Nadja B; Madsen, Mia L; Hansen, Tue H; Allin, Kristine H; Hoppe, Camilla; Fagt, Sisse; Lausten, Mia S; Gøbel, Rikke J; Vestergaard, Henrik; Hansen, Torben; Pedersen, Oluf

2015-10-30

Since information about macro- and micronutrient intake among vegans is limited we aimed to determine and evaluate their dietary and supplementary intake. Seventy 18-61 years old Danish vegans completed a four-day weighed food record from which their daily intake of macro- and micronutrients was assessed and subsequently compared to an age-range-matched group of 1,257 omnivorous individuals from the general Danish population. Moreover, the vegan dietary and supplementary intake was compared to the 2012 Nordic Nutrition Recommendations (NNR). Dietary intake differed significantly between vegans and the general Danish population in all measured macro- and micronutrients (p < 0.05), except for energy intake among women and intake of carbohydrates among men. For vegans the intake of macro- and micronutrients (including supplements) did not reach the NNR for protein, vitamin D, iodine and selenium. Among vegan women vitamin A intake also failed to reach the recommendations. With reference to the NNR, the dietary content of added sugar, sodium and fatty acids, including the ratio of PUFA to SFA, was more favorable among vegans. At the macronutrient level, the diet of Danish vegans is in better accordance with the NNR than the diet of the general Danish population. At the micronutrient level, considering both diet and supplements, the vegan diet falls short in certain nutrients, suggesting a need for greater attention toward ensuring recommended daily intake of specific vitamins and minerals.

Meticulous plasma isolation is essential to avoid false low-level viraemia in Roche Cobas HIV-1 viral load assays.

PubMed

Mortier, Virginie; Vancoillie, Leen; Dauwe, Kenny; Staelens, Delfien; Demecheleer, Els; Schauvliege, Marlies; Dinakis, Sylvie; Van Maerken, Tom; Dessilly, Géraldine; Ruelle, Jean; Verhofstede, Chris

2017-10-24

Pre-analytical sample processing is often overlooked as a potential cause of inaccurate assay results. Here we demonstrate how plasma, extracted from standard EDTA-containing blood collection tubes, may contain traces of blood cells consequently resulting in a false low-level HIV-1 viral load when using Roche Cobas HIV-1 assays. The presence of human DNA in Roche Cobas 4800 RNA extracts and in RNA extracts from the Abbott HIV-1 RealTime assay was assessed by quantifying the human albumin gene by means of quantitative PCR. RNA was extracted from plasma samples before and after an additional centrifugation and tested for viral load and DNA contamination. The relation between total DNA content and viral load was defined. Elevated concentrations of genomic DNA were detected in 28 out of 100 Cobas 4800 extracts and were significantly more frequent in samples processed outside of the AIDS Reference Laboratory. An association between genomic DNA presence and spurious low-level viraemia results was demonstrated. Supplementary centrifugation of plasma before RNA extraction eliminated the contamination and the false viraemia. Plasma isolated from standard EDTA-containing blood collection tubes may contain traces of HIV DNA leading to false viral load results above the clinical cutoff. Supplementary centrifugation of plasma before viral load analysis may eliminate the occurrence of this spurious low-level viraemia.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

PubMed Central

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun; Ibrahim, Yehia M.; Wilkins, Christopher S.; Renslow, Ryan S.; Thomas, Dennis G.; Payne, Samuel H.; Monroe, Matthew E.; Smith, Richard D.; Teeguarden, Justin G.; Baker, Erin S.; Metz, Thomas O.

2017-01-01

Abstract Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation: PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Contact: erin.baker@pnnl.gov or thomas.metz@pnnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28505286

Traceability of pH measurements by glass electrode cells: performance characteristic of pH electrodes by multi-point calibration.

PubMed

Naumann, R; Alexander-Weber, Ch; Eberhardt, R; Giera, J; Spitzer, P

2002-11-01

Routine pH measurements are carried out with pH meter-glass electrode assemblies. In most cases the glass and reference electrodes are thereby fashioned into a single probe, the so-called 'combination electrode' or simply 'the pH electrode'. The use of these electrodes is subject to various effects, described below, producing uncertainties of unknown magnitude. Therefore, the measurement of pH of a sample requires a suitable calibration by certified standard buffer solutions (CRMs) traceable to primary pH standards. The procedures in use are based on calibrations at one point, at two points bracketing the sample pH and at a series of points, the so-called multi-point calibration. The multi-point calibration (MPC) is recommended if minimum uncertainty and maximum consistency are required over a wide range of unknown pH values. Details of uncertainty computations for the two-point and MPC procedure are given. Furthermore, the multi-point calibration is a useful tool to characterise the performance of pH electrodes. This is demonstrated with different commercial pH electrodes. ELECTRONIC SUPPLEMENTARY MATERIAL is available if you access this article at http://dx.doi.org/10.1007/s00216-002-1506-5. On that page (frame on the left side), a link takes you directly to the supplementary material.

The effects of different UV-B radiation intensities on morphological and biochemical characteristics in Ocimum basilicum L.

PubMed

Sakalauskaitė, Jurga; Viskelis, Pranas; Dambrauskienė, Edita; Sakalauskienė, Sandra; Samuolienė, Giedrė; Brazaitytė, Aušra; Duchovskis, Pavelas; Urbonavičienė, Dalia

2013-04-01

The effects of short-term ultraviolet B (UV-B) irradiation on sweet basil (Ocimum basilicum L. cv. Cinnamon) plants at the 3-4 leaf pair and flowering stages were examined in controlled environment growth chambers. Plants were exposed to 0 (reference), 2 and 4 kJ UV-B m(-2) day(-1) over 7 days. Exposure of basil plants to supplementary UV-B light resulted in increased assimilating leaf area, fresh biomass and dry biomass. Stimulation of physiological functions in young basil plants under either applied UV-B dose resulted in increased total chlorophyll content but no marked variation in carotenoid content. At the flowering stage the chlorophyll and carotenoid contents of basil were affected by supplementary UV-B radiation, decreasing with enhanced UV-B exposure. Both total antioxidant activity (2,2-diphenyl-1-picrylhydrazyl free radical assay) and total phenolic compound content were increased by UV-B light supplementation. Young and mature basil plants differed in their ascorbic acid content, which was dependent on UV-B dose and plant age. UV-B radiation resulted in decreased nitrate content in young basil plants (3-4 leaf pair stage). These results indicate that the application of short-exposure UV-B radiation beneficially influenced both growth parameters and biochemical constituents in young and mature basil plants. © 2012 Society of Chemical Industry.

Historical Evolution of NASA Standard Materials Testing with Hypergolic Propellants and Ammonia (NASA Standard 6001 Test 15)

NASA Technical Reports Server (NTRS)

Greene, Benjamin; McClure, Mark B.

2012-01-01

The NASA Johnson Space Center White Sands Test Facility (WSTF) has performed testing of hazardous and reactive aerospace fluids, including hypergolic propellants, with materials since the 1960s with the Apollo program. Amongst other test activities, Test 15 is a NASA standard test for evaluating the reactivity of materials with selected aerospace fluids, in particular hydrazine, monomethylhydrazine, uns-dimethylhydrazine, Aerozine 50, dinitrogen tetroxide oxidizers, and ammonia. This manuscript provides an overview of the history of Test 15 over a timeline ranging from prior to its development and first implementation as a NASA standard test in 1974 to its current refinement. Precursor documents to NASA standard tests, as they are currently known, are reviewed. A related supplementary test, international standardization, and enhancements to Test 15 are also discussed. Because WSTF was instrumental in the development and implementation of Test 15, WSTF experience and practices are referred to in this manuscript.

13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA.

PubMed

Icazatti, A A; Martin, O A; Villegas, M; Szleifer, I; Vila, J A

2018-06-19

Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for correct assignments of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one. This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license. Supplementary data are available at Bioinformatics online.

VizieR Online Data Catalog: Dwarf novae outbursts properties (Otulakowska-Hypka+, 2016)

NASA Astrophysics Data System (ADS)

Otulakowska-Hypka, M.; Olech, A.; Patterson, J.

2017-11-01

In this study, we used the following available catalogue data sources. The catalogue and atlas of CVs (https://archive.stsci.edu/prepds/cvcat/) by Downes et al. (2001PASP..113..764D, Cat. V/123) which contains 1830 objects that have been classified as a CV before 2006 February 1, when the catalogue was frozen. Catalogue of cataclysmic binaries, low-mass X-ray binaries and related objects (http://www.mpa-garching.mpg.de/RKcat/) by Ritter & Kolb (2003A&A...404..301R, Cat. B/cb). Although the reference corresponds to a catalogue which is over 10yr old, its newest edition 7.21 (2013 December 31) has been used in this study. This catalogue contains 1094 CVs. Catalogue of J. Patterson, that is the supplementary electronic material to the publication Patterson (2011) containing properties of 292 non-magnetic CVs with orbital periods smaller than 3h (http://cbastro.org/dwarfnovashort/) (1 data file).

Reflections on the Journal of Applied Psychology for 1989 to 1994: Changes in major research themes and practices over 25 years.

PubMed

Schmitt, Neal

2017-03-01

Informal observations concerning journal content indicates that research investigating organizational behavior topics, including work on the structure of groups and determinants and consequences of group process along with the role of leadership in groups, has increased. Some topics have disappeared (e.g., job analysis, human factors, union-related work, consumer behavior) and others are declining (e.g., research methods, psychometrics). Perhaps the biggest change is in the length of articles, which is mostly a function of the inclusion of greater numbers of references and appendix material. Publishing some of this material in supplementary online materials is now current practice in the Journal of Applied Psychology. Concerns about use of journal space may also be entirely moot, if electronic publishing as opposed to print publishing becomes the norm. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Long-lived states to sustain SABRE hyperpolarised magnetisation† †Electronic supplementary information (ESI) available: Experimental details, sample specification, substrate characterisation, SABRE studies, pulse sequence details, simulations. See DOI: 10.1039/c6cp02844f Click here for additional data file.

PubMed Central

Roy, Soumya S.; Rayner, Peter J.; Norcott, Philip; Green, Gary G. R.

2016-01-01

The applicability of the magnetic resonance (MR) technique in the liquid phase is limited by poor sensitivity and short nuclear spin coherence times which are insufficient for many potential applications. Here we illustrate how it is possible to address both of these issues simultaneously by harnessing long-lived hyperpolarised spin states that are formed by adapting the Signal Amplification by Reversible Exchange (SABRE) technique. We achieve more than 4% net 1H-polarisation in a long-lived form that remains detectable for over ninety seconds by reference to proton pairs in the biologically important molecule nicotinamide and a pyrazine derivative whose in vivo imaging will offer a new route to probe disease in the future. PMID:27711398

Visible light powered self-disinfecting coatings for influenza viruses

NASA Astrophysics Data System (ADS)

Weng, Ding; Qi, Hangfei; Wu, Ting-Ting; Yan, Ming; Sun, Ren; Lu, Yunfeng

2012-04-01

Influenza A viruses, the pathogens responsible for the recent swine flu outbreak and many historical pandemics, remain a threat to the public health. We report herein the fabrication of self-disinfecting surfaces from photoactive building nanocrystals, which can inactivate influenza viruses rapidly, spontaneously and continuously under visible light illumination.Influenza A viruses, the pathogens responsible for the recent swine flu outbreak and many historical pandemics, remain a threat to the public health. We report herein the fabrication of self-disinfecting surfaces from photoactive building nanocrystals, which can inactivate influenza viruses rapidly, spontaneously and continuously under visible light illumination. Electronic supplementary information (ESI) available: XRD, UV-Vis absorbance, TEM, AFM of as-prepared nanocrystals and as-fabricated self-disinfecting surfaces, disinfection of influenza A virus by TiO2 (P25) with UV irradiation as reference control, photoinactivation of influenza A virus envelope proteins and photoinactivation of trypsin. See DOI: 10.1039/c2nr30388d

A Strategy for Origins of Life Research

PubMed Central

Scharf, Caleb; Virgo, Nathaniel; Aono, Masashi; Aubert-Kato, Nathanael; Aydinoglu, Arsev; Barahona, Ana; Barge, Laura M.; Benner, Steven A.; Biehl, Martin; Brasser, Ramon; Butch, Christopher J.; Chandru, Kuhan; Cronin, Leroy; Danielache, Sebastian; Fischer, Jakob; Hernlund, John; Hut, Piet; Ikegami, Takashi; Kimura, Jun; Kobayashi, Kensei; Mariscal, Carlos; McGlynn, Shawn; Menard, Brice; Packard, Norman; Pascal, Robert; Pereto, Juli; Rajamani, Sudha; Sinapayen, Lana; Smith, Eric; Switzer, Christopher; Takai, Ken; Tian, Feng; Ueno, Yuichiro; Voytek, Mary; Witkowski, Olaf; Yabuta, Hikaru

2015-01-01

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes—key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap  Appendix I  Appendix II  Supplementary Materials  References PMID:26684503

Synthesis of carbon-11, fluorine-18, and nitrogen-13 labeled radiotracers for biomedical applications

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

Fowler, J.S.; Wolf, A.P.

A number of reviews, many of them recent, have appeared on various aspects of /sup 11/C, /sup 18/F and /sup 13/N-labeled radiotracers. This monograph treats the topic principally from the standpoint of synthetic organic chemistry while keeping in perspective the necessity of integrating the organic chemistry with the design and ultimate application of the radiotracer. Where possible, recent examples from the literature of organic synthesis are introduced to suggest potentially new routes which may be applied to problems in labeling organic molecules with the short-lived positron emitters, carbon-11, fluorine-18, and nitrogen-13. The literature survey of carbon-11, fluorine-18 and nitrogen-13 labeledmore » compounds presented are of particular value to scientists working in this field. Two appendices are also included to provide supplementary general references. A subject index concludes this volume.« less

A molecular-sized tunnel-porous crystal with a ratchet gear structure and its one-way guest-molecule transportation property

NASA Astrophysics Data System (ADS)

Kataoka, Keisuke; Yasumoto, Tetsuaki; Manabe, Yousuke; Sato, Hiroyasu; Yamano, Akihito; Katagiri, Toshimasa

2013-01-01

An anisotropic tunnel microporous crystal was prepared. Active transportation of anthracene as a guest molecule in the anisotropic tunnels was observed. The direction of anthracene movement implies that the anisotropic tunnel did not work as a flap-check valve. The direction of the movement was consistent with that caused by a Brownian ratchet.An anisotropic tunnel microporous crystal was prepared. Active transportation of anthracene as a guest molecule in the anisotropic tunnels was observed. The direction of anthracene movement implies that the anisotropic tunnel did not work as a flap-check valve. The direction of the movement was consistent with that caused by a Brownian ratchet. Electronic supplementary information (ESI) available. CCDC reference numbers 837539 and 837540. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr30880k

Understanding the Natural and Socioeconomic Factors behind Regional Longevity in Guangxi, China: Is the Centenarian Ratio a Good Enough Indicator for Assessing the Longevity Phenomenon?

PubMed

Deng, Qucheng; Wei, Yongping; Zhao, Yan; Han, Xuerong; Yin, Juan

2018-05-08

Despite a number of longevity indicators having been used in previous longevity studies, few studies have critically evaluated whether these indicators are suitable to assess the regional longevity level. In addition, an increasing number of studies have attempted to determine the influence of socioeconomic and natural factors on regional longevity, but only certain factors were considered. This study aims to bridge this gap by determining the relationship between the 7 longevity indicators and selecting 24 natural and socioeconomic indicators in 109 selected counties and urban districts in Guangxi, China. This study has applied spatial analysis and geographically weighted regression as the main research methods. The seven longevity indicators here refer to centenarian ratio, longevity index, longevity level, aging tendency, 80⁺ ratio, 90⁺ ratio, and 95⁺ ratio. Natural indicators in this study mainly refer to atmospheric pressure, temperature, difference in temperature, humidity, rainfall, radiation, water vapor, and altitude. Socioeconomic indicators can be categorized into those related to economic status, education, local infrastructure, and health care facilities. The results show that natural factors such as the difference in temperature and altitude, along with socioeconomic factors such as GDP, might be the most significant contributors to the longevity of people aged 60⁻90 years in Guangxi. The longevity index and longevity level are useful supplementary indexes to the centenarian ratio for assessing the regional longevity.

Performance of the CORDEX regional climate models in simulating offshore wind and wind potential

NASA Astrophysics Data System (ADS)

Kulkarni, Sumeet; Deo, M. C.; Ghosh, Subimal

2018-03-01

This study is oriented towards quantification of the skill addition by regional climate models (RCMs) in the parent general circulation models (GCMs) while simulating wind speed and wind potential with particular reference to the Indian offshore region. To arrive at a suitable reference dataset, the performance of wind outputs from three different reanalysis datasets is evaluated. The comparison across the RCMs and their corresponding parent GCMs is done on the basis of annual/seasonal wind statistics, intermodel bias, wind climatology, and classes of wind potential. It was observed that while the RCMs could simulate spatial variability of winds, well for certain subregions, they generally failed to replicate the overall spatial pattern, especially in monsoon and winter. Various causes of biases in RCMs were determined by assessing corresponding maps of wind vectors, surface temperature, and sea-level pressure. The results highlight the necessity to carefully assess the RCM-yielded winds before using them for sensitive applications such as coastal vulnerability and hazard assessment. A supplementary outcome of this study is in form of wind potential atlas, based on spatial distribution of wind classes. This could be beneficial in suitably identifying viable subregions for developing offshore wind farms by intercomparing both the RCM and GCM outcomes. It is encouraging that most of the RCMs and GCMs indicate that around 70% of the Indian offshore locations in monsoon would experience mean wind potential greater than 200 W/m2.

Indexed variation graphs for efficient and accurate resistome profiling.

PubMed

Rowe, Will P M; Winn, Martyn D

2018-05-14

Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

Mineral oil certified reference materials for the determination of polychlorinated biphenyls from the National Metrology Institute of Japan (NMIJ)

PubMed Central

Aoyagi, Yoshie; Matsuo, Mayumi; Ishikawa, Keiichiro; Hanari, Nobuyasu; Otsuka, Satoko; Tsuda, Yoko; Yarita, Takashi

2008-01-01

Four mineral oil certified reference materials (CRMs), NMIJ CRM 7902-a, CRM 7903-a, CRM 7904-a, and CRM 7905-a, have been issued by the National Metrology Institute of Japan, which is part of the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST), for the determination of polychlorinated biphenyls (PCBs). The raw materials for the CRMs were an insulation oil (CRM 7902-a and CRM 7903-a) and a fuel oil (CRM7904-a and CRM 7905-a). A solution of PCB3, PCB8, and technical PCB products, comprising four types of Kaneclor, was added to the oil matrices. The total PCB concentrations in the PCB-fortified oils (CRM 7902-a and CRM 7904-a) are approximately 6 mg kg−1. In addition, the mineral oils which were not fortified with PCBs were also distributed as CRMs (CRM 7903-a and CRM 7905-a). Characterization of these CRMs was conducted by the NMIJ/AIST, where the mineral oils and the PCB solution were analyzed using multiple analytical methods such as dimethylsulfoxide extraction, normal-phase liquid chromatography, gel permeation chromatography, reversed-phase liquid chromatography, and chromatography using sulfoxide-bonded silica; and/or various capillary columns for gas chromatography, and two ionization modes for mass spectrometry. The target compounds in the mineral oils and those in the PCB solution were determined by one of the primary methods of measurement, isotope dilution–mass spectrometry (ID-MS). Certified values have been provided for 11 PCB congeners (PCB3, 8, 28, 52, 101, 118, 138, 153, 180, 194, and 206) in the CRMs. These CRMs have information values for PCB homologue concentrations determined by using a Japanese official method for determination of PCBs in wastes and densities determined with an oscillational density meter. Because oil samples having arbitrary PCB concentrations between respective property values of the PCB-fortified and nonfortified CRMs can be prepared by gravimetric mixing of the CRM pairs, these CRMs can be used for validation of PCB analyses using various instruments which have different sensitivities. Figure Preparation and certification processes of the mineral oil CRMs (example shown is polychlorinated biphenyls in insulation oil, high/low concentrations) Electronic supplementary material The online version of this article (doi:10.1007/s00216-008-2010-3) contains supplementary material, which is available to authorized users. PMID:18415091

Supplement to CCM.D-K4 'Hydrometer' report: linkage of EURAMET.M.D-K4 comparison, SIM.M.D-K4 comparison and the supplementary SIM.M.D-S2 to CCM.D-K4 'Hydrometer'

NASA Astrophysics Data System (ADS)

Lorefice, S.; Becerra, L. O.

2017-01-01

Evaluation of different types of comparisons to a common set of reference values of a CIPM key comparison is essential to satisfy the concept of the CIPM Mutual Recognition Arrangement (CIPM MRA), where the DoEs of any participant who took part in comparisons should be within the Calibration and Measurement Capability (CMC) section of the CIPM MRA Key Comparison Data Base. The subject of this supplementary report is therefore to present the equivalence of each National Metrological Institute (NMI) participant in the CCM.D-K4 'Hydrometer' key comparison, which was performed in the density range 600 kg/m3 to 2000 kg/m3 at the temperature of 20 °C, and the linkage of the European and Inter-American NMI results performed in the RMO.M.D-K4 comparisons as well as those of the supplementary SIM.M.D-S2 to the common set of KCRVs of the CCM.D-K4 'Hydrometer'. The linking procedure has been obtained by numerical simulation, based on the Monte Carlo method, in which the differences in the results of the different comparison between the intended laboratory and one or more linking laboratory/ies, which took part in both comparisons, are correlated with a continuous function describing the DoEs of the linking laboratory/ies with respect to the common set of KCRVs of the CCM.D-K4. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Evaluation of the acceptability of improved supplementary foods for the treatment of moderate acute malnutrition in Burkina Faso using a mixed method approach.

PubMed

Iuel-Brockdorf, Ann-Sophie; Draebel, Tania Aase; Ritz, Christian; Fabiansen, Christian; Cichon, Bernardette; Brix Christensen, Vibeke; Yameogo, Charles; Oummani, Rouafi; Briend, André; Michaelsen, Kim F; Ashorn, Per; Filteau, Suzanne; Friis, Henrik

2016-04-01

The objective of this study was to evaluate, within the context of a randomized controlled trial of product effectiveness, the acceptability of new formulations of six corn-soy blended flours (CSB) and six lipid-based nutrient supplements (LNS) with different quantities of milk and qualities of soy for the treatment of children with moderate acute malnutrition (MAM). Our study included 1546 children aged 6-23 months and involved questionnaires after one month of supplementation home visits and interviews with a sub-sample of 20 trial participants and their caretakers, and nine focus group discussion. All 12 products were well accepted in terms of organoleptic qualities and received good ratings. However, LNS were more appreciated by caretakers and children. Additionally, an effect of soy isolate was detected on child appreciation where products with high milk content also received better ratings. CSB were not consumed as readily; 33.9% (n = 257) of children receiving CSB were reported to have leftovers compared to 17.3% (n = 134) of children receiving LNS (p=<0.001). Both CSB and LNS were referred to as foods with medicinal properties and perceived as beneficial to child health. They were both reported to have high priority in the daily feeding of the child. In conclusion, there were minimal differences in acceptability of the various CSB and LNS formulations, although CSB were less readily consumed and required smaller meal volumes. Since all products were well-accepted, decisions regarding whether the more expensive products should be used for the treatment of MAM will need to be based on their effect on child nutrition, growth and health. Future supplementary feeding programs in similar contexts could furthermore consider introducing supplementary foods as a medical treatment, as this may increase adherence and decrease sharing. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Direct-to-digital holography reduction of reference hologram noise and fourier space smearing

DOEpatents

Voelkl, Edgar

2006-06-27

Systems and methods are described for reduction of reference hologram noise and reduction of Fourier space smearing, especially in the context of direct-to-digital holography (off-axis interferometry). A method of reducing reference hologram noise includes: recording a plurality of reference holograms; processing the plurality of reference holograms into a corresponding plurality of reference image waves; and transforming the corresponding plurality of reference image waves into a reduced noise reference image wave. A method of reducing smearing in Fourier space includes: recording a plurality of reference holograms; processing the plurality of reference holograms into a corresponding plurality of reference complex image waves; transforming the corresponding plurality of reference image waves into a reduced noise reference complex image wave; recording a hologram of an object; processing the hologram of the object into an object complex image wave; and dividing the complex image wave of the object by the reduced noise reference complex image wave to obtain a reduced smearing object complex image wave.

The SwissLipids knowledgebase for lipid biology

PubMed Central

Liechti, Robin; Hyka-Nouspikel, Nevila; Niknejad, Anne; Gleizes, Anne; Götz, Lou; Kuznetsov, Dmitry; David, Fabrice P.A.; van der Goot, F. Gisou; Riezman, Howard; Bougueleret, Lydie; Xenarios, Ioannis; Bridge, Alan

2015-01-01

Motivation: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it. Results: To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology—SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge. Availability: SwissLipids is freely available at http://www.swisslipids.org/. Contact: alan.bridge@isb-sib.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25943471

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

PubMed Central

Dröge, J.; Gregor, I.; McHardy, A. C.

2015-01-01

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

Starting and Operating Live Virtual Reference Services: A How-To-Do-It Manual for Librarians. How-To-Do-It Manuals for Librarians, Number 118.

ERIC Educational Resources Information Center

Meola, Marc; Stormont, Sam

This guide discusses the essentials of live virtual reference, preparing for virtual reference, and implementing and incorporating virtual reference. Chapter 1, "Understanding Live Virtual Reference," lays out what virtual reference is and how it compares to other forms of reference. Chapter 2, "Offering Live Virtual Reference," presents ten…

Critical appraisal of apparently evidence-based written advertising in Pakistan.

PubMed

Rohra, Dileep Kumar; Bashir, Muhammad Umair; Khwaja, Ummey Aymen; Nazir, Muhammad Ressam

2008-06-01

The objective of the study was to critically assess references cited in support of claims in drug advertisements. Drug advertising brochures were collected from privately practicing General Practitioners from different parts of Karachi. Three blinded reviewers then categorized each reference in the brochure according to the sources viz: journals (both Medline indexed and non-indexed), medical reference books, web addresses, personal communications or testimonials, abstracts presented at symposia/conferences, WHO and National Health Guidelines, 'data on file' and 'others' (which included a diverse set of references). Each reviewer then assessed and analyzed the references further into 2 broad categories: traceable and non-traceable. Traceable references were appraised and, depending upon the claim with which the reference was attached, were classified into justifiable, inaccurate/false, exaggerated and ambiguous. We collected a total of 175 different brochures. Thirty-nine (22.3%) brochures did not cite any references and were not subjected to further analysis. The remaining 136 (77.7%) contained a total of 559 references. 305 (54.6%) of these references were from Medline-indexed journals; 67 (12.0%) were from non-indexed journals; 55 (9.8%) references quoted medical reference books; 27 (4.8%) references cited web addresses; 12 (2.1%) references were personal communications/testimonials; 11 (2.0%) references referred to abstracts presented at symposia/conferences; 12 (2.1%) references were from WHO and National Health Guidelines; 8 (1.4%) references were listed as 'data on file', while the remainder that could not be defined were classified as 'others' (13.1%). Out of a total of 559 references, 249 (44.5%) could not be traced. After critically analyzing the 310 traceable references, 197 (63.5%) were adjudged justifiable, 30 (9.7%) inaccurate/false, 79 (25.5%) exaggerated and 15 (4.8%) ambiguous. Results of this study show for the first time that the claims substantiated with references in the pharmaceutical advertisements in Pakistan are highly unreliable.

Establishing physico-chemical reference conditions in Mediterranean streams according to the European Water Framework Directive.

PubMed

Sánchez-Montoya, María del Mar; Arce, Maria Isabel; Vidal-Abarca, María Rosario; Suárez, María Luisa; Prat, Narcís; Gómez, Rosa

2012-05-01

Type-specific physico-chemical reference conditions are required for the assessment of ecological status in the Water Framework Directive context, similarly to the biological and hydro-morphological elements. This directive emphasises that natural variability of quality elements in high status (reference condition) needs to be quantified. Mediterranean streams often present a marked seasonal pattern in hydrological, biological and geochemical processes which could affect physico-chemical reference conditions. This study establishes general physico-chemical reference conditions (oxygenation, nutrient, salinity and acidification conditions) for different Mediterranean stream types. 116 potential reference sites located in 23 Mediterranean catchments in Spain were sampled in spring, summer and autumn in 2003. All sites were subjected to a screening method for the selection of reference sites in Mediterranean streams (Mediterranean Reference Criteria) and classified using a pre-established stream typology that establishes five different stream types (temporary streams, evaporite-calcareous at medium altitude, siliceous headwaters, calcareous headwaters and large watercourses). Reference conditions (reference value and reference threshold equivalents to high-good class boundary) were calculated using two different methods according to the availability of reference sites: the reference site 75th percentile approach of all reference sites and the 25th percentile of the population approach. The majority of the studied potential reference sites (76 out of 116) were selected as reference sites. Regarding type-specific reference conditions, only siliceous headwaters could be considered different from the rest of stream types because lower conductivity and pH. All reference stream types presented seasonal differences as regards some parameters, except for temporary streams due to the high natural variation of this stream type. For those parameters which presented seasonal differences in a specific stream type, the least restrictive values were proposed as reference conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.

PubMed

Tang, Haiming; Thomas, Paul D

2016-07-15

PANTHER-PSEP is a new software tool for predicting non-synonymous genetic variants that may play a causal role in human disease. Several previous variant pathogenicity prediction methods have been proposed that quantify evolutionary conservation among homologous proteins from different organisms. PANTHER-PSEP employs a related but distinct metric based on 'evolutionary preservation': homologous proteins are used to reconstruct the likely sequences of ancestral proteins at nodes in a phylogenetic tree, and the history of each amino acid can be traced back in time from its current state to estimate how long that state has been preserved in its ancestors. Here, we describe the PSEP tool, and assess its performance on standard benchmarks for distinguishing disease-associated from neutral variation in humans. On these benchmarks, PSEP outperforms not only previous tools that utilize evolutionary conservation, but also several highly used tools that include multiple other sources of information as well. For predicting pathogenic human variants, the trace back of course starts with a human 'reference' protein sequence, but the PSEP tool can also be applied to predicting deleterious or pathogenic variants in reference proteins from any of the ∼100 other species in the PANTHER database. PANTHER-PSEP is freely available on the web at http://pantherdb.org/tools/csnpScoreForm.jsp Users can also download the command-line based tool at ftp://ftp.pantherdb.org/cSNP_analysis/PSEP/ CONTACT: pdthomas@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Data requirements for simulation of hydrogeologic effects of liquid waste injection, Harrison and Jackson Counties, Mississippi

USGS Publications Warehouse

Rebich, Richard A.

1994-01-01

Available literature and data were reviewed to quantify data requirements for computer simulation of hydrogeologic effects of liquid waste injection in southeastern Mississippi. Emphasis of each review was placed on quantifying physical properties of current Class I injection zones in Harrison and Jackson Counties. Class I injection zones are zones that are used for injection of hazardous or non-hazardous liquid waste below a formation containing the lowermost underground source of drinking water located within one-quarter of a mile of the injection well. Several mathematical models have been developed to simulate injection effects. The Basic Plume Method was selected because it is commonly used in permit applications, and the Intercomp model was selected because it is generally accepted and used in injection-related research. The input data requirements of the two models were combined into a single data requirement list inclusive of physical properties of injection zones only; injected waste and well properties are not included because such information is site-specific by industry, which is beyond the scope of this report. Results of the reviews of available literature and data indicated that Class I permit applications and standard-reference chemistry and physics texts were the primary sources of information to quantify physical properties of injection zones in Harrison and Jackson Counties. With the exception of a few reports and supplementary data for one injection zone in Jackson County, very little additional information pertaining to physical properties of the injection zones was available in sources other than permit applications and standard-reference texts.

Rapid access to information resources in clinical biochemistry: medical applications of Personal Digital Assistants (PDA).

PubMed

Serdar, Muhittin A; Turan, Mustafa; Cihan, Murat

2008-06-01

Laboratory specialists currently need to access scientific-based information at anytime and anywhere. A considerable period of time and too much effort are required to access this information through existing accumulated data. Personal digital assistants (PDA) are supposed to provide an effective solution with commercial software for this problem. In this study, 11 commercial software products (UpToDate, ePocrates, Inforetrive, Pepid, eMedicine, FIRST Consult, and 5 laboratory e-books released by Skyscape and/or Isilo) were selected and the benefits of their use were evaluated by seven laboratory specialists. The assessment of the software was performed based on the number of the tests included, the software content of detailed information for each test-like process, method, interpretation of results, reference ranges, critical values, interferences, equations, pathophysiology, supplementary technical details such as sample collection principles, and additional information such as linked references, evidence-based data, test cost, etc. In terms of technique, the following items are considered: the amount of memory required to run the software, the graphical user interface, which is a user-friendly instrument, and the frequency of new and/or up-date releases. There is still no perfect program, as we have anticipated. Interpretation of laboratory results may require software with an integrated program. However, methodological data are mostly not included in the software evaluated. It seems that these shortcomings will be fixed in the near future, and PDAs and relevant medical applications will also become indispensable for all physicians including laboratory specialists in the field of training/education and in patient care.

Outlier detection for particle image velocimetry data using a locally estimated noise variance

NASA Astrophysics Data System (ADS)

Lee, Yong; Yang, Hua; Yin, ZhouPing

2017-03-01

This work describes an adaptive spatial variable threshold outlier detection algorithm for raw gridded particle image velocimetry data using a locally estimated noise variance. This method is an iterative procedure, and each iteration is composed of a reference vector field reconstruction step and an outlier detection step. We construct the reference vector field using a weighted adaptive smoothing method (Garcia 2010 Comput. Stat. Data Anal. 54 1167-78), and the weights are determined in the outlier detection step using a modified outlier detector (Ma et al 2014 IEEE Trans. Image Process. 23 1706-21). A hard decision on the final weights of the iteration can produce outlier labels of the field. The technical contribution is that the spatial variable threshold motivation is embedded in the modified outlier detector with a locally estimated noise variance in an iterative framework for the first time. It turns out that a spatial variable threshold is preferable to a single spatial constant threshold in complicated flows such as vortex flows or turbulent flows. Synthetic cellular vortical flows with simulated scattered or clustered outliers are adopted to evaluate the performance of our proposed method in comparison with popular validation approaches. This method also turns out to be beneficial in a real PIV measurement of turbulent flow. The experimental results demonstrated that the proposed method yields the competitive performance in terms of outlier under-detection count and over-detection count. In addition, the outlier detection method is computational efficient and adaptive, requires no user-defined parameters, and corresponding implementations are also provided in supplementary materials.

Technical Report: Reference photon dosimetry data for Varian accelerators based on IROC-Houston site visit data.

PubMed

Kerns, James R; Followill, David S; Lowenstein, Jessica; Molineu, Andrea; Alvarez, Paola; Taylor, Paige A; Stingo, Francesco C; Kry, Stephen F

2016-05-01

Accurate data regarding linear accelerator (Linac) radiation characteristics are important for treatment planning system modeling as well as regular quality assurance of the machine. The Imaging and Radiation Oncology Core-Houston (IROC-H) has measured the dosimetric characteristics of numerous machines through their on-site dosimetry review protocols. Photon data are presented and can be used as a secondary check of acquired values, as a means to verify commissioning a new machine, or in preparation for an IROC-H site visit. Photon data from IROC-H on-site reviews from 2000 to 2014 were compiled and analyzed. Specifically, data from approximately 500 Varian machines were analyzed. Each dataset consisted of point measurements of several dosimetric parameters at various locations in a water phantom to assess the percentage depth dose, jaw output factors, multileaf collimator small field output factors, off-axis factors, and wedge factors. The data were analyzed by energy and parameter, with similarly performing machine models being assimilated into classes. Common statistical metrics are presented for each machine class. Measurement data were compared against other reference data where applicable. Distributions of the parameter data were shown to be robust and derive from a student's t distribution. Based on statistical and clinical criteria, all machine models were able to be classified into two or three classes for each energy, except for 6 MV for which there were eight classes. Quantitative analysis of the measurements for 6, 10, 15, and 18 MV photon beams is presented for each parameter; supplementary material has also been made available which contains further statistical information. IROC-H has collected numerous data on Varian Linacs and the results of photon measurements from the past 15 years are presented. The data can be used as a comparison check of a physicist's acquired values. Acquired values that are well outside the expected distribution should be verified by the physicist to identify whether the measurements are valid. Comparison of values to this reference data provides a redundant check to help prevent gross dosimetric treatment errors.

The surface chemistry of sapphire-c: A literature review and a study on various factors influencing its IEP.

PubMed

Lützenkirchen, J; Franks, G V; Plaschke, M; Zimmermann, R; Heberling, F; Abdelmonem, A; Darbha, G K; Schild, D; Filby, A; Eng, P; Catalano, J G; Rosenqvist, J; Preocanin, T; Aytug, T; Zhang, D; Gan, Y; Braunschweig, B

2018-01-01

A wide range of isoelectric points (IEPs) has been reported in the literature for sapphire-c (α-alumina), also referred to as basal plane, (001) or (0001), single crystals. Interestingly, the available data suggest that the variation of IEPs is comparable to the range of IEPs encountered for particles, although single crystals should be much better defined in terms of surface structure. One explanation for the range of IEPs might be the obvious danger of contaminating the small surface areas of single crystal samples while exposing them to comparatively large solution reservoirs. Literature suggests that factors like origin of the sample, sample treatment or the method of investigation all have an influence on the surfaces and it is difficult to clearly separate the respective, individual effects. In the present study, we investigate cause-effect relationships to better understand the individual effects. The reference IEP of our samples is between 4 and 4.5. High temperature treatment tends to decrease the IEP of sapphire-c as does UV treatment. Increasing the initial miscut (i.e. the divergence from the expected orientation of the crystal) tends to increase the IEP as does plasma cleaning, which can be understood assuming that the surfaces have become less hydrophobic due to the presence of more and/or larger steps with increasing miscut or due to amorphisation of the surface caused by plasma cleaning. Pre-treatment at very high pH caused an increase in the IEP. Surface treatments that led to IEPs different from the stable value of reference samples typically resulted in surfaces that were strongly affected by subsequent exposure to water. The streaming potential data appear to relax to the reference sample behavior after a period of time of water exposure. Combination of the zeta-potential measurements with AFM investigations support the idea that atomically smooth surfaces exhibit lower IEPs, while rougher surfaces (roughness on the order of nanometers) result in higher IEPs compared to reference samples. Two supplementary investigations resulted in either surprising or ambiguous results. On very rough surfaces (roughness on the order of micrometers) the IEP lowered compared to the reference sample with nanometer-scale roughness and transient behavior of the rough surfaces was observed. Furthermore, differences in the IEP as obtained from streaming potential and static colloid adhesion measurements may suggest that hydrodynamics play a role in streaming potential experiments. We finally relate surface diffraction data from previous studies to possible interpretations of our electrokinetic data to corroborate the presence of a water film that can explain the low IEP. Calculations show that the surface diffraction data are in line with the presence of a water film, however, they do not allow to unambiguously resolve critical features of this film which might explain the observed surface chemical characteristics like the dangling OH-bond reported in sum frequency generation studies. A broad literature review on properties of related surfaces shows that the presence of such water films could in many cases affect the interfacial properties. Persistence or not of the water film can be crucial. The presence of the water film can in principle affect important processes like ice-nucleation, wetting behavior, electric charging, etc. Copyright © 2017 Elsevier B.V. All rights reserved.

78 FR 38769 - Self-Regulatory Organizations; NYSE MKT LLC; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-27

... Replacing References to ``Principle Executive'' With References to ``Principal Executive'' in the Exchange's... Rule Change The Exchange proposes to replace references to ``principle executive'' with references to... replace references to ``principle executive'' with references to ``principal executive'' in the Exchange's...

Reference Service Policy Statement.

ERIC Educational Resources Information Center

Young, William F.

This reference service policy manual provides general guidelines to encourage reference service of the highest possible quality and to insure uniform practice. The policy refers only to reference service in the University Libraries and is intended for use in conjunction with other policies and procedures issued by the Reference Services Division.…

Quantifying the climate effects of bioenergy – Choice of reference system

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

Koponen, Kati; Soimakallio, Sampo; Kline, Keith L.

In order to understand the climate effects of a bioenergy system, a comparison between the bioenergy system and a reference system is required. The reference system describes the situation that occurs in the absence of the bioenergy system with respect to the use of land, energy, and materials. The importance of reference systems is discussed in the literature but guidance on choosing suitable reference systems for assessing climate effects of bioenergy is limited. The reference system should align with the purpose of the study. Transparency of reference system assumptions is essential for proper interpretation of bioenergy assessments. This paper presentsmore » guidance for selecting suitable reference systems. Particular attention is given to choosing the land reference. If the goal is to study the climate effects of bioenergy as a part of total anthropogenic activity the reference system should illustrate what is expected in the absence of human activities. In such a case the suitable land reference is natural regeneration, and energy or material reference systems are not relevant. If the goal is to assess the effect of a change in bioenergy use, the reference system should incorporate human activities. In this case suitable reference systems describe the most likely alternative uses of the land, energy and materials in the absence of the change in bioenergy use. The definition of the reference system is furthermore subject to the temporal scope of the study. In practice, selecting and characterizing reference systems will involve various choices and uncertainties which should be considered carefully. As a result, it can be instructive to consider how alternative reference systems influence the results and conclusions drawn from bioenergy assessments.« less

Quantifying the climate effects of bioenergy – Choice of reference system

DOE PAGES

Koponen, Kati; Soimakallio, Sampo; Kline, Keith L.; ...

2017-06-27

In order to understand the climate effects of a bioenergy system, a comparison between the bioenergy system and a reference system is required. The reference system describes the situation that occurs in the absence of the bioenergy system with respect to the use of land, energy, and materials. The importance of reference systems is discussed in the literature but guidance on choosing suitable reference systems for assessing climate effects of bioenergy is limited. The reference system should align with the purpose of the study. Transparency of reference system assumptions is essential for proper interpretation of bioenergy assessments. This paper presentsmore » guidance for selecting suitable reference systems. Particular attention is given to choosing the land reference. If the goal is to study the climate effects of bioenergy as a part of total anthropogenic activity the reference system should illustrate what is expected in the absence of human activities. In such a case the suitable land reference is natural regeneration, and energy or material reference systems are not relevant. If the goal is to assess the effect of a change in bioenergy use, the reference system should incorporate human activities. In this case suitable reference systems describe the most likely alternative uses of the land, energy and materials in the absence of the change in bioenergy use. The definition of the reference system is furthermore subject to the temporal scope of the study. In practice, selecting and characterizing reference systems will involve various choices and uncertainties which should be considered carefully. As a result, it can be instructive to consider how alternative reference systems influence the results and conclusions drawn from bioenergy assessments.« less

National Survey of Adult and Pediatric Reference Intervals in Clinical Laboratories across Canada: A Report of the CSCC Working Group on Reference Interval Harmonization.

PubMed

Adeli, Khosrow; Higgins, Victoria; Seccombe, David; Collier, Christine P; Balion, Cynthia M; Cembrowski, George; Venner, Allison A; Shaw, Julie

2017-11-01

Reference intervals are widely used decision-making tools in laboratory medicine, serving as health-associated standards to interpret laboratory test results. Numerous studies have shown wide variation in reference intervals, even between laboratories using assays from the same manufacturer. Lack of consistency in either sample measurement or reference intervals across laboratories challenges the expectation of standardized patient care regardless of testing location. Here, we present data from a national survey conducted by the Canadian Society of Clinical Chemists (CSCC) Reference Interval Harmonization (hRI) Working Group that examines variation in laboratory reference sample measurements, as well as pediatric and adult reference intervals currently used in clinical practice across Canada. Data on reference intervals currently used by 37 laboratories were collected through a national survey to examine the variation in reference intervals for seven common laboratory tests. Additionally, 40 clinical laboratories participated in a baseline assessment by measuring six analytes in a reference sample. Of the seven analytes examined, alanine aminotransferase (ALT), alkaline phosphatase (ALP), and creatinine reference intervals were most variable. As expected, reference interval variation was more substantial in the pediatric population and varied between laboratories using the same instrumentation. Reference sample results differed between laboratories, particularly for ALT and free thyroxine (FT4). Reference interval variation was greater than test result variation for the majority of analytes. It is evident that there is a critical lack of harmonization in laboratory reference intervals, particularly for the pediatric population. Furthermore, the observed variation in reference intervals across instruments cannot be explained by the bias between the results obtained on instruments by different manufacturers. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Application of a global reference for fetal-weight and birthweight percentiles in predicting infant mortality.

PubMed

Ding, G; Tian, Y; Zhang, Y; Pang, Y; Zhang, J S; Zhang, J

2013-12-01

To determine whether the recently published A global reference for fetal-weight and birthweight percentiles (Global Reference) improves small- (SGA), appropriate- (AGA), and large-for-gestational-age (LGA) definitions in predicting infant mortality. Population-based cohort study. The US Linked Livebirth and Infant Death records between 1995 and 2004. Singleton births with birthweight >500 g born at 24-41 weeks of gestation. We compared infant mortality rates of SGA, AGA, and LGA infants classified by three different references: the Global Reference; a commonly used birthweight reference; and Hadlock's ultrasound reference. Infant mortality rates. Among 33 997 719 eligible liveborn singleton births, 25% of preterm and 9% of term infants were classified differently for SGA, AGA, and LGA by the Global Reference and the birthweight reference. The Global Reference indicated higher mortality rates in preterm SGA and preterm LGA infants than the birthweight reference. The mortality rate was considerably higher in infants classified as preterm SGA by the Global Reference but not by the birthweight reference, compared with the corresponding infants classified by the birthweight reference but not by the Global Reference (105.7 versus 12.9 per 1000, RR 8.17, 95% CI 7.38-9.06). Yet, the differences in mortality rates were much smaller in term infants than in preterm infants. Black infants had a particularly higher mortality rate than other races in AGA and LGA preterm and term infants. In respect to the commonly used birthweight reference, the Global Reference increases the identification of infant deaths by improved classification of abnormal newborn size at birth, and these advantages were more obvious in preterm than in term infants. © 2013 RCOG.

A reference estimator based on composite sensor pattern noise for source device identification

NASA Astrophysics Data System (ADS)

Li, Ruizhe; Li, Chang-Tsun; Guan, Yu

2014-02-01

It has been proved that Sensor Pattern Noise (SPN) can serve as an imaging device fingerprint for source camera identification. Reference SPN estimation is a very important procedure within the framework of this application. Most previous works built reference SPN by averaging the SPNs extracted from 50 images of blue sky. However, this method can be problematic. Firstly, in practice we may face the problem of source camera identification in the absence of the imaging cameras and reference SPNs, which means only natural images with scene details are available for reference SPN estimation rather than blue sky images. It is challenging because the reference SPN can be severely contaminated by image content. Secondly, the number of available reference images sometimes is too few for existing methods to estimate a reliable reference SPN. In fact, existing methods lack consideration of the number of available reference images as they were designed for the datasets with abundant images to estimate the reference SPN. In order to deal with the aforementioned problem, in this work, a novel reference estimator is proposed. Experimental results show that our proposed method achieves better performance than the methods based on the averaged reference SPN, especially when few reference images used.

Reference Frames and Relativity.

ERIC Educational Resources Information Center

Swartz, Clifford

1989-01-01

Stresses the importance of a reference frame in mechanics. Shows the Galilean transformation in terms of relativity theory. Discusses accelerated reference frames and noninertial reference frames. Provides examples of reference frames with diagrams. (YP)

The influence of sex difference on self-reference effects in a male-dominated culture.

PubMed

Song, Xuan; Shang, Rui; Bi, Qi; Zhang, Xin; Wu, Yanhong

2012-10-01

52 secondary school students from the Chaoshan, China, area, where males are highly valued, were examined for self-reference, mother-reference, and father-reference effects. Because the father is the primary role model in Chaoshan culture, it was predicted that male participants would demonstrate a father-reference effect while females would show a mother-reference effect. The results confirmed that females showed significant self-, mother-, and father-reference effects in terms of memory performance, while males showed only a significant father-reference effect and a marginally significant self-reference effect. This study highlights the importance of researching subcultures such as the Chaoshan subculture to gain a comprehensive understanding of self-construct.

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

Koponen, Kati; Soimakallio, Sampo; Kline, Keith L.

In order to understand the climate effects of a bioenergy system, a comparison between the bioenergy system and a reference system is required. The reference system describes the situation that occurs in the absence of the bioenergy system with respect to the use of land, energy, and materials. The importance of reference systems is discussed in the literature but guidance on choosing suitable reference systems for assessing climate effects of bioenergy is limited. The reference system should align with the purpose of the study. Transparency of reference system assumptions is essential for proper interpretation of bioenergy assessments. This paper presentsmore » guidance for selecting suitable reference systems. Particular attention is given to choosing the land reference. If the goal is to study the climate effects of bioenergy as a part of total anthropogenic activity the reference system should illustrate what is expected in the absence of human activities. In such a case the suitable land reference is natural regeneration, and energy or material reference systems are not relevant. If the goal is to assess the effect of a change in bioenergy use, the reference system should incorporate human activities. In this case suitable reference systems describe the most likely alternative uses of the land, energy and materials in the absence of the change in bioenergy use. The definition of the reference system is furthermore subject to the temporal scope of the study. In practice, selecting and characterizing reference systems will involve various choices and uncertainties which should be considered carefully. As a result, it can be instructive to consider how alternative reference systems influence the results and conclusions drawn from bioenergy assessments.« less

Endogenous versus exogenous generic reference pricing for pharmaceuticals.

PubMed

Antoñanzas, F; Juárez-Castelló, C A; Rodríguez-Ibeas, R

2017-12-01

In this paper we carry out a vertical differentiation duopoly model applied to pharmaceutical markets to analyze how endogenous and exogenous generic reference pricing influence competition between generic and branded drugs producers. Unlike the literature, we characterize for the exogenous case the equilibrium prices for all feasible relevant reference prices. Competition is enhanced after the introduction of a reference pricing system. We also compare both reference pricing systems on welfare grounds, assuming two different objective functions for health authorities: (i) standard social welfare and (ii) gross consumer surplus net of total pharmaceutical expenditures. We show that regardless of the objective function, health authorities will never choose endogenous reference pricing. When health authorities are paternalistic, the exogenous reference price that maximizes standard social welfare is such that the price of the generic drug is the reference price while the price of the branded drug is higher than the reference price. When health authorities are not paternalistic, the optimal exogenous reference price is such that the price of the branded drug is the reference price while the price of the generic drug is lower than the reference price.

Inflight views of the crew of STS-7

NASA Technical Reports Server (NTRS)

1983-01-01

Inflight views of the crew of STS-7. Views include Astronaut Sally K. Ride, misison specialist, using a screw driver to clean out an air filtering system in the middeck of the Challenger. Dr. Ride's constant wear garment bears a cartoon of 35 busy astronauts around a space shuttle and the acronym TFNG, below which is written, 'We deliver!'. TFNG stands for thirty five new guys, referring to the 1978 class of astronauts from which Dr. Ride and three of her crewmates hail (35768); Astronaut Robert L. Crippen, crew commander, chooses to remain in the commander's station to shave his face using an electric razor. Forward control panels (L1, L5, O5), and windows appear in this view (35769); On middeck, Dr. Norman E. Thagard, mission specialist, conducts Detailed Supplementary Objective (DSO) 404 - On Orbit Head and Eye Tracking Tasks. Seated in the mission specialists seat, Thagard, wearing unicorn cap (pantograph attached) and with electrodes on his face and forehead, monitors DC Ampere (A

First principles electron-correlated calculations of optical absorption in magnesium clusters★

NASA Astrophysics Data System (ADS)

Shinde, Ravindra; Shukla, Alok

2017-11-01

In this paper, we report large-scale configuration interaction (CI) calculations of linear optical absorption spectra of various isomers of magnesium clusters Mgn (n = 2-5), corresponding to valence transitions. Geometry optimization of several low-lying isomers of each cluster was carried out using coupled-cluster singles doubles (CCSD) approach, and these geometries were subsequently employed to perform ground and excited state calculations using either the full-CI (FCI) or the multi-reference singles-doubles configuration interaction (MRSDCI) approach, within the frozen-core approximation. Our calculated photoabsorption spectrum of magnesium dimer (Mg2) is in excellent agreement with the experiments both for peak positions, and intensities. Owing to the sufficiently inclusive electron-correlation effects, these results can serve as benchmarks against which future experiments, as well as calculations performed using other theoretical approaches, can be tested. Supplementary material in the form of one pdf fille available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80356-6.

FaStore - a space-saving solution for raw sequencing data.

PubMed

Roguski, Lukasz; Ochoa, Idoia; Hernaez, Mikel; Deorowicz, Sebastian

2018-03-29

The affordability of DNA sequencing has led to the generation of unprecedented volumes of raw sequencing data. These data must be stored, processed, and transmitted, which poses significant challenges. To facilitate this effort, we introduce FaStore, a specialized compressor for FASTQ files. FaStore does not use any reference sequences for compression, and permits the user to choose from several lossy modes to improve the overall compression ratio, depending on the specific needs. FaStore in the lossless mode achieves a significant improvement in compression ratio with respect to previously proposed algorithms. We perform an analysis on the effect that the different lossy modes have on variant calling, the most widely used application for clinical decision making, especially important in the era of precision medicine. We show that lossy compression can offer significant compression gains, while preserving the essential genomic information and without affecting the variant calling performance. FaStore can be downloaded from https://github.com/refresh-bio/FaStore. sebastian.deorowicz@polsl.pl. Supplementary data are available at Bioinformatics online.

Differentiation of Cronobacter spp. by tryptic digestion of the cell suspension followed by MALDI-TOF MS analysis.

PubMed

Krásný, Lukáš; Rohlová, Eva; Růžičková, Helena; Santrůček, Jiří; Hynek, Radovan; Hochel, Igor

2014-03-01

Intact cell MALDI-TOF mass spectrometry is a rapid tool for the identification and classification of microorganisms, now widely used even in clinical laboratories. However, its distinctive power is not sufficient for some closely-related species. The genus Cronobacter, formerly known as Enterobacter sakazakii, contains such species. In this work, a new method for the differentiation of five Cronobacter species is presented involving the tryptic digestion of cytoplasmatic proteins followed by MALDI mass spectrometry analysis. A database was developed for use in Bruker Biotyper software including 52 reference spectra and tested on a set of 45 samples with an overall accuracy of about 80%. The possibility of measurement automation and the short time and low cost requirements of this method compared to those of biochemical tests or PCR methods make it a supplementary option to intact cell MALDI, providing additional information about the differentiation of problematic species. Copyright © 2014 Elsevier B.V. All rights reserved.

77-year-old female with syncope.

PubMed

Abdelsalam, Mahmoud A; Geske, Jeffrey B

2017-02-15

A 77-year-old female was referred for evaluation of an episode of syncope while eating breakfast. There was no history of fall, syncope, prodrome, dyspnoea, chest discomfort or palpitations. Medical history was notable for hyperlipidaemia and treated hypertension. Blood pressure was 140/90 mm Hg, pulse 85  beats per minute (BPM). No murmurs were present on cardiac examination. ECG revealed normal sinus rhythm with left ventricular (LV) hypertrophy (see online supplementary figure S1). Holter monitor demonstrated rare premature ventricular complexes (<1% of beats), without heart block or ventricular tachycardia. Transthoracic echocardiogram is shown in figure 1. Which of the following is the explanation for the flow indicated by the yellow arrow? Aortic stenosisCoronary artery flow, indicative of coronary fistulaHypertrophic cardiomyopathy with apical pouchHypertensive heart diseaseMitral stenosis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Frequency-noise measurements of optical frequency combs by multiple fringe-side discriminator

PubMed Central

Coluccelli, Nicola; Cassinerio, Marco; Gambetta, Alessio; Laporta, Paolo; Galzerano, Gianluca

2015-01-01

The frequency noise of an optical frequency comb is routinely measured through the hetherodyne beat of one comb tooth against a stable continuous-wave laser. After frequency-to-voltage conversion, the beatnote is sent to a spectrum analyzer to retrive the power spectral density of the frequency noise. Because narrow-linewidth continuous-wave lasers are available only at certain wavelengths, heterodyning the comb tooth can be challenging. We present a new technique for direct characterization of the frequency noise of an optical frequency comb, requiring no supplementary reference lasers and easily applicable in all spectral regions from the terahertz to the ultraviolet. The technique is based on the combination of a low finesse Fabry-Perot resonator and the so-called “fringe-side locking” method, usually adopted to characterize the spectral purity of single-frequency lasers, here generalized to optical frequency combs. The effectiveness of this technique is demonstrated with an Er-fiber comb source across the wavelength range from 1 to 2 μm. PMID:26548900

Consistent Quantum Theory

NASA Astrophysics Data System (ADS)

Griffiths, Robert B.

2001-11-01

Quantum mechanics is one of the most fundamental yet difficult subjects in physics. Nonrelativistic quantum theory is presented here in a clear and systematic fashion, integrating Born's probabilistic interpretation with Schrödinger dynamics. Basic quantum principles are illustrated with simple examples requiring no mathematics beyond linear algebra and elementary probability theory. The quantum measurement process is consistently analyzed using fundamental quantum principles without referring to measurement. These same principles are used to resolve several of the paradoxes that have long perplexed physicists, including the double slit and Schrödinger's cat. The consistent histories formalism used here was first introduced by the author, and extended by M. Gell-Mann, J. Hartle and R. Omnès. Essential for researchers yet accessible to advanced undergraduate students in physics, chemistry, mathematics, and computer science, this book is supplementary to standard textbooks. It will also be of interest to physicists and philosophers working on the foundations of quantum mechanics. Comprehensive account Written by one of the main figures in the field Paperback edition of successful work on philosophy of quantum mechanics

Citation success of different publication types: a case study on all references in psychology publications from the German-speaking countries (D-A-CH-L-L) in 2009, 2010, and 2011.

PubMed

Krampen, Günter; Weiland, Peter; Wiesenhütter, Jürgen

Scientometric data on the citation success of different publication types and publication genres in psychology publications are presented. Data refer to references that are cited in these scientific publications and that are documented in PSYNDEX, the exhaustive database of psychology publications from the German-speaking countries either published in German or in English language. Firstly, data analyses refer to the references that are cited in publications of 2009 versus 2010 versus 2011. With reference to all cited references, the portion of journal articles ranges from 57 to 61 %, of books from 22 to 24 %, and of book chapters from 14 to 15 %, with a rather high stability across the three publication years analysed. Secondly, data analyses refer to the numbers of cited references from the German-speaking countries, which are also documented in PSYNDEX. These compose about 11 % of all cited references indicating that nearly 90 % of the references cited are of international and/or interdisciplinary publications not stemming from the German-speaking countries. The subsample shows the proportion of journal articles, books, and chapters, and these are very similar to the percentages identified for all references that are cited. Thirdly, analyses refer to document type, scientific genre, and psychological sub-discipline of the most frequently cited references in the psychology publications. The frequency of top-cited references of books and book chapters is almost equal to that of journal articles; two-thirds of the top-cited references are non-empirical publications, only one-third are empirical publications. Top-cited references stem particularly from clinical psychology, experimental psychology, as well as tests, testing and psychometrics. In summary, the results point to the fact that citation analyses, which are limited to journal papers, tend to neglect very high portions of references that are cited in scientific publications.

IFCC primary reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C. Part 9: reference procedure for the measurement of catalytic concentration of alkaline phosphatase International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Scientific Division, Committee on Reference Systems of Enzymes (C-RSE) (1)).

PubMed

Schumann, Gerhard; Klauke, Rainer; Canalias, Francesca; Bossert-Reuther, Steffen; Franck, Paul F H; Gella, F-Javier; Jørgensen, Poul J; Kang, Dongchon; Lessinger, Jean-Marc; Panteghini, Mauro; Ceriotti, Ferruccio

2011-09-01

Abstract This paper is the ninth in a series dealing with reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C and the certification of reference preparations. Other parts deal with: Part 1. The concept of reference procedures for the measurement of catalytic activity concentrations of enzymes; Part 2. Reference procedure for the measurement of catalytic concentration of creatine kinase; Part 3. Reference procedure for the measurement of catalytic concentration of lactate dehydrogenase; Part 4. Reference procedure for the measurement of catalytic concentration of alanine aminotransferase; Part 5. Reference procedure for the measurement of catalytic concentration of aspartate aminotransferase; Part 6. Reference procedure for the measurement of catalytic concentration of γ-glutamyltransferase; Part 7. Certification of four reference materials for the determination of enzymatic activity of γ-glutamyltransferase, lactate dehydrogenase, alanine aminotransferase and creatine kinase at 37 °C; Part 8. Reference procedure for the measurement of catalytic concentration of α-amylase. The procedure described here is derived from the previously described 30 °C IFCC reference method. Differences are tabulated and commented on in Appendix 1.

Language in Context: MEG Evidence for Modality-General and -Specific Responses to Reference Resolution

PubMed Central

2016-01-01

Abstract Successful language comprehension critically depends on our ability to link linguistic expressions to the entities they refer to. Without reference resolution, newly encountered language cannot be related to previously acquired knowledge. The human experience includes many different types of referents, some visual, some auditory, some very abstract. Does the neural basis of reference resolution depend on the nature of the referents, or do our brains use a modality-general mechanism for linking meanings to referents? Here we report evidence for both. Using magnetoencephalography (MEG), we varied both the modality of referents, which consisted either of visual or auditory objects, and the point at which reference resolution was possible within sentences. Source-localized MEG responses revealed brain activity associated with reference resolution that was independent of the modality of the referents, localized to the medial parietal lobe and starting ∼415 ms after the onset of reference resolving words. A modality-specific response to reference resolution in auditory domains was also found, in the vicinity of auditory cortex. Our results suggest that referential language processing cannot be reduced to processing in classical language regions and representations of the referential domain in modality-specific neural systems. Instead, our results suggest that reference resolution engages medial parietal cortex, which supports a mechanism for referential processing regardless of the content modality. PMID:28058272

[Errors in Peruvian medical journals references].

PubMed

Huamaní, Charles; Pacheco-Romero, José

2009-01-01

References are fundamental in our studies; an adequate selection is asimportant as an adequate description. To determine the number of errors in a sample of references found in Peruvian medical journals. We reviewed 515 scientific papers references selected by systematic randomized sampling and corroborated reference information with the original document or its citation in Pubmed, LILACS or SciELO-Peru. We found errors in 47,6% (245) of the references, identifying 372 types of errors; the most frequent were errors in presentation style (120), authorship (100) and title (100), mainly due to spelling mistakes (91). References error percentage was high, varied and multiple. We suggest systematic revision of references in the editorial process as well as to extend the discussion on this theme. references, periodicals, research, bibliometrics.

Capillary reference half-cell

DOEpatents

Hall, Stephen H.

1996-01-01

The present invention is a reference half-cell electrode wherein intermingling of test fluid with reference fluid does not affect the performance of the reference half-cell over a long time. This intermingling reference half-cell may be used as a single or double junction submersible or surface reference electrode. The intermingling reference half-cell relies on a capillary tube having a first end open to reference fluid and a second end open to test fluid wherein the small diameter of the capillary tube limits free motion of fluid within the capillary to diffusion. The electrode is placed near the first end of the capillary in contact with the reference fluid. The method of operation of the present invention begins with filling the capillary tube with a reference solution. After closing the first end of the capillary, the capillary tube may be fully submerged or partially submerged with the second open end inserted into test fluid. Since the electrode is placed near the first end of the capillary, and since the test fluid may intermingle with the reference fluid through the second open end only by diffusion, this intermingling capillary reference half-cell provides a stable voltage potential for long time periods.

Capillary reference half-cell

DOEpatents

Hall, S.H.

1996-02-13

The present invention is a reference half-cell electrode wherein intermingling of test fluid with reference fluid does not affect the performance of the reference half-cell over a long time. This intermingling reference half-cell may be used as a single or double junction submersible or surface reference electrode. The intermingling reference half-cell relies on a capillary tube having a first end open to reference fluid and a second end open to test fluid wherein the small diameter of the capillary tube limits free motion of fluid within the capillary to diffusion. The electrode is placed near the first end of the capillary in contact with the reference fluid. The method of operation of the present invention begins with filling the capillary tube with a reference solution. After closing the first end of the capillary, the capillary tube may be fully submerged or partially submerged with the second open end inserted into test fluid. Since the electrode is placed near the first end of the capillary, and since the test fluid may intermingle with the reference fluid through the second open end only by diffusion, this intermingling capillary reference half-cell provides a stable voltage potential for long time periods. 11 figs.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715

Respiratory consequences of prematurity: evolution of a diagnosis and development of a comprehensive approach.

PubMed

Maitre, Nathalie L; Ballard, Roberta A; Ellenberg, Jonas H; Davis, Stephanie D; Greenberg, James M; Hamvas, Aaron; Pryhuber, Gloria S

2015-05-01

Bronchopulmonary dysplasia (BPD) is the most common respiratory consequence of premature birth and contributes to significant short- and long-term morbidity, mortality and resource utilization. Initially defined as a radiographic, clinical and histopathological entity, the chronic lung disease known as BPD has evolved as obstetrical and neonatal care have improved the survival of lower gestational age infants. Now, definitions based on the need for supplementary oxygen at 28 days and/or 36 weeks provide a useful reference point in the neonatal intensive-care unit (NICU), but are no longer based on histopathological findings, and are neither designed to predict longer term respiratory consequences nor to study the evolution of a multifactorial disease. The aims of this review are to critically examine the evolution of the diagnosis of BPD and the challenges inherent to current classifications. We found that the increasing use of respiratory support strategies that administer ambient air without supplementary oxygen confounds oxygen-based definitions of BPD. Furthermore, lack of reproducible, genetic, biochemical and physiological biomarkers limits the ability to identify an impending BPD for early intervention, quantify disease severity for standardized classification and approaches and reliably predict the long-term outcomes. More comprehensive, multidisciplinary approaches to overcome these challenges involve longitudinal observation of extremely preterm infants, not only those with BPD, using genetic, environmental, physiological and clinical data as well as large databases of patient samples. The Prematurity and Respiratory Outcomes Program (PROP) will provide such a framework to address these challenges through high-resolution characterization of both NICU and post-NICU discharge outcomes.

A computational genomics pipeline for prokaryotic sequencing projects

PubMed Central

Kislyuk, Andrey O.; Katz, Lee S.; Agrawal, Sonia; Hagen, Matthew S.; Conley, Andrew B.; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C.; Sammons, Scott A.; Govil, Dhwani; Mair, Raydel D.; Tatti, Kathleen M.; Tondella, Maria L.; Harcourt, Brian H.; Mayer, Leonard W.; Jordan, I. King

2010-01-01

Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems. Contact: king.jordan@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20519285

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms

PubMed Central

Xu, Min; Chai, Xiaoqi; Muthakana, Hariank; Liang, Xiaodan; Yang, Ge; Zeev-Ben-Mordehai, Tzviya; Xing, Eric P.

2017-01-01

Abstract Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. Results: To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Availability and Implementation: Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. Contact: mxu1@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881965

SwiSpot: modeling riboswitches by spotting out switching sequences.

PubMed

Barsacchi, Marco; Novoa, Eva Maria; Kellis, Manolis; Bechini, Alessio

2016-11-01

Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the presence of a specific ligand. Although there are a handful of known riboswitches, our knowledge in this field has been greatly limited due to our inability to identify their alternate structures from their sequences. Indeed, current methods are not able to predict the presence of the two functionally distinct conformations just from the knowledge of the plain RNA nucleotide sequence. Whether this would be possible, for which cases, and what prediction accuracy can be achieved, are currently open questions. Here we show that the two alternate secondary structures of riboswitches can be accurately predicted once the 'switching sequence' of the riboswitch has been properly identified. The proposed SwiSpot approach is capable of identifying the switching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors, which are evaluated on proper sets of configurations. Moreover, it is able to model the switching behavior of riboswitches whose generated ensemble covers both alternate configurations. Beyond structural predictions, the approach can also be paired to homology-based riboswitch searches. SwiSpot software, along with the reference dataset files, is available at: http://www.iet.unipi.it/a.bechini/swispot/Supplementary information: Supplementary data are available at Bioinformatics online. a.bechini@ing.unipi.it. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

PubMed Central

Mahmud, Md Pavel; Wiedenhoeft, John; Schliep, Alexander

2012-01-01

Motivation: Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics. Results: For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L1 distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L1 distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants. Availability and implementation: TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net. Contact: pavelm@cs.rutgers.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22962448

Southwestern Power Administration Combined Financial Statements, 2006-2009

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

None

2009-09-01

We have audited the accompanying combined balance sheets of the Southwestern Federal Power System (SWFPS), as of September 30, 2009, 2008, 2007, and 2006, and the related combined statements of revenues and expenses, changes in capitalization, and cash flows for the years then ended. As described in note 1(a), the combined financial statement presentation includes the hydroelectric generation functions of another Federal agency (hereinafter referred to as the generating agency), for which Southwestern Power Administration (Southwestern) markets and transmits power. These combined financial statements are the responsibility of the management of Southwestern and the generating agency. Our responsibility is tomore » express an opinion on these combined financial statements based on our audits. We conducted our audits in accordance with auditing standards generally accepted in the United States of America. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the combined financial statements are free of material misstatement. An audit includes consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of Southwestern and the generating agency’s internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the combined financial statements, assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall combined financial statement presentation. We believe that our audits provide a reasonable basis for our opinion. In our opinion, the combined financial statements referred to above present fairly, in all material respects, the respective financial position of the Southwestern Federal Power System, as of September 30, 2009, 2008, 2007, and 2006, and the results of its operations and its cash flow for the years then ended, in conformity with U.S. generally accepted accounting principles. Our audits were conducted for the purpose of forming an opinion on the 2009, 2008, 2007, and 2006 SWFPS’s combined financial statements taken as a whole. The supplementary information in the combining financial statements is presented for purposes of additional analysis and is not a required part of the basic combined financial statements. The supplementary information has been subjected to the auditing procedures applied in the audit of the basic combined financial statements and, in our opinion, is fairly stated in all material respects in relation to the basic combined financial statements taken as a whole.« less

Nationwide Multicenter Reference Interval Study for 28 Common Biochemical Analytes in China.

PubMed

Xia, Liangyu; Chen, Ming; Liu, Min; Tao, Zhihua; Li, Shijun; Wang, Liang; Cheng, Xinqi; Qin, Xuzhen; Han, Jianhua; Li, Pengchang; Hou, Li'an; Yu, Songlin; Ichihara, Kiyoshi; Qiu, Ling

2016-03-01

A nationwide multicenter study was conducted in the China to explore sources of variation of reference values and establish reference intervals for 28 common biochemical analytes, as a part of the International Federation of Clinical Chemistry and Laboratory Medicine, Committee on Reference Intervals and Decision Limits (IFCC/C-RIDL) global study on reference values. A total of 3148 apparently healthy volunteers were recruited in 6 cities covering a wide area in China. Blood samples were tested in 2 central laboratories using Beckman Coulter AU5800 chemistry analyzers. Certified reference materials and value-assigned serum panel were used for standardization of test results. Multiple regression analysis was performed to explore sources of variation. Need for partition of reference intervals was evaluated based on 3-level nested ANOVA. After secondary exclusion using the latent abnormal values exclusion method, reference intervals were derived by a parametric method using the modified Box-Cox formula. Test results of 20 analytes were made traceable to reference measurement procedures. By the ANOVA, significant sex-related and age-related differences were observed in 12 and 12 analytes, respectively. A small regional difference was observed in the results for albumin, glucose, and sodium. Multiple regression analysis revealed BMI-related changes in results of 9 analytes for man and 6 for woman. Reference intervals of 28 analytes were computed with 17 analytes partitioned by sex and/or age. In conclusion, reference intervals of 28 common chemistry analytes applicable to Chinese Han population were established by use of the latest methodology. Reference intervals of 20 analytes traceable to reference measurement procedures can be used as common reference intervals, whereas others can be used as the assay system-specific reference intervals in China.

Nationwide Multicenter Reference Interval Study for 28 Common Biochemical Analytes in China

PubMed Central

Xia, Liangyu; Chen, Ming; Liu, Min; Tao, Zhihua; Li, Shijun; Wang, Liang; Cheng, Xinqi; Qin, Xuzhen; Han, Jianhua; Li, Pengchang; Hou, Li’an; Yu, Songlin; Ichihara, Kiyoshi; Qiu, Ling

2016-01-01

Abstract A nationwide multicenter study was conducted in the China to explore sources of variation of reference values and establish reference intervals for 28 common biochemical analytes, as a part of the International Federation of Clinical Chemistry and Laboratory Medicine, Committee on Reference Intervals and Decision Limits (IFCC/C-RIDL) global study on reference values. A total of 3148 apparently healthy volunteers were recruited in 6 cities covering a wide area in China. Blood samples were tested in 2 central laboratories using Beckman Coulter AU5800 chemistry analyzers. Certified reference materials and value-assigned serum panel were used for standardization of test results. Multiple regression analysis was performed to explore sources of variation. Need for partition of reference intervals was evaluated based on 3-level nested ANOVA. After secondary exclusion using the latent abnormal values exclusion method, reference intervals were derived by a parametric method using the modified Box–Cox formula. Test results of 20 analytes were made traceable to reference measurement procedures. By the ANOVA, significant sex-related and age-related differences were observed in 12 and 12 analytes, respectively. A small regional difference was observed in the results for albumin, glucose, and sodium. Multiple regression analysis revealed BMI-related changes in results of 9 analytes for man and 6 for woman. Reference intervals of 28 analytes were computed with 17 analytes partitioned by sex and/or age. In conclusion, reference intervals of 28 common chemistry analytes applicable to Chinese Han population were established by use of the latest methodology. Reference intervals of 20 analytes traceable to reference measurement procedures can be used as common reference intervals, whereas others can be used as the assay system-specific reference intervals in China. PMID:26945390

The effect of reference choices on the spatio-temporal analysis of brain evoked potentials: the use of infinite reference.

PubMed

Yao, Dezhong; Wang, Li; Arendt-Nielsen, Lars; Chen, Andrew C N

2007-11-01

Reference is a very virtual issue in EEG and ERP. Understanding the difference of various references will make the applications more confident. In this work, somatosensory evoked potential (SEP) with stimulation on the right hand was studied. The SEP spatio-temporal analysis was conducted comparatively on six references, left mastoid (contralateral mastoid reference, CM), right mastoid (ipsilateral mastoid reference, IM), linked mastoids (LM), average reference (AR), vertex reference (Cz) and the infinity reference (IR) newly proposed in 2001. Among the six, CM is the one used in actual recordings, and the other five are obtained by off-line re-referencing. The comparison is conducted on four selected components (P30 ms, P40 ms, N90 ms and P230 ms) in both temporal and spatial aspects. The results show that references may have a distinct influence on the amplitudes of the scalp potentials, with relative error at some electrodes larger than 500%, and for some electrodes it may even change the polarity. Pair-wise multiple comparison (Tukey test) shows that the differences of peak values among various references are very significant (P<0.001) between Cz and IR\\CM\\IM\\LM, and significant (P<0.01) between Cz and AR for component N90 ms; very significant (P<0.001) between Cz and IR\\CM\\IM\\LM\\AR, significant between IMLM and AR (P<0.01), CM and AR (P<0.05) for component P230 ms. The amplitude value order is CM/IM> or =LM>IR>AR>Cz. The two-ways (the six references vs. the four Peaks) repeated measures ANOVA test shows the effect of different references depends on various components; there is a statistically significant interaction between reference and the peak (P=<0.001). While for the spatial map of the potential amplitude, references will not affect the amplitude map shape if the color-bar is selected automatically, but if a fixed color-bar is chosen for data of various references, they may show some differences. These results mean a common reference is important for producing a comparable result between labs. As IR is theoretically a constant reference, we recommend it as the common choice in the future.

Blending the Trends: A Holistic Approach to Reference Services

ERIC Educational Resources Information Center

Dempsey, Megan

2011-01-01

The growing trends of tiered reference, roving librarians, and virtual reference offer academic libraries several options for providing the most effective reference service. Increased enrollment at community colleges has prompted a reconsideration of how librarians can balance reference, teaching, and faculty responsibilities. This article…

Statistical Reference Datasets

National Institute of Standards and Technology Data Gateway

Statistical Reference Datasets (Web, free access)   The Statistical Reference Datasets is also supported by the Standard Reference Data Program. The purpose of this project is to improve the accuracy of statistical software by providing reference datasets with certified computational results that enable the objective evaluation of statistical software.

Reference values of thirty-one frequently used laboratory markers for 75-year-old males and females

PubMed Central

Ryden, Ingvar; Lind, Lars

2012-01-01

Background We have previously reported reference values for common clinical chemistry tests in healthy 70-year-old males and females. We have now repeated this study 5 years later to establish reference values also at the age of 75. It is important to have adequate reference values for elderly patients as biological markers may change over time, and adequate reference values are essential for correct clinical decisions. Methods We have investigated 31 frequently used laboratory markers in 75-year-old males (n = 354) and females (n = 373) without diabetes. The 2.5 and 97.5 percentiles for these markers were calculated according to the recommendations of the International Federation of Clinical Chemistry. Results Reference values are reported for 75-year-old males and females for 31 frequently used laboratory markers. Conclusion There were minor differences between reference intervals calculated with and without individuals with cardiovascular diseases. Several of the reference intervals differed from Scandinavian reference intervals based on younger individuals (Nordic Reference Interval Project). PMID:22300333

A Proposal of New Reference System for the Standard Axial, Sagittal, Coronal Planes of Brain Based on the Serially-Sectioned Images

PubMed Central

Park, Jin Seo; Park, Hyo Seok; Shin, Dong Sun; Har, Dong-Hwan; Cho, Zang-Hee; Kim, Young-Bo; Han, Jae-Yong; Chi, Je-Geun

2010-01-01

Sectional anatomy of human brain is useful to examine the diseased brain as well as normal brain. However, intracerebral reference points for the axial, sagittal, and coronal planes of brain have not been standardized in anatomical sections or radiological images. We made 2,343 serially-sectioned images of a cadaver head with 0.1 mm intervals, 0.1 mm pixel size, and 48 bit color and obtained axial, sagittal, and coronal images based on the proposed reference system. This reference system consists of one principal reference point and two ancillary reference points. The two ancillary reference points are the anterior commissure and the posterior commissure. And the principal reference point is the midpoint of two ancillary reference points. It resides in the center of whole brain. From the principal reference point, Cartesian coordinate of x, y, z could be made to be the standard axial, sagittal, and coronal planes. PMID:20052359

Semantics, Cross-Cultural Style

ERIC Educational Resources Information Center

Machery, Edouard; Mallon, Ron; Nichols, Shaun; Stich, Stephen P.

2004-01-01

Theories of reference have been central to analytic philosophy, and two views, "the descriptivist view of reference" and "the causal-historical view of reference," have dominated the field. In this research tradition, theories of reference are assessed by consulting one's intuitions about the reference of terms in hypothetical situations. However,…

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

PubMed

Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

2017-03-15

The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Sedentary behavior in Brazilian children and adolescents: a systematic review

PubMed Central

Guerra, Paulo Henrique; de Farias, José Cazuza; Florindo, Alex Antonio

2016-01-01

ABSTRACT OBJECTIVE To describe the methodological characteristics of the studies selected and assess variables associated with sedentary behavior in Brazilian children and adolescents. METHODS For this systematic review, we searched four electronic databases: PubMed, Web of Knowledge, LILACS, SciELO. Also, electronic searches were applied in Google Scholar. A supplementary search was conducted in the references lists of the included articles and in non-indexed journals. We included observational studies with children and adolescents aged from three to 19 years developed in Brazil, presenting analyses of associations based on regression methods and published until September 30, 2014. RESULTS Of the 255 potential references retrieved by the searches, 49 met the inclusion criteria and composed the descriptive synthesis. In this set, we identified a great number of cross-sectional studies (n = 43; 88.0%) and high methodological variability on the types of sedentary behavior assessed, measurement tools and cut-off points used. The variables most often associated with sedentary behavior were “high levels of body weight” (in 15 out of 27 studies; 55.0%) and “lower level of physical activity” (in eight out of 16 studies; 50.0%). CONCLUSIONS The findings of this review raise the following demands to the Brazilian agenda of sedentary behavior research geared to children and adolescents: development of longitudinal studies, validation of measuring tools, establishment of risk cut-offs, measurement of sedentary behavior beyond screen time and use of objective measures in addition to questionnaires. In the articles available, the associations between sedentary behavior with “high levels of body weight” and “low levels of physical activity” were observed in different regions of Brazil. PMID:27007685

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

PubMed

Stavrovskaya, Elena D; Niranjan, Tejasvi; Fertig, Elana J; Wheelan, Sarah J; Favorov, Alexander V; Mironov, Andrey A

2017-10-15

Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features. These features may represent high-throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. We apply our method to numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicability. We observe the changes in the correlation between epigenomic features across developmental trajectories of several tissue types consistent with known biology and find a novel spatial correlation of CAGE clusters with donor splice sites and with poly(A) sites. These analyses provide examples for the broad applicability of StereoGene for regulatory genomics. The StereoGene C ++ source code, program documentation, Galaxy integration scripts and examples are available from the project homepage http://stereogene.bioinf.fbb.msu.ru/. favorov@sensi.org. 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

Machine learning for the structure–energy–property landscapes of molecular crystals† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04665k

PubMed Central

Yang, Jack; Campbell, Joshua E.; Day, Graeme M.; Ceriotti, Michele

2017-01-01

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol–1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure–property relations in molecular crystal engineering. PMID:29675175

Results of delayed triage by HPV testing and cytology in the Norwegian Cervical Cancer Screening Programme.

PubMed

Haldorsen, Tor; Skare, Gry Baadstrand; Ursin, Giske; Bjørge, Tone

2015-02-01

High-risk human papilloma virus (hrHPV) testing was added to the cytology triage of women with equivocal screening smears in the Norwegian programme for cervical cancer screening in 2005. In this population-based observational before and after study we assessed the effect of changing the screening algorithm. In periods before and after the change 75 852 and 66 616 women, respectively, were eligible for triage, i.e. they had smear results of unsatisfactory, atypical squamous cells of undetermined significance (ASC-US), or low-grade squamous intraepithelial lesion (LSIL) at routine screening. The triage was delayed as supplementary testing started six months after the initial screening. The groups were compared with respect to results of triage and later three-year cumulative incidence of cervical intraepithelial neoplasia grade 2 or worse (CIN2+). Before and after the change in the screening algorithm 5.2% (3964/75 852) and 8.1% (5417/66 616) of women, respectively, were referred to colposcopy. Among women referred to colposcopy cumulative incidence of CIN2+ (positive predictive value of referral) increased from 42.0% [95% confidence interval (CI): 40.3 - 43.7%] in the period with cytology only to 48.0% (95% CI 46.6 - 49.4%) after the start of HPV testing. For women recalled to ordinary screening the three-year cumulative incidence decreased from 2.7% (95% CI 2.5 - 2.9%) to 1.0% (95% CI 0.9 - 1.2%) during the same period. Among women with LSIL at routine screening and HPV testing in triage, 52.5% (1976/3766) were HPV positive. The new algorithm with HPV testing implemented in 2005 resulted in an increased rate of referral to colposcopy, but in a better risk stratification with respect to precancerous disease.

Fundamentals of Reference

ERIC Educational Resources Information Center

Mulac, Carolyn M.

2012-01-01

The all-in-one "Reference reference" you've been waiting for, this invaluable book offers a concise introduction to reference sources and services for a variety of readers, from library staff members who are asked to work in the reference department to managers and others who wish to familiarize themselves with this important area of…

33 CFR 241.3 - References.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Information Services, 5285 Port Royal Road, Springfield, VA 22161. References (a), (b) and (c) may be reviewed... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false References. 241.3 Section 241.3... CONTROL COST-SHARING REQUIREMENTS UNDER THE ABILITY TO PAY PROVISION § 241.3 References. References cited...

40 CFR 63.1502 - Incorporation by reference.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Incorporation by reference. 63.1502... reference. (a) The following material is incorporated by reference in the corresponding sections noted. The incorporation by reference (IBR) of certain publications listed in the rule will be approved by the Director of...

Indians and Eskimos of Canada: A Student's Guide to Reference Resources.

ERIC Educational Resources Information Center

Slavin, Suzy M.

Emphasizing reference resources for ethnological research on Canadian American Indians and Eskimos, this guide constitutes a revised and expanded edition of an earlier student's guide entitled "Canadian Ethnology" and includes both reference sources and annotated bibliographic references for the following: (1) Handbooks (8 references);…

49 CFR 384.107 - Matter incorporated by reference.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 5 2012-10-01 2012-10-01 false Matter incorporated by reference. 384.107 Section... COMPLIANCE WITH COMMERCIAL DRIVER'S LICENSE PROGRAM General § 384.107 Matter incorporated by reference. (a) Incorporation by reference. This part includes references to certain matter or materials. The text of the...

49 CFR 385.4 - Matter incorporated by reference.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 5 2011-10-01 2011-10-01 false Matter incorporated by reference. 385.4 Section... FITNESS PROCEDURES General § 385.4 Matter incorporated by reference. (a) Incorporation by reference. Part 385 includes references to certain matter or materials, as listed in paragraph (b) of this section...

49 CFR 384.107 - Matter incorporated by reference.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 5 2014-10-01 2014-10-01 false Matter incorporated by reference. 384.107 Section... COMPLIANCE WITH COMMERCIAL DRIVER'S LICENSE PROGRAM General § 384.107 Matter incorporated by reference. (a) Incorporation by reference. This part includes references to certain matter or materials. The text of the...

49 CFR 385.4 - Matter incorporated by reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false Matter incorporated by reference. 385.4 Section... FITNESS PROCEDURES General § 385.4 Matter incorporated by reference. (a) Incorporation by reference. Part 385 includes references to certain matter or materials, as listed in paragraph (b) of this section...

An Ideological Analysis of Digital Reference Service Models.

ERIC Educational Resources Information Center

Dilevko, Juris

2001-01-01

Looks at some of the new paradigms for reference service, in particular the ideological implications of the digital reference call-center model, demonstrates how they lead to a "deprofessionalization" of reference work, and provides examples of how extensive reading can help reference librarians provide better service and become an…

Effect of Transitioning from Standard Reference Material 2806a to Standard Reference Material 2806b for Light Obscuration Particle Countering

DTIC Science & Technology

2016-04-01

Reference Material 2806b for Light Obscuration Particle Countering April 2016 UNCLASSIFIED UNCLASSIFIED Joel Schmitigal 27809 Standard Form 298 (Rev...Standard Reference Material 2806b for Light Obscuration Particle Countering 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...Reference Material 2806a to Standard Reference Material 2806b for Light Obscuration Particle Countering Joel Schmitigal Force Projection

Superconductor rotor cooling system

DOEpatents

Gamble, Bruce B.; Sidi-Yekhlef, Ahmed; Schwall, Robert E.; Driscoll, David I.; Shoykhet, Boris A.

2004-11-02

A system for cooling a superconductor device includes a cryocooler located in a stationary reference frame and a closed circulation system external to the cryocooler. The closed circulation system interfaces the stationary reference frame with a rotating reference frame in which the superconductor device is located. A method of cooling a superconductor device includes locating a cryocooler in a stationary reference frame, and transferring heat from a superconductor device located in a rotating reference frame to the cryocooler through a closed circulation system external to the cryocooler. The closed circulation system interfaces the stationary reference frame with the rotating reference frame.

Superconductor rotor cooling system

DOEpatents

Gamble, Bruce B.; Sidi-Yekhlef, Ahmed; Schwall, Robert E.; Driscoll, David I.; Shoykhet, Boris A.

2002-01-01

A system for cooling a superconductor device includes a cryocooler located in a stationary reference frame and a closed circulation system external to the cryocooler. The closed circulation system interfaces the stationary reference frame with a rotating reference frame in which the superconductor device is located. A method of cooling a superconductor device includes locating a cryocooler in a stationary reference frame, and transferring heat from a superconductor device located in a rotating reference frame to the cryocooler through a closed circulation system external to the cryocooler. The closed circulation system interfaces the stationary reference frame with the rotating reference frame.

Predictors of early person reference development: maternal language input, attachment and neurodevelopmental markers.

PubMed

Lemche, Erwin; Joraschky, Peter; Klann-Delius, Gisela

2013-12-01

In a longitudinal natural language development study in Germany, the acquisition of verbal symbols for present persons, absent persons, inanimate things and the mother-toddler dyad was investigated. Following the notion that verbal referent use is more developed in ostensive contexts, symbolic play situations were coded for verbal person reference by means of noun and pronoun use. Depending on attachment classifications at twelve months of age, effects of attachment classification and maternal language input were studied up to 36 months in four time points. Hierarchical regression analyses revealed that, except for mother absence, maternal verbal referent input rates at 17 and 36 months were stronger predictors for all referent types than any of the attachment organizations, or any other social or biological predictor variable. Attachment effects accounted for up to 9.8% of unique variance proportions in the person reference variables. Perinatal and familial measures predicted person references dependent on reference type. The results of this investigation indicate that mother-reference, self-reference and thing-reference develop in similar quantities measured from the 17-month time point, but are dependent of attachment quality. Copyright © 2013 Elsevier Inc. All rights reserved.

Postoperative hand therapy in Dupuytren's disease.

PubMed

Herweijer, Hester; Dijkstra, Pieter U; Nicolai, Jean-Philippe A; Van der Sluis, Corry K

2007-11-30

Postoperative hand therapy in patients after surgery for Dupuytren's contracture is common medical practice to improve outcomes. Until now, patients are referred for postoperative hand rehabilitation on an empirical basis. To evaluate whether referral criteria after surgery because of Dupuytren's disease were actually adhered to, and, to analyse differences in outcomes between patients who were referred according to the criteria (correctly referred) and those who were not referred but should have been (incorrectly not referred). Referral pattern was evaluated prospectively in 46 patients. Total active/passive range of joint motion (TAM/ TPM), sensibility, pinch force, Disability Arm Shoulder Hand questionnaire (DASH) and Michigan Hand outcomes Questionnaire (MHQ) were used as outcome measures preoperatively and 10 months postoperatively. In total 21 patients were referred correctly and 17 patients were incorrectly not referred. Significant improvements on TAM/TPM, DASH and MHQ were found at follow-up for the total group. No differences in outcomes were found between patients correctly referred and patients incorrectly not referred for postoperative hand therapy. Referral criteria were not adhered to. Given the lack of differences in outcomes between patients correctly referred and patients incorrectly not referred, postoperative hand therapy in Dupuytren's disease should be reconsidered.

Deviation of landmarks in accordance with methods of establishing reference planes in three-dimensional facial CT evaluation.

PubMed

Yoon, Kaeng Won; Yoon, Suk-Ja; Kang, Byung-Cheol; Kim, Young-Hee; Kook, Min Suk; Lee, Jae-Seo; Palomo, Juan Martin

2014-09-01

This study aimed to investigate the deviation of landmarks from horizontal or midsagittal reference planes according to the methods of establishing reference planes. Computed tomography (CT) scans of 18 patients who received orthodontic and orthognathic surgical treatment were reviewed. Each CT scan was reconstructed by three methods for establishing three orthogonal reference planes (namely, the horizontal, midsagittal, and coronal reference planes). The horizontal (bilateral porions and bilateral orbitales) and midsagittal (crista galli, nasion, prechiasmatic point, opisthion, and anterior nasal spine) landmarks were identified on each CT scan. Vertical deviation of the horizontal landmarks and horizontal deviation of the midsagittal landmarks were measured. The porion and orbitale, which were not involved in establishing the horizontal reference plane, were found to deviate vertically from the horizontal reference plane in the three methods. The midsagittal landmarks, which were not used for the midsagittal reference plane, deviated horizontally from the midsagittal reference plane in the three methods. In a three-dimensional facial analysis, the vertical and horizontal deviations of the landmarks from the horizontal and midsagittal reference planes could vary depending on the methods of establishing reference planes.

Determination of reference ranges for elements in human scalp hair.

PubMed

Druyan, M E; Bass, D; Puchyr, R; Urek, K; Quig, D; Harmon, E; Marquardt, W

1998-06-01

Expected values, reference ranges, or reference limits are necessary to enable clinicians to apply analytical chemical data in the delivery of health care. Determination of references ranges is not straightforward in terms of either selecting a reference population or performing statistical analysis. In light of logistical, scientific, and economic obstacles, it is understandable that clinical laboratories often combine approaches in developing health associated reference values. A laboratory may choose to: 1. Validate either reference ranges of other laboratories or published data from clinical research or both, through comparison of patients test data. 2. Base the laboratory's reference values on statistical analysis of results from specimens assayed by the clinical reference laboratory itself. 3. Adopt standards or recommendations of regulatory agencies and governmental bodies. 4. Initiate population studies to validate transferred reference ranges or to determine them anew. Effects of external contamination and anecdotal information from clinicians may be considered. The clinical utility of hair analysis is well accepted for some elements. For others, it remains in the realm of clinical investigation. This article elucidates an approach for establishment of reference ranges for elements in human scalp hair. Observed levels of analytes from hair specimens from both our laboratory's total patient population and from a physician-defined healthy American population have been evaluated. Examination of levels of elements often associated with toxicity serves to exemplify the process of determining reference ranges in hair. In addition the approach serves as a model for setting reference ranges for analytes in a variety of matrices.

CLSI-based transference of CALIPER pediatric reference intervals to Beckman Coulter AU biochemical assays.

PubMed

Abou El Hassan, Mohamed; Stoianov, Alexandra; Araújo, Petra A T; Sadeghieh, Tara; Chan, Man Khun; Chen, Yunqi; Randell, Edward; Nieuwesteeg, Michelle; Adeli, Khosrow

2015-11-01

The CALIPER program has established a comprehensive database of pediatric reference intervals using largely the Abbott ARCHITECT biochemical assays. To expand clinical application of CALIPER reference standards, the present study is aimed at transferring CALIPER reference intervals from the Abbott ARCHITECT to Beckman Coulter AU assays. Transference of CALIPER reference intervals was performed based on the CLSI guidelines C28-A3 and EP9-A2. The new reference intervals were directly verified using up to 100 reference samples from the healthy CALIPER cohort. We found a strong correlation between Abbott ARCHITECT and Beckman Coulter AU biochemical assays, allowing the transference of the vast majority (94%; 30 out of 32 assays) of CALIPER reference intervals previously established using Abbott assays. Transferred reference intervals were, in general, similar to previously published CALIPER reference intervals, with some exceptions. Most of the transferred reference intervals were sex-specific and were verified using healthy reference samples from the CALIPER biobank based on CLSI criteria. It is important to note that the comparisons performed between the Abbott and Beckman Coulter assays make no assumptions as to assay accuracy or which system is more correct/accurate. The majority of CALIPER reference intervals were transferrable to Beckman Coulter AU assays, allowing the establishment of a new database of pediatric reference intervals. This further expands the utility of the CALIPER database to clinical laboratories using the AU assays; however, each laboratory should validate these intervals for their analytical platform and local population as recommended by the CLSI. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Selection of reference genes for gene expression studies related to intramuscular fat deposition in Capra hircus skeletal muscle.

PubMed

Zhu, Wuzheng; Lin, Yaqiu; Liao, Honghai; Wang, Yong

2015-01-01

The identification of suitable reference genes is critical for obtaining reliable results from gene expression studies using quantitative real-time PCR (qPCR) because the expression of reference genes may vary considerably under different experimental conditions. In most cases, however, commonly used reference genes are employed in data normalization without proper validation, which may lead to incorrect data interpretation. Here, we aim to select a set of optimal reference genes for the accurate normalization of gene expression associated with intramuscular fat (IMF) deposition during development. In the present study, eight reference genes (PPIB, HMBS, RPLP0, B2M, YWHAZ, 18S, GAPDH and ACTB) were evaluated by three different algorithms (geNorm, NormFinder and BestKeeper) in two types of muscle tissues (longissimus dorsi muscle and biceps femoris muscle) across different developmental stages. All three algorithms gave similar results. PPIB and HMBS were identified as the most stable reference genes, while the commonly used reference genes 18S and GAPDH were the most variably expressed, with expression varying dramatically across different developmental stages. Furthermore, to reveal the crucial role of appropriate reference genes in obtaining a reliable result, analysis of PPARG expression was performed by normalization to the most and the least stable reference genes. The relative expression levels of PPARG normalized to the most stable reference genes greatly differed from those normalized to the least stable one. Therefore, evaluation of reference genes must be performed for a given experimental condition before the reference genes are used. PPIB and HMBS are the optimal reference genes for analysis of gene expression associated with IMF deposition in skeletal muscle during development.

With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies.

PubMed

Chapman, Joanne R; Waldenström, Jonas

2015-01-01

The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.

Reference Books in Special Media. Reference Circular No. 82-4.

ERIC Educational Resources Information Center

Library of Congress, Washington, DC. National Library Service for the Blind and Physically Handicapped.

Based on information contained in producers' catalogs and on responses to a survey conducted by the Reference Section of the Library of Congress National Library Service (NLS) for the Blind and Physically Handicapped, this publication lists reference materials produced in braille or in large type, and sound recordings of reference works available…

Metonymy and Reference-Point Errors in Novice Programming

ERIC Educational Resources Information Center

Miller, Craig S.

2014-01-01

When learning to program, students often mistakenly refer to an element that is structurally related to the element that they intend to reference. For example, they may indicate the attribute of an object when their intention is to reference the whole object. This paper examines these reference-point errors through the context of metonymy.…

The Peer Reference Counseling Program at Odum Library. Training Manual.

ERIC Educational Resources Information Center

Lawrence, Tamiko Danielle; Thomas, Susan; Winston, Mark

The Peer Reference Counseling Program at Valdosta State University (Georgia) is a program designed to provide students with a unique opportunity to work at the Reference Desk at Odum Library. This program employs minority students and trains them to work at the Reference Desk answering basic reference questions and utilizing as well as…

78 FR 56150 - Airworthiness Directives; Piper Aircraft, Inc. Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-12

..., PA-46-350P, PA-46R-350T, and PA-46-500TP airplanes. There is an incorrect reference to a paragraph designation, four instances of an incorrect reference to the paragraph in the service bulletin that references... instances of an incorrect reference to the paragraph in the service bulletin that references an...

Land-use history and contemporary management inform an ecological reference model for longleaf pine woodland understory plant communities

Treesearch

Lars A. Brudvig; John L. Orrock; Ellen I. Damschen; Cathy D. Collins; Philip G. Hahn; W. Brett Mattingly; Joseph W. Veldman; Joan L. Walker

2014-01-01

Ecological restoration is frequently guided by reference conditions describing a successfully restored ecosystem; however, the causes and magnitude of ecosystem degradation vary, making simple knowledge of reference conditions insufficient for prioritizing and guiding restoration. Ecological reference models provide further guidance by quantifying reference conditions...

Digital Reference Service in the New Millennium: Planning, Management, and Evaluation. The New Library Series, Number 6.

ERIC Educational Resources Information Center

Lankes, R. David, Ed.; Collins, John W., III, Ed.; Kasowitz, Abby S., Ed.

This book on digital reference services begins with an introduction entitled "The Foundations of Digital Reference" (R. David Lankes). Part 1, "The New Reference Culture: Traits and Trends," includes the following papers: "Why Reference Is about To Change Forever (but Not Completely)" (Joseph Janes);…

30 CFR 285.115 - Documents incorporated by reference.

Code of Federal Regulations, 2011 CFR

2011-07-01

... incorporating by reference the documents listed in the table in paragraph (e) of this section. The Director of...: ER29AP09.104 (e) This paragraph lists documents incorporated by reference. To easily reference text of the... 30 Mineral Resources 2 2011-07-01 2011-07-01 false Documents incorporated by reference. 285.115...

Soilcrust References

Science.gov Websites

Soil Crust Home Crust 101 Advanced Gallery References CCERS Site Links Updated: April 24, 2006 References The complete biological soil crust reference list is available in three formats: HTML Version

Testing the causal theory of reference.

PubMed

Domaneschi, Filippo; Vignolo, Massimiliano; Di Paola, Simona

2017-04-01

Theories of reference are a crucial research topic in analytic philosophy. Since the publication of Kripke's Naming and Necessity, most philosophers have endorsed the causal/historical theory of reference. The goal of this paper is twofold: (i) to discuss a method for testing experimentally the causal theory of reference for proper names by investigating linguistic usage and (ii) to present the results from two experiments conducted with that method. Data collected in our experiments confirm the causal theory of reference for people proper names and for geographical proper names. A secondary but interesting result is that the semantic domain affects reference assignment: while with people proper names speakers tend to assign the semantic reference, with geographical proper names they are prompted to assign the speaker's reference. Copyright © 2016 Elsevier B.V. All rights reserved.

[Study on ethnic medicine quantitative reference herb,Tibetan medicine fruits of Capsicum frutescens as a case].

PubMed

Zan, Ke; Cui, Gan; Guo, Li-Nong; Ma, Shuang-Cheng; Zheng, Jian

2018-05-01

High price and difficult to get of reference substance have become obstacles to HPLC assay of ethnic medicine. A new method based on quantitative reference herb (QRH) was proposed. Specific chromatograms in fruits of Capsicum frutescens were employed to determine peak positions, and HPLC quantitative reference herb was prepared from fruits of C. frutescens. The content of capsaicin and dihydrocapsaicin in the quantitative control herb was determined by HPLC. Eleven batches of fruits of C. frutescens were analyzed with quantitative reference herb and reference substance respectively. The results showed no difference. The present method is feasible for quality control of ethnic medicines and quantitative reference herb is suitable to replace reference substances in assay. Copyright© by the Chinese Pharmaceutical Association.

The presence of African American race predicts improvement in coronary endothelial function after supplementary L-arginine.

PubMed

Houghton, Jan L; Philbin, Edward F; Strogatz, David S; Torosoff, Mikhail T; Fein, Steven A; Kuhner, Patricia A; Smith, Vivienne E; Carr, Albert A

2002-04-17

The purpose of our study was to determine if the presence of African American ethnicity modulates improvement in coronary vascular endothelial function after supplementary L-arginine. Endothelial dysfunction is an early stage in the development of coronary atherosclerosis and has been implicated in the pathogenesis of hypertension and cardiomyopathy. Amelioration of endothelial dysfunction has been demonstrated in patients with established coronary atherosclerosis or with risk factors in response to infusion of L-arginine, the precursor of nitric oxide. Racial and gender patterns in L-arginine responsiveness have not, heretofore, been studied. Invasive testing of coronary artery and microvascular reactivity in response to graded intracoronary infusions of acetylcholine (ACh) +/- L-arginine was carried out in 33 matched pairs of African American and white subjects with no angiographic coronary artery disease. Pairs were matched for age, gender, indexed left ventricular mass, body mass index and low-density lipoprotein cholesterol. In addition to the matching parameters, there were no significant differences in peak coronary blood flow (CBF) response to intracoronary adenosine or in the peak CBF response to ACh before L-arginine infusion. However, absolute percentile improvement in CBF response to ACh infusion after L-arginine, as compared with before, was significantly greater among African Americans as a group (45 +/- 10% vs. 4 +/- 6%, p = 0.0016) and after partitioning by gender. The mechanism of this increase was mediated through further reduction in coronary microvascular resistance. L-arginine infusion also resulted in greater epicardial dilator response after ACh among African Americans. We conclude that intracoronary infusion of L-arginine provides significantly greater augmentation of endothelium-dependent vascular relaxation in those of African American ethnicity when compared with matched white subjects drawn from a cohort electively referred for coronary angiography. Our findings suggest that there are target populations in which supplementary L-arginine may be of therapeutic benefit in the amelioration of microvascular endothelial dysfunction. In view of the excess prevalence of cardiomyopathy among African Americans, pharmacologic correction of microcirculatory endothelial dysfunction in this group is an important area of further investigation and may ultimately prove to be clinically indicated.

Reflectance characteristics of the Viking lander camera reference test charts

NASA Technical Reports Server (NTRS)

Wall, S. D.; Burcher, E. E.; Jabson, D. J.

1975-01-01

Reference test charts provide radiometric, colorimetric, and spatial resolution references for the Viking lander cameras on Mars. Reflectance measurements of these references are described, including the absolute bidirectional reflectance of the radiometric references and the relative spectral reflectance of both radiometric and colorimetric references. Results show that the bidirection reflectance of the radiometric references is Lambertian to within + or - 7% for incidence angles between 20 deg and 60 deg, and that their spectral reflectance is constant with wavelength to within + or - 5% over the spectral range of the cameras. Estimated accuracy of the measurements is + or - 0.05 in relative spectral reflectance.

Stuttering Thoughts: Negative Self-Referent Thinking Is Less Sensitive to Aversive Outcomes in People with Higher Levels of Depressive Symptoms

PubMed Central

Iijima, Yudai; Takano, Keisuke; Boddez, Yannick; Raes, Filip; Tanno, Yoshihiko

2017-01-01

Learning theories of depression have proposed that depressive cognitions, such as negative thoughts with reference to oneself, can develop through a reinforcement learning mechanism. This negative self-reference is considered to be positively reinforced by rewarding experiences such as genuine support from others after negative self-disclosure, and negatively reinforced by avoidance of potential aversive situations. The learning account additionally predicts that negative self-reference would be maintained by an inability to adjust one’s behavior when negative self-reference no longer leads to such reward. To test this prediction, we designed an adapted version of the reversal-learning task. In this task, participants were reinforced to choose and engage in either negative or positive self-reference by probabilistic economic reward and punishment. Although participants were initially trained to choose negative self-reference, the stimulus-reward contingencies were reversed to prompt a shift toward positive self-reference (Study 1) and a further shift toward negative self-reference (Study 2). Model-based computational analyses showed that depressive symptoms were associated with a low learning rate of negative self-reference, indicating a high level of reward expectancy for negative self-reference even after the contingency reversal. Furthermore, the difficulty in updating outcome predictions of negative self-reference was significantly associated with the extent to which one possesses negative self-images. These results suggest that difficulty in adjusting action-outcome estimates for negative self-reference increases the chance to be faced with negative aspects of self, which may result in depressive symptoms. PMID:28824511

Defining the Reference Condition for Wadeable Streams in the Sand Hills Subdivision of the Southeastern Plains Ecoregion, USA

NASA Astrophysics Data System (ADS)

Kosnicki, Ely; Sefick, Stephen A.; Paller, Michael H.; Jarrell, Miller S.; Prusha, Blair A.; Sterrett, Sean C.; Tuberville, Tracey D.; Feminella, Jack W.

2014-09-01

The Sand Hills subdivision of the Southeastern Plains ecoregion has been impacted by historical land uses over the past two centuries and, with the additive effects of contemporary land use, determining reference condition for streams in this region is a challenge. We identified reference condition based on the combined use of 3 independent selection methods. Method 1 involved use of a multivariate disturbance gradient derived from several stressors, method 2 was based on variation in channel morphology, and method 3 was based on passing 6 of 7 environmental criteria. Sites selected as reference from all 3 methods were considered primary reference, whereas those selected by 2 or 1 methods were considered secondary or tertiary reference, respectively. Sites not selected by any of the methods were considered non-reference. In addition, best professional judgment (BPJ) was used to exclude some sites from any reference class, and comparisons were made to examine the utility of BPJ. Non-metric multidimensional scaling indicated that use of BPJ may help designate non-reference sites when unidentified stressors are present. The macroinvertebrate community measures Ephemeroptera, Plecoptera, Trichoptera richness and North Carolina Biotic Index showed no differences between primary and secondary reference sites when BPJ was ignored. However, there was no significant difference among primary, secondary, and tertiary reference sites when BPJ was used. We underscore the importance of classifying reference conditions, especially in regions that have endured significant anthropogenic activity. We suggest that the use of secondary reference sites may enable construction of models that target a broader set of management interests.

Stuttering Thoughts: Negative Self-Referent Thinking Is Less Sensitive to Aversive Outcomes in People with Higher Levels of Depressive Symptoms.

PubMed

Iijima, Yudai; Takano, Keisuke; Boddez, Yannick; Raes, Filip; Tanno, Yoshihiko

2017-01-01

Learning theories of depression have proposed that depressive cognitions, such as negative thoughts with reference to oneself, can develop through a reinforcement learning mechanism. This negative self-reference is considered to be positively reinforced by rewarding experiences such as genuine support from others after negative self-disclosure, and negatively reinforced by avoidance of potential aversive situations. The learning account additionally predicts that negative self-reference would be maintained by an inability to adjust one's behavior when negative self-reference no longer leads to such reward. To test this prediction, we designed an adapted version of the reversal-learning task. In this task, participants were reinforced to choose and engage in either negative or positive self-reference by probabilistic economic reward and punishment. Although participants were initially trained to choose negative self-reference, the stimulus-reward contingencies were reversed to prompt a shift toward positive self-reference (Study 1) and a further shift toward negative self-reference (Study 2). Model-based computational analyses showed that depressive symptoms were associated with a low learning rate of negative self-reference, indicating a high level of reward expectancy for negative self-reference even after the contingency reversal. Furthermore, the difficulty in updating outcome predictions of negative self-reference was significantly associated with the extent to which one possesses negative self-images. These results suggest that difficulty in adjusting action-outcome estimates for negative self-reference increases the chance to be faced with negative aspects of self, which may result in depressive symptoms.

Metonymy and reference-point errors in novice programming

NASA Astrophysics Data System (ADS)

Miller, Craig S.

2014-07-01

When learning to program, students often mistakenly refer to an element that is structurally related to the element that they intend to reference. For example, they may indicate the attribute of an object when their intention is to reference the whole object. This paper examines these reference-point errors through the context of metonymy. Metonymy is a rhetorical device where the speaker states a referent that is structurally related to the intended referent. For example, the following sentence states an office bureau but actually refers to a person working at the bureau: The tourist asked the travel bureau for directions to the museum. Drawing upon previous studies, I discuss how student reference errors may be consistent with the use of metonymy. In particular, I hypothesize that students are more likely to reference an identifying element even when a structurally related element is intended. I then present two experiments, which produce results consistent with this analysis. In both experiments, students are more likely to produce reference-point errors that involve identifying attributes than descriptive attributes. Given these results, I explore the possibility that students are relying on habits of communication rather than the mechanistic principles needed for successful programming. Finally I discuss teaching interventions using live examples and how metonymy may be presented to non-computing students as pedagogy for computational thinking.

What Is the Reference? An Examination of Alternatives to the Reference Sources Used in IES TM-30-15

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

Royer, Michael P.

A study was undertaken to document the role of the reference illuminant in the IES TM-30-15 method for evaluating color rendition. TM-30-15 relies on a relative reference scheme; that is, the reference illuminant and test source always have the same correlated color temperature (CCT). The reference illuminant is a Planckian radiator, model of daylight, or combination of those two, depending on the exact CCT of the test source. Three alternative reference schemes were considered: 1) either using all Planckian radiators or all daylight models; 2) using only one of ten possible illuminants (Planckian, daylight, or equal energy), regardless of themore » CCT of the test source; 3) using an off-Planckian reference illuminant (i.e., a source with a negative Duv). No reference scheme is inherently superior to another, with differences in metric values largely a result of small differences in gamut shape of the reference alternatives. While using any of the alternative schemes is more reasonable in the TM-30-15 evaluation framework than it was with the CIE CRI framework, the differences still ultimately manifest only as changes in interpretation of the results. References are employed in color rendering measures to provide a familiar point of comparison, not to establish an ideal source.« less

Gene Expression Profile Analysis is Directly Affected by the Selected Reference Gene: The Case of Leaf-Cutting Atta Sexdens

PubMed Central

Máximo, Wesley P. F.; Zanetti, Ronald; Paiva, Luciano V.

2018-01-01

Although several ant species are important targets for the development of molecular control strategies, only a few studies focus on identifying and validating reference genes for quantitative reverse transcription polymerase chain reaction (RT-qPCR) data normalization. We provide here an extensive study to identify and validate suitable reference genes for gene expression analysis in the ant Atta sexdens, a threatening agricultural pest in South America. The optimal number of reference genes varies according to each sample and the result generated by RefFinder differed about which is the most suitable reference gene. Results suggest that the RPS16, NADH and SDHB genes were the best reference genes in the sample pool according to stability values. The SNF7 gene expression pattern was stable in all evaluated sample set. In contrast, when using less stable reference genes for normalization a large variability in SNF7 gene expression was recorded. There is no universal reference gene suitable for all conditions under analysis, since these genes can also participate in different cellular functions, thus requiring a systematic validation of possible reference genes for each specific condition. The choice of reference genes on SNF7 gene normalization confirmed that unstable reference genes might drastically change the expression profile analysis of target candidate genes. PMID:29419794

A Method for Evaluating Outcomes of Restoration When No Reference Sites Exist

Treesearch

J. Stephen Brewer; Timothy Menzel

2009-01-01

Ecological restoration typically seeks to shift species composition toward that of existing reference sites. Yet, comparing the assemblages in restored and reference habitats assumes that similarity to the reference habitat is the optimal outcome of restoration and does not provide a perspective on regionally rare off-site species. When no such reference assemblages of...

Reference and Information Services: An Introduction. Second Edition. Library Science Text Series.

ERIC Educational Resources Information Center

Bopp, Richard E., Ed.; Smith, Linda C., Ed.

This document provides an overview of the concepts and processes behind reference services and the most important sources consulted in answering common reference questions. The book is divided into two parts. Part 1 deals with concepts and theory. It covers ethical aspects of reference service, the reference interview, the principles and goals of…

Geometric Cues, Reference Frames, and the Equivalence of Experienced-Aligned and Novel-Aligned Views in Human Spatial Memory

ERIC Educational Resources Information Center

Kelly, Jonathan W.; Sjolund, Lori A.; Sturz, Bradley R.

2013-01-01

Spatial memories are often organized around reference frames, and environmental shape provides a salient cue to reference frame selection. To date, however, the environmental cues responsible for influencing reference frame selection remain relatively unknown. To connect research on reference frame selection with that on orientation via…

Evaluating a Chat Reference Service at the University of South Alabama's Baugh Biomedical Library

ERIC Educational Resources Information Center

Clanton, Clista C.; Staggs, Geneva B.; Williams, Thomas L.

2006-01-01

The University of South Alabama's Baugh Biomedical Library recently initiated a chat reference service targeted at distance education students in the biomedical sciences. After one year of service, the library conducted an evaluation of the chat reference to assess the success of this mode of reference service. Both traditional reference and…

76 FR 6648 - Self-Regulatory Organizations; The Options Clearing Corporation; Notice of Filing of Proposed...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-07

... accommodate the clearance of options on certain indexes measuring the relative performance of one reference... performance of one reference security or reference index relative to a second reference security or reference..., an Alpha Index may measure the relative total return of two non-ETF securities, two ETFs, or one ETF...

78 FR 8640 - Self-Regulatory Organizations; BATS Exchange, Inc.; Order Approving Proposed Rule Change To...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-06

... disseminate the lesser of the Reference Buy Shares \\15\\ and the Reference Sell Shares,\\16\\ rather than... Reference Buy Shares and Reference Sell Share information could allow a market participant to discern the... auction occurs, the Exchange believes that a market participant could use both the Reference Buy Shares...

Laboratory Surveillance of Polio and Other Enteroviruses in High-Risk Populations and Environmental Samples.

PubMed

Pogka, Vasiliki; Labropoulou, Stavroula; Emmanouil, Mary; Voulgari-Kokota, Androniki; Vernardaki, Alexandra; Georgakopoulou, Theano; Mentis, Andreas F

2017-03-01

In the context of poliomyelitis eradication, a reinforced supplementary laboratory surveillance of enteroviruses was implemented in Greece. Between 2008 and 2014, the Hellenic Polioviruses/Enteroviruses Reference Laboratory performed detailed supplementary surveillance of circulating enteroviruses among healthy individuals in high-risk population groups, among immigrants from countries in which poliovirus is endemic, and in environmental samples. In total, 722 stool samples and 179 sewage water samples were included in the study. No wild-type polioviruses were isolated during these 7 years of surveillance, although two imported vaccine polioviruses were detected. Enterovirus presence was recorded in 25.3 and 25.1% of stool and sewage water samples, respectively. Nonpolio enteroviruses isolated from stool samples belonged to species A, B, or C; coxsackievirus A24 was the most frequently identified serotype. Only enteroviruses of species B were identified in sewage water samples, including four serotypes of echoviruses and four serotypes of coxsackie B viruses. Phylogenetic analysis revealed close genetic relationships among virus isolates from sewage water samples and stool samples, which in most cases fell into the same cluster. To the best of our knowledge, this is the first study to compare enterovirus serotypes circulating in fecal specimens of healthy individuals and environmental samples, emphasizing the burden of enterovirus circulation in asymptomatic individuals at high risk. Given that Greece continues to receive a large number of short-term arrivals, students, migrants, and refugees from countries in which poliovirus is endemic, it is important to guarantee high-quality surveillance in order to maintain its polio-free status until global eradication is achieved. IMPORTANCE This article summarizes the results of supplementary poliovirus surveillance in Greece and the subsequent characterization of enteroviral circulation in human feces and the environment. The examination of stool samples from healthy refugees and other individuals in "high-risk" groups for poliovirus enables the identification of enterovirus cases and forms the basis for further investigation of the community-level risk of viral transmission. In addition, the examination of composite human fecal samples through environmental surveillance links poliovirus and nonpoliovirus isolates from unknown individuals to populations served by the sewage or wastewater system. Supplementary surveillance is necessary to comply with the prerequisites imposed by the World Health Organization for monitoring the emergence of vaccine-derived polioviruses, reemergence of wild polioviruses, or disappearance of all vaccine-related strains in order for countries such as Greece to maintain their polio-free status and contribute to global poliovirus eradication. Copyright © 2017 American Society for Microbiology.

Laboratory Surveillance of Polio and Other Enteroviruses in High-Risk Populations and Environmental Samples

PubMed Central

Pogka, Vasiliki; Labropoulou, Stavroula; Emmanouil, Mary; Voulgari-Kokota, Androniki; Vernardaki, Alexandra; Georgakopoulou, Theano

2017-01-01

ABSTRACT In the context of poliomyelitis eradication, a reinforced supplementary laboratory surveillance of enteroviruses was implemented in Greece. Between 2008 and 2014, the Hellenic Polioviruses/Enteroviruses Reference Laboratory performed detailed supplementary surveillance of circulating enteroviruses among healthy individuals in high-risk population groups, among immigrants from countries in which poliovirus is endemic, and in environmental samples. In total, 722 stool samples and 179 sewage water samples were included in the study. No wild-type polioviruses were isolated during these 7 years of surveillance, although two imported vaccine polioviruses were detected. Enterovirus presence was recorded in 25.3 and 25.1% of stool and sewage water samples, respectively. Nonpolio enteroviruses isolated from stool samples belonged to species A, B, or C; coxsackievirus A24 was the most frequently identified serotype. Only enteroviruses of species B were identified in sewage water samples, including four serotypes of echoviruses and four serotypes of coxsackie B viruses. Phylogenetic analysis revealed close genetic relationships among virus isolates from sewage water samples and stool samples, which in most cases fell into the same cluster. To the best of our knowledge, this is the first study to compare enterovirus serotypes circulating in fecal specimens of healthy individuals and environmental samples, emphasizing the burden of enterovirus circulation in asymptomatic individuals at high risk. Given that Greece continues to receive a large number of short-term arrivals, students, migrants, and refugees from countries in which poliovirus is endemic, it is important to guarantee high-quality surveillance in order to maintain its polio-free status until global eradication is achieved. IMPORTANCE This article summarizes the results of supplementary poliovirus surveillance in Greece and the subsequent characterization of enteroviral circulation in human feces and the environment. The examination of stool samples from healthy refugees and other individuals in “high-risk” groups for poliovirus enables the identification of enterovirus cases and forms the basis for further investigation of the community-level risk of viral transmission. In addition, the examination of composite human fecal samples through environmental surveillance links poliovirus and nonpoliovirus isolates from unknown individuals to populations served by the sewage or wastewater system. Supplementary surveillance is necessary to comply with the prerequisites imposed by the World Health Organization for monitoring the emergence of vaccine-derived polioviruses, reemergence of wild polioviruses, or disappearance of all vaccine-related strains in order for countries such as Greece to maintain their polio-free status and contribute to global poliovirus eradication. PMID:28039136

Effectiveness of supplementary blended flour based on chickpea and cereals for the treatment of infants with moderate acute malnutrition in Iran: A randomized clinical trial.

PubMed

Javan, Roghayeh; Kooshki, Akram; Afzalaghaee, Monavvar; Aldaghi, Mitra; Yousefi, Mahdi

2017-12-01

Despite the decreasing rate of under nutrition children in recent years overall, the negative affect in growth and development make it as a main concern in the world. Applying an available and appropriate supplementary food is a major approach in treating children with Moderate Acute Malnutrition (MAM). To compare the effectiveness of a new supplementary blended flour (containing chickpea, rice, wheat and barley, named Shadameen) in combination with multivitamin/mineral supplement and nutritional counseling versus multivitamin/mineral supplement and nutritional counseling alone, in the treatment of children with MAM. This randomized controlled trial study was conducted at Heshmatiyeh Hospital in Sabzevar city in Iran, from January 2016 to December 2016. Seventy infants, aged 9 to 24 months with MAM who were referred from urban health centers to the hospital clinic were included. They were randomly assigned to receive, for about 3 months, either multivitamin / mineral supplement and nutritional counseling alone or in combination with an extra supplementary blended food. We analyzed weight, length, weight for length Z score (WLZ), weight for age Z score (WAZ) and length for weight Z score (LAZ), along with recovery rate and adverse events among the two groups. The data were analyzed using SPSS version 16. We used statistics, Chi-square, independent t-test, and Fisher's exact test for the analyses of primary and secondary outcomes. The food supplementation infant's mean weight and WLZ and WAZ were greater compared with the other group (0.81±0.29 gr and 0.55±0.33 gr, p=0.002), (0.36±0.36 and 0.02±0.52, p=0.003), (0.40±0.33 and 0.09±0.37, p=0.001). The recovery rate in the food supplemented group was significantly higher than the other group (68.4%, 31.6%, p=0.001). No adverse reactions were observed. There were no significant differences in LAZ at the end of the study between the two groups (p=0.53). This study showed that Shadameen in combination with multivitamin/mineral and counselling therapy can be more effective in decreasing the wasting rate of children with MAM than vitamin/mineral and counseling therapy alone. The trial was registered at the Iranian Registry of Clinical Trials (http://www.irct.ir) with the Irct ID: IRCT2015040921670N1. This study was financially supported by the vice chancellor for research office, Mashhad University of Medical Sciences.

Resampling methods in Microsoft Excel® for estimating reference intervals

PubMed Central

Theodorsson, Elvar

2015-01-01

Computer- intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles.
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples. PMID:26527366

Resampling methods in Microsoft Excel® for estimating reference intervals.

PubMed

Theodorsson, Elvar

2015-01-01

Computer-intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles. 
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
 Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples.

Identification of appropriate reference genes for human mesenchymal stem cell analysis by quantitative real-time PCR.

PubMed

Li, Xiuying; Yang, Qiwei; Bai, Jinping; Xuan, Yali; Wang, Yimin

2015-01-01

Normalization to a reference gene is the method of choice for quantitative reverse transcription-PCR (RT-qPCR) analysis. The stability of reference genes is critical for accurate experimental results and conclusions. We have evaluated the expression stability of eight commonly used reference genes found in four different human mesenchymal stem cells (MSC). Using geNorm, NormFinder and BestKeeper algorithms, we show that beta-2-microglobulin and peptidyl-prolylisomerase A were the optimal reference genes for normalizing RT-qPCR data obtained from MSC, whereas the TATA box binding protein was not suitable due to its extensive variability in expression. Our findings emphasize the significance of validating reference genes for qPCR analyses. We offer a short list of reference genes to use for normalization and recommend some commercially-available software programs as a rapid approach to validate reference genes. We also demonstrate that the two reference genes, β-actin and glyceraldehyde-3-phosphate dehydrogenase, are frequently used are not always successful in many cases.

Predictive value and efficiency of laboratory testing.

PubMed

Galen, R S

1980-11-01

Literature on determining reference values and reference intervals on "normal" or "healthy" individuals is abundant. It is impossible, however, to evaluate a data set of reference values and select a suitable reference interval that will be meaningful for the practice of medicine. The reference interval, no matter how derived statistically, tells us nothing about disease. This is the main reason the concepts of "normal values" have failed us and why "reference values" will prove similarly disappointing. By studying these same constituents in a variety of disease states as well, it will be possible to select "referent values" that will make the test procedure meaningful for diagnostic purposes. In order to obtain meaningful referent values for predicting disease, it is necessary to study not only the "healthy" reference population, but patients with the disease in question, and patients who are free of the disease in question but who have other diseases. Studies of this type are not frequently found for laboratory tests that are in common use today.

An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

PubMed Central

Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S.; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M.; Bhak, Jong

2016-01-01

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. PMID:27882922

What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments.

PubMed

Kerr, Kathleen F; Serikawa, Kyle A; Wei, Caimiao; Peters, Mette A; Bumgarner, Roger E

2007-01-01

The reference design is a practical and popular choice for microarray studies using two-color platforms. In the reference design, the reference RNA uses half of all array resources, leading investigators to ask: What is the best reference RNA? We propose a novel method for evaluating reference RNAs and present the results of an experiment that was specially designed to evaluate three common choices of reference RNA. We found no compelling evidence in favor of any particular reference. In particular, a commercial reference showed no advantage in our data. Our experimental design also enabled a new way to test the effectiveness of pre-processing methods for two-color arrays. Our results favor using intensity normalization and foregoing background subtraction. Finally, we evaluate the sensitivity and specificity of data quality filters, and we propose a new filter that can be applied to any experimental design and does not rely on replicate hybridizations.

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

PubMed

Dee, Cheryl R

2003-01-01

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

Astrophysics of Reference Frame Tie Objects

NASA Technical Reports Server (NTRS)

Johnston, Kenneth J.; Boboltz, David; Fey, Alan Lee; Gaume, Ralph A.; Zacharias, Norbert

2004-01-01

The Astrophysics of Reference Frame Tie Objects Key Science program will investigate the underlying physics of SIM grid objects. Extragalactic objects in the SIM grid will be used to tie the SIM reference frame to the quasi-inertial reference frame defined by extragalactic objects and to remove any residual frame rotation with respect to the extragalactic frame. The current realization of the extragalactic frame is the International Celestial Reference Frame (ICRF). The ICRF is defined by the radio positions of 212 extragalactic objects and is the IAU sanctioned fundamental astronomical reference frame. This key project will advance our knowledge of the physics of the objects which will make up the SIM grid, such as quasars and chromospherically active stars, and relates directly to the stability of the SIM reference frame. The following questions concerning the physics of reference frame tie objects will be investigated.

Actinide ion sensor for pyroprocess monitoring

DOEpatents

Jue, Jan-fong; Li, Shelly X.

2014-06-03

An apparatus for real-time, in-situ monitoring of actinide ion concentrations which comprises a working electrode, a reference electrode, a container, a working electrolyte, a separator, a reference electrolyte, and a voltmeter. The container holds the working electrolyte. The voltmeter is electrically connected to the working electrode and the reference electrode and measures the voltage between those electrodes. The working electrode contacts the working electrolyte. The working electrolyte comprises an actinide ion of interest. The reference electrode contacts the reference electrolyte. The reference electrolyte is separated from the working electrolyte by the separator. The separator contacts both the working electrolyte and the reference electrolyte. The separator is ionically conductive to the actinide ion of interest. The reference electrolyte comprises a known concentration of the actinide ion of interest. The separator comprises a beta double prime alumina exchanged with the actinide ion of interest.

Database of Geoscientific References Through 2007 for Afghanistan, Version 2

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2007-01-01

This report describes an accompanying database of geoscientific references for the country of Afghanistan. Included is an accompanying Microsoft? Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan's energy, mineral, and water resources, and geologic hazards, currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,462) and unpublished (n = 174) references compiled through September, 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable, interface and only minimum knowledge of the use of Microsoft? Access is required.

Reference Reviewed and Re-Envisioned: Revamping Librarian and Desk-Centric Services with LibStARs and LibAnswers

ERIC Educational Resources Information Center

Stevens, Christy R.

2013-01-01

The first section of this article reviews the literature on the changing face of reference, beginning with a discussion of the national decline in reference transactions, its causes, and the likelihood that online reference services might one day halt or reverse the decline. It then analyzes definitions of the term "reference," pointing…

In vitro vaccine potency testing: a proposal for reducing animal use for requalification testing.

PubMed

Brown, K; Stokes, W

2012-01-01

This paper proposes a program under which the use of animals for requalification of in vitro potency tests could be eliminated. Standard References (USDA/CVB nomenclature) would be developed, characterized, stored and monitored by selected reference laboratories worldwide. These laboratories would employ scientists skilled in protein and glycoprotein chemistry and equipped with state-of-the-art instruments for required analyses. After Standard References are established, the reference laboratories would provide them to the animal health industry as "gold standards". Companies would then establish and validate a correlation between the Standard Reference and the company Master Reference (USDA/CVB nomenclature) using an internal in vitro assay. After this correlation is established, the company could use the Standard References for qualifying, monitoring and requalifying company Master References without the use of animals. Such a program would eliminate the need for animals for requalification of Master References and the need for each company to develop and validate a battery of Master Reference Monitoring assays. It would also provide advantages in terms of reduced costs and reduced time for requalification testing. As such it would provide a strong incentive for companies to develop and use in vitro assays for potency testing.

Use of internal references for assessing CT density measurements of the pelvis as replacement for use of an external phantom.

PubMed

Boomsma, Martijn F; Slouwerhof, Inge; van Dalen, Jorn A; Edens, Mireille A; Mueller, Dirk; Milles, Julien; Maas, Mario

2015-11-01

The purpose of this research is to study the use of an internal reference standard for fat- and muscle as a replacement for an external reference standard with a phantom. By using a phantomless internal reference standard, Hounsfield unit (HU) measurements of various tissues can potentially be assessed in patients with a CT scan of the pelvis without an added phantom at time of CT acquisition. This paves the way for development of a tool for quantification of the change in tissue density in one patient over time and between patients. This could make every CT scan made without contrast available for research purposes. Fifty patients with unilateral metal-on-metal total hip replacements, scanned together with a calibration reference phantom used in bone mineral density measurements, were included in this study. On computed tomography scans of the pelvis without the use of intravenous iodine contrast, reference values for fat and muscle were measured in the phantom as well as within the patient's body. The conformity between the references was examined with the intra-class correlation coefficient. The mean HU (± SD) of reference values for fat for the internal- and phantom references were -91.5 (±7.0) and -90.9 (±7.8), respectively. For muscle, the mean HU (± SD) for the internal- and phantom references were 59.2 (±6.2) and 60.0 (±7.2), respectively. The intra-class correlation coefficients for fat and muscle were 0.90 and 0.84 respectively and show excellent agreement between the phantom and internal references. Internal references can be used with similar accuracy as references from an external phantom. There is no need to use an external phantom to asses CT density measurements of body tissue.

Reference Value Advisor: a new freeware set of macroinstructions to calculate reference intervals with Microsoft Excel.

PubMed

Geffré, Anne; Concordet, Didier; Braun, Jean-Pierre; Trumel, Catherine

2011-03-01

International recommendations for determination of reference intervals have been recently updated, especially for small reference sample groups, and use of the robust method and Box-Cox transformation is now recommended. Unfortunately, these methods are not included in most software programs used for data analysis by clinical laboratories. We have created a set of macroinstructions, named Reference Value Advisor, for use in Microsoft Excel to calculate reference limits applying different methods. For any series of data, Reference Value Advisor calculates reference limits (with 90% confidence intervals [CI]) using a nonparametric method when n≥40 and by parametric and robust methods from native and Box-Cox transformed values; tests normality of distributions using the Anderson-Darling test and outliers using Tukey and Dixon-Reed tests; displays the distribution of values in dot plots and histograms and constructs Q-Q plots for visual inspection of normality; and provides minimal guidelines in the form of comments based on international recommendations. The critical steps in determination of reference intervals are correct selection of as many reference individuals as possible and analysis of specimens in controlled preanalytical and analytical conditions. Computing tools cannot compensate for flaws in selection and size of the reference sample group and handling and analysis of samples. However, if those steps are performed properly, Reference Value Advisor, available as freeware at http://www.biostat.envt.fr/spip/spip.php?article63, permits rapid assessment and comparison of results calculated using different methods, including currently unavailable methods. This allows for selection of the most appropriate method, especially as the program provides the CI of limits. It should be useful in veterinary clinical pathology when only small reference sample groups are available. ©2011 American Society for Veterinary Clinical Pathology.

CLSI-based transference of the CALIPER database of pediatric reference intervals from Abbott to Beckman, Ortho, Roche and Siemens Clinical Chemistry Assays: direct validation using reference samples from the CALIPER cohort.

PubMed

Estey, Mathew P; Cohen, Ashley H; Colantonio, David A; Chan, Man Khun; Marvasti, Tina Binesh; Randell, Edward; Delvin, Edgard; Cousineau, Jocelyne; Grey, Vijaylaxmi; Greenway, Donald; Meng, Qing H; Jung, Benjamin; Bhuiyan, Jalaluddin; Seccombe, David; Adeli, Khosrow

2013-09-01

The CALIPER program recently established a comprehensive database of age- and sex-stratified pediatric reference intervals for 40 biochemical markers. However, this database was only directly applicable for Abbott ARCHITECT assays. We therefore sought to expand the scope of this database to biochemical assays from other major manufacturers, allowing for a much wider application of the CALIPER database. Based on CLSI C28-A3 and EP9-A2 guidelines, CALIPER reference intervals were transferred (using specific statistical criteria) to assays performed on four other commonly used clinical chemistry platforms including Beckman Coulter DxC800, Ortho Vitros 5600, Roche Cobas 6000, and Siemens Vista 1500. The resulting reference intervals were subjected to a thorough validation using 100 reference specimens (healthy community children and adolescents) from the CALIPER bio-bank, and all testing centers participated in an external quality assessment (EQA) evaluation. In general, the transferred pediatric reference intervals were similar to those established in our previous study. However, assay-specific differences in reference limits were observed for many analytes, and in some instances were considerable. The results of the EQA evaluation generally mimicked the similarities and differences in reference limits among the five manufacturers' assays. In addition, the majority of transferred reference intervals were validated through the analysis of CALIPER reference samples. This study greatly extends the utility of the CALIPER reference interval database which is now directly applicable for assays performed on five major analytical platforms in clinical use, and should permit the worldwide application of CALIPER pediatric reference intervals. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Degrading and non-degrading sex in popular music: a content analysis.

PubMed

Primack, Brian A; Gold, Melanie A; Schwarz, Eleanor B; Dalton, Madeline A

2008-01-01

Those exposed to more degrading sexual references in popular music are more likely to initiate intercourse at a younger age. The purpose of this study was to perform a content analysis of contemporary popular music with particular attention paid to the prevalence of degrading and non-degrading sexual references. We also aimed to determine if sexual references of each subtype were associated with other song characteristics and/or content. We used Billboard magazine to identify the top popular songs in 2005. Two independent coders each analyzed all of these songs (n = 279) for degrading and non-degrading sexual references. As measured with Cohen's kappa scores, inter-rater agreement on degrading vs. non-degrading sex was substantial. Mentions of substance use, violence, and weapon carrying were also coded. Of the 279 songs identified, 103 (36.9%) contained references to sexual activity. Songs with references to degrading sex were more common than songs with references to non-degrading sex (67 [65.0%] vs. 36 [35.0%], p < 0.001). Songs with degrading sex were most commonly Rap (64.2%), whereas songs with non-degrading sex were most likely Country (44.5%) or Rhythm & Blues/Hip-Hop (27.8%). Compared with songs that had no mention of sexual activity, songs with degrading sex were more likely to contain references to substance use, violence, and weapon carrying. Songs with non-degrading sex were no more likely to mention these other risk behaviors. References to sexual activity are common in popular music, and degrading sexual references are more prevalent than non-degrading references. References to degrading sex also frequently appear with references to other risky behaviors.

When a Stone Tries to Climb up a Slope: The Interplay between Lexical and Perceptual Animacy in Referential Choices

PubMed Central

Vogels, Jorrig; Krahmer, Emiel; Maes, Alfons

2013-01-01

Several studies suggest that referential choices are influenced by animacy. On the one hand, animate referents are more likely to be mentioned as subjects than inanimate referents. On the other hand, animate referents are more frequently pronominalized than inanimate referents. These effects have been analyzed as effects of conceptual accessibility. In this paper, we raise the question whether these effects are driven only by lexical concepts, such that referents described by animate lexical items (e.g., “toddler”) are more accessible than referents described by inanimate lexical items (e.g., “shoe”), or can also be influenced by context-derived conceptualizations, such that referents that are perceived as animate in a particular context are more accessible than referents that are not. In two animation-retelling experiments, conducted in Dutch, we investigated the influence of lexical and perceptual animacy on the choice of referent and the choice of referring expression. If the effects of animacy are context-dependent, entities that are perceived as animate should yield more subject references and more pronouns than entities that are perceived as inanimate, irrespective of their lexical animacy. If the effects are tied to lexical concepts, entities described with animate lexical items should be mentioned as the subject and pronominalized more frequently than entities described with inanimate lexical items, irrespective of their perceptual animacy. The results show that while only lexical animacy appears to affect the choice of subject referent, perceptual animacy may overrule lexical animacy in the choice of referring expression. These findings suggest that referential choices can be influenced by conceptualizations based on the perceptual context. PMID:23554600

GNSS RTK-networks: The significance and issues to realize a recent reference coordinate system

NASA Astrophysics Data System (ADS)

Umnig, Elke; Möller, Gregor; Weber, Robert

2014-05-01

The upcoming release of the new global reference frame ITRF2013 will provide high accurate reference station positions and station velocities at the mm- and mm/year level, respectively. ITRF users benefit from this development in various ways. For example, this new frame allows for embedding high accurate GNSS baseline observations to an underlying reference of at least the same accuracy. Another advantage is that the IGS products are fully consistent with this frame and therefore all GNSS based zero-difference positioning results (Precise Point Positioning (PPP)) will be aligned to the ITRF2013. Unfortunately the transistion to a new frame (or just to a new epoch) implies also issues in particular for providers and users of real time positioning services. Thus providers have to perform arrangements, such as the readjustment of the reference station coordinates and the update of the transformation parameters from the homogenous GNSS coordinate frame into the national datum. Finally providers have to inform their clients appropriately about these changes and significant adjustments. Furthermore the aspect of the continental reference frame has to be considered: In Europe the use of the continental reference system/reference frame ETRS89/ETRF2000 is, due to cross-national guidelines, recommend by most national mapping authorities. Subsequently GNSS post-processing applications are degraded by the concurrent use of the reference systems and reference frames, to which terrestrial site coordinates and satellite coordinates are aligned. In this presentation we highlight all significant steps and hurdles which have to be jumped over when introducing a new reference frame from point of view of a typical regional RTK-reference station network provider. This network is located in Austria and parts of the neighbouring countries and consists of about 40 reference stations. Moreover, we discuss the significance of permanently monitoring the stability of the reference network sites and the determination of station velocities/rates for geodynamical investigations.

Serum TSH reference interval in healthy Finnish adults using the Abbott Architect 2000i Analyzer.

PubMed

Schalin-Jäntti, Camilla; Tanner, Pirjo; Välimäki, Matti J; Hämäläinen, Esa

2011-07-01

Current serum TSH reference intervals have been criticized as they were established from unselected background populations. A special concern is that the upper limit, which defines subclinical hypothyroidism, is too high. The objective was to redefine the TSH reference interval in the adult Finnish population. The current reference interval for the widely used Abbott Architect method in Finland is 0.4-4.0 mU/L. Serum TSH and free T4 concentrations were derived from 606 healthy, non-pregnant, 18-91-year-old Finns from the Nordic Reference Interval Project (NORIP) and the possible effects of age, sex and thyroid peroxidase antibody (TPOAb) status were evaluated. After excluding TPOAb-positive subjects and outliers, a reference population of 511 subjects was obtained. In the reference population, no statistically significant gender- or age-specific differences in mean TSH (1.55 ± 3.30 mU/L) or TSH reference intervals were observed. The new reference interval was 0.5-3.6 mU/L (2.5th-97.5th percentiles). The current upper TSH reference limit is 10% too high. A TSH > 3.6 mU/L, confirmed with a repeat TSH sampling, may indicate subclinical hypothyroidism. Differences in ethnicity, regional iodine-intake and analytical methods underline the need for redefining the TSH reference interval in central laboratories in different countries.

[Tasks and duties of veterinary reference laboratories for food borne zoonoses].

PubMed

Ellerbroek, Lüppo; Alter, T; Johne, R; Nöckler, K; Beutin, L; Helmuth, R

2009-02-01

Reference laboratories are of central importance for consumer protection. Field expertise and high scientific competence are basic requirements for the nomination of a national reference laboratory. To ensure a common approach in the analysis of zoonotic hazards, standards have been developed by the reference laboratories together with national official laboratories on the basis of Art. 33 of Directive (EG) No. 882/2004. Reference laboratories function as arbitrative boards in the case of ambivalent or debatable results. New methods for detection of zoonotic agents are developed and validated to provide tools for analysis, e. g., in legal cases, if results from different parties are disputed. Besides these tasks, national reference laboratories offer capacity building and advanced training courses and control the performance of ring trials to ensure consistency in the quality of analyses in official laboratories. All reference laboratories work according to the ISO standard 17025 which defines the grounds for strict laboratory quality rules and in cooperation with the respective Community Reference Laboratories (CRL). From the group of veterinary reference laboratories for food-borne zoonoses, the national reference laboratories are responsible for Listeria monocytogenes, for Campylobacter, for the surveillance and control of viral and bacterial contamination of bivalve molluscs, for E. coli, for the performance of analysis and tests on zoonoses (Salmonella), and from the group of parasitological zoonotic agents, the national reference laboratory for Trichinella.

[Saarland Growth Study: sampling design].

PubMed

Danker-Hopfe, H; Zabransky, S

2000-01-01

The use of reference data to evaluate the physical development of children and adolescents is part of the daily routine in the paediatric ambulance. The construction of such reference data is based on the collection of extensive reference data. There are different kinds of reference data: cross sectional references, which are based on data collected from a big representative cross-sectional sample of the population, longitudinal references, which are based on follow-up surveys of usually smaller samples of individuals from birth to maturity, and mixed longitudinal references, which are a combination of longitudinal and cross-sectional reference data. The advantages and disadvantages of the different methods of data collection and the resulting reference data are discussed. The Saarland Growth Study was conducted for several reasons: growth processes are subject to secular changes, there are no specific reference data for children and adolescents from this part of the country and the growth charts in use in the paediatric praxis are possibly not appropriate any more. Therefore, the Saarland Growth Study served two purposes a) to create actual regional reference data and b) to create a database for future studies on secular trends in growth processes of children and adolescents from Saarland. The present contribution focusses on general remarks on the sampling design of (cross-sectional) growth surveys and its inferences for the design of the present study.

43 CFR 3.8 - Applications referred for recommendation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Applications referred for recommendation... AMERICAN ANTIQUITIES § 3.8 Applications referred for recommendation. Applications for permits shall be referred to the Smithsonian Institution for recommendation. ...

43 CFR 3.8 - Applications referred for recommendation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Applications referred for recommendation... AMERICAN ANTIQUITIES § 3.8 Applications referred for recommendation. Applications for permits shall be referred to the Smithsonian Institution for recommendation. ...

Reference Materials and Subject Matter Knowledge Codes for Airman Knowledge Testing

DOT National Transportation Integrated Search

2004-06-08

The listings of reference materials and subject matter knowledge codes have been : prepared by the Federal Aviation Administration (FAA) to establish specific : references for all knowledge standards. The listings contain reference materials : to be ...

Eliminating traditional reference services in an academic health sciences library: a case study

PubMed Central

Schulte, Stephanie J

2011-01-01

Question: How were traditional librarian reference desk services successfully eliminated at one health sciences library? Setting: The analysis was done at an academic health sciences library at a major research university. Method: A gap analysis was performed, evaluating changes in the first eleven months through analysis of reference transaction and instructional session data. Main Results: Substantial increases were seen in the overall number of specialized reference transactions and those conducted by librarians lasting more than thirty minutes. The number of reference transactions overall increased after implementing the new model. Several new small-scale instructional initiatives began, though perhaps not directly related to the new model. Conclusion: Traditional reference desk services were eliminated at one academic health sciences library without negative impact on reference and instructional statistics. Eliminating ties to the confines of the physical library due to staffing reference desk hours removed one significant barrier to a more proactive liaison program. PMID:22022221

Requirements for data integration platforms in biomedical research networks: a reference model.

PubMed

Ganzinger, Matthias; Knaup, Petra

2015-01-01

Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure, we developed a reference model for the requirements. The reference model consists of five reference goals and 15 reference requirements. Using the Unified Modeling Language, the goals and requirements are set into relation to each other. In addition, all goals and requirements are described textually in tables. This reference model can be used by research networks as a basis for a resource efficient acquisition of their project specific requirements. Furthermore, a concrete instance of the reference model is described for a research network on liver cancer. The reference model is transferred into a requirements model of the specific network. Based on this concrete requirements model, a service-oriented information technology architecture is derived and also described in this paper.

Subjective Social Status and Well-Being: The Role of Referent Abstraction.

PubMed

Haught, Heather M; Rose, Jason; Geers, Andrew; Brown, Jill A

2015-01-01

Subjective social status (SSS) has been shown to predict well-being and mental health, above and beyond objective social status (OSS). However, little is known about the factors that moderate this relationship. Two studies explored whether the link between SSS and well-being varied depending upon the referent used for comparison in SSS judgments. Participants judged their well-being and SSS in comparison to referents that varied in abstraction. A confirmatory factor analysis on SSS judgments yielded two factors: (a) SSS perceptions toward global referents and (b) SSS perceptions toward local referents. SSS relative to a global referent was a better predictor of depression (Studies 1 and 2), life satisfaction (Studies 1 and 2), and self-esteem (Study 2) than SSS relative to a local referent. These findings have theoretical implications for understanding how people differentiate between local vs. global referents and practical implications for status-related health disparities.

Devices for the Production of Reference Gas Mixtures.

PubMed

Fijało, Cyprian; Dymerski, Tomasz; Gębicki, Jacek; Namieśnik, Jacek

2016-09-02

For many years there has been growing demand for gaseous reference materials, which is connected with development in many fields of science and technology. As a result, new methodological and instrumental solutions appear that can be used for this purpose. Appropriate quality assurance/quality control (QA/QC) must be used to make sure that measurement data are a reliable source of information. Reference materials are a significant element of such systems. In the case of gas samples, such materials are generally called reference gas mixtures. This article presents the application and classification of reference gas mixtures, which are a specific type of reference materials, and the methods for obtaining them are described. Construction solutions of devices for the production of reference gas mixtures are detailed, and a description of a prototype device for dynamic production of reference gas mixtures containing aroma compounds is presented.

Bibliographical search for reliable seismic moments of large earthquakes during 1900-1979 to compute MW in the ISC-GEM Global Instrumental Reference Earthquake Catalogue

NASA Astrophysics Data System (ADS)

Lee, William H. K.; Engdahl, E. Robert

2015-02-01

Moment magnitude (MW) determinations from the online GCMT Catalogue of seismic moment tensor solutions (GCMT Catalog, 2011) have provided the bulk of MW values in the ISC-GEM Global Instrumental Reference Earthquake Catalogue (1900-2009) for almost all moderate-to-large earthquakes occurring after 1975. This paper describes an effort to determine MW of large earthquakes that occurred prior to the start of the digital seismograph era, based on credible assessments of thousands of seismic moment (M0) values published in the scientific literature by hundreds of individual authors. MW computed from the published M0 values (for a time period more than twice that of the digital era) are preferable to proxy MW values, especially for earthquakes with MW greater than about 8.5, for which MS is known to be underestimated or "saturated". After examining 1,123 papers, we compile a database of seismic moments and related information for 1,003 earthquakes with published M0 values, of which 967 were included in the ISC-GEM Catalogue. The remaining 36 earthquakes were not included in the Catalogue due to difficulties in their relocation because of inadequate arrival time information. However, 5 of these earthquakes with bibliographic M0 (and thus MW) are included in the Catalogue's Appendix. A search for reliable seismic moments was not successful for earthquakes prior to 1904. For each of the 967 earthquakes a "preferred" seismic moment value (if there is more than one) was selected and its uncertainty was estimated according to the data and method used. We used the IASPEI formula (IASPEI, 2005) to compute direct moment magnitudes (MW[M0]) based on the seismic moments (M0), and assigned their errors based on the uncertainties of M0. From 1900 to 1979, there are 129 great or near great earthquakes (MW ⩾ 7.75) - the bibliographic search provided direct MW values for 86 of these events (or 67%), the GCMT Catalog provided direct MW values for 8 events (or 6%), and the remaining 35 (or 27%) earthquakes have empirically determined proxy MW estimates. An electronic supplementary file is included with this paper in order to provide our M0/MW catalogue of earthquakes (1904-1978) from the published literature, and a reference list of the 1,123 papers that we examined.

7 CFR 1.626 - What regulations apply to a case referred for a hearing?

Code of Federal Regulations, 2014 CFR

2014-01-01

... referred for a hearing? (a) If NFS refers the case to OALJ, these regulations will continue to apply to the hearing process. (b) If NFS refers the case to the Department of the Interior's Office of Hearing and Appeals, the regulations at 43 CFR 45.1 et seq. will apply from that point. (c) If NFS refers the case to...

7 CFR 1.626 - What regulations apply to a case referred for a hearing?

Code of Federal Regulations, 2013 CFR

2013-01-01

... referred for a hearing? (a) If NFS refers the case to OALJ, these regulations will continue to apply to the hearing process. (b) If NFS refers the case to the Department of the Interior's Office of Hearing and Appeals, the regulations at 43 CFR 45.1 et seq. will apply from that point. (c) If NFS refers the case to...

7 CFR 1.626 - What regulations apply to a case referred for a hearing?

Code of Federal Regulations, 2012 CFR

2012-01-01

... referred for a hearing? (a) If NFS refers the case to OALJ, these regulations will continue to apply to the hearing process. (b) If NFS refers the case to the Department of the Interior's Office of Hearing and Appeals, the regulations at 43 CFR 45.1 et seq. will apply from that point. (c) If NFS refers the case to...

7 CFR 1.626 - What regulations apply to a case referred for a hearing?

Code of Federal Regulations, 2011 CFR

2011-01-01

... referred for a hearing? (a) If NFS refers the case to OALJ, these regulations will continue to apply to the hearing process. (b) If NFS refers the case to the Department of the Interior's Office of Hearing and Appeals, the regulations at 43 CFR 45.1 et seq. will apply from that point. (c) If NFS refers the case to...

7 CFR 1.626 - What regulations apply to a case referred for a hearing?

Code of Federal Regulations, 2010 CFR

2010-01-01

... referred for a hearing? (a) If NFS refers the case to OALJ, these regulations will continue to apply to the hearing process. (b) If NFS refers the case to the Department of the Interior's Office of Hearing and Appeals, the regulations at 43 CFR 45.1 et seq. will apply from that point. (c) If NFS refers the case to...

The Hidden Agenda in the Measurement and Evaluation of Reference Service, or, how to Make a Case for Yourself.

ERIC Educational Resources Information Center

Rothstein, Samuel

1989-01-01

Discusses measurement and evaluation as ways to justify reference work to users and library administration. A trivia contest is cited as a way to achieve public recognition, and measuring use of reference materials rather than the number of reference questions is recommended. User surveys and other measures of reference activity and value are also…

The availability of references and the sponsorship of original research cited in pharmaceutical advertisements

PubMed Central

Cooper, Richelle J.; Schriger, David L.

2005-01-01

Background The primary goal of pharmaceutical advertisements is to convince physicians to prescribe the manufacturer's product. We sought to determine what materials are cited in support of claims in pharmaceutical ads and medical research articles, and whether health care professionals seeking to verify the claims could obtain these references. Methods We reviewed 438 unique ads from the 1999 issues of 10 American medical journals, and a random sample of 400 references in medical research articles selected from the same journals. We classified references as journal article, data on file, meeting abstract or presentation, book or monograph, marketing report, prescribing information, government document or Internet site. We attempted to confirm or obtain each reference through library and Internet searches or by direct request from the manufacturer. The main outcome we sought to determine was the availability of the reference to a clinician. We also ascertained the source of funding for original research cited in the ads and the research articles. Results In the 438 ads with medical claims, 126 contained no references and 312 contained 721 unique references. Of these ad references, 55% (396/721) cited journal articles and 19% (135/721) cited data on file. In contrast, in the sample of research article references, 88% (351/400) cited journal articles and 8% (33/400) cited books. Overall, 84% of the citations from the ads were available: 98% of journal articles, 86% of books, 71% of meeting abstracts or presentations and 20% of data-on-file references. In all, 99% of the sample of research article references were available. We determined that 58% of the original research cited in the pharmaceutical ads was sponsored by or had an author affiliated with the product's manufacturer, as compared with 8% of the articles cited in the research articles. Interpretation Many pharmaceutical ads contain no references for medical claims. Although references to journal articles were usually obtainable, other published sources were not as easily acquired. The majority of unpublished data-on-file references were not available, and the majority of original research cited to substantiate claims in the pharmaceutical ads was funded by or had authors affiliated with the product's manufacturer. PMID:15710940

The availability of references and the sponsorship of original research cited in pharmaceutical advertisements.

PubMed

Cooper, Richelle J; Schriger, David L

2005-02-15

The primary goal of pharmaceutical advertisements is to convince physicians to prescribe the manufacturer's product. We sought to determine what materials are cited in support of claims in pharmaceutical ads and medical research articles, and whether health care professionals seeking to verify the claims could obtain these references. We reviewed 438 unique ads from the 1999 issues of 10 American medical journals, and a random sample of 400 references in medical research articles selected from the same journals. We classified references as journal article, data on file, meeting abstract or presentation, book or monograph, marketing report, prescribing information, government document or Internet site. We attempted to confirm or obtain each reference through library and Internet searches or by direct request from the manufacturer. The main outcome we sought to determine was the availability of the reference to a clinician. We also ascertained the source of funding for original research cited in the ads and the research articles. In the 438 ads with medical claims, 126 contained no references and 312 contained 721 unique references. Of these ad references, 55% (396/721) cited journal articles and 19% (135/721) cited data on file. In contrast, in the sample of research article references, 88% (351/400) cited journal articles and 8% (33/400) cited books. Overall, 84% of the citations from the ads were available: 98% of journal articles, 86% of books, 71% of meeting abstracts or presentations and 20% of data-on-file references. In all, 99% of the sample of research article references were available. We determined that 58% of the original research cited in the pharmaceutical ads was sponsored by or had an author affiliated with the product's manufacturer, as compared with 8% of the articles cited in the research articles. Many pharmaceutical ads contain no references for medical claims. Although references to journal articles were usually obtainable, other published sources were not as easily acquired. The majority of unpublished data-on-file references were not available, and the majority of original research cited to substantiate claims in the pharmaceutical ads was funded by or had authors affiliated with the product's manufacturer.

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events.

PubMed

Demeke, Tigst; Eng, Monika

2018-05-01

Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences ( HMG-I/Y , FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.

Accuracy of body mass index for age to diagnose obesity in Mexican schoolchildren.

PubMed

Mendoza Pablo, Pedro A; Valdés, Jesús; Ortiz-Hernández, Luis

2015-06-01

To compare the accuracy of three BMI-forage references (World Health Organization reference, WHO; the updated International Obesity Task Force reference, IOTF; and Centers for Disease Control and Prevention (CDC) growth charts) to diagnose obesity in Mexican children. A convenience sample of Mexican schoolchildren (n = 218) was assessed. The gold standard was the percentage of body fat estimated by deuterium dilution technique. Sensitivity and specificity of the classical cutoff point of BMI-for-age to identify obesity (i.e. > 2.00 standard deviation, SD) were estimated. The accuracy (i.e. area under the curve, AUC) of three BMI-for-age references for the diagnosis of obesity was estimated with the receiver operating characteristic (ROC) curves method. The optimal cutoff point (OCP) was determined. The cutoff points to identify obesity had low (WHO reference: 57.6%, CDC: 53.5%) to very low (IOTF reference: 40.4%) sensitivities, but adequate specificities (91.6%, 95.0%, and, 97.5%, respectively). The AUC of the three references were adequate (0.89). For the IOTF reference, the AUC was lower among the older children. The OCP for the CDC reference (1.24 SD) was lower than the OCP for WHO (1.53 SD) and IOTF charts (1.47 SD). The classical cutoff point for obesity has low sensitivity--especially for the IOTF reference. The accuracy of the three references was similar. However, to obtain comparable diagnosis of obesity different cutoff points should be used depending of the reference. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

PubMed

Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

2017-12-01

To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

Impact of a product-specific reference standard for the measurement of a PEGylated rFVIII activity: the Swiss Multicentre Field Study.

PubMed

Bulla, O; Poncet, A; Alberio, L; Asmis, L M; Gähler, A; Graf, L; Nagler, M; Studt, J-D; Tsakiris, D A; Fontana, P

2017-07-01

Measuring factor VIII (FVIII) activity can be challenging when it has been modified, such as when FVIII is pegylated to increase its circulating half-life. Use of a product-specific reference standard may help avoid this issue. Evaluate the impact of using a product-specific reference standard for measuring the FVIII activity of BAX 855 - a pegylated FVIII - in eight of Switzerland's main laboratories. Factor VIII-deficient plasma, spiked with five different concentrations of BAX 855, plus a control FVIII sample, was sent to the participating laboratories. They measured FVIII activity by using either with a one-stage (OSA) or the chromogenic assay (CA) against their local or a product-specific reference standard. When using a local reference standard, there was an overestimation of BAX 855 activity compared to the target concentrations, both with the OSA and CA. The use of a product-specific reference standard reduced this effect: mean recovery ranged from 127.7% to 213.5% using the OSA with local reference standards, compared to 110% to 183.8% with a product-specific reference standard, and from 146.3% to 182.4% using the CA with local reference standards compared to 72.7% to 103.7% with a product-specific reference standard. In this in vitro study, the type of reference standard had a major impact on the measurement of BAX 855 activity. Evaluation was more accurate and precise when using a product-specific reference standard. © 2017 John Wiley & Sons Ltd.

High frequency reference electrode

DOEpatents

Kronberg, J.W.

1994-05-31

A high frequency reference electrode for electrochemical experiments comprises a mercury-calomel or silver-silver chloride reference electrode with a layer of platinum around it and a layer of a chemically and electrically resistant material such as TEFLON around the platinum covering all but a small ring or halo' at the tip of the reference electrode, adjacent to the active portion of the reference electrode. The voltage output of the platinum layer, which serves as a redox electrode, and that of the reference electrode are coupled by a capacitor or a set of capacitors and the coupled output transmitted to a standard laboratory potentiostat. The platinum may be applied by thermal decomposition to the surface of the reference electrode. The electrode provides superior high-frequency response over conventional electrodes. 4 figs.

High frequency reference electrode

DOEpatents

Kronberg, James W.

1994-01-01

A high frequency reference electrode for electrochemical experiments comprises a mercury-calomel or silver-silver chloride reference electrode with a layer of platinum around it and a layer of a chemically and electrically resistant material such as TEFLON around the platinum covering all but a small ring or "halo" at the tip of the reference electrode, adjacent to the active portion of the reference electrode. The voltage output of the platinum layer, which serves as a redox electrode, and that of the reference electrode are coupled by a capacitor or a set of capacitors and the coupled output transmitted to a standard laboratory potentiostat. The platinum may be applied by thermal decomposition to the surface of the reference electrode. The electrode provides superior high-frequency response over conventional electrodes.

Beam masking to reduce cyclic error in beam launcher of interferometer

NASA Technical Reports Server (NTRS)

Ames, Lawrence L. (Inventor); Bell, Raymond Mark (Inventor); Dutta, Kalyan (Inventor)

2005-01-01

Embodiments of the present invention are directed to reducing cyclic error in the beam launcher of an interferometer. In one embodiment, an interferometry apparatus comprises a reference beam directed along a reference path, and a measurement beam spatially separated from the reference beam and being directed along a measurement path contacting a measurement object. The reference beam and the measurement beam have a single frequency. At least a portion of the reference beam and at least a portion of the measurement beam overlapping along a common path. One or more masks are disposed in the common path or in the reference path and the measurement path to spatially isolate the reference beam and the measurement beam from one another.

Research notes : evaluation of the performance of reference electrodes embedded in reinforced concrete.

DOT National Transportation Integrated Search

1995-07-01

The objectives of this work were to examine placement strategies for reference electrodes and to evaluate the suitability of graphite reference electrodes as imbedded reference electrodes in reinforced concrete structures that are cathodically protec...

Adaptive optimization of reference intensity for optical coherence imaging using galvanometric mirror tilting method

NASA Astrophysics Data System (ADS)

Kim, Ji-hyun; Han, Jae-Ho; Jeong, Jichai

2015-09-01

Integration time and reference intensity are important factors for achieving high signal-to-noise ratio (SNR) and sensitivity in optical coherence tomography (OCT). In this context, we present an adaptive optimization method of reference intensity for OCT setup. The reference intensity is automatically controlled by tilting a beam position using a Galvanometric scanning mirror system. Before sample scanning, the OCT system acquires two dimensional intensity map with normalized intensity and variables in color spaces using false-color mapping. Then, the system increases or decreases reference intensity following the map data for optimization with a given algorithm. In our experiments, the proposed method successfully corrected the reference intensity with maintaining spectral shape, enabled to change integration time without manual calibration of the reference intensity, and prevented image degradation due to over-saturation and insufficient reference intensity. Also, SNR and sensitivity could be improved by increasing integration time with automatic adjustment of the reference intensity. We believe that our findings can significantly aid in the optimization of SNR and sensitivity for optical coherence tomography systems.

Passive serialization in a multitasking environment

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

Hennessey, J.P.; Osisek, D.L.; Seigh, J.W. II

1989-02-28

In a multiprocessing system having a control program in which data objects are shared among processes, this patent describes a method for serializing references to a data object by the processes so as to prevent invalid references to the data object by any process when an operation requiring exclusive access is performed by another process, comprising the steps of: permitting the processes to reference data objects on a shared access basis without obtaining a shared lock; monitoring a point of execution of the control program which is common to all processes in the system, which occurs regularly in the process'more » execution and across which no references to any data object can be maintained by any process, except references using locks; establishing a system reference point which occurs after each process in the system has passed the point of execution at least once since the last such system reference point; requesting an operation requiring exclusive access on a selected data object; preventing subsequent references by other processes to the selected data object; waiting until two of the system references points have occurred; and then performing the requested operation.« less

How Flexible is the Use of Egocentric Versus Allocentric Frame of Reference in the Williams Syndrome Population?

PubMed

Heiz, J; Majerus, S; Barisnikov, K

2017-09-28

This study examined the spontaneous use of allocentric and egocentric frames of reference and their flexible use as a function of instructions. The computerized spatial reference task created by Heiz and Barisnikov (2015) was used. Participants had to choose a frame of reference according to three types of instructions: spontaneous, allocentric and egocentric. The performances of 16 Williams Syndrome participants between 10 and 41 years were compared to those of two control groups (chronological age and non-verbal intellectual ability). The majority of Williams Syndrome participants did not show a preference for a particular frame of reference. When explicitly inviting participants to use an allocentric frame of reference, all three groups showed an increased use of the allocentric frame of reference. At the same time, an important heterogeneity of type of frame of reference used by Williams Syndrome participants was observed. Results demonstrate that despite difficulties in the spontaneous use of allocentric and egocentric frames of reference, some Williams Syndrome participants show flexibility in the use of an allocentric frame of reference when an explicit instruction is provided. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress.

PubMed

Chen, Jingchao; Huang, Zhaofeng; Huang, Hongjuan; Wei, Shouhui; Liu, Yan; Jiang, Cuilan; Zhang, Jie; Zhang, Chaoxian

2017-04-21

Goosegrass (Eleusine indica) is one of the most serious annual grassy weeds worldwide, and its evolved herbicide-resistant populations are more difficult to control. Quantitative real-time PCR (qPCR) is a common technique for investigating the resistance mechanism; however, there is as yet no report on the systematic selection of stable reference genes for goosegrass. This study proposed to test the expression stability of 9 candidate reference genes in goosegrass in different tissues and developmental stages and under stress from three types of herbicide. The results show that for different developmental stages and organs (control), eukaryotic initiation factor 4 A (eIF-4) is the most stable reference gene. Chloroplast acetolactate synthase (ALS) is the most stable reference gene under glyphosate stress. Under glufosinate stress, eIF-4 is the best reference gene. Ubiquitin-conjugating enzyme (UCE) is the most stable reference gene under quizalofop-p-ethyl stress. The gene eIF-4 is the recommended reference gene for goosegrass under the stress of all three herbicides. Moreover, pairwise analysis showed that seven reference genes were sufficient to normalize the gene expression data under three herbicides treatment. This study provides a list of reliable reference genes for transcript normalization in goosegrass, which will facilitate resistance mechanism studies in this weed species.

Selection of Reference Genes for Quantitative Gene Expression in Porcine Mesenchymal Stem Cells Derived from Various Sources along with Differentiation into Multilineages

PubMed Central

Lee, Won-Jae; Jeon, Ryoung-Hoon; Jang, Si-Jung; Park, Ji-Sung; Lee, Seung-Chan; Baregundi Subbarao, Raghavendra; Lee, Sung-Lim; Park, Bong-Wook; King, William Allan; Rho, Gyu-Jin

2015-01-01

The identification of stable reference genes is a prerequisite for ensuring accurate validation of gene expression, yet too little is known about stable reference genes of porcine MSCs. The present study was, therefore, conducted to assess the stability of reference genes in porcine MSCs derived from bone marrow (BMSCs), adipose (AMSCs), and skin (SMSCs) with their in vitro differentiated cells into mesenchymal lineages such as adipocytes, osteocytes, and chondrocytes. Twelve commonly used reference genes were investigated for their threshold cycle (Ct) values by qRT-PCR. The Ct values of candidate reference genes were analyzed by geNorm software to clarify stable expression regardless of experimental conditions. Thus, Pearson's correlation was applied to determine correlation between the three most stable reference genes (NF3) and optimal number of reference genes (NFopt). In assessment of stability of reference gene across experimental conditions by geNorm analysis, undifferentiated MSCs and each differentiated status into mesenchymal lineages showed slightly different results but similar patterns about more or less stable rankings. Furthermore, Pearson's correlation revealed high correlation (r > 0.9) between NF3 and NFopt. Overall, the present study showed that HMBS, YWHAZ, SDHA, and TBP are suitable reference genes for qRT-PCR in porcine MSCs. PMID:25972899

Identification and validation of reference genes for qRT-PCR studies of the obligate aphid pathogenic fungus Pandora neoaphidis during different developmental stages.

PubMed

Zhang, Shutao; Chen, Chun; Xie, Tingna; Ye, Sudan

2017-01-01

The selection of stable reference genes is a critical step for the accurate quantification of gene expression. To identify and validate the reference genes in Pandora neoaphidis-an obligate aphid pathogenic fungus-the expression of 13classical candidate reference genes were evaluated by quantitative real-time reverse transcriptase polymerase chain reaction(qPCR) at four developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae). Four statistical algorithms, including geNorm, NormFinder, BestKeeper and Delta Ct method were used to rank putative reference genes according to their expression stability and indicate the best reference gene or combination of reference genes for accurate normalization. The analysis of comprehensive ranking revealed that ACT1and 18Swas the most stably expressed genes throughout the developmental stages. To further validate the suitability of the reference genes identified in this study, the expression of cell division control protein 25 (CDC25) and Chitinase 1(CHI1) genes were used to further confirm the validated candidate reference genes. Our study presented the first systematic study of reference gene(s) selection for P. neoaphidis study and provided guidelines to obtain more accurate qPCR results for future developmental efforts.

Pointing to potential reference areas to assess soil mutagenicity.

PubMed

Meyer, D D; Da Silva, F M R; Souza, J W M; Pohren, R S; Rocha, J A V; Vargas, V M F

2015-04-01

Several have been performed to evaluate the mutagenicity of soil samples in urban and industrial areas. The use of uncontaminated reference areas has been an obstacle to the study of environmental mutagenesis. The study aimed to indicate a methodology to define reference areas in studies of environmental contamination based on "Ambient Background Concentration" of metallic elements associated with the Salmonella/microsome assay. We looked at three potential reference areas, two of them close by the industrial sources of contamination (São Jerônimo reference, near the coal-fired power plant, and Triunfo reference, near the wood preservative plant), but not directly influenced by them and an area located inside a protected area (Itapuã reference). We also carried out chemical analyses of some metals to plot the metal profile of these potential reference areas and define basal levels of these metals in the soils. After examining the mutagenicity of the inorganic extracts using strains TA98, TA97a, and TA100, in the presence and absence of S9 mix, we indicated the São Jerônimo reference and the Itapuã reference as two sites that could be used in future studies of mutagenicity of soils in southern Brazil. The association between a mutagenicity bioassay and the "Ambient Background Concentration" seems to be a useful method to indicate the reference areas in studies of contamination by environmental mutagens, where these results were corroborated by canonical correspondence analysis.

Reference in human and non-human primate communication: What does it take to refer?

PubMed

Sievers, Christine; Gruber, Thibaud

2016-07-01

The concept of functional reference has been used to isolate potentially referential vocal signals in animal communication. However, its relatedness to the phenomenon of reference in human language has recently been brought into question. While some researchers have suggested abandoning the concept of functional reference altogether, others advocate a revision of its definition to include contextual cues that play a role in signal production and perception. Empirical and theoretical work on functional reference has also put much emphasis on how the receiver understands the referential signal. However, reference, as defined in the linguistic literature, is an action of the producer, and therefore, any definition describing reference in non-human animals must also focus on the producer. To successfully determine whether a signal is used to refer, we suggest an approach from the field of pragmatics, taking a closer look at specific situations of signal production, specifically at the factors that influence the production of a signal by an individual. We define the concept of signaller's reference to identify intentional acts of reference produced by a signaller independently of the communicative modality, and illustrate it with a case study of the hoo vocalizations produced by wild chimpanzees during travel. This novel framework introduces an intentional approach to referentiality. It may therefore permit a closer comparison of human and non-human animal referential behaviour and underlying cognitive processes, allowing us to identify what may have emerged solely in the human lineage.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

A Comparative Study of Different EEG Reference Choices for Diagnosing Unipolar Depression.

PubMed

Mumtaz, Wajid; Malik, Aamir Saeed

2018-06-02

The choice of an electroencephalogram (EEG) reference has fundamental importance and could be critical during clinical decision-making because an impure EEG reference could falsify the clinical measurements and subsequent inferences. In this research, the suitability of three EEG references was compared while classifying depressed and healthy brains using a machine-learning (ML)-based validation method. In this research, the EEG data of 30 unipolar depressed subjects and 30 age-matched healthy controls were recorded. The EEG data were analyzed in three different EEG references, the link-ear reference (LE), average reference (AR), and reference electrode standardization technique (REST). The EEG-based functional connectivity (FC) was computed. Also, the graph-based measures, such as the distances between nodes, minimum spanning tree, and maximum flow between the nodes for each channel pair, were calculated. An ML scheme provided a mechanism to compare the performances of the extracted features that involved a general framework such as the feature extraction (graph-based theoretic measures), feature selection, classification, and validation. For comparison purposes, the performance metrics such as the classification accuracies, sensitivities, specificities, and F scores were computed. When comparing the three references, the diagnostic accuracy showed better performances during the REST, while the LE and AR showed less discrimination between the two groups. Based on the results, it can be concluded that the choice of appropriate reference is critical during the clinical scenario. The REST reference is recommended for future applications of EEG-based diagnosis of mental illnesses.

Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans

PubMed Central

Haagensen, Brian N.; Christensen, Mark S.; Madsen, Kristoffer H.; Rowe, James B.; Løkkegaard, Annemette; Siebner, Hartwig R.

2015-01-01

Dopaminergic signalling in the striatum contributes to reinforcement of actions and motivational enhancement of motor vigour. Parkinson's disease leads to progressive dopaminergic denervation of the striatum, impairing the function of cortico-basal ganglia networks. While levodopa therapy alleviates basal ganglia dysfunction in Parkinson's disease, it often elicits involuntary movements, referred to as levodopa-induced peak-of-dose dyskinesias. Here, we used a novel pharmacodynamic neuroimaging approach to identify the changes in cortico-basal ganglia connectivity that herald the emergence of levodopa-induced dyskinesias. Twenty-six patients with Parkinson's disease (age range: 51–84 years; 11 females) received a single dose of levodopa and then performed a task in which they had to produce or suppress a movement in response to visual cues. Task-related activity was continuously mapped with functional magnetic resonance imaging. Dynamic causal modelling was applied to assess levodopa-induced modulation of effective connectivity between the pre-supplementary motor area, primary motor cortex and putamen when patients suppressed a motor response. Bayesian model selection revealed that patients who later developed levodopa-induced dyskinesias, but not patients without dyskinesias, showed a linear increase in connectivity between the putamen and primary motor cortex after levodopa intake during movement suppression. Individual dyskinesia severity was predicted by levodopa-induced modulation of striato-cortical feedback connections from putamen to the pre-supplementary motor area (Pcorrected = 0.020) and primary motor cortex (Pcorrected = 0.044), but not feed-forward connections from the cortex to the putamen. Our results identify for the first time, aberrant dopaminergic modulation of striatal-cortical connectivity as a neural signature of levodopa-induced dyskinesias in humans. We argue that excessive striato-cortical connectivity in response to levodopa produces an aberrant reinforcement signal producing an abnormal motor drive that ultimately triggers involuntary movements. PMID:25882651

Impact of Participation in a Community-Based Intimate Partner Violence Prevention Program on Medical Students: A Multi-Center Study

PubMed Central

Guiton, Gretchen; Chirra, Annapoorna; Núñez, Ana E.; Bigby, JudyAnn; Stahl, Christiane; Robertson, Candace; Thul, Elizabeth C.; Miller, Elizabeth; Sims, Abigail; Sachs, Carolyn J.; Pregler, Janet P.

2008-01-01

Background Physicians are generally poorly trained to recognize, treat or refer adolescents at risk for intimate partner violence (IPV). Participation in community programs may improve medical students’ knowledge, skills, and attitudes about IPV prevention. Objective To determine whether the experience of serving as educators in a community-based adolescent IPV prevention program improves medical students’ knowledge, skills, and attitudes toward victims of IPV, beyond that of didactic training. Participants One hundred and seventeen students attending 4 medical schools. Design Students were randomly assigned to didactic training in adolescent IPV prevention with or without participation as educators in a community-based adolescent IPV prevention program. Students assigned to didactic training alone served as community educators after the study was completed. Measurement Knowledge, self-assessment of skills and attitudes about intimate partner violence and future plans to pursue outreach work. Results The baseline mean knowledge score of 10.25 improved to 21.64 after didactic training (p ≤ .001). Medical students in the “didactic plus outreach” group demonstrated higher levels of confidence in their ability to address issues of intimate partner violence, (mean = 41.91) than did students in the “didactic only” group (mean = 38.94) after controlling for initial levels of confidence (p ≤ .002). Conclusions Experience as educators in a community-based program to prevent adolescent IPV improved medical students’ confidence and attitudes in recognizing and taking action in situations of adolescent IPV, whereas participation in didactic training alone significantly improved students’ knowledge. Electronic supplementary material The online version of this article (doi:10.1007/s11606-008-0624-y) contains supplementary material, which is available to authorized users. PMID:18612741

Approaches to the implementation of the Water Framework Directive: targeting mitigation measures at critical source areas of diffuse phosphorus in Irish catchments.

PubMed

Doody, D G; Archbold, M; Foy, R H; Flynn, R

2012-01-01

The Water Framework Directive (WFD) has initiated a shift towards a targeted approach to implementation through its focus on river basin districts as management units and the natural ecological characteristics of waterbodies. Due to its role in eutrophication, phosphorus (P) has received considerable attention, resulting in a significant body of research, which now forms the evidence base for the programme of measures (POMs) adopted in WFD River Basin Management Plans (RBMP). Targeting POMs at critical sources areas (CSAs) of P could significantly improve environmental efficiency and cost effectiveness of proposed mitigation strategies. This paper summarises the progress made towards targeting mitigation measures at CSAs in Irish catchments. A review of current research highlights that knowledge related to P export at field scale is relatively comprehensive however; the availability of site-specific data and tools limits widespread identification of CSA at this scale. Increasing complexity of hydrological processes at larger scales limits accurate identification of CSA at catchment scale. Implementation of a tiered approach, using catchment scale tools in conjunction with field-by-field surveys could decrease uncertainty and provide a more practical and cost effective method of delineating CSA in a range of catchments. Despite scientific and practical uncertainties, development of a tiered CSA-based approach to assist in the development of supplementary measures would provide a means of developing catchment-specific and cost-effective programmes of measures for diffuse P. The paper presents a conceptual framework for such an approach, which would have particular relevance for the development of supplementary measures in High Status Waterbodies (HSW). The cost and resources necessary for implementation are justified based on HSWs' value as undisturbed reference condition ecosystems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Distinct [18F]THK5351 binding patterns in primary progressive aphasia variants.

PubMed

Schaeverbeke, Jolien; Evenepoel, Charlotte; Declercq, Lieven; Gabel, Silvy; Meersmans, Karen; Bruffaerts, Rose; Adamczuk, Kate; Dries, Eva; Van Bouwel, Karen; Sieben, Anne; Pijnenburg, Yolande; Peeters, Ronald; Bormans, Guy; Van Laere, Koen; Koole, Michel; Dupont, Patrick; Vandenberghe, Rik

2018-06-26

To assess the binding of the PET tracer [ 18 F]THK5351 in patients with different primary progressive aphasia (PPA) variants and its correlation with clinical deficits. The majority of patients with nonfluent variant (NFV) and logopenic variant (LV) PPA have underlying tauopathy of the frontotemporal lobar or Alzheimer disease type, respectively, while patients with the semantic variant (SV) have predominantly transactive response DNA binding protein 43-kDa pathology. The study included 20 PPA patients consecutively recruited through a memory clinic (12 NFV, 5 SV, 3 LV), and 20 healthy controls. All participants received an extensive neurolinguistic assessment, magnetic resonance imaging and amyloid biomarker tests. [ 18 F]THK5351 binding patterns were assessed on standardized uptake value ratio (SUVR) images with the cerebellar grey matter as the reference using statistical parametric mapping. Whole-brain voxel-wise regression analysis was performed to evaluate the association between [ 18 F]THK5351 SUVR images and neurolinguistic scores. Analyses were performed with and without partial volume correction. Patients with NFV showed increased binding in the supplementary motor area, left premotor cortex, thalamus, basal ganglia and midbrain compared with controls and patients with SV. Patients with SV had increased binding in the temporal lobes bilaterally and in the right ventromedial frontal cortex compared with controls and patients with NFV. The whole-brain voxel-wise regression analysis revealed a correlation between agrammatism and motor speech impairment, and [ 18 F]THK5351 binding in the left supplementary motor area and left postcentral gyrus. Analysis of [ 18 F]THK5351 scans without partial volume correction revealed similar results. [ 18 F]THK5351 imaging shows a topography closely matching the anatomical distribution of predicted underlying pathology characteristic of NFV and SV PPA. [ 18 F]THK5351 binding correlates with the severity of clinical impairment.

Bayesian correlated clustering to integrate multiple datasets

PubMed Central

Kirk, Paul; Griffin, Jim E.; Savage, Richard S.; Ghahramani, Zoubin; Wild, David L.

2012-01-01

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct—but often complementary—information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. Results: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI’s performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation–chip and protein–protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques—as well as to non-integrative approaches—demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods. Availability: A Matlab implementation of MDI is available from http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/. Contact: D.L.Wild@warwick.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23047558

Final report on APMP supplementary comparison of industrial platinum resistance thermometer for range -50 °C to 400 °C. (APMP.T-S6)

NASA Astrophysics Data System (ADS)

Ali, Nurulaini Md; Othman, Hafidzah; Ho, Mong-Kim; Yang, Inseok; Gabi, Victor; Zhang, Zhe; Sheng, Ying; Hu, Jing; Zhang, Jintao; Tsai, Shu-Fei; Liao, Su-Chuion; Shafiqul Alam, Md; Norranim, Uthai; Yaokulbodee, Charuayrat; Liedberg, Hans; Gamal Ahmed, Mohamed; Harba, Naser; Fuad Flaifel, Mustafa; Suherlan; Achmadi, Aditya; Haoyuan, Kho; Yan, Fan; Boon Kwee, Neoh; Thanh Binh, Pham; Ragay, Monalisa

2017-01-01

The National Metrology Laboratory, Malaysia (NML-SIRIM) had coordinated the Supplementary Comparison of Industrial Platinum Resistance Thermometer (IPRT) started from July 2009 until April 2011 together with the National Measurement Institute of Australia (NMIA) and Korea Research Institute of Standards and Science (KRISS). This comparison was opened to all APMP members and 16 participants had taken part in order to consolidate or improve their calibration and measurement capabilities (CMCs). Three units of artefacts 100-ohm IPRT belonging to NML-SIRIM, NMIA and KRISS were used and three loops of measurement were run in parallel to shorten the circulation time. The stability of artefacts was monitored with initial and final ice point measurement by each laboratory. The participants need to perform measurement at temperature points (0,-50,-30, 0, 100, 200, 300, 400,0) °C. All submitted data were compiled and adjusted at nominal temperature and by using the linkage from NMIA and KRISS as reference value for all three loops , the temperature deviation from participants from different loops can be compared. The approach of Birge Ratio for final exclusion comprised all the excluded results from the analysis of each loop and the measurement performance for each participant were summarized by the En number value. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

PubMed Central

Zhang, Yanju; Lameijer, Eric-Wubbo; 't Hoen, Peter A. C.; Ning, Zemin; Slagboom, P. Eline; Ye, Kai

2012-01-01

Motivation: RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies. Moreover, it may be used for cellular phenotyping and help establishing the etiology of diseases characterized by abnormal splicing patterns. In RNA-Seq, the exact nature of splicing events is buried in the reads that span exon–exon boundaries. The accurate and efficient mapping of these reads to the reference genome is a major challenge. Results: We developed PASSion, a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads. Comparing the performance of PASSion to three existing RNA-Seq analysis pipelines, TopHat, MapSplice and HMMSplicer, revealed that PASSion is competitive with these packages. Moreover, the performance of PASSion is not affected by read length and coverage. It performs better than the other three approaches when detecting junctions in highly abundant transcripts. PASSion has the ability to detect junctions that do not have known splicing motifs, which cannot be found by the other tools. Of the two public RNA-Seq datasets, PASSion predicted ∼ 137 000 and 173 000 splicing events, of which on average 82 are known junctions annotated in the Ensembl transcript database and 18% are novel. In addition, our package can discover differential and shared splicing patterns among multiple samples. Availability: The code and utilities can be freely downloaded from https://trac.nbic.nl/passion and ftp://ftp.sanger.ac.uk/pub/zn1/passion Contact: y.zhang@lumc.nl; k.ye@lumc.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22219203

GTRAC: fast retrieval from compressed collections of genomic variants

PubMed Central

Tatwawadi, Kedar; Hernaez, Mikel; Ochoa, Idoia; Weissman, Tsachy

2016-01-01

Motivation: The dramatic decrease in the cost of sequencing has resulted in the generation of huge amounts of genomic data, as evidenced by projects such as the UK10K and the Million Veteran Project, with the number of sequenced genomes ranging in the order of 10 K to 1 M. Due to the large redundancies among genomic sequences of individuals from the same species, most of the medical research deals with the variants in the sequences as compared with a reference sequence, rather than with the complete genomic sequences. Consequently, millions of genomes represented as variants are stored in databases. These databases are constantly updated and queried to extract information such as the common variants among individuals or groups of individuals. Previous algorithms for compression of this type of databases lack efficient random access capabilities, rendering querying the database for particular variants and/or individuals extremely inefficient, to the point where compression is often relinquished altogether. Results: We present a new algorithm for this task, called GTRAC, that achieves significant compression ratios while allowing fast random access over the compressed database. For example, GTRAC is able to compress a Homo sapiens dataset containing 1092 samples in 1.1 GB (compression ratio of 160), while allowing for decompression of specific samples in less than a second and decompression of specific variants in 17 ms. GTRAC uses and adapts techniques from information theory, such as a specialized Lempel-Ziv compressor, and tailored succinct data structures. Availability and Implementation: The GTRAC algorithm is available for download at: https://github.com/kedartatwawadi/GTRAC Contact: kedart@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27587665

An Updated Catalog of Taiwan Earthquakes (1900-2011) with Homogenized Mw Magnitudes

NASA Astrophysics Data System (ADS)

Chen, K.; Tsai, Y.; Chang, W.

2012-12-01

A complete and consistent catalog of earthquakes can provide good data for studying the distribution of earthquakes in a region as function of space, time and magnitude. Therefore, it is a basic tool for studying seismic hazard and mitigating hazard, and we can get the seismicity with magnitude equal to or greater than Mw from the data set. In the article for completeness and consistence, we apply a catalog of earthquakes from 1900 to 2006 with homogenized magnitude (Mw) (Chen and Tsai, 2008) as a base, and we also refer to the Hsu (1989) to incorporate available supplementary data (total 188 data) for the period 1900-1935, the supplementary data lead the cutoff threshold magnitude to be from Mw 5.5 down to 5.0, this indicates that we add the additional data has enriched the magnitude > 5.0 content. For this study, the catalog has been updated to include earthquakes up to 2011, and it is complete for Mw > 5.0, this will increase the reliability for studying seismic hazard. It is found that it is saturated for original catalog of Taiwan earthquakes compared with Harvard Mw or USGS M for magnitude > 6.5. Although, we modified the original catalog into seismic moment magnitude Mw, it still does not overcome the drawback. But, it is found for Mw < 6.5, our unified Mw are most greater than Harvard Mw or USGS M, the phenomenon indicates our unified Mw to supplement the gap above magnitude > 6.0 and somewhere magnitude > 5.5 during the time period 1973-1991 for original catalog. Therefore, it is better with Mw to report the earthquake magnitude.

Adherence to Clinical Practice Guidelines during Dementia Work-Up in a Real-World Setting: A Study from the Registry of Dementias of Girona.

PubMed

Turró-Garriga, Oriol; Calvó-Perxas, Laia; Vilalta-Franch, Joan; Hernández-Ferrándiz, Marta; Flaqué, Margarita; Linares, Marta; Cullell, Marta; Gich, Jordi; Casas, Isabel; Perkal, Héctor; Garre-Olmo, Josep

2017-01-01

There are several position statements and clinical practice guidelines (CPG) for diagnosing dementia. Our aims were to evaluate the adherence to CPG among specialists in the 7 memory clinics included in the Registry of Dementias of Girona (ReDeGi), and to compare the results between 2007-2011 and 2012-2015. We also determined the time and number of visits required to achieve a diagnosis, the supplementary tests ordered, and the drugs prescribed according to dementia subtypes. Medical charts of a stratified random sample of 475 ReDeGi cases were reviewed. Basic dementia work-up was evaluated using as a reference evidence-based CPG. An Index of Adherence (AI) was calculated using the following items in the medical chart: cognitive symptomatology; functional disability evaluation; physical examination; neurological examination; psychiatric examination; brief cognitive examination; activities of daily living performance examination; blood test; structural neuroimaging (CT-scan or MRI). The mean AI to CPG among specialists was of 8.2 points, and it improved from 7.9 points in 2007-2011 to 8.5 points in 2012-2015 (Cohen's d = 0.46). A lower adherence was detected in the most severe cases. A dementia diagnosis required 3.5 visits, regardless of the subtype of dementia, although milder cases required more time, more visits, and more supplementary tests than severe cases. The adherence to CPG in the catchment area of the ReDeGi is high, and an epidemiological surveillance system such as the ReDeGi may help in improving it. Dementia guidelines should establish procedures adapted to clinical practice, with simplified recommendations for most severe cases.

HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics.

PubMed

Zheng, Jie; Rodriguez, Santiago; Laurin, Charles; Baird, Denis; Trela-Larsen, Lea; Erzurumluoglu, Mesut A; Zheng, Yi; White, Jon; Giambartolomei, Claudia; Zabaneh, Delilah; Morris, Richard; Kumari, Meena; Casas, Juan P; Hingorani, Aroon D; Evans, David M; Gaunt, Tom R; Day, Ian N M

2017-01-01

Fine mapping is a widely used approach for identifying the causal variant(s) at disease-associated loci. Standard methods (e.g. multiple regression) require individual level genotypes. Recent fine mapping methods using summary-level data require the pairwise correlation coefficients ([Formula: see text]) of the variants. However, haplotypes rather than pairwise [Formula: see text], are the true biological representation of linkage disequilibrium (LD) among multiple loci. In this article, we present an empirical iterative method, HAPlotype Regional Association analysis Program (HAPRAP), that enables fine mapping using summary statistics and haplotype information from an individual-level reference panel. Simulations with individual-level genotypes show that the results of HAPRAP and multiple regression are highly consistent. In simulation with summary-level data, we demonstrate that HAPRAP is less sensitive to poor LD estimates. In a parametric simulation using Genetic Investigation of ANthropometric Traits height data, HAPRAP performs well with a small training sample size (N < 2000) while other methods become suboptimal. Moreover, HAPRAP's performance is not affected substantially by single nucleotide polymorphisms (SNPs) with low minor allele frequencies. We applied the method to existing quantitative trait and binary outcome meta-analyses (human height, QTc interval and gallbladder disease); all previous reported association signals were replicated and two additional variants were independently associated with human height. Due to the growing availability of summary level data, the value of HAPRAP is likely to increase markedly for future analyses (e.g. functional prediction and identification of instruments for Mendelian randomization). The HAPRAP package and documentation are available at http://apps.biocompute.org.uk/haprap/ CONTACT: : jie.zheng@bristol.ac.uk or tom.gaunt@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

DISSCO: direct imputation of summary statistics allowing covariates

PubMed Central

Xu, Zheng; Duan, Qing; Yan, Song; Chen, Wei; Li, Mingyao; Lange, Ethan; Li, Yun

2015-01-01

Background: Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be valuable, for example in meta-analyses where individual level genotype data are not available. Two methods (DIST and ImpG-Summary/LD), that assume a multivariate Gaussian distribution for the association summary statistics, have been proposed for imputing association summary statistics. However, both methods assume that the correlations between association summary statistics are the same as the correlations between the corresponding genotypes. This assumption can be violated in the presence of confounding covariates. Methods: We analytically show that in the absence of covariates, correlation among association summary statistics is indeed the same as that among the corresponding genotypes, thus serving as a theoretical justification for the recently proposed methods. We continue to prove that in the presence of covariates, correlation among association summary statistics becomes the partial correlation of the corresponding genotypes controlling for covariates. We therefore develop direct imputation of summary statistics allowing covariates (DISSCO). Results: We consider two real-life scenarios where the correlation and partial correlation likely make practical difference: (i) association studies in admixed populations; (ii) association studies in presence of other confounding covariate(s). Application of DISSCO to real datasets under both scenarios shows at least comparable, if not better, performance compared with existing correlation-based methods, particularly for lower frequency variants. For example, DISSCO can reduce the absolute deviation from the truth by 3.9–15.2% for variants with minor allele frequency <5%. Availability and implementation: http://www.unc.edu/∼yunmli/DISSCO. Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25810429

Fast and accurate inference of local ancestry in Latino populations

PubMed Central

Baran, Yael; Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Burchard, Esteban Gonzàlez; Halperin, Eran

2012-01-01

Motivation: It is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease loci, to understand recombination rate variation and to detect recent selection events. The utility of such studies crucially depends on accurate and unbiased estimation of the ancestry at every genomic locus in recently admixed populations. Although various methods have been proposed and shown to be extremely accurate in two-way admixtures (e.g. African Americans), only a few approaches have been proposed and thoroughly benchmarked on multi-way admixtures (e.g. Latino populations of the Americas). Results: To address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos. Availability: http://lamp.icsi.berkeley.edu/lamp/lampld/ Contact: bpasaniu@hsph.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22495753

45 CFR 164.105 - Organizational requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) A reference in such provision to “protected health information” refers to protected health...; and (D) A reference in such provision to “electronic protected health information” refers to electronic protected health information that is created, received, maintained, or transmitted by or on behalf...

RECENT REFERENCES: JULY 1, 2005 TO SEPTEMBER 30, 2005

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

WINCHELL, D.F.

2005-09-30

This document lists experimental references added to Nuclear Science References (NSR) during the period July 1, 2005 to September 30, 2005. The first section lists keynumbers and keywords sorted by mass and nuclide. The second section lists all references, ordered by keynumber.

RECENT REFERENCES: OCTOBER 1, 2005 TO DECEMBER 31, 2005

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

WINCHELL, D.F.

2005-12-31

This document lists experimental references added to Nuclear Science References (NSR) during the period October 1, 2005 to December 31, 2005. The first section lists keynumbers and keywords sorted by mass and nuclide. The second section lists all references, ordered by keynumber.

5 CFR 294.401 - References.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false References. 294.401 Section 294.401 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS AVAILABILITY OF OFFICIAL INFORMATION Cross References § 294.401 References. The table below provides assistance in locating other OPM...

Putting "Reference" in the Publications Reference File.

ERIC Educational Resources Information Center

Zink, Steven D.

1980-01-01

Argues for more widespread utilization of the U.S. Government Printing Office's Publications Reference File, a reference tool in microfiche format used to answer questions about current U.S. government documents and their availability. Ways to accomplish this task are suggested. (Author/JD)

49 CFR 385.4 - Matter incorporated by reference.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 5 2014-10-01 2014-10-01 false Matter incorporated by reference. 385.4 Section 385.4 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER... FITNESS PROCEDURES General § 385.4 Matter incorporated by reference. (a) Incorporation by reference...

49 CFR 385.4 - Matter incorporated by reference.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 5 2012-10-01 2012-10-01 false Matter incorporated by reference. 385.4 Section 385.4 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER... FITNESS PROCEDURES General § 385.4 Matter incorporated by reference. (a) Incorporation by reference...

Kerlinger's Criterial Referents Theory Revisited.

ERIC Educational Resources Information Center

Zak, Itai; Birenbaum, Menucha

1980-01-01

Kerlinger's criterial referents theory of attitudes was tested cross-culturally by administering an education attitude referents summated-rating scale to 713 individuals in Israel. The response pattern to criterial and noncriterial referents was examined. Results indicated empirical cross-cultural validity of theory, but questioned measuring…

A systematic review of reference pricing: implications for US prescription drug spending.

PubMed

Lee, Joy Li-Yueh; Fischer, Micahel A; Shrank, William H; Polinski, Jennifer M; Choudhry, Niteesh K

2012-11-01

Given rising pharmaceutical expenditures and the widespread use of reference pricing as a costcontainment instrument abroad, we systematically reviewed the evidence evaluating reference pricing policies. We performed a structured electronic search of peer-reviewed journals for studies published before that reported on the effects of reference pricing policies on medication use, payer and patient spending, and resource consumption. Our search yielded 16 studies describing 9 reference-pricing policies from 6 countries. Reference-pricing policies led to decreases in drug prices and increases in utilization of targeted medications, while also reducing payer and patient expenditures. In addition, these policies did not lead to increased use of medical services, such as physician office visits and hospitalization. These results suggest that reference pricing may be an attractive policy strategy for the US healthcare system.

Enhancing the effectiveness of antismoking messages via self-congruent appeals.

PubMed

Chang, Chingching

2009-01-01

A self-congruent effect model was applied to understand adolescents' responses to antismoking advertising that referred to the self or others. Experiment 1 showed that self-referring ads generated more negative smoking attitudes than other-referring ads among adolescents with independent self-construals, whereas other-referring ads generated more negative smoking attitudes than self-referring ads among adolescents with interdependent self-construals. A survey further showed that smokers rated themselves higher on a measure of independent self-construal than nonsmokers. Experiment 2 then found that self-referring ads are more effective than other-referring ads for smokers, who have independent self-construals. Findings supported the idea that health communication campaign designers can maximize message effectiveness by developing different messages for different target segments of the population based on their self-construals.

Locating and parsing bibliographic references in HTML medical articles

PubMed Central

Zou, Jie; Le, Daniel; Thoma, George R.

2010-01-01

The set of references that typically appear toward the end of journal articles is sometimes, though not always, a field in bibliographic (citation) databases. But even if references do not constitute such a field, they can be useful as a preprocessing step in the automated extraction of other bibliographic data from articles, as well as in computer-assisted indexing of articles. Automation in data extraction and indexing to minimize human labor is key to the affordable creation and maintenance of large bibliographic databases. Extracting the components of references, such as author names, article title, journal name, publication date and other entities, is therefore a valuable and sometimes necessary task. This paper describes a two-step process using statistical machine learning algorithms, to first locate the references in HTML medical articles and then to parse them. Reference locating identifies the reference section in an article and then decomposes it into individual references. We formulate this step as a two-class classification problem based on text and geometric features. An evaluation conducted on 500 articles drawn from 100 medical journals achieves near-perfect precision and recall rates for locating references. Reference parsing identifies the components of each reference. For this second step, we implement and compare two algorithms. One relies on sequence statistics and trains a Conditional Random Field. The other focuses on local feature statistics and trains a Support Vector Machine to classify each individual word, followed by a search algorithm that systematically corrects low confidence labels if the label sequence violates a set of predefined rules. The overall performance of these two reference-parsing algorithms is about the same: above 99% accuracy at the word level, and over 97% accuracy at the chunk level. PMID:20640222

Locating and parsing bibliographic references in HTML medical articles.

PubMed

Zou, Jie; Le, Daniel; Thoma, George R

2010-06-01

The set of references that typically appear toward the end of journal articles is sometimes, though not always, a field in bibliographic (citation) databases. But even if references do not constitute such a field, they can be useful as a preprocessing step in the automated extraction of other bibliographic data from articles, as well as in computer-assisted indexing of articles. Automation in data extraction and indexing to minimize human labor is key to the affordable creation and maintenance of large bibliographic databases. Extracting the components of references, such as author names, article title, journal name, publication date and other entities, is therefore a valuable and sometimes necessary task. This paper describes a two-step process using statistical machine learning algorithms, to first locate the references in HTML medical articles and then to parse them. Reference locating identifies the reference section in an article and then decomposes it into individual references. We formulate this step as a two-class classification problem based on text and geometric features. An evaluation conducted on 500 articles drawn from 100 medical journals achieves near-perfect precision and recall rates for locating references. Reference parsing identifies the components of each reference. For this second step, we implement and compare two algorithms. One relies on sequence statistics and trains a Conditional Random Field. The other focuses on local feature statistics and trains a Support Vector Machine to classify each individual word, followed by a search algorithm that systematically corrects low confidence labels if the label sequence violates a set of predefined rules. The overall performance of these two reference-parsing algorithms is about the same: above 99% accuracy at the word level, and over 97% accuracy at the chunk level.

Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues.

PubMed

Kou, Shu-Jun; Wu, Xiao-Meng; Liu, Zheng; Liu, Yuan-Long; Xu, Qiang; Guo, Wen-Wu

2012-12-01

miRNAs have recently been reported to modulate somatic embryogenesis (SE), a key pathway of plant regeneration in vitro. For expression level detection and subsequent function dissection of miRNAs in certain biological processes, qRT-PCR is one of the most effective and sensitive techniques, for which suitable reference gene selection is a prerequisite. In this study, three miRNAs and eight non-coding RNAs (ncRNA) were selected as reference candidates, and their expression stability was inspected in developing citrus SE tissues cultured at 20, 25, and 30 °C. Stability of the eight non-miRNA ncRNAs was further validated in five adult tissues without temperature treatment. The best single reference gene for SE tissues was snoR14 or snoRD25, while for the adult tissues the best one was U4; although they were not as stable as the optimal multiple references snoR14 + U6 for SE tissues and snoR14 + U5 for adult tissues. For expression normalization of less abundant miRNAs in SE tissues, miR3954 was assessed as a viable reference. Single reference gene snoR14 outperformed multiple references for the overall SE and adult tissues. As one of the pioneer systematic studies on reference gene identification for plant miRNA normalization, this study benefits future exploration on miRNA function in citrus and provides valuable information for similar studies in other higher plants. Three miRNAs and eight non-coding RNAs were tested as reference candidates on developing citrus SE tissues. Best single references snoR14 or snoRD25 and optimal multiple references snoR14 + U6, snoR14 + U5 were identified.

Estimation of reference intervals from small samples: an example using canine plasma creatinine.

PubMed

Geffré, A; Braun, J P; Trumel, C; Concordet, D

2009-12-01

According to international recommendations, reference intervals should be determined from at least 120 reference individuals, which often are impossible to achieve in veterinary clinical pathology, especially for wild animals. When only a small number of reference subjects is available, the possible bias cannot be known and the normality of the distribution cannot be evaluated. A comparison of reference intervals estimated by different methods could be helpful. The purpose of this study was to compare reference limits determined from a large set of canine plasma creatinine reference values, and large subsets of this data, with estimates obtained from small samples selected randomly. Twenty sets each of 120 and 27 samples were randomly selected from a set of 1439 plasma creatinine results obtained from healthy dogs in another study. Reference intervals for the whole sample and for the large samples were determined by a nonparametric method. The estimated reference limits for the small samples were minimum and maximum, mean +/- 2 SD of native and Box-Cox-transformed values, 2.5th and 97.5th percentiles by a robust method on native and Box-Cox-transformed values, and estimates from diagrams of cumulative distribution functions. The whole sample had a heavily skewed distribution, which approached Gaussian after Box-Cox transformation. The reference limits estimated from small samples were highly variable. The closest estimates to the 1439-result reference interval for 27-result subsamples were obtained by both parametric and robust methods after Box-Cox transformation but were grossly erroneous in some cases. For small samples, it is recommended that all values be reported graphically in a dot plot or histogram and that estimates of the reference limits be compared using different methods.

Time Series Analysis on the Impact of Generic Substitution and Reference Pricing on Antipsychotic Costs in Finland.

PubMed

Koskinen, Hanna; Mikkola, Hennamari; Saastamoinen, Leena K; Ahola, Elina; Martikainen, Jaana E

2015-12-01

To analyze the medium- to long-term impact of generic substitution and the reference price system on the daily cost of antipsychotics in Finland. The additional impact of reference pricing over and above previously implemented generic substitution was also assessed. An interrupted time series design with a control group and segmented regression analysis was used to estimate the effect of the implementation of generic substitution and the reference price system on the daily cost of antipsychotics. The data have 69 monthly values of the average daily cost for each of the studied antipsychotics: 39 months before and 30 months after the introduction of reference pricing. For one of the studied antipsychotic, the time before the introduction of reference pricing could be further divided into time before and after the introduction of generic substitution. According to the model, 2.5 years after the implementation of reference pricing, the daily cost of the studied antipsychotics was 24.6% to 50.6% lower than it would have been if reference pricing had not been implemented. Two and a half years after the implementation of the reference price system, however, the additional impact of reference pricing over and above previously implemented generic substitution was modest, less than 1 percentage point. Although the price competition induced by reference pricing decreased the prices of antipsychotics in Finland in the short-term, the prices had a tendency to stagnate or even to turn in an upward direction in the medium- to long-term. Furthermore, the additional impact of reference pricing over and above previously implemented generic substitution remained quite modest. Copyright © 2015 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

PubMed Central

Yatsenko, Svetlana A.; Shaw, Chad A.; Ou, Zhishuo; Pursley, Amber N.; Patel, Ankita; Bi, Weimin; Cheung, Sau Wai; Lupski, James R.; Chinault, A. Craig; Beaudet, Arthur L.

2009-01-01

In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately one-half of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sex-matched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sex-mismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs. PMID:19324990

Evaluation of New Reference Genes in Papaya for Accurate Transcript Normalization under Different Experimental Conditions

PubMed Central

Chen, Weixin; Chen, Jianye; Lu, Wangjin; Chen, Lei; Fu, Danwen

2012-01-01

Real-time reverse transcription PCR (RT-qPCR) is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s) validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP) treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s) or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A), TBP1 (TATA binding protein 1) and TBP2 (TATA binding protein 2) genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2), 18S rRNA (18S ribosomal RNA) and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental conditions. PMID:22952972

Thermal radiation transfer calculations in combustion fields using the SLW model coupled with a modified reference approach

NASA Astrophysics Data System (ADS)

Darbandi, Masoud; Abrar, Bagher

2018-01-01

The spectral-line weighted-sum-of-gray-gases (SLW) model is considered as a modern global model, which can be used in predicting the thermal radiation heat transfer within the combustion fields. The past SLW model users have mostly employed the reference approach to calculate the local values of gray gases' absorption coefficient. This classical reference approach assumes that the absorption spectra of gases at different thermodynamic conditions are scalable with the absorption spectrum of gas at a reference thermodynamic state in the domain. However, this assumption cannot be reasonable in combustion fields, where the gas temperature is very different from the reference temperature. Consequently, the results of SLW model incorporated with the classical reference approach, say the classical SLW method, are highly sensitive to the reference temperature magnitude in non-isothermal combustion fields. To lessen this sensitivity, the current work combines the SLW model with a modified reference approach, which is a particular one among the eight possible reference approach forms reported recently by Solovjov, et al. [DOI: 10.1016/j.jqsrt.2017.01.034, 2017]. The combination is called "modified SLW method". This work shows that the modified reference approach can provide more accurate total emissivity calculation than the classical reference approach if it is coupled with the SLW method. This would be particularly helpful for more accurate calculation of radiation transfer in highly non-isothermal combustion fields. To approve this, we use both the classical and modified SLW methods and calculate the radiation transfer in such fields. It is shown that the modified SLW method can almost eliminate the sensitivity of achieved results to the chosen reference temperature in treating highly non-isothermal combustion fields.

Current Practices of Measuring and Reference Range Reporting of Free and Total Testosterone in the United States.

PubMed

Le, Margaret; Flores, David; May, Danica; Gourley, Eric; Nangia, Ajay K

2016-05-01

The evaluation and management of male hypogonadism should be based on symptoms and on serum testosterone levels. Diagnostically this relies on accurate testing and reference values. Our objective was to define the distribution of reference values and assays for free and total testosterone by clinical laboratories in the United States. Upper and lower reference values, assay methodology and source of published reference ranges were obtained from laboratories across the country. A standardized survey was reviewed with laboratory staff via telephone. Descriptive statistics were used to tabulate results. We surveyed a total of 120 laboratories in 47 states. Total testosterone was measured in house at 73% of laboratories. At the remaining laboratories studies were sent to larger centralized reference facilities. The mean ± SD lower reference value of total testosterone was 231 ± 46 ng/dl (range 160 to 300) and the mean upper limit was 850 ± 141 ng/dl (range 726 to 1,130). Only 9% of laboratories where in-house total testosterone testing was performed created a reference range unique to their region. Others validated the instrument recommended reference values in a small number of internal test samples. For free testosterone 82% of laboratories sent testing to larger centralized reference laboratories where equilibrium dialysis and/or liquid chromatography with mass spectrometry was done. The remaining laboratories used published algorithms to calculate serum free testosterone. Reference ranges for testosterone assays vary significantly among laboratories. The ranges are predominantly defined by limited population studies of men with unknown medical and reproductive histories. These poorly defined and variable reference values, especially the lower limit, affect how clinicians determine treatment. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Reference surfaces for bridge scour depths

USGS Publications Warehouse

Landers, Mark N.; Mueller, David S.; ,

1993-01-01

Depth of scour is measured as the vertical distance between scoured channel geometry and a measurement reference surface. A scour depth measurement can have a wide range depending on the method used to establish the reference surface. A consistent method to establish reference surfaces for bridge scour measurements is needed to facilitate transferability of scour data an scour analyses. This paper describes and evaluates techniques for establishing reference surfaces from which local and contraction scour are measured.

BrainSnail: A dynamic information display system for the Sciences

PubMed Central

Telefont, Martin; Asaithambi, Asai

2009-01-01

Scientific reference management has become crucial in rapidly expanding fields of biology. Many of the reference management systems currently employed are reference centric and not object/process focused. BrainSnail is a reference management/knowledge representation application that tries to bridge disconnect between subject and reference in the fields of neuropharmacology, neuroanatomy and neurophysiology. BrainSnail has been developed with considering both individual researcher and research group efforts. PMID:19293992

E&V (Evaluation and Validation) Reference Manual, Version 1.0.

DTIC Science & Technology

1988-07-01

references featured in the Reference Manual. G-05097a GENERAL REFERENCE INFORMATION EXTRACTED , FROM * INDEXES AND CROSS REFERENCES CHAPTER 4...at E&V techniques through many different paths, and provides a means to extract useful information along the way. /^c^^s; /r^ ^yr*•**•»» * L...electronically (preferred) to szymansk@ajpo.sei.cmu.edu or by regular mail to Mr. Raymond Szymanski . AFWAUAAAF, Wright Patterson AFB, OH 45433-6543. ES-2

Identification of Suitable Reference Genes for Gene Expression Normalization in qRT-PCR Analysis in Watermelon

PubMed Central

Gao, Lingyun; Zhao, Shuang; Jiang, Wei; Huang, Yuan; Bie, Zhilong

2014-01-01

Watermelon is one of the major Cucurbitaceae crops and the recent availability of genome sequence greatly facilitates the fundamental researches on it. Quantitative real-time reverse transcriptase PCR (qRT–PCR) is the preferred method for gene expression analyses, and using validated reference genes for normalization is crucial to ensure the accuracy of this method. However, a systematic validation of reference genes has not been conducted on watermelon. In this study, transcripts of 15 candidate reference genes were quantified in watermelon using qRT–PCR, and the stability of these genes was compared using geNorm and NormFinder. geNorm identified ClTUA and ClACT, ClEF1α and ClACT, and ClCAC and ClTUA as the best pairs of reference genes in watermelon organs and tissues under normal growth conditions, abiotic stress, and biotic stress, respectively. NormFinder identified ClYLS8, ClUBCP, and ClCAC as the best single reference genes under the above experimental conditions, respectively. ClYLS8 and ClPP2A were identified as the best reference genes across all samples. Two to nine reference genes were required for more reliable normalization depending on the experimental conditions. The widely used watermelon reference gene 18SrRNA was less stable than the other reference genes under the experimental conditions. Catalase family genes were identified in watermelon genome, and used to validate the reliability of the identified reference genes. ClCAT1and ClCAT2 were induced and upregulated in the first 24 h, whereas ClCAT3 was downregulated in the leaves under low temperature stress. However, the expression levels of these genes were significantly overestimated and misinterpreted when 18SrRNA was used as a reference gene. These results provide a good starting point for reference gene selection in qRT–PCR analyses involving watermelon. PMID:24587403

Non-linear Analysis of Scalp EEG by Using Bispectra: The Effect of the Reference Choice

PubMed Central

Chella, Federico; D'Andrea, Antea; Basti, Alessio; Pizzella, Vittorio; Marzetti, Laura

2017-01-01

Bispectral analysis is a signal processing technique that makes it possible to capture the non-linear and non-Gaussian properties of the EEG signals. It has found various applications in EEG research and clinical practice, including the assessment of anesthetic depth, the identification of epileptic seizures, and more recently, the evaluation of non-linear cross-frequency brain functional connectivity. However, the validity and reliability of the indices drawn from bispectral analysis of EEG signals are potentially biased by the use of a non-neutral EEG reference. The present study aims at investigating the effects of the reference choice on the analysis of the non-linear features of EEG signals through bicoherence, as well as on the estimation of cross-frequency EEG connectivity through two different non-linear measures, i.e., the cross-bicoherence and the antisymmetric cross-bicoherence. To this end, four commonly used reference schemes were considered: the vertex electrode (Cz), the digitally linked mastoids, the average reference, and the Reference Electrode Standardization Technique (REST). The reference effects were assessed both in simulations and in a real EEG experiment. The simulations allowed to investigated: (i) the effects of the electrode density on the performance of the above references in the estimation of bispectral measures; and (ii) the effects of the head model accuracy in the performance of the REST. For real data, the EEG signals recorded from 10 subjects during eyes open resting state were examined, and the distortions induced by the reference choice in the patterns of alpha-beta bicoherence, cross-bicoherence, and antisymmetric cross-bicoherence were assessed. The results showed significant differences in the findings depending on the chosen reference, with the REST providing superior performance than all the other references in approximating the ideal neutral reference. In conclusion, this study highlights the importance of considering the effects of the reference choice in the interpretation and comparison of the results of bispectral analysis of scalp EEG. PMID:28559790

First Definition of Reference Intervals of Liver Function Tests in China: A Large-Population-Based Multi-Center Study about Healthy Adults

PubMed Central

Zhang, Chuanbao; Guo, Wei; Huang, Hengjian; Ma, Yueyun; Zhuang, Junhua; Zhang, Jie

2013-01-01

Background Reference intervals of Liver function tests are very important for the screening, diagnosis, treatment, and monitoring of liver diseases. We aim to establish common reference intervals of liver function tests specifically for the Chinese adult population. Methods A total of 3210 individuals (20–79 years) were enrolled in six representative geographical regions in China. Analytes of ALT, AST, GGT, ALP, total protein, albumin and total bilirubin were measured using three analytical systems mainly used in China. The newly established reference intervals were based on the results of traceability or multiple systems, and then validated in 21 large hospitals located nationwide qualified by the National External Quality Assessment (EQA) of China. Results We had been established reference intervals of the seven liver function tests for the Chinese adult population and found there were apparent variances of reference values for the variables for partitioning analysis such as gender(ALT, GGT, total bilirubin), age(ALP, albumin) and region(total protein). More than 86% of the 21 laboratories passed the validation in all subgroup of reference intervals and overall about 95.3% to 98.8% of the 1220 validation results fell within the range of the new reference interval for all liver function tests. In comparison with the currently recommended reference intervals in China, the single side observed proportions of out of range of reference values from our study for most of the tests deviated significantly from the nominal 2.5% such as total bilirubin (15.2%), ALP (0.2%), albumin (0.0%). Most of reference intervals in our study were obviously different from that of other races. Conclusion These used reference intervals are no longer applicable for the current Chinese population. We have established common reference intervals of liver function tests that are defined specifically for Chinese population and can be universally used among EQA-approved laboratories located all over China. PMID:24058449

Encounter risk analysis of rainfall and reference crop evapotranspiration in the irrigation district

NASA Astrophysics Data System (ADS)

Zhang, Jinping; Lin, Xiaomin; Zhao, Yong; Hong, Yang

2017-09-01

Rainfall and reference crop evapotranspiration are random but mutually affected variables in the irrigation district, and their encounter situation can determine water shortage risks under the contexts of natural water supply and demand. However, in reality, the rainfall and reference crop evapotranspiration may have different marginal distributions and their relations are nonlinear. In this study, based on the annual rainfall and reference crop evapotranspiration data series from 1970 to 2013 in the Luhun irrigation district of China, the joint probability distribution of rainfall and reference crop evapotranspiration are developed with the Frank copula function. Using the joint probability distribution, the synchronous-asynchronous encounter risk, conditional joint probability, and conditional return period of different combinations of rainfall and reference crop evapotranspiration are analyzed. The results show that the copula-based joint probability distributions of rainfall and reference crop evapotranspiration are reasonable. The asynchronous encounter probability of rainfall and reference crop evapotranspiration is greater than their synchronous encounter probability, and the water shortage risk associated with meteorological drought (i.e. rainfall variability) is more prone to appear. Compared with other states, there are higher conditional joint probability and lower conditional return period in either low rainfall or high reference crop evapotranspiration. For a specifically high reference crop evapotranspiration with a certain frequency, the encounter risk of low rainfall and high reference crop evapotranspiration is increased with the decrease in frequency. For a specifically low rainfall with a certain frequency, the encounter risk of low rainfall and high reference crop evapotranspiration is decreased with the decrease in frequency. When either the high reference crop evapotranspiration exceeds a certain frequency or low rainfall does not exceed a certain frequency, the higher conditional joint probability and lower conditional return period of various combinations likely cause a water shortage, but the water shortage is not severe.

Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon.

PubMed

Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Shuang; Jiang, Wei; Huang, Yuan; Bie, Zhilong

2014-01-01

Watermelon is one of the major Cucurbitaceae crops and the recent availability of genome sequence greatly facilitates the fundamental researches on it. Quantitative real-time reverse transcriptase PCR (qRT-PCR) is the preferred method for gene expression analyses, and using validated reference genes for normalization is crucial to ensure the accuracy of this method. However, a systematic validation of reference genes has not been conducted on watermelon. In this study, transcripts of 15 candidate reference genes were quantified in watermelon using qRT-PCR, and the stability of these genes was compared using geNorm and NormFinder. geNorm identified ClTUA and ClACT, ClEF1α and ClACT, and ClCAC and ClTUA as the best pairs of reference genes in watermelon organs and tissues under normal growth conditions, abiotic stress, and biotic stress, respectively. NormFinder identified ClYLS8, ClUBCP, and ClCAC as the best single reference genes under the above experimental conditions, respectively. ClYLS8 and ClPP2A were identified as the best reference genes across all samples. Two to nine reference genes were required for more reliable normalization depending on the experimental conditions. The widely used watermelon reference gene 18SrRNA was less stable than the other reference genes under the experimental conditions. Catalase family genes were identified in watermelon genome, and used to validate the reliability of the identified reference genes. ClCAT1and ClCAT2 were induced and upregulated in the first 24 h, whereas ClCAT3 was downregulated in the leaves under low temperature stress. However, the expression levels of these genes were significantly overestimated and misinterpreted when 18SrRNA was used as a reference gene. These results provide a good starting point for reference gene selection in qRT-PCR analyses involving watermelon.

46 CFR 109.105 - Incorporation by reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Incorporation by reference. 109.105 Section 109.105 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS OPERATIONS General § 109.105 Incorporation by reference. (a) Certain material is incorporated by reference...

46 CFR 109.105 - Incorporation by reference.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 4 2013-10-01 2013-10-01 false Incorporation by reference. 109.105 Section 109.105 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS OPERATIONS General § 109.105 Incorporation by reference. (a) Certain material is incorporated by reference...

46 CFR 109.105 - Incorporation by reference.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 4 2014-10-01 2014-10-01 false Incorporation by reference. 109.105 Section 109.105 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS OPERATIONS General § 109.105 Incorporation by reference. (a) Certain material is incorporated by reference...

46 CFR 109.105 - Incorporation by reference.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 4 2012-10-01 2012-10-01 false Incorporation by reference. 109.105 Section 109.105 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS OPERATIONS General § 109.105 Incorporation by reference. (a) Certain material is incorporated by reference...

46 CFR 109.105 - Incorporation by reference.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 4 2011-10-01 2011-10-01 false Incorporation by reference. 109.105 Section 109.105 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) A-MOBILE OFFSHORE DRILLING UNITS OPERATIONS General § 109.105 Incorporation by reference. (a) Certain material is incorporated by reference...

40 CFR 53.16 - Supersession of reference methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Supersession of reference methods. 53... (CONTINUED) AMBIENT AIR MONITORING REFERENCE AND EQUIVALENT METHODS General Provisions § 53.16 Supersession of reference methods. (a) This section prescribes procedures and criteria applicable to requests that...

Knowledge Management and Reference Services

ERIC Educational Resources Information Center

Gandhi, Smiti

2004-01-01

Many corporations are embracing knowledge management (KM) to capture the intellectual capital of their employees. This article focuses on KM applications for reference work in libraries. It defines key concepts of KM, establishes a need for KM for reference services, and reviews various KM initiatives for reference services.

Spatial interpolation of daily reference evapotranspiration in the Texas High Plains

USDA-ARS?s Scientific Manuscript database

The Texas High Plains Evapotranspiration (ET) Network collects meteorological data from 18 grass reference weather stations at hourly intervals and estimates hourly and daily reference ET using the American Society of Civil Engineers (ASCE) Standardized Reference ET equation. Producers in the Texas ...

Effects of norm referent salience on young people's dietary orientation.

PubMed

Tarrant, Mark; Khan, Sammyh S; Qin, Qi

2015-02-01

We examined the effects of making salient different norm referents on young people's dietary orientation. Participants were exposed to a referent who was either of similar age to themselves or older before reporting their normative beliefs, attitudes and intentions concerning dietary behavior. As predicted, exposure to the older referent was associated with stronger perceptions that eating five portions of fruit and vegetables each day was normative. Compared to those exposed to the same-age referent, participants exposed to the older referent reported more positive attitudes towards eating "five-a-day" and stronger intentions to do so over the coming week. Referent salience was also associated with a behavioral outcome, with those participants exposed to the older referent more likely to take a piece of fruit upon completion of the study (OR: 4.97, 95% CI: 1.39-17.82). The implications of these findings for norms-based interventions for changing dietary behavior are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Requirements for data integration platforms in biomedical research networks: a reference model

PubMed Central

Knaup, Petra

2015-01-01

Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure, we developed a reference model for the requirements. The reference model consists of five reference goals and 15 reference requirements. Using the Unified Modeling Language, the goals and requirements are set into relation to each other. In addition, all goals and requirements are described textually in tables. This reference model can be used by research networks as a basis for a resource efficient acquisition of their project specific requirements. Furthermore, a concrete instance of the reference model is described for a research network on liver cancer. The reference model is transferred into a requirements model of the specific network. Based on this concrete requirements model, a service-oriented information technology architecture is derived and also described in this paper. PMID:25699205

Reference pricing with endogenous generic entry.

PubMed

Brekke, Kurt R; Canta, Chiara; Straume, Odd Rune

2016-12-01

Reference pricing intends to reduce pharmaceutical expenditures by increasing demand elasticity and stimulating generic competition. We develop a novel model where a brand-name producer competes in prices with several generics producers in a market with brand-biased and brand-neutral consumers. Comparing with coinsurance, we show that reference pricing, contrary to policy makers' intentions, discourages generic entry, as it induces the brand-name producer to price more aggressively. Thus, the net effect of reference pricing on drug prices is ambiguous, implying that reference pricing can be counterproductive in reducing expenditures. However, under price regulation, we show that reference pricing may stimulate generic entry, since a binding price cap weakens the aggressive price response by the brand-name producer. This may explain mixed empirical results on the competitive effects of reference pricing. Finally, we show that reference pricing may be welfare improving when accounting for brand preferences despite its adverse effects on entry and prices. Copyright © 2016 Elsevier B.V. All rights reserved.

Electronic reporting of all reference laboratory results: An important step toward a truly all-encompassing, integrated health record.

PubMed

Kratz, Alexander

2016-09-01

Results from reference laboratories are often not easily available in electronic health records. This article describes a multi-pronged, long-term approach that includes bringing send-out tests in-house, upgrading the laboratory information system, interfacing more send-out tests and more reference laboratories, utilizing the "miscellaneous assay" option offered by some reference laboratories, and scanning all remaining paper reports from reference laboratories for display in the electronic health record. This allowed all laboratory results obtained in association with a patient visit, whether performed in-house or at a reference laboratory, to be available in the integrated electronic health record. This was achieved without manual data entry of reference laboratory results, thereby avoiding the risk of transcription errors. A fully integrated electronic health record that contains all laboratory results can be achieved by maximizing the number of interfaced reference laboratory assays and making all non-interfaced results available as scanned documents. © The Author(s) 2015.

Methods, systems and apparatus for controlling third harmonic voltage when operating a multi-space machine in an overmodulation region

DOEpatents

Perisic, Milun; Kinoshita, Michael H; Ranson, Ray M; Gallegos-Lopez, Gabriel

2014-06-03

Methods, system and apparatus are provided for controlling third harmonic voltages when operating a multi-phase machine in an overmodulation region. The multi-phase machine can be, for example, a five-phase machine in a vector controlled motor drive system that includes a five-phase PWM controlled inverter module that drives the five-phase machine. Techniques for overmodulating a reference voltage vector are provided. For example, when the reference voltage vector is determined to be within the overmodulation region, an angle of the reference voltage vector can be modified to generate a reference voltage overmodulation control angle, and a magnitude of the reference voltage vector can be modified, based on the reference voltage overmodulation control angle, to generate a modified magnitude of the reference voltage vector. By modifying the reference voltage vector, voltage command signals that control a five-phase inverter module can be optimized to increase output voltages generated by the five-phase inverter module.

Recent developments in the field of environmental reference materials at the JRC Ispra.

PubMed

Muntau, H

2001-06-01

The production of reference materials for environmental analysis started in the Joint Research Centre at Ispra/Italy in 1972 with the objective of later certification by the BCR, but for obvious budget reasons only a fraction of the total production achieved at Ispra ever reached certification level, although all materials were produced according to the severe quality requirements requested for certified reference materials. Therefore, the materials not destinated to certification are in growing demand as inter-laboratory test materials and as laboratory reference materials, for internal quality control, e.g., by control charts. The history of reference material production within the Joint Research Centre is briefly reviewed and the latest additions described. New developments such as micro-scale reference materials intended for analytical methods requiring sample intakes at milligram or sub-milligram level and therefor not finding supply on the reference material market, and "wet" environmental reference materials, which meet more precisely the "real-world" environmental analysis conditions, are presented and the state-of-the-art discussed.

Asymptomatic young man with an incidental murmur.

PubMed

Shojaeifard, Maryam; Pouraliakbar, Hamid Reza; Houshmand, Golnaz

2018-05-31

A 32-year old man was referred to our institution for transthoracic echocardiography (TTE) following detection of an incidental murmur on physical examination before blood donation. He was asymptomatic with no significant medical history. Physical examination revealed dual heart sounds with a grade II/VI systolic murmur heard in the left sternal border. An ECG was in normal sinus rhythm. TTE was performed (figure 1A-C, online supplementary videos 1-4) followed by cardiac CT angiography (CTA) (figure 1D,E).heartjnl;heartjnl-2018-313223v1/F1F1F1Figure 1(A) Transthoracic echocardiography, parasternal left ventricular long axis view. (B) Colour Doppler of modified short axis in the mid-left ventricular level. (C) Doppler flow velocity profile. (D) Cardiac CT angiography (CTA) sagittal reconstruction. (E) Three-dimensional CTA reconstruction of the heart. What is the diagnosis?Pericardial cyst.Ventricular septal defect.Kawasaki.Anomalous left coronary artery from pulmonary artery (ALCAPA). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Ground-water conditions in Utah, spring of 2002

USGS Publications Warehouse

Burden, Carole B.; Enright, Michael; Danner, M.R.; Fisher, M.J.; Haraden, Peter L.; Kenney, T.A.; Wilkowske, C.D.; Eacret, Robert J.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.

2002-01-01

This is the thirty-ninth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 2001. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Division of Water Rights and Division of Water Resources.

Ground-water conditions in Utah, spring of 1997

USGS Publications Warehouse

Gerner, S.J.; Steiger, J.I.; Sory, J.D.; Burden, Carole B.; Loving, B.L.; Brockner, S.J.; Danner, M.R.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.; Herbert, L.R.

1997-01-01

This is the thirty-fourth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources, provide data to enable interested parties to keep aware of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas for which applicable data are available and are important to a discussion of changing ground-water conditions.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 1996. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Divisions of Water Rights and Water Resources.

Ground-water conditions in Utah, spring of 1999

USGS Publications Warehouse

Burden, Carole B.; Spangler, L.E.; Sory, J.D.; Eacret, Robert J.; Kenney, T.A.; Johnson, K.K.; Loving, B.L.; Brockner, S.J.; Danner, M.R.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.; Fisher, M.J.

1999-01-01

This is the thirty-sixth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 1998. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Divisions of Water Rights and Water Resources.

Ground-water conditions in Utah, spring of 2001

USGS Publications Warehouse

Burden, Carole B.; Sory, J.D.; Danner, M.R.; Fisher, M.J.; Haraden, Peter L.; Kenney, T.A.; Eacret, Robert J.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.

2001-01-01

This is the thirty-eighth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 2000. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Division of Water Rights and Division of Water Resources.

Ground-water conditions in Utah, spring of 1998

USGS Publications Warehouse

Susong, David D.; Burden, Carole B.; Sory, J.D.; Eacret, Robert J.; Johnson, K.K.; Loving, B.L.; Brockner, S.J.; Danner, M.R.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.; Herbert, L.R.

1998-01-01

This is the thirty-fifth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 1997. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Divisions of Water Rights and Water Resources.

Ground-water conditions in Utah, spring of 2003

USGS Publications Warehouse

Burden, Carole B.; Enright, Michael; Danner, M.R.; Fisher, M.J.; Haraden, Peter L.; Kenney, T.A.; Wilkowske, C.D.; Eacret, Robert J.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.

2003-01-01

This is the fortieth in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 2002. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Division of Water Rights and Division of Water Resources.

Ground-water conditions in Utah, spring of 2000

USGS Publications Warehouse

Burden, Carole B.; Sory, J.D.; Danner, M.R.; Johnson, K.K.; Kenny, T.A.; Brockner, S.J.; Eacret, Robert J.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.; Fisher, M.J.

2000-01-01

This is the thirty-seventh in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 1999. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Divisions of Water Rights and Water Resources.

Ground-water conditions in Utah, spring of 2004

USGS Publications Warehouse

Burden, Carole B.; Allen, David V.; Danner, M.R.; Walzem, Vince; Cillessen, J.L.; Kenney, T.A.; Wilkowske, C.D.; Eacret, Robert J.; Downhour, Paul; Slaugh, B.A.; Swenson, R.L.; Howells, J.H.; Christiansen, H.K.; Fisher, M.J.

2004-01-01

This is the forty-first in a series of annual reports that describe ground-water conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Resources and Division of Water Rights, provide data to enable interested parties to maintain awareness of changing ground-water conditions.This report, like the others in the series, contains information on well construction, ground-water withdrawal from wells, water-level changes, precipitation, streamflow, and chemical quality of water. Information on well construction included in this report refers only to wells constructed for new appropriations of ground water. Supplementary data are included in reports of this series only for those years or areas which are important to a discussion of changing ground-water conditions and for which applicable data are available.This report includes individual discussions of selected significant areas of ground-water development in the State for calendar year 2003. Most of the reported data were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources, Division of Water Rights and Division of Water Resources.

Final report of supplementary comparison AFRIMETS.AUV.A-S1: primary pressure calibration of LS2aP microphones according to IEC 61094-2, over the frequency range 1 Hz to 31.5 kHz.

NASA Astrophysics Data System (ADS)

Nel, R.; Barrera-Figueroa, S.; Dobrowolska, D.; Defilippo Soares, Z. M.; Maina, A. K.; Hof, C.

2016-01-01

This is the final report of the AFRIMETS.AUV-S1 comparison of the pressure sensitivity, modulus and phase, of LS2aP microphones in the frequency range 1 Hz to 31.5 kHz in accordance with IEC 61094-2. Six national metrology institutes from three different regional metrology organisations participated in the comparison for which two LS2aP microphones were circulated simultaneously to all the participants in a hybrid-star configuration. The comparison reference values were calculated as the weighted mean for modulus and phase for each individual microphone. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

COOMET.QM-K93 (COOMET 615/RU/13): key comparison in the field of measuring of the ethanol amount fraction in nitrogen (120 μmol/mol)

NASA Astrophysics Data System (ADS)

Konopelko, L. A.; Efremova, O. V.; Fatina, O. V.; Orshanskaia, A. A.; Rozhnov, M. S.; Melnyk, D. M.; Petryshyn, P. V.

2016-01-01

The relevance of the COOMET.QM-K93 comparison is founded on paying particular attention to reliability of measurements which are performed during the medical examination of drivers of vehicles in order to assess the degree of alcoholic intoxication. Standard gas mixtures of ethanol in nitrogen in cylinders under pressure play a key role in providing metrological assurance of breath-alcohol analyzers. Participating laboratories: VNIIM and Ukrmetrteststandart. This comparison was carried out in 2014-2015. This supplementary comparison supports CMC claims for: ethanol in the range 50-500 μmol/mol in a matrix of either nitrogen or synthetic air. Results: The results are consistent with the reference values. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

The primary structure of aspartate aminotransferase from pig heart muscle. Digestion with a proteinase having specificity for lysine residues.

PubMed Central

Doonan, S; Doonan, H J; Hanford, R; Vernon, C A; Walker, J M; da Airold, L P; Bossa, F; Barra, D; Carloni, M; Fasella, P; Riva, F

1975-01-01

Carboxymethylated aspartate aminotransferase was digested with a proteinase claimed to be specific for lysine residues. Complete cleavage occurred at 12 of the 19 lysine residues in the protein, but at the remaining seven residues cleavage was either restricted or absent. In addition, cleavage was observed at three of the 26 arginine residues. These results are discussed with reference to the amino acid residues adjacent to points of complete or restricted cleavage. The complete primary structure of aspartate aminotransferase, based on these and other studies, is given. Evidence for the assignment of some acid and amide side chains has been deposited as Supplementary Publication SUP 50050 (11 pp.) at the British Library (Lending Division), Boston Spa, Wetherby, W. Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1975) 145, 5. The evidence for the assignment of residue 366 was less conclusive than for the other acid and amide side chains and is, therefore, given in the main paper. PMID:1239277

Investigation of suspected chronic fatigue syndrome/myalgic encephalopathy.

PubMed

Owe, Jone Furlund; Næss, Halvor; Gjerde, Ivar Otto; Bødtker, Jørn Eilert; Tysnes, Ole-Bjørn

2016-02-09

Chronic fatigue is a frequently occurring problem in both the primary and specialist health services. The Department of Neurology at Haukeland University Hospital has established a standard assessment for patients referred with suspected CFS/ME. This study reports diagnoses and findings upon assessment, and considers the benefit of supplementary examinations. Diagnoses and findings from examinations of 365 patients assessed for suspected CFS/ME are retrospectively reported. A total of 48 patients (13.2%) were diagnosed with CFS/ME, while a further 18 patients (4.9%) were diagnosed with post-infectious fatigue. Mental and behavioural disorders were diagnosed in 169 patients (46.3%), and these represented by far the largest group. Serious, but unrecognised somatic illness was discovered in two patients, while changes of uncertain significance were identified by MRI and lumbar puncture in a few patients. Fatigue is a frequently occurring symptom in the population. Thorough somatic and psychiatric investigation is necessary before referral to the specialist health services. Mental disorders and reactions to life crises are common and important differential diagnoses for CFS/ME. Long waiting times in the specialist health services may result in delayed diagnosis for these patients.

Data-dependent bucketing improves reference-free compression of sequencing reads.

PubMed

Patro, Rob; Kingsford, Carl

2015-09-01

The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data. We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes. Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http://www.cs.cmu.edu/∼ckingsf/software/mince. carlk@cs.cmu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

[The contradictions between the universal Unified Health System and the transfer of public funds to private health plans and insurances].

PubMed

Bahia, Ligia

2008-01-01

Trailing the whole group of trends and changes in the scenario of relations between the public and the private, this article analyses the effects of the rise in the rates of return of health plan operators and health insurance companies in 2007. Special attention is given to the segmentation of the system, the complaints about the naturalization of inequitable access to health services and to the depreciation of the original concepts of the Unified Health System. The study also gathers information regarding the production of knowledge about supplementary care with the intent to systemize the bases and methodological approaches adopted by a selected sub-group of scientific papers. Finally, the article develops conjectures and hypotheses with regard to possible associations between growth and stability of the health plan and insurance market and as refers to the nature of scientific production about this issue, taking into consideration the contradictions between the political and economical circuit in which the health plan and insurance companies are operating and the universality of the Brazilian Health System.

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.

PubMed

Van Landeghem, Sofie; Van Parys, Thomas; Dubois, Marieke; Inzé, Dirk; Van de Peer, Yves

2016-01-05

Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time. In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator. Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.

Incentives and pharmaceutical reimbursement reforms in Spain.

PubMed

Puig-Junoy, Jaume

2004-02-01

The aim of this paper is to assess whether cost containment has been affected by recent pharmaceutical reimbursement reforms that have been introduced in the Spanish health care system over the period 1996-2002, under the conservative Popular Party Government. Four main reimbursement policies can be observed in the Spanish pharmaceutical market after 1996, each of them largely unintegrated with the other three. First, a second supplementary negative list of excluded pharmaceutical products was introduced in 1998. Second, a reference pricing (RP) system was introduced in December 2000, with annual updating and enlargement. Third, the pharmacies' payment system has moved from the traditional set margin on the consumer price to a margin that varies according to the consumer price of the product, the generic status of the product, and the volume of sales by pharmacies. And fourth, general agreements between the government and the industry have been reached with cost containment objectives. In the final section of this paper, we present an overall assessment of the impact of these pharmaceutical reimbursement policies on the behaviour of the agents in the pharmaceutical market.